en Advisors for this project come from the IFOMIS group, Saarbruecken and from the Co-ODE group in Manchester Alan Ruttenberg Allyson Lister Barry Smith Bill Bug Bjoern Peters Carlo Torniai Chris Mungall Chris Stoeckert Chris Taylor Christian Bolling Cristian Cocos Daniel Rubin Daniel Schober Dawn Field Dirk Derom Elisabetta Manduchi Eric Deutsch Frank Gibson Gilberto Fragoso Helen C. Causton Helen Parkinson Holger Stenzhorn James A. Overton James Malone Jay Greenbaum Jeffrey Grethe Jennifer Fostel Jessica Turner Jie Zheng Joe White John Westbrook Kevin Clancy Larisa Soldatova Lawrence Hunter Liju Fan Luisa Montecchi Matthew Brush Matthew Pocock Melanie Courtot Melissa Haendel Mervi Heiskanen Monnie McGee Norman Morrison Philip Lord Philippe Rocca-Serra Pierre Grenon Richard Bruskiewich Richard Scheuermann Robert Stevens Ryan R. Brinkman Stefan Wiemann Steve Pittard Susanna-Assunta Sansone Tanya Gray Tina Hernandez-Boussard Trish Whetzel Yongqun He Yongqun Oliver He (YH) Zhaohui Steve Qin 2009-07-31 2016-03-13 The Epigenome Ontology (EGO) is an ontology in the domain of epigenome. The Ontology for Biomedical Investigations (OBI) is build in a collaborative, international effort and will serve as a resource for annotating biomedical investigations, including the study design, protocols and instrumentation used, the data generated and the types of analysis performed on the data. This ontology arose from the Functional Genomics Investigation Ontology (FuGO) and will contain both terms that are common to all biomedical investigations, including functional genomics investigations and those that are more domain specific. OWL-DL An ontology for the annotation of biomedical and functional genomics experiments. Ontology for Biomedical Investigation Please cite the OBI consortium http://purl.obolibrary.org/obo/obi where traditional citation is called for. However it is adequate that individual terms be attributed simply by use of the identifying PURL for the term, in projects that refer to them. 2015-12-07 Arbor version; 1.0.1 BFO OWL specification label Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification. Really of interest to developers only BFO OWL specification label BFO CLIF specification label Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2 Person:Alan Ruttenberg Really of interest to developers only BFO CLIF specification label editor preferred term~editor preferred label The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> editor preferred label editor preferred term editor preferred term editor preferred term~editor preferred label example of usage A phrase describing how a class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms, examples for low level terms (e.g., Affymetrix HU133 array) are not PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> example of usage in branch An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet. GROUP:OBI OBI_0000277 in branch has curation status PERSON:Alan Ruttenberg PERSON:Bill Bug PERSON:Melanie Courtot OBI_0000281 has curation status definition The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. 2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition definition textual definition editor note An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. PERSON:Daniel Schober GROUP:OBI:<http://purl.obfoundry.org/obo/obi> editor note term editor Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people 20110707, MC: label update to term editor and definition modified accordingly. See http://code.google.com/p/information-artifact-ontology/issues/detail?id=115. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> term editor alternative term An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent) PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> alternative term definition source formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 PERSON:Daniel Schober Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition source has obsolescence reason Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification. PERSON:Alan Ruttenberg PERSON:Melanie Courtot has obsolescence reason curator note An administrative note of use for a curator but of no use for a user PERSON:Alan Ruttenberg curator note is denotator type relates an class defined in an ontology, to the type of it's denotator In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type') Alan Ruttenberg is denotator type imported from For external terms/classes, the ontology from which the term was imported PERSON:Alan Ruttenberg PERSON:Melanie Courtot GROUP:OBI:<http://purl.obolibrary.org/obo/obi> imported from expand expression to ObjectProperty: RO_0002104 Label: has plasma membrane part Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones Chris Mungall expand expression to expand assertion to ObjectProperty: RO??? Label: spatially disjoint from Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom. Chris Mungall expand assertion to first order logic expression PERSON:Alan Ruttenberg first order logic expression antisymmetric property part_of antisymmetric property xsd:true use boolean value xsd:true to indicate that the property is an antisymmetric property Alan Ruttenberg antisymmetric property OBO foundry unique label An alternative name for a class or property which is unique across the OBO Foundry. The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools . PERSON:Alan Ruttenberg PERSON:Bjoern Peters PERSON:Chris Mungall PERSON:Melanie Courtot GROUP:OBO Foundry <http://obofoundry.org/> OBO foundry unique label has ID digit count Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO" Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix" annotation property value concatenated with an integer in the id range (left padded with "0"s to make this many digits) Person:Alan Ruttenberg has ID digit count has ID range allocated to Datatype: idrange:1 Annotations: 'has ID range allocated to': "Chris Mungall" EquivalentTo: xsd:integer[> 2151 , <= 2300] Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new terms Person:Alan Ruttenberg has ID range allocated to has ID policy for Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO" Relating an ontology used to record id policy to the ontology namespace whose policy it manages Person:Alan Ruttenberg has ID policy for has ID prefix Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO" Relates an ontology used to record id policy to a prefix concatenated with an integer in the id range (left padded with "0"s to make this many digits) to construct an ID for a term being created. Person:Alan Ruttenberg has ID prefix elucidation person:Alan Ruttenberg Person:Barry Smith Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms elucidation has associated axiom(nl) Person:Alan Ruttenberg Person:Alan Ruttenberg An axiom associated with a term expressed using natural language has associated axiom(nl) has associated axiom(fol) Person:Alan Ruttenberg Person:Alan Ruttenberg An axiom expressed in first order logic using CLIF syntax has associated axiom(fol) is allocated id range Add as annotation triples in the granting ontology Relates an ontology IRI to an (inclusive) range of IRIs in an OBO name space. The range is give as, e.g. "IAO_0020000-IAO_0020999" PERSON:Alan Ruttenberg is allocated id range retired from use as of relates a class of CRID to the date after which further instances should not be made, according to the central authority In OWL 2 add AnnotationPropertyRange xsd:dateTimeStamp Alan Ruttenberg retired from use as of has axiom label Person:Alan Ruttenberg Person:Alan Ruttenberg A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI has axiom label term replaced by Add as annotation triples in the granting ontology Use on obsolete terms, relating the term to another term that can be used as a substitute Person:Alan Ruttenberg Person:Alan Ruttenberg term replaced by ISA alternative term An alternative term used by the ISA tools project (http://isa-tools.org). Requested by Alejandra Gonzalez-Beltran https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891&atid=886178 Person: Alejandra Gonzalez-Beltran Person: Philippe Rocca-Serra ISA tools project (http://isa-tools.org) ISA alternative term NIAID GSCID-BRC alternative term An alternative term used by the National Institute of Allergy and Infectious Diseases (NIAID) Genomic Sequencing Centers for Infectious Diseases (GSCID) and Bioinformatics Resource Centers (BRC). PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group NIAID GSCID-BRC alternative term IEDB alternative term An alternative term used by the IEDB. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IEDB alternative term FGED alternative term An alternative term used by the Functional Genomics Data (FGED) Society. PERSON: Chris Stoeckert, Jie Zheng Penn Group FGED alternative term temporal interpretation temporal interpretation https://code.google.com/p/obo-relations/wiki/ROAndTime https://github.com/oborel/obo-relations/wiki/ROAndTime Examples of a Contributor include a person, an organisation, or a service. Typically, the name of a Contributor should be used to indicate the entity. An entity responsible for making contributions to the content of the resource. Contributor Contributor Coverage will typically include spatial location (a place name or geographic coordinates), temporal period (a period label, date, or date range) or jurisdiction (such as a named administrative entity). Recommended best practice is to select a value from a controlled vocabulary (for example, the Thesaurus of Geographic Names [TGN]) and that, where appropriate, named places or time periods be used in preference to numeric identifiers such as sets of coordinates or date ranges. The extent or scope of the content of the resource. Coverage Coverage Examples of a Creator include a person, an organisation, or a service. Typically, the name of a Creator should be used to indicate the entity. An entity primarily responsible for making the content of the resource. Creator Creator Typically, Date will be associated with the creation or availability of the resource. Recommended best practice for encoding the date value is defined in a profile of ISO 8601 [W3CDTF] and follows the YYYY-MM-DD format. A date associated with an event in the life cycle of the resource. Date Date Description may include but is not limited to: an abstract, table of contents, reference to a graphical representation of content or a free-text account of the content. An account of the content of the resource. Description Description Typically, Format may include the media-type or dimensions of the resource. Format may be used to determine the software, hardware or other equipment needed to display or operate the resource. Examples of dimensions include size and duration. Recommended best practice is to select a value from a controlled vocabulary (for example, the list of Internet Media Types [MIME] defining computer media formats). The physical or digital manifestation of the resource. Format Format Recommended best practice is to identify the resource by means of a string or number conforming to a formal identification system. Example formal identification systems include the Uniform Resource Identifier (URI) (including the Uniform Resource Locator (URL)), the Digital Object Identifier (DOI) and the International Standard Book Number (ISBN). An unambiguous reference to the resource within a given context. Resource Identifier Resource Identifier Recommended best practice is to use RFC 3066 [RFC3066], which, in conjunction with ISO 639 [ISO639], defines two- and three-letter primary language tags with optional subtags. Examples include "en" or "eng" for English, "akk" for Akkadian, and "en-GB" for English used in the United Kingdom. A language of the intellectual content of the resource. Language Language Examples of a Publisher include a person, an organisation, or a service. Typically, the name of a Publisher should be used to indicate the entity. An entity responsible for making the resource available Publisher Publisher Recommended best practice is to reference the resource by means of a string or number conforming to a formal identification system. A reference to a related resource. Relation Relation Typically, a Rights element will contain a rights management statement for the resource, or reference a service providing such information. Rights information often encompasses Intellectual Property Rights (IPR), Copyright, and various Property Rights. If the Rights element is absent, no assumptions can be made about the status of these and other rights with respect to the resource. Information about rights held in and over the resource. Rights Management Rights Management The present resource may be derived from the Source resource in whole or in part. Recommended best practice is to reference the resource by means of a string or number conforming to a formal identification system. A reference to a resource from which the present resource is derived. Source Source Typically, a Subject will be expressed as keywords, key phrases or classification codes that describe a topic of the resource. Recommended best practice is to select a value from a controlled vocabulary or formal classification scheme. The topic of the content of the resource. Subject and Keywords Subject and Keywords Typically, a Title will be a name by which the resource is formally known. A name given to the resource. Title Title Type includes terms describing general categories, functions, genres, or aggregation levels for content. Recommended best practice is to select a value from a controlled vocabulary (for example, the DCMI Type Vocabulary [DCMITYPE]). To describe the physical or digital manifestation of the resource, use the Format element. The nature or genre of the content of the resource. Resource Type Resource Type shorthand shorthand label part of my brain is part of my body (continuant parthood, two material entities) my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) this day is part of this year (occurrent parthood) a core relation that holds between a part and its whole Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. part_of part of http://www.obofoundry.org/ro/#OBO_REL:part_of realized in this disease is realized in this disease course this fragility is realized in this shattering this investigator role is realized in this investigation is realized by realized_in [copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process realized in contains process [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant contains process ChIP-seq binding at obsolete_specifically denotes The process of creation is, for example, writing down on paper the name of a friend by deliberately creating a certain pattern using ink. Here the ink + paper is the independent continuant and the carrier is the pattern in the ink. c = pattern in the ink b = paper + ink r = friend c specifically denotes r =def r is a portion of reality & c is a particular quality & c depends specifically on some independent continuant b & b acquired c as the result of the achievement of an objective to enable pointing to r repeatedly. Marked means there is a changed or additional quality of the bearer - the quality is the information carrier. Case 1 Memory trace as mark created when reading some description of some friend. The trace can denote. Case 2 Pattern of ink arrayed on paper as mark when writing down a friend's name Case 3 Pattern of magnetic domains on scattered pieces of a hard disk platter as mark when saving a file. 8/6/2009 Alan Ruttenberg: The suggestions is to deprecate specific and generically denotes in favor of a single denote relationship that corresponds to the generic sense see http://code.google.com/p/information-artifact-ontology/issues/detail?id=25&q=denote Alan Ruttenberg Smith, Ceusters, Ruttenberg, 2000 years of philosophy obsolete_specifically denotes true mentions An information artifact IA mentions an entity E exactly when it has a component/part that denotes E 7/6/2009 Alan Ruttenberg. P4 RC1 munges our GCI so remove it for now: mentions some entity equivalentTo has_part some ('generically denotes' some entity) 7/6/2009 Alan Ruttenberg: Add this relation following conversation with Jonathan Rees that N&S GCI for is_about was too strong. Really it was simply sufficient. To effect this change we introduce this relation, which is subproperty of is_about, and have previous GCI use this relation "mentions" in it's (logical) definition PERSON: Jonathan Rees Person: Alan Ruttenberg mentions obsolete_materially denotes see http://code.google.com/p/information-artifact-ontology/issues/detail?id=25&q=denote obsolete_materially denotes true obsolete_describes obsolete_describes true obsolete_represents obsolete_represents true has coordinate unit label relating a cartesian spatial coordinate datum to a unit label that together with the values represent a point has coordinate unit label is quality measured as inverse of the relation of is quality measurement of 2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship Person:Alan Ruttenberg is quality measured as is quality specification of a relation between a data item and a quality of a material entity where the material entity is the specified output of a material transformation which achieves an objective specification that indicates the intended value of the specified quality. Person:Alan Ruttenberg Person:Bjoern Peters is quality specification of quality is specified as inverse of the relation of is quality specification of 2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship Person:Alan Ruttenberg Person:Bjoern Peters quality is specified as has time stamp relates a time stamped measurement datum to the time measurement datum that denotes the time when the measurement was taken Alan Ruttenberg has time stamp has measurement datum relates a time stamped measurement datum to the measurement datum that was measured Alan Ruttenberg has measurement datum obsolete_is_concretization_of Is a relationship between a generically dependent continuant and a specifically dependent continuant. A generically dependent continuant may inhere in more than one entity. It does so by virtue of the fact that there is, for each entity that it inheres, a specifically dependent *concretization* of the generically dependent continuant that is specifically dependent. For instance, consider a story, which is an information artifact that inheres in some number of books. Each book bears some quality that carries the story. The relation between this quality and the generically dependent continuant is that the former is the concretization of the latter. replaced by: http://purl.obolibrary.org/obo/BFO_0000058 PERSON: Alan Ruttenburg PERSON: Barry Smith obsolete_is_concretization_of true is_specified_input_of some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. Alan Ruttenberg PERSON:Bjoern Peters is_specified_input_of obsolete_is_concretized_as Is a relationship between a specifically dependent continuant and a generically dependent continuant. A generically dependent continuant may inhere in more than one entity. It does so by virtue of the fact that there is, for each entity that it inheres, a specifically dependent *concretization* of the generically dependent continuant that is specifically dependent. For instance, consider a story, which is an information artifact that inheres in some number of books. Each book bears some quality that carries the story. The relation between this quality and the generically dependent continuant is that the former is the concretization of the latter. replaced by: http://purl.obolibrary.org/obo/BFO_0000059 PERSON: Alan Ruttenberg PERSON: Barry Smith obsolete_is_concretized_as true obsolete_has_quality A relation between an entity and a quality. For types: E has_quality Q iff: for any eEt, exists qQt such that q inheres_in e at t. For instances: e has_quality q at t iff q inheres_in e at t and q instance-of Quality [GOC:cjm] replaced by: http://purl.obolibrary.org/obo/BFO_0000086 GROUP:OBI:<http://obi.sourceforge.net> PERSON: Chris Mungall obsolete_has_quality true obsolete_is_realized_by Relation between a realizable and a process. Reciprocal relation of realizes [GOC:cjm] replaced by http://purl.obolibrary.org/obo/BFO_0000054: 'is realized by' GROUP:OBI:<http://obi.sourceforge.net> PERSON: Chris Mungall executed_during has_realization is_realized_as obsolete_is_realized_by true obsoleted_has_specified_output_information A relation between a participant in a process, that produces a data set . The process is the realization of a concretization of a realizable information entity (objective specification or plan specification). In general, not all data present at the end of the process are specified_data. PERSON: Alan Ruttenberg PERSON: Frank Gibson obsoleted_has_specified_output_information true obsolete_has_function heart has_function to-pump-blood Relation between an independent continuant and a function. replaced by: http://purl.obolibrary.org/obo/BFO_0000085 GROUP:OBI:<http://obi.sourceforge.net> PERSON: Chris Mungall obsolete_has_function true obsoleted_is_reagent_in some Triton X-100 (Sigma-Aldrich) is_reagent_in instance of Chromium Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay Relationship between a substance and a protocol application in which it participates, where the substance has a ReagentRole Alan Ruttenberg obsoleted_is_reagent_in true obsolete_realizes example of usage: The process of 'histidine catabolism' (GO:0006548) realizes the function 'histidine ammonia lyase activity' (GO:0004397) (note: here 'activity' denotes a function and not a process). We leave open the possibility of defining in future the sub-relations directly_realizes (as bewteen a function and it's functioning) and indirectly_realizes. Relation between a process and a function, where the unfolding of the process requires the execution of the function. Class level: P realizes F iff: given any p that instantiates P, there exists some f, t such that f instantiates F at t and p *realizes* f. Here, *realizes* is the primitive instance level relation [GOC:cjm] replaced by http://purl.obolibrary.org/obo/BFO_0000055: 'realizes' GROUP:OBI:<http://obi.sourceforge.net> PERSON: Chris Mungal executes has_function_part involves_execution_of is_realization_of obsolete_realizes true obsoleted_utilizes_reagent see example_of_usage for is_reagent_in Relationship between a protocol application and a substance that has role reagent that participates in the protocol application Alan Ruttenberg obsoleted_utilizes_reagent true obsoleted_is_device_for some LKB 1272 Clinigamma counter is_device_for instance of Chromium Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay Relationship between a device and a protocol application in which it participates Alan Ruttenberg obsoleted_is_device_for true obsoleted_utilizes_device see example_of_usage for is_device_for Relationship between protocol application and an intrument in which it participates Alan Ruttenberg obsoleted_utilizes_device true is_proxy_for position on a gel is_proxy_for mass and charge of molecule in an western blot. Florescent intensity is_proxy_for amount of protein labeled with GFP. Examples: A260/A280 (of a DNA sample) is_proxy_for DNA-purity. NMR Sample scan is a proxy for sample quality. Within the assay mentioned here: https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay level of radioactivity is_proxy_for level of toxicity A relation between continuant instances c1 and c2 where within an experiment/ protocol application, measurement of c1 is used to determine what a measurement of c2 would be. A relation between continuant instances c1 and c2 where within a protocol application, measurement of c1 is related to a what would be the measurement of c2. (another definition) Alan Ruttenberg is_proxy_for obsoleted_has_specified_input_information A relation between a process and a participant in that process, that consumes a data set . The process is the realization of a concretization of a directive information entity (objective specification or plan specification). In general, not all data present at the beginning of the process are specified_data. PERSON: Frank Gibson PERSON:Alan Ruttenberg consumes data obsoleted_has_specified_input_information true obsolete_has_role A relation between a continuant C and a role R. The reciprocal relation of role_of. replaced by: http://purl.obolibrary.org/obo/BFO_0000087 GROUP:OBI:<http://obi.sourceforge.net> PERSON:Chris Mungal obsolete_has_role true obsolete_results_from 2009/11/23: BP, dev call:o bsoleted as discussed in tracker https://sourceforge.net/tracker/?func=detail&aid=2899860&group_id=177891&atid=886178 . Should be replaced by instead creating defined classes for materials, which are specified output of the process that conveys the obsolete_results_from true obsoleted_is_specified_information_output_of A relation between a data set and the process in which it participates and was produced. Inverse of outputs_specified_data relation. is replaced by has_specified_output_of PERSON: James Malone Editor obsoleted_is_specified_information_output_of true obsoleted_is_specified_information_intput_of Is the inverse relation of has_specfied_input_information is replaced by is_specified_intput_of obsoleted_is_specified_information_intput_of true is grain of A relation between granular parts and the whole of which they are a part. Granular parts have indeterminate number such that removing one granular part does not necessarily damage or diminish the whole. JAO: Added definition 2013-10-25 based on 'has grain', but both these terms seem problematic. PERSON: Alan Ruttenberg Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. With inspiration from the paper Granularity, scale and collectivity: When size does and does not matter, Alan Recto, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349 is grain of supplies A relation between an organisation or person and a material entity who owned or has license to the material entity and there was a legal transfer of ownership or licensing of the material entity to the current owner. GROUP: Relations branch supplies has_supplier A relation between a material entity and an organisation or person who owned or has license to the material entity and there was a legal transfer of ownership or licensing of the material entity to the current owner. PERSON: Alan Rutternberg PERSON: Cristian Cocos PERSON: Frank Gibson PERSON: Melanie Courtot has_supplier objective_achieved_by This relation obtains between a a objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process. OBI OBI objective_achieved_by is member of organization Relating a legal person or organization to an organization in the case where the legal person or organization has a role as member of the organization. 2009/10/01 Alan Ruttenberg. Barry prefers generic is-member-of. Question of what the range should be. For now organization. Is organization a population? Would the same relation be used to record members of a population JZ: Discussed on May 7, 2012 OBI dev call. Bjoern points out that we need to allow for organizations to be members of organizations. And agreed by the other OBI developers. So, human and organization were specified in 'Domains'. The textual definition was updated based on it. Person:Alan Ruttenberg Person:Helen Parkinson Person:Alan Ruttenberg Person:Helen Parkinson 2009/09/28 Alan Ruttenberg. Fucoidan-use-case is member of organization has category label A relation between a categorical measurement data item and the categorical label that indicates the value of that data item on the categorical scale. has category label has disposition to bind A relationship between two material entitites that each have disposition to form a complex with the other. This is a shortcut relation, and should expand to say that the two material entities have dispositions, point to the process in which they from a complex that realizes those dispositions, and points to the complex in which the two entities are 'bound to' each other IEDB has disposition to bind has organization member Relating an organization to a legal person or organization. See tracker: https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_id=177891&atid=886178 Person: Jie Zheng has organization member has performer performer relation covers the need to report on who performed a planned processed. it has to cover processes done by People or Devices (such as a robot controlled by software WF management system) has performer process is result of The production of IFN-gamma by effector T cells is a process result of T cell stimulation through the TCR is a relationship between a process and a preceding occurrent that directly caused the later one to occur IEDB PERSON:Bjoern Peters process is result of obsolete_is_described_by obsolete_is_described_by true bound_to A relationship between two material entities that form a complex based on a selective, non-covalent interaction. The definition of this term is modeled after the Chebi:50967 and GO:0005488 terms. Further alignment of the logical definitions with those ontologies will require agreement on the placement of GO:molecular function in BFO among other things. OBI will retire this term once such an alignment is achieved as 'bound to' is not in the primary OBI scope. bound_to participates in this blood clot participates in this blood coagulation this input material (or this output material) participates in this process this investigator participates in this investigation a relation between a continuant and a process, in which the continuant is somehow involved in the process participates_in participates in is concretized as A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants. is concretized as concretizes A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant. concretizes quality of this red color is a quality of this apple a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence A quality inheres in its bearer at all times for which the quality exists. is quality of quality_of quality of role of this investigator role is a role of this person a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. is role of role_of role of has quality this apple has quality this red color a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. has_quality has quality derives into this parent cell derives into this cell (cell division) this parent nucleus derives into this nucleus (nuclear division) a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'. derives_into derives into location of my head is the location of my brain this cage is the location of this rat a relation between two independent continuants, the location and the target, in which the target is entirely within the location Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime location_of location of located in my brain is located in my head this rat is located in this cage a relation between two independent continuants, the target and the location, in which the target is entirely within the location Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime located_in http://www.obofoundry.org/ro/#OBO_REL:located_in located in 2D boundary of the surface of my skin is a 2D boundary of my body a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. 2D_boundary_of boundary of is 2D boundary of is boundary of 2D boundary of has 2D boundary my body has 2D boundary the surface of my skin a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. has boundary has_2D_boundary has 2D boundary immediately precedes David Osumi-Sutherland ends_at_start_of meets X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) immediately precedes surrounded by x surrounded_by y if and only if x is adjacent to y and for every region r that is adjacent to x, r overlaps y surrounded by adjacent to adjacent to temporal relation move to BFO? Allen A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. temporal relation starts inverse of starts with Chris Mungall Allen starts member of An organism that is a member of a population of organisms is member of is a mereological relation between a item and a collection. is member of member part of SIO member of has member has member is a mereological relation between a collection and an item. SIO has member has measurement value has measurement value has x coordinate value has x coordinate value has z coordinate value has z coordinate value has y coordinate value has y coordinate value has_feature_value has_feature_value datatype property is used to describe the feature values which the feature class can contain, for example has_base can have feature values of nonNegativeInteger values. James Malone has_feature_value has specified value A relation between a value specification and a number that quantifies it. A range of 'real' might be better than 'float'. For now we follow 'has measurement value' until we can consider technical issues with SPARQL queries and reasoning. PERSON: James A. Overton OBI has specified value BFO:0000001 entity Entity entity Julius Caesar Verdi’s Requiem the Second World War your body mass index BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) entity Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf per discussion with Barry Smith An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) BFO:0000002 continuant Continuant continuant An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] continuant Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] BFO:0000003 occurrent Occurrent occurrent An entity that has temporal parts and that happens, unfolds or develops through time. BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players. Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] occurrent Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. per discussion with Barry Smith Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] BFO:0000004 ic IndependentContinuant independent continuant a chair a heart a leg a molecule a spatial region an atom an orchestra. an organism the bottom right portion of a human torso the interior of your mouth A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] independent continuant b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] BFO:0000005 obsolete dependent continuant A continuant that is either dependent on one or other independent continuant bearers or inheres in or is borne by other entities. obsolete dependent continuant true BFO:0000006 s-region SpatialRegion spatial region BFO 2 Reference: Spatial regions do not participate in processes. Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional. A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001]) All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] spatial region Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional. per discussion with Barry Smith A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001]) All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] BFO:0000008 t-region TemporalRegion temporal region Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001]) All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001]) Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] temporal region Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional per discussion with Barry Smith A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001]) All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001]) Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] BFO:0000009 2d-s-region TwoDimensionalSpatialRegion two-dimensional spatial region an infinitely thin plane in space. the surface of a sphere-shaped part of space A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001]) (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] two-dimensional spatial region A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001]) (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] BFO:0000011 st-region SpatiotemporalRegion spatiotemporal region the spatiotemporal region occupied by a human life the spatiotemporal region occupied by a process of cellular meiosis. the spatiotemporal region occupied by the development of a cancer tumor A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001]) All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001]) Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001]) Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001]) Every spatiotemporal region occupies_spatiotemporal_region itself. Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002]) (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] spatiotemporal region A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001]) All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001]) Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001]) Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001]) Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002]) (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] BFO:0000015 process Process process a process of cell-division, \ a beating of the heart a process of meiosis a process of sleeping the course of a disease the flight of a bird the life of an organism your process of aging. An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war) (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] process p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] BFO:0000016 disposition Disposition disposition an atom of element X has the disposition to decay to an atom of element Y certain people have a predisposition to colon cancer children are innately disposed to categorize objects in certain ways. the cell wall is disposed to filter chemicals in endocytosis and exocytosis BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type. b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] disposition b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] BFO:0000017 realizable RealizableEntity realizable entity the disposition of this piece of metal to conduct electricity. the disposition of your blood to coagulate the function of your reproductive organs the role of being a doctor the role of this boundary to delineate where Utah and Colorado meet A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] realizable entity To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] BFO:0000018 0d-s-region ZeroDimensionalSpatialRegion zero-dimensional spatial region A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001]) (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] zero-dimensional spatial region A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001]) (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] BFO:0000019 quality Quality quality the ambient temperature of this portion of air the color of a tomato the length of the circumference of your waist the mass of this piece of gold. the shape of your nose the shape of your nostril a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] quality a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] BFO:0000020 sdc SpecificallyDependentContinuant specifically dependent continuant Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key of one-sided specifically dependent continuants: the mass of this tomato of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates. the disposition of this fish to decay the function of this heart: to pump blood the mutual dependence of proton donors and acceptors in chemical reactions [79 the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction the pink color of a medium rare piece of grilled filet mignon at its center the role of being a doctor the shape of this hole. the smell of this portion of mozzarella A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] specifically dependent continuant b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. per discussion with Barry Smith (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] BFO:0000023 role Role role John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. the priest role the role of a boundary to demarcate two neighboring administrative territories the role of a building in serving as a military target the role of a stone in marking a property boundary the role of subject in a clinical trial the student role A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives. b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] role b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] BFO:0000024 fiat-object FiatObjectPart fiat object or with divisions drawn by cognitive subjects for practical reasons, such as the division of a cake (before slicing) into (what will become) slices (and thus member parts of an object aggregate). However, this does not mean that fiat object parts are dependent for their existence on divisions or delineations effected by cognitive subjects. If, for example, it is correct to conceive geological layers of the Earth as fiat object parts of the Earth, then even though these layers were first delineated in recent times, still existed long before such delineation and what holds of these layers (for example that the oldest layers are also the lowest layers) did not begin to hold because of our acts of delineation.Treatment of material entity in BFOExamples viewed by some as problematic cases for the trichotomy of fiat object part, object, and object aggregate include: a mussel on (and attached to) a rock, a slime mold, a pizza, a cloud, a galaxy, a railway train with engine and multiple carriages, a clonal stand of quaking aspen, a bacterial community (biofilm), a broken femur. Note that, as Aristotle already clearly recognized, such problematic cases – which lie at or near the penumbra of instances defined by the categories in question – need not invalidate these categories. The existence of grey objects does not prove that there are not objects which are black and objects which are white; the existence of mules does not prove that there are not objects which are donkeys and objects which are horses. It does, however, show that the examples in question need to be addressed carefully in order to show how they can be fitted into the proposed scheme, for example by recognizing additional subdivisions [29 the FMA:regional parts of an intact human body. the Western hemisphere of the Earth the division of the brain into regions the division of the planet into hemispheres the dorsal and ventral surfaces of the body the upper and lower lobes of the left lung BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] fiat object b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] BFO:0000026 1d-s-region OneDimensionalSpatialRegion one-dimensional spatial region an edge of a cube-shaped portion of space. A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001]) (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] one-dimensional spatial region A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001]) (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] BFO:0000027 object-aggregate ObjectAggregate object aggregate a collection of cells in a blood biobank. a swarm of bees is an aggregate of members who are linked together through natural bonds a symphony orchestra an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team) defined by fiat: the aggregate of members of an organization defined through physical attachment: the aggregate of atoms in a lump of granite defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container defined via attributive delimitations such as: the patients in this hospital the aggregate of bearings in a constant velocity axle joint the aggregate of blood cells in your body the nitrogen atoms in the atmosphere the restaurants in Palo Alto your collection of Meissen ceramic plates. An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee). ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] object aggregate An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] BFO:0000028 3d-s-region ThreeDimensionalSpatialRegion three-dimensional spatial region a cube-shaped region of space a sphere-shaped region of space, A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001]) (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] three-dimensional spatial region A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001]) (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] BFO:0000029 site Site site Manhattan Canyon) a hole in the interior of a portion of cheese a rabbit hole an air traffic control region defined in the airspace above an airport the Grand Canyon the Piazza San Marco the cockpit of an aircraft the hold of a ship the interior of a kangaroo pouch the interior of the trunk of your car the interior of your bedroom the interior of your office the interior of your refrigerator the lumen of your gut your left nostril (a fiat part – the opening – of your left nasal cavity) b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] site b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] BFO:0000030 object Object object atom cell cells and organisms engineered artifacts grain of sand molecule organelle organism planet solid portions of matter star BFO 2 Reference: BFO rests on the presupposition that at multiple micro-, meso- and macroscopic scales reality exhibits certain stable, spatially separated or separable material units, combined or combinable into aggregates of various sorts (for example organisms into what are called ‘populations’). Such units play a central role in almost all domains of natural science from particle physics to cosmology. Many scientific laws govern the units in question, employing general terms (such as ‘molecule’ or ‘planet’) referring to the types and subtypes of units, and also to the types and subtypes of the processes through which such units develop and interact. The division of reality into such natural units is at the heart of biological science, as also is the fact that these units may form higher-level units (as cells form multicellular organisms) and that they may also form aggregates of units, for example as cells form portions of tissue and organs form families, herds, breeds, species, and so on. At the same time, the division of certain portions of reality into engineered units (manufactured artifacts) is the basis of modern industrial technology, which rests on the distributed mass production of engineered parts through division of labor and on their assembly into larger, compound units such as cars and laptops. The division of portions of reality into units is one starting point for the phenomenon of counting. BFO 2 Reference: Each object is such that there are entities of which we can assert unproblematically that they lie in its interior, and other entities of which we can assert unproblematically that they lie in its exterior. This may not be so for entities lying at or near the boundary between the interior and exterior. This means that two objects – for example the two cells depicted in Figure 3 – may be such that there are material entities crossing their boundaries which belong determinately to neither cell. Something similar obtains in certain cases of conjoined twins (see below). BFO 2 Reference: To say that b is causally unified means: b is a material entity which is such that its material parts are tied together in such a way that, in environments typical for entities of the type in question,if c, a continuant part of b that is in the interior of b at t, is larger than a certain threshold size (which will be determined differently from case to case, depending on factors such as porosity of external cover) and is moved in space to be at t at a location on the exterior of the spatial region that had been occupied by b at t, then either b’s other parts will be moved in coordinated fashion or b will be damaged (be affected, for example, by breakage or tearing) in the interval between t and t.causal changes in one part of b can have consequences for other parts of b without the mediation of any entity that lies on the exterior of b. Material entities with no proper material parts would satisfy these conditions trivially. Candidate examples of types of causal unity for material entities of more complex sorts are as follows (this is not intended to be an exhaustive list):CU1: Causal unity via physical coveringHere the parts in the interior of the unified entity are combined together causally through a common membrane or other physical covering\. The latter points outwards toward and may serve a protective function in relation to what lies on the exterior of the entity [13, 47 BFO 2 Reference: an object is a maximal causally unified material entity BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74 b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001]) object b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001]) BFO:0000031 gdc GenericallyDependentContinuant generically dependent continuant The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. the pdf file on your laptop, the pdf file that is a copy thereof on my laptop the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] generically dependent continuant b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] BFO:0000034 function Function function the function of a hammer to drive in nails the function of a heart pacemaker to regulate the beating of a heart through electricity the function of amylase in saliva to break down starch into sugar BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc. A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] function A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] BFO:0000035 p-boundary ProcessBoundary process boundary the boundary between the 2nd and 3rd year of your life. p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001]) Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002]) (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] process boundary p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001]) Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002]) (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] BFO:0000038 1d-t-region OneDimensionalTemporalRegion one-dimensional temporal region the temporal region during which a process occurs. BFO 2 Reference: A temporal interval is a special kind of one-dimensional temporal region, namely one that is self-connected (is without gaps or breaks). A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] one-dimensional temporal region A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] BFO:0000040 material MaterialEntity material entity a flame a forest fire a human being a hurricane a photon a puff of smoke a sea wave a tornado an aggregate of human beings. an energy wave an epidemic the undetached arm of a human being An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] material entity A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] BFO:0000140 cf-boundary ContinuantFiatBoundary continuant fiat boundary b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001]) BFO 2 Reference: In BFO 1.1 the assumption was made that the external surface of a material entity such as a cell could be treated as if it were a boundary in the mathematical sense. The new document propounds the view that when we talk about external surfaces of material objects in this way then we are talking about something fiat. To be dealt with in a future version: fiat boundaries at different levels of granularity.More generally, the focus in discussion of boundaries in BFO 2.0 is now on fiat boundaries, which means: boundaries for which there is no assumption that they coincide with physical discontinuities. The ontology of boundaries becomes more closely allied with the ontology of regions. BFO 2 Reference: a continuant fiat boundary is a boundary of some material entity (for example: the plane separating the Northern and Southern hemispheres; the North Pole), or it is a boundary of some immaterial entity (for example of some portion of airspace). Three basic kinds of continuant fiat boundary can be distinguished (together with various combination kinds [29 Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions. Every continuant fiat boundary is located at some spatial region at every time at which it exists (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] continuant fiat boundary b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001]) Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions. (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] BFO:0000141 immaterial ImmaterialEntity immaterial entity BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10 immaterial entity BFO:0000142 1d-cf-boundary OneDimensionalContinuantFiatBoundary one-dimensional continuant fiat boundary The Equator all geopolitical boundaries all lines of latitude and longitude the line separating the outer surface of the mucosa of the lower lip from the outer surface of the skin of the chin. the median sulcus of your tongue a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001]) (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] one-dimensional continuant fiat boundary a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001]) (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] BFO:0000144 process-profile ProcessProfile process profile On a somewhat higher level of complexity are what we shall call rate process profiles, which are the targets of selective abstraction focused not on determinate quality magnitudes plotted over time, but rather on certain ratios between these magnitudes and elapsed times. A speed process profile, for example, is represented by a graph plotting against time the ratio of distance covered per unit of time. Since rates may change, and since such changes, too, may have rates of change, we have to deal here with a hierarchy of process profile universals at successive levels One important sub-family of rate process profiles is illustrated by the beat or frequency profiles of cyclical processes, illustrated by the 60 beats per minute beating process of John’s heart, or the 120 beats per minute drumming process involved in one of John’s performances in a rock band, and so on. Each such process includes what we shall call a beat process profile instance as part, a subtype of rate process profile in which the salient ratio is not distance covered but rather number of beat cycles per unit of time. Each beat process profile instance instantiates the determinable universal beat process profile. But it also instantiates multiple more specialized universals at lower levels of generality, selected from rate process profilebeat process profileregular beat process profile3 bpm beat process profile4 bpm beat process profileirregular beat process profileincreasing beat process profileand so on.In the case of a regular beat process profile, a rate can be assigned in the simplest possible fashion by dividing the number of cycles by the length of the temporal region occupied by the beating process profile as a whole. Irregular process profiles of this sort, for example as identified in the clinic, or in the readings on an aircraft instrument panel, are often of diagnostic significance. The simplest type of process profiles are what we shall call ‘quality process profiles’, which are the process profiles which serve as the foci of the sort of selective abstraction that is involved when measurements are made of changes in single qualities, as illustrated, for example, by process profiles of mass, temperature, aortic pressure, and so on. b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002]) b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005]) (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] process profile b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002]) b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005]) (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] BFO:0000145 r-quality RelationalQuality relational quality John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. a marriage bond, an instance of love, an obligation between one person and another. b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001]) (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] relational quality b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001]) (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] BFO:0000146 2d-cf-boundary TwoDimensionalContinuantFiatBoundary two-dimensional continuant fiat boundary a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001]) (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] two-dimensional continuant fiat boundary a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001]) (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] BFO:0000147 0d-cf-boundary ZeroDimensionalContinuantFiatBoundary zero-dimensional continuant fiat boundary the geographic North Pole the point of origin of some spatial coordinate system. the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona. a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001]) (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] zero-dimensional continuant fiat boundary zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona. requested by Melanie Courtot a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001]) (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] BFO:0000148 0d-t-region ZeroDimensionalTemporalRegion zero-dimensional temporal region a temporal region that is occupied by a process boundary right now the moment at which a child is born the moment at which a finger is detached in an industrial accident the moment of death. temporal instant. A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001]) (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] zero-dimensional temporal region A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001]) (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] BFO:0000182 history History history A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001]) history A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001]) CARO:0000004 portion of organism substance Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body. portion of organism substance CARO:0000043 portion of tissue Anatomical structure, that consists of similar cells and intercellular matrix, aggregated according to genetically determined spatial relationships. portion of tissue CARO:0000055 multi-tissue structure Anatomical structure that has as its parts two or more portions of tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types. multi-tissue structure CARO:0000066 epithelium Portion of tissue, that consists of one or more layers of epithelial cells connected to each other by cell junctions and which is underlain by a basal lamina. epithelium CARO:0001008 gross anatomical part Anatomical structure that is part of a multicellular organism and is at the gross anatomical level, e.g. above the level of a cell. Included are portions of organism substances such as blood, multi-cell-part structures such as axon tracts, acellular anatomical structures such as hair, and organism subdivisions such as head. Excluded is the whole organism and more granular parts of the organism, such as atoms, molecules, macromolecular complexes and cells. gross anatomical part CHEBI:15377 water An inorganic hydroxy compound that has formula H2O. water CHEBI:15956 biotin An organic heterobicyclic compound that consists of 2-oxohexahydro-1H-thieno[3,4-d]imidazole having a valeric acid substituent attached to the tetrahydrothiophene ring. The parent of the class of biotins. biotin CHEBI:16670 peptide Amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from alpha-amino acids, but it includes those derived from any amino carboxylic acid. X = OH, OR, NH2, NHR, etc. peptide CHEBI:16991 deoxyribonucleic acid High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms. deoxyribonucleic acid CHEBI:17137 hydrogensulfite A sulfur oxoanion that has formula HO3S. hydrogensulfite CHEBI:17234 glucose An aldohexose used as a source of energy and metabolic intermediate. glucose CHEBI:17709 5'-adenylyl sulfate An adenosine 5'-phosphate having a sulfo group attached to one the phosphate OH groups. 5'-adenylyl sulfate CHEBI:23367 molecular entity Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. We are assuming that every molecular entity has to be completely connected by chemical bonds. This excludes protein complexes, which are comprised of minimally two separate molecular entities. We will follow up with Chebi to ensure this is their understanding as well molecular entity CHEBI:23528 cytochalasin cytochalasin CHEBI:23995 N-ethyl-N-nitrosourea A member of the class of N-nitrosoureas that is urea in which one of the nitrogens is substituted by ethyl and nitroso groups. N-ethyl-N-nitrosourea CHEBI:24636 proton Nuclear particle of charge number +1, spin 1/2 and rest mass of 1.007276470(12) u. proton CHEBI:25078 luciferin A low-molecular-mass compound present in bioluminescent organisms that emits light when oxidized in presence of enzyme luciferase. luciferin CHEBI:26710 sodium chloride An inorganic chloride salt having sodium(1+) as the counterion. sodium chloride CHEBI:27889 lead(0) An elemental lead that has formula Pb. lead(0) CHEBI:28619 acrylamide A member of the class of acrylamides that results from the formal condensation of acrylic acid with ammonia. acrylamide CHEBI:29191 hydroxyl An oxygen radical that has formula HO. hydroxyl CHEBI:29237 deuterium atom The stable isotope of hydrogen with relative atomic mass 2.014102 and a natural abundance of 0.0115 atom percent (from Greek deltaepsilonupsilontauepsilonrhoomicronnu, second). deuterium atom CHEBI:30682 ruthenium atom An iron group element atom that has formula Ru. ruthenium atom CHEBI:31624 fluorescein A xanthene dye that is a highly fluorescent dye, detectable even when present in minute quantities. Used forensically to detect traces of blood, in analytical chemistry as an indicator in silver nitrate titrations and in microscopy. fluorescein CHEBI:31642 gadodiamide hydrate The hydrate of gadodiamide. gadodiamide hydrate CHEBI:31643 gadoteridol A non-ionic gadolinium chelate having a macrocyclic tetraamine framework. It is used as a paramagnetic contrast agent in magnetic resonance imaging (MRI). gadoteridol CHEBI:31991 phenol red 3H-2,1-Benzoxathiole 1,1-dioxide in which both of the hydrogens at position 3 have been substituted by 4-hydroxyphenyl groups. A pH indicator changing colour from yellow below pH 6.8 to bright pink above pH 8.2, it is commonly used as an indicator in cell cultures and in home swimming pool test kits. It is also used in the (now infrequently performed) phenolsulfonphthalein (PSP) test for estimation of overall blood flow through the kidney. phenol red CHEBI:32142 sodium citrate dihydrate The dihydrate of trisodium citrate. sodium citrate dihydrate CHEBI:33250 atom A chemical entity constituting the smallest component of an element having the chemical properties of the element. atom CHEBI:33359 rhodium atom A cobalt group element atom that has formula Rh. rhodium atom CHEBI:33375 gadolinium atom A lanthanoid atom that has formula Gd. gadolinium atom CHEBI:33376 terbium atom A lanthanoid atom that has formula Tb. terbium atom CHEBI:33696 nucleic acid A macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid. nucleic acid CHEBI:33697 ribonucleic acid High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds; RNA is central to the synthesis of proteins. ribonucleic acid CHEBI:33709 amino acid A carboxylic acid containing one or more amino groups. amino acid CHEBI:33839 macromolecule A macromolecule is a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. polymer macromolecule CHEBI:35729 gadolinium molecular entity gadolinium molecular entity CHEBI:37333 gadodiamide A non-ionic gadolinium chelate having a macrocyclic triamine framework. It is used as a paramagnetic contrast agent in magnetic resonance imaging (MRI). gadodiamide CHEBI:37586 sodium phosphate sodium phosphate CHEBI:37972 phosphorus-32 atom The radioactive isotope of phosphorus with relative atomic mass 31.973907 and half-life of 14.26 days. phosphorus-32 atom CHEBI:37973 phosphorus-33 atom The radioactive isotope of phosphorus with relative atomic mass 32.971725, half-life of 25.34 days and nuclear spin (1)/2. phosphorus-33 atom CHEBI:37987 Cy3 dye Cy3 dye CHEBI:37989 Cy5 dye Cy5 dye CHEBI:42098 digoxigenin A hydroxy steroid that consists of 5beta-cardanolide having a double bond at the 20(22)-position as well as hydroxy groups at the 3beta-, 12beta- and 14beta-positions. It has been isolated from the plant species of the genus Digitalis. digoxigenin CHEBI:42191 ethylenediaminetetraacetic acid A polyamino carboxylic acid that has formula C10H16N2O8. ethylenediaminetetraacetic acid CHEBI:4705 double-stranded DNA double-stranded DNA CHEBI:472552 5-bromo-2'-deoxyuridine A pyrimidine 2'-deoxyribonucleoside compound having 5-bromouracil as the nucleobase. 5-bromo-2'-deoxyuridine CHEBI:50076 chromium-51 A synthetic radioactive isotope of chromium having a half-life of 27.7 days and decaying by electron capture with emission of gamma rays (0.32 MeV); it is used to label red blood cells for measurement of mass or volume, survival time, and sequestration studies, for the diagnosis of gastrointestinal bleeding, and to label platelets to study their survival. chromium-51 CHEBI:51756 Alexa Fluor 532 An organosulfonic acid that has formula C34H33N3O11S2. Alexa Fluor 532 CHEBI:51760 Alexa Fluor 546 An organic heteropentacyclic compound that has formula C44H46Cl3N4NaO14S3. Alexa Fluor 546 CHEBI:52673 Alexa Fluor 555 A fluorescent dye of absorption wavelength 555 nm and emission wavelength 565 nm, derived from a 3,6-diaminoxanthene-4,5-disulfate. Alexa Fluor 555 CHEBI:53526 tritiated thymidine Thymidine linked to the radioisotope tritium. Used to label DNA in the study of cellular and viral DNA synthesis. tritiated thymidine CHEBI:59050 dimethyl sulfate The dimethyl ester of sulfuric acid. dimethyl sulfate CHEBI:59051 diethyl pyrocarbonate The diethyl ester of dicarbonic acid. diethyl pyrocarbonate CHEBI:59052 1,1-dihydroxy-3-ethoxy-2-butanone A butanone derivative having two hydroxy substituents at the 1-position and an ethoxy substituent at the 3-position. 1,1-dihydroxy-3-ethoxy-2-butanone CHEBI:59053 N-cyclohexyl-N'-(2-(4-morpholinyl)ethyl)carbodiimide A carbodiimide having cyclcohexyl and 2-(4-morpholinyl)ethyl as the two N-substituents. N-cyclohexyl-N'-(2-(4-morpholinyl)ethyl)carbodiimide CHEBI:59054 N-methylisatoic anhydride A 3,1-benzoxazin-1,4-dione having an N-methyl substituent. N-methylisatoic anhydride CHEBI:59055 (S)-1-(4-bromoacetamidobenzyl)EDTA A tetracarboxylic acid consisting of ethylenediaminetetraacetic acid having a 4-bromoacetamidobenzyl group at the C1-position and (S)-configuration. (S)-1-(4-bromoacetamidobenzyl)EDTA CHEBI:59056 EDTA methidiumpropylamide A combined intercalating and chelating reagent. The iron chelate, prepared by adding Fe(NH4)2(SO4)2, effects random oxidative cleavage of DNA in the presence of O2 and a reducing agent. This activity is useful as a footprinting probe. EDTA methidiumpropylamide CHEBI:59424 bromophenol blue 3H-2,1-Benzoxathiole 1,1-dioxide in which both of the hydrogens at position 3 have been substituted by 3,5-dibromo-4-hydroxyphenyl groups. It is used as a laboratory indicator, changing from yellow below pH 3 to purple at pH 4.6, and as a size marker for monitoring the progress of agarose gel and polyacrylamide gel electrophoresis. It has also been used as an industrial dye. bromophenol blue CHEBI:9754 tris A primary amino compound that is tert-butylamine in which one hydrogen attached to each methyl group is replaced by a hydroxy group. A compound widely used as a biological buffer substance in the pH range 7--9; pKa = 8.3 at 20 degreeC; pKa = 7.82 at 37 degreeC. tris CLO:0000001 cell line cell A cultured cell that is part of a cell line - a stable and homogeneous population of cells with a common biological origin and propagation history in culture cell line cell 'derives from' is transitive, so even cell line cells created through modification of an existing cell line cell have derived_from some initial primary cultured cell that existed at some point in time. CLO:0000018 mortal cell line cell A cell line cell that is capable of replicating a limited number of times in culture before undergoing senescence. mortal cell line cell CLO:0000019 immortal cell line cell A cell line cell that is expected to be capable of an unlimited number of divisions, and is thus able to support indefinite propagation in vitro as part of an immortal cell line. immortal cell line cell CLO:0000031 cell line A cultured cell population that represents a genetically stable and homogenous population of cultured cells that shares a common propagation history (i.e. has been successively passaged together in culture). cell line CLO:0000578 CLO:0007599 CLO:0007605 CLO:0009251 CLO:0009828 immortal cell line A cell line that is expected to be capable of indefinite propagation in an vitro culture. immortal cell line 0 CLO:0009829 mortal cell line A cell line is able to support only a limited number of passages in vitro. mortal cell line CL:0000000 cell PMID:18089833.Cancer Res. 2007 Dec 15;67(24):12018-25. "...Epithelial cells were harvested from histologically confirmed adenocarcinomas .." A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. cell CL:0000001 primary cultured cell A cultured cell that is freshly isolated from a organismal source, or derives in culture from such a cell prior to the culture being passaged. primary cultured cell CL:0000003 native cell A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment). native cell CL:0000010 cultured cell A cell in vitro that is or has been maintained or propagated as part of a cell culture. cultured cell CL:0000057 fibroblast A connective tissue cell which secretes an extracellular matrix rich in collagen and other macromolecules. Flattened and irregular in outline with branching processes; appear fusiform or spindle-shaped. fibroblast CL:0000066 epithelial cell A cell that is usually found in a two-dimensional sheet with a free surface. The cell has a cytoskeleton that allows for tight cell to cell contact and for cell polarity where apical part is directed towards the lumen and the basal part to the basal lamina. epithelial cell CL:0000084 T cell A type of lymphocyte whose defining characteristic is the expression of a T cell receptor complex. T cell CL:0000097 mast cell A cell that is found in almost all tissues containing numerous basophilic granules and capable of releasing large amounts of histamine and heparin upon activation. Progenitors leave bone marrow and mature in connective and mucosal tissue. Mature mast cells are found in all tissues, except the bloodstream. Their phenotype is CD117-high, CD123-negative, CD193-positive, CD200R3-positive, and FceRI-high. Stem-cell factor (KIT-ligand; SCF) is the main controlling signal of their survival and development. mast cell CL:0000182 hepatocyte The main structural component of the liver. They are specialized epithelial cells that are organized into interconnected plates called lobules. Majority of cell population of liver, polygonal in shape, arranged in plates or trabeculae between sinusoids; may have single nucleus or binucleated. hepatocyte CL:0000232 erythrocyte A red blood cell. In mammals, mature erythrocytes are biconcave disks containing hemoglobin whose function is to transport oxygen. erythrocyte CL:0000235 macrophage A mononuclear phagocyte present in variety of tissues, typically differentiated from monocytes, capable of phagocytosing a variety of extracellular particulate material, including immune complexes, microorganisms, and dead cells. macrophage CL:0000236 B cell A lymphocyte of B lineage with the phenotype CD19-positive, CD20-positive, and capable of B cell mediated immunity. B cell CL:0000451 dendritic cell A cell of hematopoietic origin, typically resident in particular tissues, specialized in the uptake, processing, and transport of antigens to lymph nodes for the purpose of stimulating an immune response via T cell activation. These cells are lineage negative (CD3-negative, CD19-negative, CD34-negative, and CD56-negative). dendritic cell CL:0000542 lymphocyte A lymphocyte is a leukocyte commonly found in the blood and lymph that has the characteristics of a large nucleus, a neutral staining cytoplasm, and prominent heterochromatin. lymphocyte CL:0000578 experimentally modified cell in vitro A cell in vitro that has undergone physical changes as a consequence of a deliberate and specific experimental procedure. experimentally modified cell in vitro CL:0000624 CD4-positive, alpha-beta T cell A mature alpha-beta T cell that expresses an alpha-beta T cell receptor and the CD4 coreceptor. CD4-positive, alpha-beta T cell CL:0000625 CD8-positive, alpha-beta T cell A T cell expressing an alpha-beta T cell receptor and the CD8 coreceptor. CD8-positive, alpha-beta T cell CL:0000767 basophil Any of the immature or mature forms of a granular leukocyte that in its mature form has an irregularly shaped, pale-staining nucleus that is partially constricted into two lobes, and with cytoplasm that contains coarse, bluish-black granules of variable size. Basophils contain vasoactive amines such as histamine and serotonin, which are released on appropriate stimulation. A basophil is CD123-positive, CD193-positive, CD203c-positive, and FceRIa-positive. basophil CL:0000786 plasma cell A terminally differentiated, post-mitotic, antibody secreting cell of the B cell lineage with the phenotype CD138-positive, surface immunonoglobulin-negative, and MHC Class II-negative. Plasma cells are oval or round with extensive rough endoplasmic reticulum, a well-developed Golgi apparatus, and a round nucleus having a characteristic cartwheel heterochromatin pattern and are devoted to producing large amounts of immunoglobulin. plasma cell CL:0000789 alpha-beta T cell A T cell that expresses an alpha-beta T cell receptor complex. alpha-beta T cell CL:0000794 CD8-positive, alpha-beta cytotoxic T cell A CD8-positive, alpha-beta T cell that is capable of killing target cells in an antigen specific manner with the phenotype perforin-positive and granzyme B-positive. CD8-positive, alpha-beta cytotoxic T cell CL:0000814 mature NK T cell A mature alpha-beta T cell of a distinct lineage that bears natural killer markers and a T cell receptor specific for a limited set of ligands. NK T cells have activation and regulatory roles particularly early in an immune response. mature NK T cell CL:0000842 mononuclear cell A leukocyte with a single non-segmented nucleus in the mature form. mononuclear cell EGO:0000000001 a material entity that is made up of chemical compounds and proteins that can attach to DNA and direct such actions as turning genes on or off, controlling the production of proteins in particular cells. WEB: https://en.wikipedia.org/wiki/Epigenome Oliver He, Steve Qin, and Steve Pittard When epigenomic compounds attach to DNA and modify its function, they are said to have "marked" the genome. These marks do not change the sequence of the DNA. Rather, they change the way cells use the DNA's instructions. The marks are sometimes passed on from cell to cell as cells divide. They also can be passed down from one generation to the next. epigenome EGO:0000000002 a genomic location in human Oliver He human genomic location EGO:0000000003 a genomic location in human chromosome I Oliver He human chromosome I location EGO:0000000004 the position 3 in a genomic location in human chromosome I Oliver He Pos 3 of human Chr I EGO:0000000005 an epigenome that exists in a eukaryotic organism WEB: https://www.genome.gov/27532724 Oliver He, Steve Qin, and Steve Pittard eukaryotic epigenome EGO:0000000006 a genomic location in mouse Oliver He mouse genomic location EGO:0000000007 MAX binding EGO:0000000009 a eukaryotic epigenome that exists in human. WEB: https://en.wikipedia.org/wiki/Epigenome Oliver He, Steve Qin, and Steve Pittard The epigenome marks the genome in two main ways, both of which play a role in turning genes on or off. The first type of mark, called DNA methylation, directly affects the DNA in a genome. In this process, proteins attach chemical tags called methyl groups to the bases of the DNA molecule in specific places. The methyl groups turn genes on or off by affecting interactions between the DNA and other proteins. In this way, cells can remember which genes are on or off. The second kind of mark, called histone modification, affects DNA indirectly. DNA in cells is wrapped around histone proteins, which form spool-like structures that enable DNA's very long molecules to be wound up neatly into chromosomes inside the cell nucleus. Proteins can attach a variety of chemical tags to histones. Other proteins in cells can detect these tags and determine whether that region of DNA should be used or ignored in that cell. Web: https://www.genome.gov/27532724 The human genome is the complete assembly of DNA (deoxyribonucleic acid)-about 3 billion base pairs - that makes each individual unique. DNA holds the instructions for building the proteins that carry out a variety of functions in a cell. Web: https://www.genome.gov/27532724 human epigenome EGO:0000000010 a eukaryotic epigenome that exists in mouse WEB: https://en.wikipedia.org/wiki/Epigenome Oliver He, Steve Qin, and Steve Pittard mouse epigenome EGO:0000000011 a site that indicates the location at a genome Oliver He genomic location EGO:0000000013 MAX binding in MCF-7 cell EGO:0000000016 the position 5 in a genomic location in human chromosome I Oliver He Pos 5 of human Chr I ENVO:00001998 soil Soil is an environmental material which is primarily composed of minerals, varying proportions of sand, silt, and clay, organic material such as humus, gases, liquids, and a broad range of resident micro- and macroorganisms. soil ENVO:00002257 podzol Podzols are soils with a typically ash-grey upper subsurface horizon, bleached by loss of organic matter and iron oxides, on top of a dark accumulation horizon with brown, reddish or black illuviated humus and/or reddish Fe compounds. Podzols occur in humid areas in the boreal and temperate zones and locally also in the tropics. podzol ENVO:00010483 environmental material A portion of environmental material is a fiat object which forms the medium or part of the medium of an environmental system. environmental material GO:0001047 core promoter binding Interacting selectively and non-covalently with the regulatory region composed of the transcription start site and binding sites for the basal transcription machinery. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors. core promoter binding GO:0001788 antibody-dependent cellular cytotoxicity Cytolysis of target cells by natural killer cells, eosinophils, neutrophils, monocytes, or macrophages following engagement of antibodies bound to the target cells by Fc receptors on the effector cells. antibody-dependent cellular cytotoxicity GO:0001806 type IV hypersensitivity An inflammatory response driven by T cell recognition of processed soluble or cell-associated antigens leading to cytokine release and leukocyte activation. type IV hypersensitivity GO:0001816 cytokine production The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. cytokine production GO:0001906 cell killing Any process in an organism that results in the killing of its own cells or those of another organism, including in some cases the death of the other organism. Killing here refers to the induction of death in one cell by another cell, not cell-autonomous death due to internal or other environmental conditions. cell killing GO:0001913 T cell mediated cytotoxicity The directed killing of a target cell by a T cell through the release of granules containing cytotoxic mediators or through the engagement of death receptors. T cell mediated cytotoxicity GO:0002250 adaptive immune response An immune response based on directed amplification of specific receptors for antigen produced through a somatic diversification process, and allowing for enhanced response to subsequent exposures to the same antigen (immunological memory). adaptive immune response GO:0002367 cytokine production involved in immune response The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus contributing to an immune response, resulting in an increase in its intracellular or extracellular levels. cytokine production involved in immune response GO:0002390 platelet activating factor production The synthesis or release of platelet activating factor following a stimulus, resulting in an increase in its intracellular or extracellular levels. platelet activating factor production GO:0002507 tolerance induction A process that directly activates any of the steps required for tolerance, a physiologic state in which the immune system does not react destructively against the components of an organism that harbors it or against antigens that are introduced to it. tolerance induction GO:0002514 B cell tolerance induction A process involving any mechanism for tolerance induction in B cells. B cell tolerance induction GO:0002517 T cell tolerance induction A process involving any mechanism for tolerance induction in T cells. T cell tolerance induction GO:0002524 hypersensitivity An inflammatory response to an exogenous environmental antigen or an endogenous antigen initiated by the adaptive immune system. hypersensitivity GO:0002534 cytokine production involved in inflammatory response The synthesis or release of a cytokine following a inflammatory stimulus as part of an inflammatory response, resulting in an increase in its intracellular or extracellular levels. cytokine production involved in inflammatory response GO:0003674 molecular_function Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions. molecular_function GO:0003823 antigen binding Interacting selectively and non-covalently with an antigen, any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen. antigen binding GO:0003824 catalytic activity Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. catalytic activity GO:0003964 RNA-directed DNA polymerase activity Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). Catalyzes RNA-template-directed extension of the 3'- end of a DNA strand by one deoxynucleotide at a time. RNA-directed DNA polymerase activity GO:0005216 ion channel activity Catalysis of facilitated diffusion of an ion (by an energy-independent process) by passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism. ion channel activity GO:0005575 cellular_component The part of a cell or its extracellular environment in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together. cellular_component GO:0005694 chromosome A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information. chromosome GO:0005739 mitochondrion A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration. mitochondrion GO:0006006 glucose metabolic process The chemical reactions and pathways involving glucose, the aldohexose gluco-hexose. D-glucose is dextrorotatory and is sometimes known as dextrose; it is an important source of energy for living organisms and is found free as well as combined in homo- and hetero-oligosaccharides and polysaccharides. glucose metabolic process GO:0006260 DNA replication The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA. DNA replication GO:0006306 DNA methylation The covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine. DNA methylation GO:0006338 chromatin remodeling Dynamic structural changes to eukaryotic chromatin occurring throughout the cell division cycle. These changes range from the local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation. chromatin remodeling GO:0006909 phagocytosis An endocytosis process that results in the engulfment of external particulate material by phagocytes. The particles are initially contained within phagocytic vacuoles (phagosomes), which then fuse with primary lysosomes to effect digestion of the particles. phagocytosis GO:0006955 immune response Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat. immune response GO:0006974 cellular response to DNA damage stimulus Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism. cellular response to DNA damage stimulus GO:0007049 cell cycle The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division. cell cycle GO:0007596 blood coagulation The sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers. blood coagulation GO:0008134 GO:0008150 biological_process Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end. biological_process GO:0008228 opsonization The process in which a microorganism (or other particulate material) is rendered more susceptible to phagocytosis by coating with an opsonin, a blood serum protein such as a complement component or antibody. opsonization GO:0008283 cell proliferation The multiplication or reproduction of cells, resulting in the expansion of a cell population. cell proliferation GO:0009566 fertilization The union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. It involves the fusion of the gametic nuclei (karyogamy) and cytoplasm (plasmogamy). fertilization GO:0009987 cellular process Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. cellular process GO:0010467 gene expression The process in which a gene's sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form. gene expression GO:0010573 vascular endothelial growth factor production The appearance of vascular endothelial growth factor production due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. vascular endothelial growth factor production GO:0016064 immunoglobulin mediated immune response An immune response mediated by immunoglobulins, whether cell-bound or in solution. immunoglobulin mediated immune response GO:0016570 histone modification The covalent alteration of one or more amino acid residues within a histone protein. histone modification GO:0019814 immunoglobulin complex A protein complex that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains, held together by disulfide bonds and sometimes complexed with additional proteins. An immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph. immunoglobulin complex GO:0019815 B cell receptor complex An immunoglobulin complex that is present in the plasma membrane of B cells and that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains and a signaling subunit, a heterodimer of the Ig-alpha and Ig-beta proteins. B cell receptor complex GO:0019882 antigen processing and presentation The process in which an antigen-presenting cell expresses antigen (peptide or lipid) on its cell surface in association with an MHC protein complex. antigen processing and presentation GO:0019904 protein domain specific binding Interacting selectively and non-covalently with a specific domain of a protein. protein domain specific binding GO:0030041 actin filament polymerization Assembly of actin filaments by the addition of actin monomers to a filament. actin filament polymerization GO:0030097 hemopoiesis The process whose specific outcome is the progression of the myeloid and lymphoid derived organ/tissue systems of the blood and other parts of the body over time, from formation to the mature structure. The site of hemopoiesis is variable during development, but occurs primarily in bone marrow or kidney in many adult vertebrates. hemopoiesis GO:0032601 connective tissue growth factor production The appearance of connective tissue growth factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. connective tissue growth factor production GO:0032602 chemokine production The appearance of a chemokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. chemokine production GO:0032604 granulocyte macrophage colony-stimulating factor production The appearance of granulocyte macrophage colony-stimulating factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. granulocyte macrophage colony-stimulating factor production GO:0032605 hepatocyte growth factor production The appearance of hepatocyte growth factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. hepatocyte growth factor production GO:0032606 type I interferon production The appearance of type I interferon due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families. type I interferon production GO:0032608 interferon-beta production The appearance of interferon-beta due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. interferon-beta production GO:0032609 interferon-gamma production The appearance of interferon-gamma due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Interferon-gamma is also known as type II interferon. interferon-gamma production GO:0032610 interleukin-1 alpha production The appearance of interleukin-1 alpha due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. interleukin-1 alpha production GO:0032611 interleukin-1 beta production The appearance of interleukin-1 beta due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. interleukin-1 beta production GO:0032612 interleukin-1 production The appearance of interleukin-1 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. interleukin-1 production GO:0032613 interleukin-10 production The appearance of interleukin-10 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. interleukin-10 production GO:0032614 interleukin-11 production The appearance of interleukin-11 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. interleukin-11 production GO:0032615 interleukin-12 production The appearance of interleukin-12 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. interleukin-12 production GO:0032616 interleukin-13 production The appearance of interleukin-13 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. interleukin-13 production GO:0032617 interleukin-14 production The appearance of interleukin-14 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. interleukin-14 production GO:0032618 interleukin-15 production The appearance of interleukin-15 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. interleukin-15 production GO:0032619 interleukin-16 production The appearance of interleukin-16 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. interleukin-16 production GO:0032620 interleukin-17 production The appearance of any member of the interleukin-17 family of cytokines due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. interleukin-17 production GO:0032621 interleukin-18 production The appearance of interleukin-18 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. interleukin-18 production GO:0032622 interleukin-19 production The appearance of interleukin-19 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. interleukin-19 production GO:0032623 interleukin-2 production The appearance of interleukin-2 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. interleukin-2 production GO:0032624 interleukin-20 production The appearance of interleukin-20 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. interleukin-20 production GO:0032625 interleukin-21 production The appearance of interleukin-21 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. interleukin-21 production GO:0032626 interleukin-22 production The appearance of interleukin-22 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. interleukin-22 production GO:0032627 interleukin-23 production The appearance of interleukin-23 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. interleukin-23 production GO:0032628 interleukin-24 production The appearance of interleukin-24 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. interleukin-24 production GO:0032629 interleukin-25 production The appearance of interleukin-25 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. interleukin-25 production GO:0032630 interleukin-26 production The appearance of interleukin-26 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. interleukin-26 production GO:0032631 interleukin-27 production The appearance of interleukin-27 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. interleukin-27 production GO:0032632 interleukin-3 production The appearance of interleukin-3 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. interleukin-3 production GO:0032633 interleukin-4 production The appearance of interleukin-4 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. interleukin-4 production GO:0032634 interleukin-5 production The appearance of interleukin-5 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. interleukin-5 production GO:0032635 interleukin-6 production The appearance of interleukin-6 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. interleukin-6 production GO:0032636 interleukin-7 production The appearance of interleukin-7 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. interleukin-7 production GO:0032637 interleukin-8 production The appearance of interleukin-8 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. interleukin-8 production GO:0032638 interleukin-9 production The appearance of interleukin-9 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. interleukin-9 production GO:0032639 TRAIL production The appearance of TRAIL due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. TRAIL production GO:0032640 tumor necrosis factor production The appearance of tumor necrosis factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. TNF alpha production tumor necrosis factor production GO:0032641 lymphotoxin A production The appearance of lymphotoxin A due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. TNF beta production lymphotoxin A production GO:0032905 transforming growth factor beta1 production The appearance of transforming growth factor-beta1 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. transforming growth factor beta1 production GO:0032906 transforming growth factor beta2 production The appearance of transforming growth factor-beta2 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. transforming growth factor beta2 production GO:0032907 transforming growth factor beta3 production The appearance of transforming growth factor-beta3 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. transforming growth factor beta3 production GO:0033036 macromolecule localization Any process in which a macromolecule is transported to, or maintained in, a specific location. macromolecule localization GO:0034061 DNA polymerase activity Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a nucleic acid template and a 3'hydroxyl group. DNA polymerase activity GO:0034343 type III interferon production The appearance of type III interferon due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Interferon lambda is the only member of the type III interferon found so far. type III interferon production GO:0035393 chemokine (C-X-C motif) ligand 9 production The appearance of chemokine (C-X-C motif) ligand 9 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. chemokine (C-X-C motif) ligand 9 production GO:0035397 helper T cell enhancement of adaptive immune response Positive regulation of an adaptive immune response mediated via cytokine production by helper T cell. helper T cell enhancement of adaptive immune response GO:0035398 helper T cell enhancement of T cell mediated immune response Positive regulation of a T cell mediated immune response mediated via cytokine production by a helper T cell. helper T cell enhancement of T cell mediated immune response GO:0035399 helper T cell enhancement of B cell mediated immune response Positive regulation of a B cell mediated immune response mediated via cytokine production by a helper T cell. helper T cell enhancement of B cell mediated immune response GO:0035746 granzyme A production The appearance of granzyme A due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. granzyme A production GO:0035944 perforin production The appearance of a perforin protein due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. perforin production GO:0036262 granulysin production The appearance of granulysin due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. granulysin production GO:0040029 regulation of gene expression, epigenetic Any process that modulates the frequency, rate or extent of gene expression; the process is mitotically or meiotically heritable, or is stably self-propagated in the cytoplasm of a resting cell, and does not entail a change in DNA sequence. regulation of gene expression, epigenetic GO:0040030 regulation of molecular function, epigenetic Any heritable epigenetic process that modulates the frequency, rate or extent of protein function by self-perpetuating conformational conversions of normal proteins in healthy cells. This is distinct from, though mechanistically analogous to, disease states associated with prion propagation and amyloidogenesis. A single protein, if it carries a glutamine/asparagine-rich ('prion') domain, can sometimes stably exist in at least two distinct physical states, each associated with a different phenotype; propagation of one of these traits is achieved by a self-perpetuating change in the protein from one form to the other, mediated by conformational changes in the glutamine/asparagine-rich domain. Prion domains are both modular and transferable to other proteins, on which they can confer a heritable epigenetic alteration of function; existing bioinformatics data indicate that they are rare in non-eukarya, but common in eukarya. regulation of molecular function, epigenetic GO:0042098 T cell proliferation The expansion of a T cell population by cell division. Follows T cell activation. T cell proliferation GO:0042101 T cell receptor complex A protein complex that contains a disulfide-linked heterodimer of T cell receptor (TCR) chains, which are members of the immunoglobulin superfamily, and mediates antigen recognition, ultimately resulting in T cell activation. The TCR heterodimer is associated with the CD3 complex, which consists of the nonpolymorphic polypeptides gamma, delta, epsilon, zeta, and, in some cases, eta (an RNA splice variant of zeta) or Fc epsilon chains. T cell receptor complex GO:0042110 T cell activation The change in morphology and behavior of a mature or immature T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific. T cell activation GO:0042571 immunoglobulin complex, circulating An immunoglobulin complex that is secreted into extracellular space and found in mucosal areas or other tissues or circulating in the blood or lymph. In its canonical form, a circulating immunoglobulin complex is composed of two identical heavy chains and two identical light chains, held together by disulfide bonds. Some forms of are polymers of the basic structure and contain additional components such as J-chain and the secretory component. antibody antibody immunoglobulin complex, circulating GO:0042575 DNA polymerase complex A protein complex that possesses DNA polymerase activity and is involved in template directed synthesis of DNA. DNA polymerase complex GO:0042605 peptide antigen binding Interacting selectively and non-covalently with an antigen peptide. peptide antigen binding GO:0042611 MHC protein complex A transmembrane protein complex composed of an MHC alpha chain and, in most cases, either an MHC class II beta chain or an invariant beta2-microglobin chain, and with or without a bound peptide, lipid, or polysaccharide antigen. MHC protein complex GO:0043227 membrane-bounded organelle Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. membrane-bounded organelle GO:0043234 protein complex A ribosome is a protein complex Any macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical. protein complex GO:0043316 cytotoxic T cell degranulation The regulated exocytosis of secretory granules containing preformed mediators such as perforin and granzymes by a cytotoxic T cell. cytotoxic T cell degranulation GO:0043565 sequence-specific DNA binding Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding. sequence-specific DNA binding GO:0044030 regulation of DNA methylation Any process that modulates the frequency, rate or extent of the covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine. regulation of DNA methylation GO:0044807 macrophage migration inhibitory factor production The appearance of macrophage migration inhibitory factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. macrophage migration inhibitory factor production GO:0044808 Oncostatin M production The appearance of Oncostatin M due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Oncostatin M production GO:0044809 chemokine (C-C motif) ligand 17 production The appearance of chemokine (C-C motif) ligand 17 (CCL17) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. chemokine (C-C motif) ligand 17 production GO:0048869 cellular developmental process A biological process whose specific outcome is the progression of a cell over time from an initial condition to a later condition. cellular developmental process GO:0050896 response to stimulus Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism. response to stimulus GO:0051276 chromosome organization A process that is carried out at the cellular level that results in the assembly, arrangement of constituent parts, or disassembly of chromosomes, structures composed of a very long molecule of DNA and associated proteins that carries hereditary information. This term covers covalent modifications at the molecular level as well as spatial relationships among the major components of a chromosome. chromosome organization GO:0070358 actin polymerization-dependent cell motility A process involved in the controlled movement of a bacterial cell powered by the continuous polymerization of actin at one pole of the cell. actin polymerization-dependent cell motility GO:0071604 transforming growth factor beta production The appearance of any member of the transforming growth factor-beta family of cytokines due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Transforming growth factor-beta family members include TGF-B1, TGF-B2, and TGF-B3. transforming growth factor beta production GO:0071605 monocyte chemotactic protein-1 production The appearance of monocyte chemotactic protein-1 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. monocyte chemotactic protein-1 production GO:0071606 chemokine (C-C motif) ligand 4 production The appearance of chemokine (C-C motif) ligand 4 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. chemokine (C-C motif) ligand 4 production GO:0071607 macrophage inflammatory protein-1 gamma production The appearance of macrophage inflammatory protein-1 gamma due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. macrophage inflammatory protein-1 gamma production GO:0071608 macrophage inflammatory protein-1 alpha production The appearance of macrophage inflammatory protein 1 alpha due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. macrophage inflammatory protein-1 alpha production GO:0071609 chemokine (C-C motif) ligand 5 production The appearance of chemokine (C-C motif) ligand 5 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. chemokine (C-C motif) ligand 5 production GO:0071610 chemokine (C-C motif) ligand 1 production The appearance of chemokine (C-C motif) ligand 1 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. chemokine (C-C motif) ligand 1 production GO:0071611 granulocyte colony-stimulating factor production The appearance of granulocyte colony-stimulating factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. granulocyte colony-stimulating factor production GO:0071612 IP-10 production The appearance of IP-10 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. IP-10 production GO:0071613 granzyme B production The appearance of granzyme B due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. granzyme B production GO:0071706 tumor necrosis factor superfamily cytokine production The appearance of any member of the TNF superfamily due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. tumor necrosis factor superfamily cytokine production GO:0071924 chemokine (C-C motif) ligand 22 production The appearance of chemokine (C-C motif) ligand 22 (CCL22) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. chemokine (C-C motif) ligand 22 production GO:0072535 tumor necrosis factor (ligand) superfamily member 11 production The appearance of tumor necrosis factor superfamily member 11 (TNFSF11; RANKL) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. tumor necrosis factor (ligand) superfamily member 11 production GO:0097087 interleukin-17A production The appearance of interleukin-17A due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. interleukin-17A production GO:0097088 interleukin-17F production The appearance of interleukin-17F due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. interleukin-17F production GO:0097278 complement-dependent cytotoxicity Lysis of a cell resulting from triggering of the complement cascade. An example can be seen with complement activation and subsequent lysis of a bacterial cell as a result of the binding of IgM to the cell surface followed by the binding of complement proteins to that antibody. complement-dependent cytotoxicity GO:0097280 histamine secretion mediated by immunoglobulin Histamine release triggered by the binding of an antigen to an immunoglobulin bound to the cell surface. histamine secretion mediated by immunoglobulin GO:0097281 immune complex formation The process that gives rise to an immune complex. Immune complexes are clusters of antibodies bound to antigen, to which complement may also be fixed, and which may precipitate or remain in solution. Examples are the clumping of cells such as bacteria or red blood cells in the presence of an antibody, precipitation of a toxin after an antibody binds to it, and clumping of viral particles as a result of antibody binding to the virus. immune complex formation GO:0097282 immunoglobulin-mediated neutralization The inhibition of an antigen's biological effects by antibody binding to it. An example is neutralization of diphtheria toxin by preventing its entry into human cells via the binding of antibody specific for diphtheria toxin. immunoglobulin-mediated neutralization GO:0097388 chemokine (C-C motif) ligand 19 production The appearance of chemokine (C-C motif) ligand 19 (CCL19) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. chemokine (C-C motif) ligand 19 production GO:0097389 chemokine (C-C motif) ligand 21 production The appearance of chemokine (C-C motif) ligand 21 (CCL21) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. chemokine (C-C motif) ligand 21 production GO:0097390 chemokine (C-X-C motif) ligand 12 production The appearance of chemokine (C-X-C motif) ligand 12 (CXCL12) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. chemokine (C-X-C motif) ligand 12 production GO:0097391 chemokine (C-X-C motif) ligand 13 production The appearance of chemokine (C-X-C motif) ligand 13 (CXCL13) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. chemokine (C-X-C motif) ligand 13 production GO:0097392 chemokine (C-X-C motif) ligand 16 production The appearance of chemokine (C-X-C motif) ligand 16 (CXCL16) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. chemokine (C-X-C motif) ligand 16 production HP:0000855 Insulin resistance Increased resistance towards insulin, that is, diminished effectiveness of insulin in reducing blood glucose levels. Insulin resistance IAO:0000001 conditional specification a directive information entity that specifies what should happen if the trigger condition is fulfilled PlanAndPlannedProcess Branch OBI branch derived OBI_0000349 conditional specification IAO:0000003 measurement unit label Examples of measurement unit labels are liters, inches, weight per volume. A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure. 2009-03-16: provenance: a term measurement unit was proposed for OBI (OBI_0000176) , edited by Chris Stoeckert and Cristian Cocos, and subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definition of this, different, term. 2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI. PERSON: Alan Ruttenberg PERSON: Melanie Courtot measurement unit label IAO:0000005 objective specification In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction. a directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved. 2009-03-16: original definition when imported from OBI read: "objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed." 2014-03-31: In the example of usage ("In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that. Answers the question, why did you do this experiment? PERSON: Alan Ruttenberg PERSON: Barry Smith PERSON: Bjoern Peters PERSON: Jennifer Fostel goal specification OBI Plan and Planned Process/Roles Branch OBI_0000217 objective specification IAO:0000006 narrative object Examples of narrative objects are reports, journal articles, and patents submission. A narrative object is an information content entity that is a set of propositions. 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity' and 'figure'. Alan restored as there are OBI dependencies and this merits further discussion agree - DENRIE. Issue(alan) do we only mean text? What about a story told by mime. Does music count? (no) what about an oral report. Regarding definition, saying it is a set of propositions means we loose the idea that wording matters. Maybe adjust saying a narrative object has some relationshop to a set of propositions person:Chris Stoeckert OBI_0000013 group:OBI narrative object IAO:0000007 action specification Pour the contents of flask 1 into flask 2 a directive information entity that describes an action the bearer will take Alan Ruttenberg OBI Plan and Planned Process branch action specification IAO:0000008 obsolete_artifact obsolete_artifact true IAO:0000009 datum label A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label http://www.golovchenko.org/cgi-bin/wnsearch?q=label#4n GROUP: IAO 9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum. datum label IAO:0000010 software Software is a plan specification composed of a series of instructions that can be interpreted by or directly executed by a processing unit. see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178 PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Chris Stoeckert PERSON: Melanie Courtot GROUP: OBI software IAO:0000012 obsolete2_digital entity A digital entity is an information entity which is a collection of bits that can be interpreted by a computer. Two digital entities are the same if they are bitwise identical. 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 Superclass was 'digitial quality' person:Chris Stoeckert OBI_0000261 group:OBI obsolete2_digital entity true IAO:0000013 journal article Examples are articles published in the journals, Nature and Science. The content can often be cited by reference to a paper based encoding, e.g. Authors, Title of article, Journal name, date or year of publication, volume and page number. a report that is published in a journal person:Alan Ruttenberg person:Chris Stoeckert OBI_0000159 group:OBI journal article IAO:0000015 information carrier In the case of a printed paperback novel the physicality of the ink and of the paper form part of the information bearer. The qualities of appearing black and having a certain pattern for the ink and appearing white for the paper form part of the information carrier in this case. A quality of an information bearer that imparts the information content 12/15/09: There is a concern that some ways that carry information may be processes rather than qualities, such as in a 'delayed wave carrier'. 2014-03-10: We are not certain that all information carriers are qualities. There was a discussion of dropping it. PERSON: Alan Ruttenberg Smith, Ceusters, Ruttenberg, 2000 years of philosophy information carrier IAO:0000017 model number A model number is an information content entity specifically borne by catalogs, design specifications, advertising materials, inventory systems and similar that is about manufactured objects of the same class. The model number is an alternative term for the class. The manufactered objects may or may not also bear the model number. Model numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots. manufactered items may have more than one model number, sometimes by rebranding, or because companies are sold and the products issued new model numbers Person: Alan Ruttenberg model number IAO:0000018 obsolete_material_entity obsolete_material_entity true IAO:0000019 obsolete2_binary digital entity MS Word document, ZIP file, DICOM file, JPEG file A binary digital entity is a digital entity that is encoded in a way that is not easily human readable and that contains other than text characters. 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 Superclass was 'digital entity' digital_entity person:Chris Stoeckert OBI_0000244 group:OBI obsolete2_binary digital entity true IAO:0000024 obsolete_unit of measure The length of a ruler. a unit of measure is the quality of some material entity compared to which another quality is some multiple of. Alan Ruttenberg Smith, Ceusters, Ruttenberg, 2000 years of philosophy obsolete_unit of measure true IAO:0000025 programming language R, Perl, Java A language in which source code is written that is intended to be executed/run by a software interpreter. Programming languages are ways to write instructions that specify what to do, and sometimes, how to do it. person:Alan Ruttenberg person:Chris Stoeckert OBI_0000058 group:OBI programming language IAO:0000027 data item Data items include counts of things, analyte concentrations, and statistical summaries. a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers. 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum. 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym. 2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/ JAR: datum -- well, this will be very tricky to define, but maybe some information-like stuff that might be put into a computer and that is meant, by someone, to denote and/or to be interpreted by some process... I would include lists, tables, sentences... I think I might defer to Barry, or to Brian Cantwell Smith JAR: A data item is an approximately justified approximately true approximate belief PERSON: Alan Ruttenberg PERSON: Chris Stoeckert PERSON: Jonathan Rees data data item IAO:0000028 symbol a serial number such as "12324X" a stop sign a written proper name such as "OBI" An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity. 20091104, MC: this needs work and will most probably change 2014-03-31: We would like to have a deeper analysis of 'mark' and 'sign' in the future (see https://code.google.com/p/information-artifact-ontology/issues/detail?id=154). PERSON: James A. Overton PERSON: Jonathan Rees based on Oxford English Dictionary symbol IAO:0000029 numeral A symbol that denotes a number. PERSON: Jonathan Rees numeral IAO:0000030 information content entity Examples of information content entites include journal articles, data, graphical layouts, and graphs. A generically dependent continuant that is about some thing. 2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ). information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity. PERSON: Chris Stoeckert OBI_0000142 information content entity IAO:0000031 integer numeral a numeral that denotes an integer PERSON: Jonathan Rees integer numeral 1 1 IAO:0000032 scalar measurement datum 10 feet. 3 ml. a scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label. 2009-03-16: we decided to keep datum singular in scalar measurement datum, as in this case we explicitly refer to the singular form Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them. PERSON: Alan Ruttenberg PERSON: Melanie Courtot scalar measurement datum IAO:0000033 directive information entity An information content entity whose concretizations indicate to their bearer how to realize them in a process. 2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. 2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it. 8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan PERSON: Alan Ruttenberg PERSON: Bjoern Peters directive information entity IAO:0000034 time trigger revisit? PlanAndPlannedProcess Branch OBI branch derived OBI_0000331 time trigger IAO:0000035 obsolete_study interpretation A study interpretation is a textual entity about the implications of a study result. Examples include discussion of whether a hypothesis is false, whether the study failed to address the hypothesis, and whether the study results have led to new hypotheses 2009-03-16: definition was "A conclusion is a narrative object which can be published in a paper summerizing and interpreting a protocol application." 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI. The obsoleting of narrative object required a modest change in the definition of this term. Circularity with "interpretation... interprets" has been removed, using "about the implications" instead. Lawrence Hunter PERSON: Alan Ruttenberg PERSON: Jennifer Fostel PERSON: Melanie Courtot conclusion OBI_0000005 obsolete_study interpretation true IAO:0000037 dot plot Dot plot of SSC-H and FSC-H. A dot plot is a report graph which is a graphical representation of data where each data point is represented by a single dot placed on coordinates corresponding to data point values in particular dimensions. person:Allyson Lister person:Chris Stoeckert OBI_0000123 group:OBI dot plot IAO:0000038 graph A diagram that presents one or more tuples of information by mapping those tuples in to a two dimensional space in a non arbitrary way. PERSON: Lawrence Hunter person:Alan Ruttenberg person:Allyson Lister OBI_0000240 group:OBI graph IAO:0000047 obsolete2_text based digital entity XML file, C++ source code file A text based digital entity is a digital entity that is encoded so that it only contains text characters. 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 superclass was 'digital document' digital_entity person:Chris Stoeckert OBI_0000132 group:OBI obsolete2_text based digital entity true IAO:0000055 rule example to be added a rule is an executable which guides, defines, restricts actions MSI PRS OBI_0500021 PRS rule IAO:0000057 contour plot Contour plot of SSC-H, FSC-H, and FL1-H. generically_dependent_continuants person:Allyson Lister person:Chris Stoeckert OBI_0000246 group:Flow Cytometry community contour plot IAO:0000059 obsolete2_report figure A report figure is a report display element that has some aspect of illustration, but may be a composite of figures, images, and other elements I prepended the 'report ' to make it clear that we mean parts of reports here. We may want a more generic version of 'figure', in which case this would become a defined class - figure and part_of some report Replaced by defined version of figure person:Alan Ruttenberg person:Allyson Lister OBI_0000027 group:OBI obsolete2_report figure true IAO:0000064 algorithm PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies. A plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata. Philippe Rocca-Serra PlanAndPlannedProcess Branch OBI_0000270 adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg) algorithm IAO:0000065 software interpreter R program, Perl interpreter, Java virtual machine A software interpreter is a software application that executes some specified input software. Do we care? Jennifer: Yes, there was a particular version of R that had a bug and it was fixed later. That would imply that we mean specific version of an interpreter. So an instance of this would be a particular version of the interpreter person:Alan Ruttenberg person:Chris Stoeckert OBI_0000199 group:OBI software interpreter IAO:0000078 curation status specification The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting) PERSON:Bill Bug GROUP:OBI:<http://purl.obolibrary.org/obo/obi> OBI_0000266 curation status specification IAO:0000079 density plot Density plot of SSC-H and FSC-H. A density plot is a report graph which is a graphical representation of data where the tint of a particular pixel corresponds to some kind of function corresponding the the amount of data points relativelly with their distance from the the pixel. person:Allyson Lister person:Chris Stoeckert OBI_0000179 group:Flow Cytometry community density plot IAO:0000088 report Examples of reports are gene lists and investigation reports. These are not published (journal) articles but may be included in a journal article. a document assembled by an author for the purpose of providing information for the audience. A report is the output of a documenting process and has the objective to be consumed by a specific audience. Topic of the report is on something that has completed. A report is not a single figure. Examples of reports are journal article, patent application, grant progress report, case report (not patient record) 2009-03-16: comment from Darren Natale: I am slightly uneasy with the sentence "Topic of the report is on something that has completed." Should it be restricted to those things that are completed? For example, a progress report is (usually) about something that definitely has *not* been completed, or may include (only) projections. I think the definition would not suffer if the whole sentence is deleted. 2009-03-16: this was report of results with definition: A report is a narrative object that is a formal statement of the results of an investigation, or of any matter on which definite information is required, made by some person or body instructed or required to do so. 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI. 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'document'. Alan restored as there are OBI dependencies and this merits further discussion disagreement about where reports go. alan: only some gene lists are reports. Is a report all the content of some document? The example of usage suggests that a report may be part of some article. Term needs clarification PERSON: Alan Ruttenberg PERSON: Melanie Courtot PERSON:Chris Stoeckert GROUP: OBI OBI_0000099 report IAO:0000091 obsolete_report element A report element is a narrative object in which information is presented and consumed by a human being, and is part of a report. Examples of report elements are figure (dot plot), table, text portion (may include a movie or audio clip on a web page). 2009-03-16: needs some more work (clarify relations). 2009-03-16: was report display element with definition: A report display element is a narrative object that is part of a report. Report display elements are set off from the textual parts of a report and are typically given a label(e.g. Figure 2) which is used to refer to the element from the text. Typically the 2d layout is part of the identity of such elements. 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI. 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity' and 'figure'. Alan restored as there are OBI dependencies and this merits further discussion Replaced by textual entity and figure There will be some issue here about whether these are defined classes. As intended these are meant to denote the parts of the report that are not textual but are typically boxed and set within the text, labelled with some identifier, and referred to in the text PERSON: Alan Ruttenberg PERSON: Allyson Lister PERSON: Melanie Courtot GROUP:OBI OBI_0000001 obsolete_report element true IAO:0000093 obsolete2_binary executable Binary executable is a digital entity consisting of the binary representation of machine instructions of a specific processor or they may be binary pseudocode for a virtual machine. A non-source executable file is also called an object program. It is assumed that the binary executable file contains properly-formatted computer instructions. (derived from Wikipedia, Nov 1, 2007) 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 superclass was 'digital entity' person:Jennifer Fostel OBI_0000222 group:OBI obsolete2_binary executable true IAO:0000096 source code module The written source code that implements part of an algorithm. Test - if you know that it was written in a specific language, then it can be source code module. We mean here, roughly, the wording of a document such as a perl script. A source code module is a directive information entity that specifies, using a programming language, some algorithm. person:Alan Ruttenberg person:Chris Stoeckert OBI_0000039 group:OBI source code module IAO:0000097 obsolete_report table A report table is a report display element consisting of a matrix of cells layed out in a grid, some set of which are filled with some information content 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity table'. Alan restored as there are OBI dependencies and this merits further discussion person:Alan Ruttenberg person:Allyson Lister OBI_0000265 group:OBI obsolete_report table true IAO:0000098 data format specification A data format specification is the information content borne by the document published defining the specification. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file 2009-03-16: provenance: term imported from OBI_0000187, which had original definition "A data format specification is a plan which organizes information. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file" PERSON: Alan Ruttenberg PlanAndPlannedProcess Branch OBI branch derived OBI_0000187 data format specification IAO:0000100 data set Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves). A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets. 2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type 2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction. person:Allyson Lister person:Chris Stoeckert OBI_0000042 group:OBI data set IAO:0000101 image An image is an affine projection to a two dimensional surface, of measurements of some quality of an entity or entities repeated at regular intervals across a spatial range, where the measurements are represented as color and luminosity on the projected on surface. person:Alan Ruttenberg person:Allyson person:Chris Stoeckert OBI_0000030 group:OBI image IAO:0000102 data about an ontology part data about an ontology part is a data item about a part of an ontology, for example a term Person:Alan Ruttenberg data about an ontology part IAO:0000104 plan specification PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice. A directive information entity with action specifications and objective specifications as parts that, when concretized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified. 2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. 2014-03-31: A plan specification can have other parts, such as conditional specifications. Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved Alan Ruttenberg OBI Plan and Planned Process branch OBI_0000344 2/3/2009 Comment from OBI review. Action specification not well enough specified. Conditional specification not well enough specified. Question whether all plan specifications have objective specifications. Request that IAO either clarify these or change definitions not to use them plan specification IAO:0000105 obsolete2_digital document A digital document is a digital entity consisting of an electronic file which can be rendered into human-readable form by one or more computational applications. The digital document does not refer to the information content of the document but to an instance of the file. 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 superclass was 'digial entity' person:Jennifer Fostel OBI_0000195 group:OBI obsolete2_digital document true IAO:0000109 measurement datum Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}. A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device. 2/2/2009 is_specified_output of some assay? person:Chris Stoeckert OBI_0000305 group:OBI measurement datum IAO:0000128 obsolete_identifier _identifier is a container under information content entity for collecting types of terms to indicate a specific instance or clas of what was used or participated in an investigation. Identifiers are borne by a product or its packaging, and can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots. Note: everybody agreed that identifier is probably a too general term. We however felt that it would be appropriate to group "identifiying" terms under some kind of umbrella. We therefore propose to use _identifier for that purpose. As per OBI conventions, the _ prefixing identifier indicates that this is a helper class and shouldn't be considered as final. obsolete_identifier true IAO:0000129 version number A version number is an information content entity which is a sequence of characters borne by part of each of a class of manufactured products or its packaging and indicates its order within a set of other products having the same name. Note: we feel that at the moment we are happy with a general version number, and that we will subclass as needed in the future. For example, see 7. genome sequence version GROUP: IAO version number IAO:0000131 serial number A serial number is an information content entity which is a unique sequence of characters borne by part of manufactured product or its packaging that is assigned to each individual in some class of products, and so can serve as a way to identify an individual product within the class. Serial numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots. Note: during the call there was some confusion between serial number and model number. We agreed that it would be very helpful for all those terms to have example of usages - please add if you have any :-) GROUP: IAO serial number IAO:0000132 lot number A lot number is an information content entity which is an identical sequence of character borne by part of manufactured product or its packaging for each instances of a product class in a discrete batch of an item. Lot numbers are usually assigned to each separate production run of an item. Manufacturing as a lot might be due to a variety of reasons, for example, a single process during which many individuals are made from the same portion of source material. Lot numbers can be encoded in a pattern of other information objects, such as bar codes, numerals, or patterns of dots. GROUP: IAO batch number lot number IAO:0000140 setting datum A settings datum is a datum that denotes some configuration of an instrument. 2/3/2009 Feedback from OBI This should be a "setting specification". There is a question of whether it is information about a realizable or not. Pro other specification are about realizables. Cons sometimes specifies a quality which is not a realizable. Alan grouped these in placeholder for the moment. Name by analogy to measurement datum. setting datum IAO:0000141 obsolete_digital quality 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 Need to rework digital entity. Digital quality was suggested by Barry. obsolete_digital quality true IAO:0000144 conclusion textual entity that fucoidan has a small statistically significant effect on AT3 level but no useful clinical effect as in-vivo anticoagulant, a paraphrase of part of the last paragraph of the discussion section of the paper 'Pilot clinical study to evaluate the anticoagulant activity of fucoidan', by Lowenthal et. al.PMID:19696660 A textual entity that expresses the results of reasoning about a problem, for instance as typically found towards the end of scientific papers. 2009/09/28 Alan Ruttenberg. Fucoidan-use-case 2009/10/23 Alan Ruttenberg: We need to work on the definition still Person:Alan Ruttenberg conclusion textual entity IAO:0000178 material information bearer A page of a paperback novel with writing on it. The paper itself is a material information bearer, the pattern of ink is the information carrier. a brain a hard drive A material entity in which a concretization of an information content entity inheres. GROUP: IAO material information bearer IAO:0000179 histogram A histogram is a report graph which is a statistical description of a distribution in terms of occurrence frequencies of different event classes. PERSON:Chris Stoeckert PERSON:James Malone PERSON:Melanie Courtot GROUP:OBI histogram IAO:0000180 heatmap A heatmap is a report graph which is a graphical representation of data where the values taken by a variable(s) are shown as colors in a two-dimensional map. PERSON:Chris Stoeckert PERSON:James Malone PERSON:Melanie Courtot GROUP:OBI heatmap IAO:0000181 Venn diagram A Venn diagram is a report graph showing all hypothetically possible logical relations between a finite collection of sets. PERSON:Chris Stoeckert PERSON:James Malone PERSON:Melanie Courtot WEB: http://en.wikipedia.org/wiki/Venn_diagram Venn diagram IAO:0000182 obsolete_survival curve A survival curve is a report graph which is a graphical representation of data where the percentage of survival is plotted as a function of time. PERSON:Chris Stoeckert PERSON:James Malone PERSON:Melanie Courtot WEB: http://www.graphpad.com/www/book/survive.htm obsolete_survival curve true IAO:0000183 dendrogram Dendrograms are often used in computational biology to illustrate the clustering of genes. A dendrogram is a report graph which is a tree diagram frequently used to illustrate the arrangement of the clusters produced by a clustering algorithm. PERSON:Chris Stoeckert PERSON:James Malone PERSON:Melanie Courtot WEB: http://en.wikipedia.org/wiki/Dendrogram dendrogram IAO:0000184 scatter plot Comparison of gene expression values in two samples can be displayed in a scatter plot A scatterplot is a graph which uses Cartesian coordinates to display values for two variables for a set of data. The data is displayed as a collection of points, each having the value of one variable determining the position on the horizontal axis and the value of the other variable determining the position on the vertical axis. PERSON:Chris Stoeckert PERSON:James Malone PERSON:Melanie Courtot scattergraph WEB: http://en.wikipedia.org/wiki/Scatterplot scatter plot IAO:0000185 photograph A photograph is created by projecting an image onto a photosensitive surface such as a chemically treated plate or film, CCD receptor, etc. PERSON:Alan Ruttenberg PERSON:Joanne Luciano PERSON:Melanie Courtot WEB: http://en.wiktionary.org/wiki/photograph photograph IAO:0000186 photographic print A photographic print is a material entity upon which a photograph generically depends. PERSON:Alan Ruttenberg PERSON:Melanie Courtot photographic print IAO:0000225 obsolescence reason specification The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology. PERSON: Alan Ruttenberg PERSON: Melanie Courtot obsolescence reason specification IAO:0000300 textual entity Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities A textual entity is a part of a manifestation (FRBR sense), a generically dependent continuant whose concretizations are patterns of glyphs intended to be interpreted as words, formulas, etc. AR, (IAO call 2009-09-01): a document as a whole is not typically a textual entity, because it has pictures in it - rather there are parts of it that are textual entities. Examples: The title, paragraph 2 sentence 7, etc. MC, 2009-09-14 (following IAO call 2009-09-01): textual entities live at the FRBR (http://en.wikipedia.org/wiki/Functional_Requirements_for_Bibliographic_Records) manifestation level. Everything is significant: line break, pdf and html versions of same document are different textual entities. PERSON: Lawrence Hunter text textual entity IAO:0000301 citation Verspoor, K., Cohen, KB., Hunter, L. Textual characteristics of traditional and Open Access scientific journals are similar, BMC Bioinformatics 2009, 10:183. a textual entity intended to identify a particular publication PERSON: Lawrence Hunter citation IAO:0000302 author identification L. Hunter A textual entity intended to identify a particular author PERSON: Lawrence Hunter author identification IAO:0000303 institutional identification University of Colorado Denver School of Medicine A textual entity intended to identify a particular institution PERSON: Lawrence Hunter institutional identification IAO:0000304 caption Figure 1: A system diagram describing the modules of the Hanalyzer. Reading methods (green) take external sources of knowledge (blue) and extract information from them, either by parsing structured data or biomedical language processing to extract information from unstructured data. Reading modules are responsible for tracking the provenance of all knowledge. Reasoning methods (yellow) enrich the knowledge that results from reading by, for example, noting two genes that are annotated to the same ontology term or database entry. All knowledge sources, read or reasoned, are assigned a reliability score, and all are combined using that score into a knowledge network (orange) that represents the integration of all sorts of relationship between a pair of genes and a combined reliability score. A data network (also orange) is created from experimental results to be analyzed. The reporting modules (pink) integrate the data and knowledge networks, producing visualizations that can be queried with the associated drill-down tool. A textual entity that describes a figure PERSON: Lawrence Hunter caption IAO:0000305 document title Textual characteristics of traditional and Open Access scientific journals are similar A textual entity that names a document PERSON: Lawrence Hunter document title IAO:0000306 table | T F --+----- T | T F F | F F A textual entity that contains a two-dimensional arrangement of texts repeated at regular intervals across a spatial range, such that the spatial relationships among the constituent texts expresses propositions PERSON: Lawrence Hunter table IAO:0000307 table of abbreviations IAO information artifact ontology OBI ontology of biomedical investiations GO gene ontology A table where the constituent texts are abbreviations and their expansions PERSON: Lawrence Hunter table of abbreviations IAO:0000308 figure Any picture, diagram or table An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something. PERSON: Lawrence Hunter figure IAO:0000309 diagram A molecular structure ribbon cartoon showing helices, turns and sheets and their relations to each other in space. A figure that expresses one or more propositions PERSON: Lawrence Hunter diagram IAO:0000310 document A journal article, patent application, laboratory notebook, or a book A collection of information content entities intended to be understood together as a whole PERSON: Lawrence Hunter document IAO:0000311 publication A journal article or book A document that has been accepted by a publisher PERSON: Lawrence Hunter publication IAO:0000312 publication about an investigation Most scientific journal articles A publication that is about an investigation PERSON: Lawrence Hunter scientific publication publication about an investigation IAO:0000313 patent US Patent 6,449,603 A document that has been accepted by a patent authority PERSON: Lawrence Hunter patent IAO:0000314 document part An abstract, introduction, method or results section. an information content entity that is part of a document PERSON: Lawrence Hunter document part IAO:0000315 abstract The profusion of high-throughput instruments and the explosion of new results in the scientific literature, particularly in molecular biomedicine, is both a blessing and a curse to the bench researcher. Even knowledgeable and experienced scientists can benefit from computational tools that help navigate this vast and rapidly evolving terrain. In this paper, we describe a novel computational approach to this challenge, a knowledge-based system that combines reading, reasoning and reporting methods to facilitate analysis of experimental data. Reading methods extract information from external resources, either by parsing structured data or biomedical language processing to extract information from unstructured data, and track knowledge provenance. Reasoning methods enrich the knowledge that results from reading by, for example, noting two genes that are annotated to the same ontology term or database entry. Reasoning is also used to combine all sources into a knowledge network that represents the integration of all sorts of relationships between a pair of genes, and to calculate a combined reliability score. Reporting methods combine the knowledge network with a congruent network constructed from experimental data and visualize the combined network in a tool that facilitates the knowledge-based analysis of that data. A summary of the entire document that is substantially smaller than the document it summarizes. It is about the document it summarizes. PERSON: Lawrence Hunter abstract IAO:0000316 introduction to a publication about an investigation Section labelled 'introduction' of a typical scientific journal article A part of a publication about an investigation that is about the objective specification (why the investigation is being done) PERSON: Lawrence Hunter introduction introduction to a publication about an investigation IAO:0000317 methods section The section labelled 'Methods' or 'Materials and Methods' in a typical scientific journal article. A part of a publication about an investigation that is about the study design of the investigation PERSON: Lawrence Hunter methods section IAO:0000318 results section The section labelled 'results' in a typical scientific journal article A part of a publication about an investigation that is about a study design execution PERSON: Lawrence Hunter results section IAO:0000319 discussion section of a publication about an investigation A part of a publication about an investigation that is about the study interpretation of the investigation PERSON: Lawrence Hunter discussion section discussion section of a publication about an investigation IAO:0000320 references section The list of citations found at the end of a scientific publication, grant proposal or patent application, sometimes called "literature cited" or "bibliography" A part of a document that has citations as parts PERSON: Lawrence Hunter references section IAO:0000321 author list Lawrence Hunter and Kevin Brettonel Cohen part of a document that enumerates the authors of the document PERSON: Lawrence Hunter author list IAO:0000322 institution list The University of Colorado Denver School of Medicine and the University of Colorado Boulder. part of a document that has parts that are institution identifications associated with the authors of the document PERSON: Lawrence Hunter institution list IAO:0000323 author contributions section LH conceived of the hypothesis, designed the study and contributed to the writing of the manuscript. KBC executed the experiments, analyzed the data, and contributed to the writing of the manuscript. A part of a publication that is about the specific contributions of each author PERSON: Lawrence Hunter author contributions section IAO:0000324 acknowledgements section The authors wish to thank Alan Ruttenberg for his constructive comments about an earlier draft of this manuscript Part of a publication that is about the contributions of people or institutions other than the authors. PERSON: Lawrence Hunter acknowledgements section IAO:0000325 footnote The referent in the text is usually indicated by a special typographic character such as * or a superscripted number, which is also used to indicate the footnote that refers to that text. A part of a document that is about a specific other part of the document. Usually footnotes are spatially segregated from the rest of the document. PERSON: Lawrence Hunter endnote footnote IAO:0000326 supplementary material to a document part of a document that is segregated from the rest of the document due to its size PERSON: Lawrence Hunter appendix supplementary material supplementary material to a document IAO:0000327 table of contents A table that relates document parts to specific locations in a document (usually page numbers). This is also a document part (subsumption there should be inferred). PERSON: Lawrence Hunter table of contents IAO:0000328 table of figures A table that relates figures in a document to specific locations in that document (usually page numbers). This is also a document part (subsumption there should be inferred). PERSON: Lawrence Hunter table of figures IAO:0000329 running title A shorter version of a document title PERSON: Lawrence Hunter running title IAO:0000330 copyright section This work is licensed under a Creative Commons Attribution-Share Alike 3.0 United States License. A document part that describes legal restrictions on making or distributing copies of the document PERSON: Lawrence Hunter copyright section 1 IAO:0000400 cartesian spatial coordinate datum A cartesian spatial coordinate datum is a representation of a point in a spatial region, in which equal changes in the magnitude of a coordinate value denote length qualities with the same magnitude 2009-08-18 Alan Ruttenberg - question to BFO list about whether the BFO sense of the lower dimensional regions is that they are always part of actual space (the three dimensional sort) http://groups.google.com/group/bfo-discuss/browse_thread/thread/9d04e717e39fb617 Alan Ruttenberg AR notes: We need to discuss whether it should include site. cartesian spatial coordinate datum http://groups.google.com/group/bfo-discuss/browse_thread/thread/9d04e717e39fb617 1 IAO:0000401 one dimensional cartesian spatial coordinate datum A cartesion spatial coordinate datum that uses one value to specify a position along a one dimensional spatial region Alan Ruttenberg one dimensional cartesian spatial coordinate datum 1 1 IAO:0000402 two dimensional cartesian spatial coordinate datum A cartesion spatial coordinate datum that uses two values to specify a position within a two dimensional spatial region Alan Ruttenberg two dimensional cartesian spatial coordinate datum 1 1 1 IAO:0000403 three dimensional cartesian spatial coordinate datum A cartesion spatial coordinate datum that uses three values to specify a position within a three dimensional spatial region Alan Ruttenberg three dimensional cartesian spatial coordinate datum IAO:0000408 length measurement datum A scalar measurement datum that is the result of measurement of length quality Alan Ruttenberg length measurement datum IAO:0000409 denotator type The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities. A denotator type indicates how a term should be interpreted from an ontological perspective. Alan Ruttenberg Barry Smith, Werner Ceusters denotator type IAO:0000414 mass measurement datum A scalar measurement datum that is the result of measurement of mass quality 2009/09/28 Alan Ruttenberg. Fucoidan-use-case Person:Alan Ruttenberg mass measurement datum IAO:0000415 hypothesis textual entity that fucoidan has a small statistically significant effect on AT3 level but no useful clinical effect as in-vivo anticoagulant, a paraphrase of part of the last paragraph of the discussion section of the paper 'Pilot clinical study to evaluate the anticoagulant activity of fucoidan', by Lowenthal et. al.PMID:19696660 A textual entity that expresses an assertion that is intended to be tested. 2009/09/28 Alan Ruttenberg. Fucoidan-use-case Person:Alan Ruttenberg hypothesis textual entity IAO:0000416 time measurement datum A scalar measurement datum that is the result of measuring a temporal interval 2009/09/28 Alan Ruttenberg. Fucoidan-use-case Person:Alan Ruttenberg time measurement datum IAO:0000422 postal address A textual entity that is used as directive to deliver something to a person, or organization 2010-05-24 Alan Ruttenberg. Use label for the string representation. See issue http://code.google.com/p/information-artifact-ontology/issues/detail?id=59 postal address IAO:0000429 email address Alan Ruttenberg 1/3/2012 - Provisional id, see issue at http://code.google.com/p/information-artifact-ontology/issues/detail?id=130&thanks=130&ts=1325636583 Person:Alan Ruttenberg Person:Chris Stoeckart email address IAO:0000442 author role A role inhering in a person or organization that is realized when the bearer participates in the work which is the basis of the document, in the writing of the document, and signs it with their name. PERSON: Alan Ruttenberg PERSON: Melanie Courtot author role IAO:0000443 data item extraction from journal article a planned process in which journal articles are read or processed and data items are extracted, typically for further analysis or indexing Person:Alan Ruttenberg data item extraction from journal article IAO:0000572 documenting Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database. a planned process in which a document is created or added to by including the specified input in it. 6/11/9: Edited at OBI workshop. We need to be able identify a child form of information artifact which corresponds to something enduring (not brain like). This used to be restricted to physical document or digital entity as the output, but that excludes e.g. an audio cassette tape Bjoern Peters wikipedia http://en.wikipedia.org/wiki/Documenting documenting IAO:0000573 line graph A line graph is a type of graph created by connecting a series of data points together with a line. PERSON:Chris Stoeckert PERSON:Melanie Courtot line chart GROUP:OBI WEB: http://en.wikipedia.org/wiki/Line_chart line graph IAO:0000574 assigning a centrally registered identifier A new pubmed ID being created for a journal article, and the associated pubmed record containing information to the journal article. A license plate number registered at the DMV to be belonging to a specific vehicle and owner. Placing a barcode on a product and entering information in a database that this barcode is assigned. a planned process in which a new CRID is created, associated with an entity, and stored in the CRID registry thereby registering it as being associated with some entity 2014-05-05: It is the CRID registry that assigns CRIDs, not the users of the registry. Person:Alan Ruttenberg Person:Bjoern Peters Person:Melanie Courtot assigning a CRID assigning a centrally registered identifier IAO:0000575 associating information with a centrally registered identifier in its registry Articles in Pubmed are reviewed by curators who add MESH terms to the Pubmed records in order to categorize them better and improve the ability to search for them. A planned process in which a CRID registry associates an information content entity with a CRID symbol PERSON:Alan Ruttenberg associating information with a CRID in the CRID registry associating information with a centrally registered identifier in its registry IAO:0000576 obsolete_establishing a CRID registry a planned process with the objective to establish a system that allows to refer to specific entities of a certain kind and store information about them, by establishing a CRID registry and plan specifications for the process of 1) assigning a CRID and 2) looking up a CRID. MC, 20101124: deprecated following discussion at IAO call 20101124. Term was deemed not necessary - no use case for now. obsolete_establishing a CRID registry true IAO:0000577 centrally registered identifier symbol The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed. A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry. PERSON: Alan Ruttenberg PERSON: Bill Hogan PERSON: Bjoern Peters PERSON: Melanie Courtot CRID symbol Original proposal from Bjoern, discussions at IAO calls centrally registered identifier symbol IAO:0000578 centrally registered identifier The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed. An information content entity that consists of a CRID symbol and additional information about the CRID registry to which it belongs. 2014-05-05: In defining this term we take no position on what the CRID denotes. In particular do not assume it denotes a *record* in the CRID registry (since the registry might not have 'records'). Alan, IAO call 20101124: potentially the CRID denotes the instance it was associated with during creation. Note, IAO call 20101124: URIs are not always CRID, as not centrally registered. We acknowledge that CRID is a subset of a larger identifier class, but this subset fulfills our current needs. OBI PURLs are CRID as they are registered with OCLC. UPCs (Universal Product Codes from AC Nielsen)are not CRID as they are not centrally registered. PERSON: Alan Ruttenberg PERSON: Bill Hogan PERSON: Bjoern Peters PERSON: Melanie Courtot CRID Original proposal from Bjoern, discussions at IAO calls centrally registered identifier IAO:0000579 centrally registered identifier registry PubMed is a CRID registry. It has a dataset of PubMed identifiers associated with journal articles. A CRID registry is a dataset of CRID records, each consisting of a CRID symbol and additional information which was recorded in the dataset through a assigning a centrally registered identifier process. PERSON: Alan Ruttenberg PERSON: Bill Hogan PERSON: Bjoern Peters PERSON: Melanie Courtot CRID registry Original proposal from Bjoern, discussions at IAO calls centrally registered identifier registry IAO:0000580 looking up a centrally registered identifier Going to the PubMed website and entering a PubMed ID in order to retrieve the Pubmed information associated with that ID. A planned process in which a request to a CRID registry is made to return the information associated with a CRID symbol PERSON: Alan Ruttenberg PERSON: Bill Hogan PERSON: Bjoern Peters PERSON: Melanie Courtot looking up a CRID looking up a centrally registered identifier IAO:0000582 time stamped measurement datum time stamped measurement datum IAO:0000584 time sampled measurement data set pmid:20604925 - time-lapse live cell microscopy A data set that is an aggregate of data recording some measurement at a number of time points. The time series data set is an ordered list of pairs of time measurement data and the corresponding measurement data acquired at that time. Alan Ruttenberg experimental time series time sampled measurement data set IAO:0000590 written name "Bill Clinton" "The Eiffel Tower" "United States of America" A textual entity that denotes a particular in reality. PERSON: Bill Hogan http://code.google.com/p/information-artifact-ontology/issues/detail?id=114 The qualifier "written" is to set it apart from spoken names. Also, note the restrictions to particulars. We are not naming universals. We could however, be naming, attributive collections which are particulars, so "All people located in the boundaries of the city of Little Rock, AR on June 18, 2011 at 9:50a CDT" would be a name. written name IAO:0000591 software method A software method (also called subroutine, subprogram, procedure, method, function, or routine) is software designed to execute a specific task. PERSON: Melanie Courtot PERSON: Michel Dumontier http://code.google.com/p/information-artifact-ontology/issues/detail?id=80 software method IAO:0000592 software module A software module is software composed of a collection of software methods. PERSON: Melanei Courtot PERSON: Michel Dumontier http://code.google.com/p/information-artifact-ontology/issues/detail?id=80 software module IAO:0000593 software library A software library is software composed of a collection of software modules and/or software methods in a form that can be statically or dynamically linked to some software application. PERSON: Melanie Courtot PERSON: Michel Dumontier http://code.google.com/p/information-artifact-ontology/issues/detail?id=80 software library IAO:0000594 software application A software application is software that can be directly executed by some processing unit. PERSON: Melanie Courtot PERSON: Michel Dumontier http://code.google.com/p/information-artifact-ontology/issues/detail?id=80 software application IAO:0000595 software script A software script is software whose instructions can be executed using a software interpreter. PERSON: Melanie Courtot PERSON: Michel Dumontier http://code.google.com/p/information-artifact-ontology/issues/detail?id=80 software script IDO:0000586 infection A part of an extended organism that itself has as part a population of one or more infectious agents and that (1) exists as a result of processes initiated by members of the infectious agent population and is (2) clinically abnormal in virtue of the presence of this infectious agent population, or (3) has a disposition to bring clinical abnormality to immunocompetent organisms of the same Species as the host (the organism corresponding to the extended organism) through transmission of a member or offspring of a member of the infectious agent population. infection IDO:0000666 human pathogenicity disposition A disposition to initiate processes that result in a disorder in a human organism. human pathogenicity disposition NCBITaxon:10090 Mus musculus house mouse mouse Mus musculus NCBITaxon:10116 Rattus norvegicus Norway rat Rattus sp. strain Wistar brown rat rat rats Rattus norvegicus NCBITaxon:10239 Viruses Viruses NCBITaxon:117571 Euteleostomi bony vertebrates Euteleostomi NCBITaxon:1206794 Ecdysozoa Ecdysozoa NCBITaxon:197562 Pancrustacea Pancrustacea NCBITaxon:2 Bacteria eubacteria Bacteria NCBITaxon:2157 Archaea Archaea NCBITaxon:2759 Eukaryota eucaryotes eukaryotes Eukaryota NCBITaxon:314146 Euarchontoglires Euarchontoglires NCBITaxon:32523 Tetrapoda tetrapods Tetrapoda NCBITaxon:32524 Amniota amniotes Amniota NCBITaxon:33154 Opisthokonta Opisthokonta NCBITaxon:33208 NCBITaxon:33213 Bilateria Bilateria NCBITaxon:3702 Arabidopsis thaliana mouse-ear cress thale cress thale-cress Arabidopsis thaliana NCBITaxon:39107 Murinae Murinae NCBITaxon:40674 Mammalia mammals Mammalia NCBITaxon:44689 Dictyostelium discoideum Dictyostelium discoideum NCBITaxon:4890 Ascomycota ascomycetes sac fungi Ascomycota NCBITaxon:4896 Schizosaccharomyces pombe fission yeast Schizosaccharomyces pombe NCBITaxon:4932 Saccharomyces cerevisiae baker's yeast brewer's yeast lager beer yeast yeast Saccharomyces cerevisiae NCBITaxon:5140 Neurospora Neurospora NCBITaxon:6239 Caenorhabditis elegans nematode Caenorhabditis elegans NCBITaxon:6668 Daphnia common water fleas Daphnia NCBITaxon:716545 saccharomyceta saccharomyceta NCBITaxon:7227 Drosophila melanogaster fruit fly Drosophila melanogaster NCBITaxon:7742 Vertebrata <Metazoa> Vertebrata vertebrates Vertebrata <Metazoa> NCBITaxon:7955 Danio rerio leopard danio zebra danio zebra fish zebrafish Danio rerio NCBITaxon:8353 Xenopus <genus> Xenopus Xenopus <genus> NCBITaxon:9031 Gallus gallus bantam chicken chickens Gallus gallus NCBITaxon:9606 Homo sapiens human human being man Homo sapiens NCBITaxon:9989 Rodentia rodents Rodentia OBI:0000006 role of being consumer safety officer Consumer safety officer; Consumer Safety Officer Positions at FDA http://69.20.19.211/jobs/cso.htm Person charged with serving as CSO, FDA official who coordinates the review the role of a human being that is realized by enforcing regulations to ensure consumer safety Jennifer Fostel Person:Helen Parkinson OBI, CDISC role of being consumer safety officer OBI:0000010 fluorescent reporter intensity A measurement datum that represents the output of a scanner measuring the intensity value for each fluorescent reporter. person:Chris Stoeckert group:OBI From the DT branch: This term and definition were originally submitted by the community to our branch, but we thought they best fit DENRIE. However we see several issues with this. First of all the name 'probe' might not be used in OBI. Instead we have a 'reporter' role. Also, albeit the term 'probe intensity' is often used in communities such as the microarray one, the name 'probe' is ambiguous (some use it to refer to what's on the array, some use it to refer to what's hybed to the array). Furthermore, this concept could possibly be encompassed by combining different OBI terms, such as the roles of analyte, detector and reporter (you need something hybed to a probe on the array to get an intensity) and maybe a more general term for 'measuring intensities'. We need to find the right balance between what is consistent with OBI and combinations of its terms and what is user-friendly. Finally, note that 'intensity' is already in the OBI .owl file and is also in PATO. Why didn't OBI import it from PATO? This might be a problem. fluorescent reporter intensity OBI:0000011 planned process Injecting mice with a vaccine in order to test its efficacy A processual entity that realizes a plan which is the concretization of a plan specification. 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.) We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some objectives is a planned process. Bjoern Peters branch derived 6/11/9: Edited at workshop. Used to include: is initiated by an agent This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call) planned process OBI:0000014 regulator role Fact sheet - Regulating the companies The role of the regulator. Ofwat is the economic regulator of the water and sewerage industry in England and Wales. http://www.ofwat.gov.uk/aptrix/ofwat/publish.nsf/Content/roleofregulator_factsheet170805 a regulatory role involved with making and/or enforcing relevant legislation and governmental orders Person:Jennifer Fostel regulator OBI regulator role OBI:0000015 biological feature identification objective Biological_feature_identification_objective is an objective role carried out by the proposition defining the aim of a study designed to examine or characterize a particular biological feature. Jennifer Fostel biological feature identification objective OBI:0000016 regulation-assigned role Approval letter Regulation-assigned role is a regulatory role defined by legislation or governmental orders Person: Jennifer Fostel regulation-assigned role OBI:0000017 regulatory role Regulatory agency, Ethics committee, Approval letter; example: Browse these EPA Regulatory Role subtopics http://www.epa.gov/ebtpages/enviregulatoryrole.html Feb 29, 2008 a role which inheres in material entities and is realized in the processes of making, enforcing or being defined by legislation or orders issued by a governmental body. GROUP: Role branch OBI, CDISC govt agents responsible for creating regulations; proxies for enforcing regulations. CDISC definition: regulatory authorities. Bodies having the power to regulate. NOTE: In the ICH GCP guideline the term includes the authorities that review submitted clinical data and those that conduct inspections. These bodies are sometimes referred to as competent regulatory role OBI:0000018 material supplier role Jackson Labs is an organization which provide mice as experimental material a role realized through the process of supplying materials such as animal subjects, reagents or other materials used in an investigation. Supplier role is a special kind of service, e.g. biobank PERSON:Jennifer Fostel material provider role supplier material supplier role OBI:0000020 contract research organization role a worker role of carrying out the study according to the protocol document or study plan delivered by the PI, under the control of the study director. This role cannot make decisions about the study execution Person: Jennifer Fostel contract research organization contract research organization role OBI:0000021 list-mode data file An example of a list-mode data file is a file following list-mode Flow Cytometry Standard (FCS) format. Since FCS files can be in histogram mode or list-mode we have to specify which data format specifically. List-mode format in the overwhelming (even universal) option used. A list-mode data file is a binary digital entity where events are stored sequentially, parameter by parameter. One example of usage is in the context of flow cytometry, however is not restricted to this community and is more widely used, e.g. by imaging people. person:Chris Stoeckert group:Flow Cytometry community list-mode data file OBI:0000023 classified data set A data set that is produced as the output of a class prediction data transformation and consists of a data set with assigned class labels. PERSON: James Malone PERSON: Monnie McGee data set with assigned class labels classified data set OBI:0000025 reference substance role Calibration standard, positive control substance, vehicle Good Laboratory Practices: Questions and Answers - Test Control and Reference Substance Characterization http://www.epa.gov/enforcement/monitoring/programs/fifra/glpqanda-character.html a role inhering in a material entity that is realized when characteristics or responses elicited by the substance are used for comparison or reference. Person:Jennifer Fostel reference substance OBI reference substance role OBI:0000026 cytological stain role haemotoxylin is a general purpose nuclear stain extracted from the wood of the logwood tree WEB: http://en.wikipedia.org/wiki/Haematoxylin A dye role that is realized when the stain is used to colour cells and or cellular components for the purposes of visualization Person:Helen Parkinson Person:Jennifer Fostel cytological stain cytological stain role OBI:0000029 centrifuge pellet role Definition of pellet :the material concentrated at the bottom of a centrifuge tube after centrifugation. http://www.everythingbio.com/glos/definition.php?word=pellet pellet role is a role which inheres in a material entity and is realized by a material separation process using gravitational force generated by a centrifuge in which the material bearing the pellet role is the heavier or heaviest component of the output material.. GROUP: Role branch OBI 9Mar09 after discussion with process branch changed definition to include use of centrifuge; centrifuge pellet role OBI:0000032 clinical research coordinator role a worker role comprised of handling the administrative duties of a trial or study. Person:Jennifer Fostel clinical research coordinator clinical research coordinator role OBI:0000034 supernatant role Precipitation is the formation of a solid in a solution during a chemical reaction. When the reaction occurs, the solid formed is called the precipitate, and the liquid remaining above the solid is called the supernate. Wikipedia supernatant role is a role which inheres in a material entity and is realized by a material separation process using gravitational force in which the material bearing the supernatant role is the liquid component of the output material. GROUP: Role branch OBI supernatant role OBI:0000038 chromatography column Chromatography column in chemistry is a tube and contents (typically glass) used to purify individual chemical compounds from mixtures of compounds. It is often used for preparative applications on scales from micrograms up to kilograms. Frank Gibson http://en.wikipedia.org/wiki/Column_chromatography open tracker https://sourceforge.net/tracker/index.php?func=detail&aid=2881353&group_id=177891&atid=886178 chromatography column OBI:0000040 drug role http://www.answers.com/topic/drug 1. A substance used in the diagnosis, treatment, or prevention of a disease or as a component of a medication. 2. Such a substance as recognized or defined by the U.S. Food, Drug, and Cosmetic Act. a role borne by a molecular entity and is realized in a process of absorption by an organism alters, or effects (or is assumed to effect) a function(s) which inhere in an organism Role Branch drug OBI, CDISC drug role OBI:0000041 pump valve switch A pump valve switch is a cardinal part of a liquid chromatography instrument that controls the flow. FG:I would assume this should be a pump valve control switch and it would not be specific to a liquid chromatography instrument OBI Instrument branch OBI pump valve switch OBI:0000043 xenotransplantation is the transplantation of living cells, tissues or \norgans from one species to another such as from pigs to humans PlanAndPlannedProcess Branch OBI branch derived xenotransplantation OBI:0000044 physical document a book is a physical document A physical document is an object serving as a record of information by means of symbolic marks. PERSON: Bjoern Peters GROUP: OBI physical document OBI:0000045 waiting not actively doing anything to a material for a duration of time. PERSON:Alan Ruttenberg OBI branch derived BP: I have doubts about the utility of this. We need a better handling/modeling of time (January 2008) waiting OBI:0000047 processed material Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples Is a material entity that is created or changed during material processing. PERSON: Alan Ruttenberg processed material OBI:0000048 chromatography device a device that facilitates the separation of mixtures. The function of a chromatography device involves passing a mixture dissolved in a "mobile phase" through a stationary phase, which separates the analyte to be measured from other molecules in the mixture and allows it to be isolated. Frank Gibson chromatography instrument http://en.wikipedia.org/wiki/Chromatography open tracker https://sourceforge.net/tracker/index.php?func=detail&aid=2881353&group_id=177891&atid=886178 chromatography device OBI:0000049 mass spectrometer LCQ Fleet Ion Trap MSn manufactured by thermo fisher scientific A mass spectrometer is an instrument which is used to measure the mass to charge ratio of ions. All mass spectrometers consist of three basic parts: an ion source, a mass analyzer, and a detector system. The stages within the mass spectrometer are: 1. Production of ions from the sample 2. Separation of ions with different masses 3. Detection of the number of ions of each mass produced 4.Collection of data to generate the mass spectrum Frank Gibson http://en.wikipedia.org/wiki/Mass_spectrometry mass spectrometer OBI:0000050 obsolete_platform A platform is an object_aggregate that is the set of instruments and software needed to perform a process. definition_source: OBI. OBI Instrument branch OBI Instrument branch rem1: We decided at the Philly workshop that consumables do not include reagents. FG: we could actully add a relation to platform which would be "has_part some instrument" DS: Sounds fine to me, with the restriction that I would assume a min. cardinality of 2 to be applicable for this crossproduct, so at least 2 instruments make it a platform... at least one is not enough AR:has_part is transitive, and transitive properties can't have cardinality constraints in OWL-DL. We can always put this particular constraint in the owl-full file. We need to make this a defined class when the class software is in the ontology suggested for deprecation https://sourceforge.net/tracker/index.php?func=detail&aid=2881353&group_id=177891&atid=886178 obsolete_platform true OBI:0000051 liquid chromatography mass spectrometry platform A liquid chromatography mass spectrometry platform is a platform that is the collection of instrument, software and reagents needed to perform a liquid chromatography mass spectrometry protocol. definition_source: OBI. OBI instrument branch OBI Instrument branch liquid chromatography mass spectrometry platform OBI:0000052 microarray platform A microarray platform is a platform that contains the instruments, software and reagents needed to perform a microarray protocol. definition_source: OBI. OBI Instrument branch OBI Instrument branch microarray platform OBI:0000054 ratio of collected to emitted light 10% A measurement datum measuring the amount of light collected s compared to the total amount of emitted light in the detector component of a flow cytometer instrument. The datum has a qualitative role person:Chris Stoeckert person:Kevin Clancy Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt ratio of collected to emitted light OBI:0000055 software optimization objective Software_optimization is a software_testing_objective role describing a study designed to identify the best software or parameters of the software. Jennifer Fostel software optimization objective OBI:0000056 notified body role The role of notified bodies presentation: http://ec.europa.eu/enterprise/electr_equipment/emc/revision/notified_bodies.pdf Notified body is regulator of consumables and medical devices charged by the Competent Authority with verifying compliance of medical devices (not drugs) with the applicable Essential Requirements stated in the Medical Device Directive Notified Body (NB). A private institution charged by the Competent Authority with verifying compliance of medical devices (not drugs) with the applicable Essential Requirements stated in the Medical Device Directive. This process, called Conformity Assessment, has EU-wide validity once completed by the NB. Person: Jennifer Fostel notified body OBI, CDISC notified body role OBI:0000057 allotransplantation is the transplantation of organs between members of the same species. PlanAndPlannedProcess Branch OBI branch derived allotransplantation OBI:0000059 gamma counter A Geiger counter A processed material which measures gamma radiation Frank Gibson http://en.wikipedia.org/wiki/Gamma_counter gamma counter OBI:0000060 trial monitor role a responsible party involved in planning, overseeing the conduct of a study or study component, and interpreting data from a study Person:Jennifer Fostel trial monitor CDISC definition: Person employed by the sponsor or CRO who is responsible for determining that a trial is being conducted in accordance with the protocol and GCP guidance. NOTE: A monitor's duties may include, but are not limited to, helping to plan and initiate a trial, assessing the conduct of trials, and assisting in data analysis, interpretation and extrapolation. Clinical Research Associate: Primary representative of the sponsor; monitors progress of investigator sites participating in a clinical study. trial monitor role OBI:0000064 positive reference substance role MMS mutagen a reference role in which the characteristics or responses elicited by the substance playing the reference substance role are used to establish a "100%" response Person: Jennifer Fostel positive reference substance positive reference substance role OBI:0000065 polyethylene glycol p-(1,1,3,3-tetramethylbutyl)-phenyl ether PMID: 30799. J Histochem Cytochem. 1978 Sep;26(9):696-712. Acid lipase: a histochemical and biochemical study using triton X100-naphtyl palmitate micelles. triton X100 is a chemical entity which belongs to the group of The pluronics which are triblock copolymers of ethylene oxide and propylene oxide. Triton x-100 is_used_as detergent due to its non-ionic surfactant properties Philippe Rocca-Serra adapted from Wikipedia before possible import from CHEBI polyethylene glycol p-(1,1,3,3-tetramethylbutyl)-phenyl ether OBI:0000066 investigation Lung cancer investigation using expression profiling, a stem cell transplant investigation, biobanking is not an investigation, though it may be part of an investigation a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s). Bjoern Peters OBI branch derived Could add specific objective specification Following OBI call November 2012,26th: it was decided there was no need for adding "achieves objective of drawing conclusion" as existing relations were providing equivalent ability. this note closes the issue and validates the class definition to be part of the OBI core editor = PRS study investigation OBI:0000067 evaluant role When a specimen of blood is assayed for glucose concentration, the blood has the evaluant role. When measuring the mass of a mouse, the evaluant is the mouse. When measuring the time of DNA replication, the evaluant is the DNA. When measuring the intensity of light on a surface, the evaluant is the light source. a role that inheres in a material entity that is realized in an assay in which data is generated about the bearer of the evaluant role Role call - 17nov-08: JF and MC think an evaluant role is always specified input of a process. Even in the case where we have an assay taking blood as evaluant and outputting blood, the blood is not the specified output at the end of the assay (the concentration of glucose in the blood is) examples of features that could be described in an evaluant: quality.... e.g. "contains 10 pg/ml IL2", or "no glucose detected") GROUP: Role Branch OBI Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. evaluant role OBI:0000068 reporting party role Person who prepares microarray data in MAGE-TAB format and submits to a database, such as ArrayExpress. The first section has been pre-designated as the 'Reporting Party' section and should be filled with the Reporting Party's personal information. http://www.mercedsheriff.com/SelfReporting.htm a study personnel role played by a party who reports the outcome of a study component MO:submitter mapped to this term. So, alternative term 'submitter' was added. Jennifer Fostel reporting party submitter OBI reporting party role OBI:0000070 assay Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house. A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies. 12/3/12: BP: the reference to the 'physical examination' is included to point out that a prediction is not an assay, as that does not require physical examiniation. PlanAndPlannedProcess Branch measuring scientific observation OBI branch derived study assay any method assay OBI:0000071 quantitative confidence value A data item which is used to indicate the degree of uncertainty about a measurement. person:Chris Stoeckert group:OBI quantitative confidence value OBI:0000073 sample preparation for assay A sample_preparation_for_assay is a protocol_application including material_enrollments and biomaterial_transformations. definition_source: OBI. PlanAndPlannedProcess Branch study OBI branch derived sample preparation for assay OBI:0000075 diagnosis textual entity diagnosis is an assessment of a disease or injury, its likely prognosis and treatment. Jennifer Fostel diagnosis textual entity OBI:0000076 unplanned occurrence effecting an investigation Earthquake that destroys the lab, an outside investigator discovering an adverse effect of the reagants used a process which is external in origin to the investigation that has an impact on the outcome. PERSON: Bjoern Peters OBI unplanned occurrence effecting an investigation OBI:0000078 eMedical record An eMedical record is a digital document derived from a computer system used primarily for patient care in a clinical setting. Not required to be compliant with requirements of 21 CFR Part 11. person:Jennifer Fostel article-without-pmid-or-doi:CDISCglossary eMedical record OBI:0000079 culture medium A growth medium or culture medium is a substance in which microorganisms or cells can grow. Wikipedia, growth medium, Feb 29, 2008 a processed material that provides the needed nourishment for microorganisms or cells grown in vitro. changed from a role to a processed material based on on Aug 22, 2011 dev call. Details see the tracker item: http://sourceforge.net/tracker/?func=detail&aid=3325270&group_id=177891&atid=886178 Modification made by JZ. Person: Jennifer Fostel, Jie Zheng OBI culture medium OBI:0000083 electronic case report tabulation An electronic case report tabulation is a digital document containing tabular data about multiple trial participants which is part of a clinical regulatory submission. An eCRT has the property that it can be audited and compliant with requirements of 21 CFR Part 11 and has format suited to review by regulators. person:Jennifer Fostel CDISC glossary electronic case report tabulation OBI:0000084 polystyrene tube Polystyrene tubes can be used to contain tissue culture cells during centrifgation a polystyrene tube is a test tube made of polystyrene PERSON: Chris Stoeckert PERSON: Chris Stoeckert polystyrene tube OBI:0000086 reagent role Buffer, dye, a catalyst, a solvating agent. A role inhering in a biological or chemical entity that is intended to be applied in a scientific technique to participate (or have molecular components that participate) in a chemical reaction that facilitates the generation of data about some entity distinct from the bearer, or the generation of some specified material output distinct from the bearer. PERSON:Matthew Brush reagent PERSON:Matthew Brush Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. May 28 2013. Updated definition taken from ReO based on discussions initiated in Philly 2011 workshop. Former defnition described a narrower view of reagents in chemistry that restricts bearers of the role to be chemical entities ("a role played by a molecular entity used to produce a chemical reaction to detect, measure, or produce other substances"). Updated definition allows for broader view of reagents in the domain of biomedical research to include larger materials that have parts that participate chemically in a molecular reaction or interaction. (copied from ReO) Reagents are distinguished from instruments or devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in or have parts that participate in some chemical interaction or reaction during their intended participation in some technique. By contrast, instruments do not participate in a chemical reaction/interaction during the technique. Reagents are distinguished from study subjects/evaluants in that study subjects and evaluants are that about which conclusions are drawn and knowledge is sought in an investigation - while reagents, by definition, are not. It should be noted, however, that reagent and study subject/evaluant roles can be borne by instances of the same type of material entity - but a given instance will realize only one of these roles in the execution of a given assay or technique. For example, taq polymerase can bear a reagent role or an evaluant role. In a DNA sequencing assay aimed at generating sequence data about some plasmid, the reagent role of the taq polymerase is realized. In an assay to evaluate the quality of the taq polymerase itself, the evaluant/study subject role of the taq is realized, but not the reagent role since the taq is the subject about which data is generated. In regard to the statement that reagents are 'distinct' from the specified outputs of a technique, note that a reagent may be incorporated into a material output of a technique, as long as the IDENTITY of this output is distinct from that of the bearer of the reagent role. For example, dNTPs input into a PCR are reagents that become part of the material output of this technique, but this output has a new identity (ie that of a 'nucleic acid molecule') that is distinct from the identity of the dNTPs that comprise it. Similarly, a biotin molecule input into a cell labeling technique are reagents that become part of the specified output, but the identity of the output is that of some modified cell specimen which shares identity with the input unmodified cell specimen, and not with the biotin label. Thus, we see that an important criteria of 'reagent-ness' is that it is a facilitator, and not the primary focus of an investigation or material processing technique (ie not the specified subject/evaluant about which knowledge is sought, or the specified output material of the technique). reagent role OBI:0000089 role of regulator of chemical manufacturer EPA; John Mollison is the registrar of chemical products in Tasmania, the body that administers the Act that regulates chemical use in that State. http://www.abc.net.au/rn/science/earth/stories/s1160346.htm a regulator involved with making and enforcing legislation and governmental orders relevant to chemical manufacture Person: Jennifer Fostel regulator of chemical manufacture OBI role of regulator of chemical manufacturer OBI:0000091 detector reagent role a role which inheres in a molecular entity and is realized by the process of recording or registering a stimulus. 19feb2009. not clear we need this term. originally if came from microarrays -- the probes on the array are termed detectors in some instances One that detects, especially a mechanical, electrical, or chemical device that automatically identifies and records or registers a stimulus, such as an environmental change in pressure or temperature, an electric signal, or radiation from a radioactive material. http://www.answers.com/topic/detector 19feb2009 detector reagent role OBI:0000092 role of certified IRB professional CIP= Certified IRB Professional; http://acronyms.thefreedictionary.com/Certified+IRB+Professional a role of which inheres in a Homo sapiens and realized during administration and oversight of the daily activities of Institutional Review Boards (IRBs) in the USA Person:Helen Parkinson Person:Jennifer Fostel certified IRB professional WEB: http://en.wikipedia.org/wiki/Certified_IRB_Professional role of certified IRB professional OBI:0000093 patient role a hospitalized person; a person with controlled diabetes; the patient's role http://www.fertilityjourney.com/testingAndDiagnosis/theRightDoctor/thePatientsRole/index.asp?C=55245395146924652778 a role which inheres in a person and is realized by the process of being under the care of a physician or health care provider GROUP:Role Branch patient OBI, CDISC CDISC definition: patient. Person under a physician's care for a particular disease or condition. NOTE: A subject in a clinical trial is not necessarily a patient, but a patient in a clinical trial is a subject. See also subject, trial subject, healthy volunteer. Often used interchangeably patient role OBI:0000094 material processing A cell lysis, production of a cloning vector, creating a buffer. A planned process which results in physical changes in a specified input material PERSON: Bjoern Peters PERSON: Frank Gibson PERSON: Jennifer Fostel PERSON: Melanie Courtot PERSON: Philippe Rocca Serra material transformation OBI branch derived material processing OBI:0000096 protocol testing objective Protocol_testing_objective is a methodology_testing_objective role describing a study designed to examine the effects of using different protocols. Jennifer Fostel protocol testing objective OBI:0000097 participant under investigation role Human subjects in a clinical trial, rats in a toxicogenomics study, tissue cutlures subjected to drug tests, fish observed in an ecotoxicology study. Parasite example: people are infected with a parasite which is then extracted; the particpant under investigation could be the parasite, the people, or a population of which the people are members, depending on the nature of the study. Lake example: a lake could realize this role in an investigation that assays pollution levels in samples of water taken from the lake. A role that is realized through the execution of a study design in which the bearer of the role participates and in which data about that bearer is collected. A participant can realize both "specimen role" and "participant under investigation role" at the same time. However "participant under investigation role" is distinct from "specimen role", since a specimen could somehow be involved in an investigation without being the thing that is under investigation. GROUP: Role Branch OBI Following OBI call November 2012,26th: 1. it was decided there was no need for moving the children class and making them siblings of study subject role. 2. it also settles the disambiguation about 'study subject'. This is about the individual participating in the investigation/study, Not the 'topic' (as in 'toxicity study') of the investigation/study This note closes the issue and validates the class definition to be part of the OBI core editor = PRS participant under investigation role OBI:0000100 obsolete_role of being first subject treated Rat 1A; first enrolled patient to receive treatment First subject treated role is a study subject role borne by the subject realized in the application of the process specified in intervention study design with no previous study subject realizing the role prior in the study first subject treated. First subject who receives the test article or placebo in a clinical trial. Role Branch OBI obsolete_role of being first subject treated true OBI:0000101 measured expression level Examples are quantified data from an expression microarray experiment, PCR measurements, etc. A measurement datum that is the outcome of the quantification of an assay for the activity of a gene, or the number of RNA transcripts. person:Chris Stoeckert OBI Data Transformation branch measured expression level OBI:0000102 responsible party role he THERAPIST has the ability to print a separate statement for the patient and each responsible party. http://www.beaverlog.com/therapist/ez_support/billing/responsible_party_statements.htm a study personnel role played by a party who is accountable for the execution of a study component and can make decisions about the conduct of the study Person: Jennifer Fostel responsible party OBI responsible party role OBI:0000103 principal investigator role a responsible party role played by a person responsible for the overall conduct of a study Person: Jennifer Fostel principal investigator CDISC definition: A person responsible for the conduct of the clinical trial at a trial site. If a trial is conducted by a team of individuals at a trial site, the investigator is the responsible leader of the team and may be called the principal investigator. 2. The individual principal investigator. 2. The individual under whose immediate direction the test article is administered or dispensed to, or used involving, a subject, or, in the event of an investigation conducted by a team of individuals, is See also sponsor-investigator.; Leiter der klinischen Prufung.Under the German Drug Law, the physician who is head of the clinical investigation (CDISC): coordinating investigator (CDISC) (also study coordinator, MUSC); sponsor-investigator. An individual who both initiates and conducts, alone or with others, a clinical trial, and under whose immediate direction the investigational product is administered to, dispensed to, or used by a subject.NOTE: The term does not include any person other than an individual, hence not a corporation, agency (CDISC) principal investigator role OBI:0000105 transplantation a protocol application to replace an organ or tissue of an organism PlanAndPlannedProcess Branch OBI branch derived transplantation OBI:0000109 biological vector role 1983 Sci. Amer. Jan. 58/2 Plasmids are routinely used as vectors for introducing foreign DNA into bacteria. Some epidemiological aspects and vector role of tick infestation on layers in the Faisalabad district (Pakistan). http://journals.cambridge.org/action/displayAbstract;jsessionid=0373164489D00868AEEF2C556EB4FD29.tomcat1?fromPage=online&aid=624280 a biological vector role is a material to be added role that is realized by the process of transmitting material to the organism that is the target of the transmission. Feb 20, 2009. The material transmitted can be genetic information (as in cloning vector) or a pathogen (as in a disease vector) false GROUP: Role Branch OBI and Wikipedia 6/12/2009 Alan made this a material to be added role, because it was, and because this speeded up reasoning biological vector role true OBI:0000110 pH indicator dye role bromophenol blue has a pH indicator dye role phenol red in RPMI; pH=4 indicator dye (also carries reference role) the role of a dye that is realized when the dye is used in an experiment to measure the pH in a material entity Person: Jennifer Fostel Person:Helen Parkinson pH indicator dye pH indicator dye role OBI:0000112 specimen role liver section; a portion of a culture of cells; a nemotode or other animal once no longer a subject (generally killed); portion of blood from a patient. a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation 22Jun09. The definition includes whole organisms, and can include a human. The link between specimen role and study subject role has been removed. A specimen taken as part of a case study is not considered to be a population representative, while a specimen taken as representing a population, e.g. person taken from a cohort, blood specimen taken from an animal) would be considered a population representative and would also bear material sample role. Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. blood taken from animal: animal continues in study, whereas blood has role specimen. something taken from study subject, leaves the study and becomes the specimen. parasite example - when parasite in people we study people, people are subjects and parasites are specimen - when parasite extracted, they become subject in the following study specimen can later be subject. GROUP: Role Branch OBI specimen role OBI:0000113 sequence feature identification objective Sequence_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize molecular features exhibited at the level of a macromolecular sequence, e.g. nucleic acid, protein, polysaccharide. Jennifer Fostel sequence feature identification objective OBI:0000115 intervention design PMID: 18208636.Br J Nutr. 2008 Jan 22;:1-11.Effect of vitamin D supplementation on bone and vitamin D status among Pakistani immigrants in Denmark: a randomised double-blinded placebo-controlled intervention study. An intervention design is a study design in which a controlled process applied to the subjects (the intervention) serves as the independent variable manipulated by the experimentalist. The treatment (perturbation or intervention) defined can be defined as a combination of values taken by independent variable manipulated by the experimentalists are applied to the recruited subjects assigned (possibly by applying specific methods) to treatment groups. The specificity of intervention design is the fact that independent variables are being manipulated and a response of the biological system is evaluated via response variables as monitored by possibly a series of assays. Philppe Rocca-Serra OBI branch derived intervention design OBI:0000116 worker role Public sector workers in states that run their own OSHA programs are covered by those states. http://www.osha.gov/as/opa/worker/index.html a personnel role played by a party who executes a component of the study plan; this can occur before, during, after or outside the study timeline "executes the study plan" includes the suppliers and manufacturers of reagents and other materials used in the study Person:Jennifer Fostel worker OBI worker role OBI:0000117 Bernoulli trial is an assay where the output data is a datum with one of two values denoted success and failure. PlanAndPlannedProcess Branch OBI branch derived Bernoulli trial OBI:0000118 gene list Gene lists may arise from analysis to determine differentially expressed genes, may be collected from the literature for involvement in a particular process or pathway (e.g., inflammation), or may be the input for gene set enrichment analysis. A data set of the names or identifiers of genes that are the outcome of an analysis or have been put together for the purpose of an analysis. person:Chris Stoeckert group:OBI kind of report. (alan) need to be careful to distinguish from output of a data transformation or calculation. A gene list is a report when it is published as such? Relates to question of whether report is a whole, or whether it can be a part of some other narrative object. gene list OBI:0000119 number of particles in subset 500, 200, 0 A measurement datum measuring the number of subjects in a defined subset in a flow cytometer instrument. The datum has a qualitative role person:Kevin Clancy Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt number of particles in subset OBI:0000125 number of lost events electronic 74, 0, 14 events lost due to data acquisition electronic coincidence. A measurement datum measuring the number of analysis events lost due to errors in data acquisition electronic coincidence in a flow cytometer instrument. The datum has a qualitative role. person:Kevin Clancy Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt number of lost events electronic OBI:0000129 calibration substance role pH buffer used to calibrate a pH meter bears a calibration substance role A reference substance role that is realized when characteristics or responses elicited by the bearer are used to ensure an instrument is within protocol specification of accuracy or performance Jennifer Fostel calibration substance role OBI:0000131 molecular feature identification objective Molecular_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize molecular features of a biological system, e.g. expression profiling, copy number of molecular components, epigenetic modifications. Jennifer Fostel molecular feature identification objective OBI:0000134 hardware testing objective Hardware_testing_objective is a methodology_testing_objective role describing a study designed to examine the effects of using different hardware, e.g. scanner. Jennifer Fostel hardware testing objective OBI:0000136 incubator Incubators are used in microbiology for culturing (growing) bacteria and other microorganisms. Incubators in tissue culture rooms are used for culturing stem cells, lymphocytes, skin fibroblasts and other types of cells a device in which environmental conditions (light, photoperiod, temperature, humidity, etc.) can be controlled Frank Gibson http://www.medterms.com/script/main/art.asp?articlekey=18426 incubator OBI:0000140 obsolete_label role Label role is a role which inheres in a material entity and which is realized in a detection of label assay MHB (9-26-12): consider deprecation of this class and replacement with REO:'molecular label role' Nucleotides synthesized with the incorporation of biotin were used to synthesize cDNA, which was then detected by adding fluorochrome-conjugated anti-biotin antibody. the fluorochrome bears label role, the antibody bears detector role, the biotin bears reporter role. may need to change the terms following discussion need to add a restriction that the material entity has the disposition / quality that permits it to be detected, and one way to say this (BP) is that the entity is such that an assay exists that detects the presence of the material entity we need to sort out probe, detector and reporter. See https://sourceforge.net/tracker/index.php?func=detail&amp;aid=1866458&amp;group_id=177891&amp;atid=886178 Role Branch label OBI http://purl.obolibrary.org/obo/REO_0000171 obsolete_label role true OBI:0000143 baseline participant role Subject at time = 0; subject before a stress test. a reference participant role which is realized by making the reference to qualities at the start of the study or intervention Person: Jennifer Fostel baseline participant baseline participant role OBI:0000144 role of independent data monitoring committee a trial monitor role charged recommending whether to continue, modify, or end the trial Person: Jennifer Fostel independent data monitoring committee role of independent data monitoring committee OBI:0000145 pathologist role a worker role of being responsible for making the histopathology diagnoses associated with data from a study; this activity occurs outside the study timeline Person:Jennifer Fostel Pathologist pathologist role OBI:0000146 supernatant collection system harvesting frame a device that is designed for collecting 90% of the supernatant in a microplate well and separating the living cell with no stress, eliminating centrifugation and other similar techniques. It can be used in a variety of release assays with different radioactive isotopes, such as Cr51 or I125. Daniel Schober google supernatant collection system harvesting frame OBI:0000151 filter paper a device manufacture with the intent to provide a porous unsized paper used for filtering. Frank Gibson sep:00107 filter paper 2 OBI:0000153 cell co-culturing Culturing cytotoxic T-lymphocytes together with target cells in order to study lysis of the target cells. See chromium_release_assay A material combination in which cell cultures of two or more different types are are combined and allowed to culture as one. PlanAndPlannedProcess Branch OBI branch derived cell co-culturing OBI:0000154 role of Institutional Review Board An institutional review board/independent ethics committee (IRB/IEC) (also known as ethical review board) is a group that has been formally designated to approve, monitor, and review biomedical and behavioral research involving humans with the alleged aim to protect the rights and welfare of the subjects. Wikipedia March 2008 Animal protocol review board the role of a organization that is realized by members reviewing study designs for their agreement with regulations Person:Helen Parkinson Person:Jennifer Fostel Internal Review Board OBI, CDISC CDISC definition: institutional review board; independent ethics committee (IEC). An independent body (a review board or a committee, institutional, regional, national, or supranational) constituted of medical/scientific professionals and non-scientific members, whose responsibility it is to ensure the protection of the rights, safety and well-being of human subjects involved in a trial. role of Institutional Review Board OBI:0000158 eSource document an eSource document is a digital document consisting of a logical collection of Source data and other eSource documents that can be presented in an ordered way and capture the time of completion, change, and any signatures person:Jennifer Fostel article-without-pmid-or-doi:CDISCglossary eSource document OBI:0000161 crossover population role a role realized when a participant serves as reference to itself Person: Jennifer Fostel crossover population crossover population role OBI:0000162 complete nutrient role Rat chow; RPMI medium + serum; use example: CNS17 (Complete Nutrient System) Grow 3-2-4, http://www.kalyx.com/store/proddetail.cfm/ItemID/552307/CategoryID/12000/SubCatID/2755/file.htm A nutrient role that inheres in a material entity and is realized in the use of that material entity by an organism to provide all needed nourishment. Person: Jennifer Fostel complete nutrient complete nutrient role OBI:0000163 radiolabel role a molecular label role which inheres in a material entity which is realized by the process of radioactivity detection Jennifer Fostel radiolabel radiolabel role OBI:0000164 cDNA library PMID:6110205. collection of cDNA derived from mouse splenocytes. Mixed population of cDNAs (complementaryDNA) made from mRNA from a defined source, usually a specific cell type. This term should be associated only to nucleic acid interactors not to their proteins product. For instance in 2h screening use living cells (MI:0349) as sample process. ALT DEF (PRS):: a cDNA library is a collection of host cells, typically E.Coli cells but not exclusively. modified by transfer of plasmid DNA molecule used as vector containing a fragment or totality of cDNA molecule (the insert) . cDNA library may have an array of role and applications. PERSON: Luisa Montecchi PERSON: Philippe Rocca-Serra GROUP: PSI PRS: 22022008. class moved under population, modification of definition and replacement of biomaterials in previous definition with 'material' addition of has_role restriction cDNA library OBI:0000167 electronic case report form An electronic case report form is a digital document used to record all of the protocol required information to be reported for each trial subject. An eCRF has the property that it can be audited and compliant with requirements of 21 CFR Part 11. person:Jennifer Fostel CDISC glossary electronic case report form OBI:0000169 placebo role Pill consisting of inert materials a negative reference substance is a reference role in which the substance playing the reference substance role is physically similar in appearance to the test substance Person:Jennifer Fostel placebo CDISC definition placebo. A pharmaceutical preparation that does not contain the investigational agent. In blinded studies, it is generally prepared to be physically indistinguishable from the preparation containing the investigational product. placebo role OBI:0000171 autotransplantation is the transplantation of tissue from one part of \nthe body to another in the same individual. ) PlanAndPlannedProcess Branch OBI branch derived autotransplantation OBI:0000172 parameter threshold 0.01, 0.03 A measurement datum measuring the minimal signal that must be detected to generate an electrical event, as compared to the maximal detected signal in a flow cytometer instrument. The datum has a qualitative role person:Kevin Clancy Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt parameter threshold OBI:0000174 study group role The group of randomized participants that are assigned to a treatment arm of the trial a study population role where the bearer is a population of material entities and the role is realized in the implementation of a study design wherein the entities bearing the study population role are observed or subjected to intervention according to the study design and are biological replicates, i.e. they receive the same treatment under the protocol Jennifer Fostel study group population study group role OBI:0000175 p-value PMID:19696660 in contrast to the in-vivo data AT-III increased significantly from 113.5% at baseline to 117% after 4 days (n = 10, P-value= 0.02; Table 2). A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone. May be outside the scope of OBI long term, is needed so is retained PERSON:Chris Stoeckert WEB: http://en.wikipedia.org/wiki/P-value p-value OBI:0000181 population PMID12564891. Environ Sci Technol. 2003 Jan 15;37(2):223-8. Effects of historic PCB exposures on the reproductive success of the Hudson River striped bass population. a population is a collection of individuals from the same taxonomic class living, counted or sampled at a particular site or in a particular area 1/28/2013, BP, on the call it was raised that we may want to switch to an external ontology for all populatin terms: http://code.google.com/p/popcomm-ontology/ PERSON: Philippe Rocca-Serra adapted from Oxford English Dictionnary rem1: collection somehow always involve a selection process population OBI:0000182 nuclear magnetic resonance 3D structure determination assay Determining the binding of epitope-specific nanobody cAb-HuL5 to wild type human lysozyme by chemical shift perturbations in NMR spectra (Erwin De Genst, J Phys Chem B 2013). A 3D structure determination assay that uses magnetic properties of atomic nuclei to determine the 3D structure and dynamics of molecules in the input sample. PlanAndPlannedProcess Branch, IEDB IEDB nuclear magnetic resonance 3D structure determination assay OBI:0000185 imaging assay An imaging assay is an assay to produce a picture of an entity. definition_source: OBI. PlanAndPlannedProcess Branch OBI branch derived imaging assay OBI:0000186 protocol optimization objective Protocol_optimization is a protocol_testing_objective role describing a study designed to identify the best protocol. This may be carried out by comparing different protocols or by modifying the parameters used within a single protocol. Jennifer Fostel protocol optimization objective OBI:0000188 role of pathology review board a worker role comprised of providing a confirmed and consensus diagnosis for histopathology results obtained during the investigation Person: Jennifer Fostel pathology review board role of pathology review board OBI:0000192 microtiter plate A microtiter plate with 6, 24, 96, 384 or 1536 sample wells used in the enzyme-linked immunosorbent assay (ELISA) A microtiter_plate is a flat plate with multiple wells used as small test tubes. Melanie Courtot microplate http://en.wikipedia.org/wiki/Microtiter_plate microtiter plate OBI:0000196 role of impartial witness According to GCP , an impartial witness should be present for an illiterate subject. PharmPK Discussion, http://www.boomer.org/pkin/PK06/PK2006253.html a role which inheres in a Homo sapiens and is realized during a clinical trial - the impartial witness is independent of the trial and cannot be unfairly influenced by people involved with the trial impartial witness. A person, who is independent of the trial, who cannot be unfairly influenced by people involved with the trial, who attends the informed consent process if the subject or the subject's legally acceptable representative cannot read, and who Person: Helen Parkinson Person: Jennifer Fostel impartial witness role of impartial witness OBI:00001975 chromatin immunoprecipitation Yang et al, Int J Clin Exp Pathol. 2015; 8(3): 2746–275 PMID:26045780. Cells were lysed and sonicated to shear DNA to lengths between 200-1000 bp. The sample was then incubated with antibodies against Acety-H3 to immunoprecipitate protein-DNA complexes using protein A agarose beads. The isolated protein-DNA complexes were treated with proteinase K digestion to remove histones. QPCR was then performed using primers specific for TGF-β1, MMP-9 and PI3K promoters at 95°C for 5 min, followed by 40 cycles at 95 °C for 20 s, 58°C for 20 s, and 72°C for 20 s. Each QPCR reaction was repeated in triplicate. QPCR was followed by a melt curve analysis to determine the reaction specificity. The relative gene expression was calculated using 2-ΔΔCt method. An immunoprecipitation in which chromatin (i.e. packaged DNA which can include protein and RNA complexes) is cut into short regions, reversibly cross linked, and antibodies or tags are used to select for pieces of chromatin with desired characteristics. Bjoern Peters, Randi Vita, James A. Overton ChIP OBI chromatin immunoprecipitation OBI:0000198 biological replicate role A member of a dose-time group; a patient in a given arm of a trial a reference participant role realized by equivalent treatment of participants Person:Jennifer Fostel biological replicate OBI biological replicate role OBI:0000201 radioactivity detection Placing the evaluant input material close to a scintillation counter which emits light upon being hit with alpha/beta/gamma radiation and counting the frequency of light blasts to determine the radioactivity of the input material. An assay that measures the amount of radiation in the radioactive spectrum (alpha, beta or gamma rays) emitted from an input material. PlanAndPlannedProcess Branch, IEDB IEDB radioactivity detection OBI:0000202 investigation agent role The person perform microarray experiments and submit microarray results (including raw data, processed data) with experiment description to ArrayExpress. A role borne by an entity and that is realized in a process that is part of an investigation in which an objective is achieved. These processes include, among others: planning, overseeing, funding, reviewing. Implementing a study means carrying out or performing the study and providing reagents or other materials used in the study and other tasks without which the study would not happen. Philly2013: Historically, this role would have been borne only by humans or organizations. However, we now also want to enable representing investigations run by robot scientists such as ADAM (King et al, Science, 2009) GROUP: Role Branch investigator OBI Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. study person role Philly2013: Historically, this role would have been borne only by humans or organizations. However, we now also want to enable investigations run by robot scientists such as ADAM (King et al, Science, 2009) investigation agent role OBI:0000204 nutrient role Luria broth; vitamin A; A nutrient is a substance used in an organism's metabolism which must be taken in from the environment. Wikipedia. a role that inheres in a material entity and is realized in the use of that material entity by an organism when it is used in that organism's metabolism and provides nourishment. GROUP: Role branch nutrient Wikipedia, feb 29, 2008 19 Feb 2009; old def: A nutrient role is a role played by a substance used in an organism's metabolism which is taken in from the environment and provides nourishment. nutrient role OBI:0000205 obsolete_dropout role Escaped rat; human who moved to another city. Rat which escapes part way through a study; a human study participant who moved to another city before the study was completed (and stopped participating in the study) Dropout is a study subject role borne by an entity realized by a process of leaving the study earlier than the protocol specified and where the bearer of the dropout role had been borne study subject role prior to bearing dropout role. Will be modelled as defined material, ouput of some 'dropout or withdrawal process' instead of role Role Branch OBI obsolete_dropout role true OBI:0000207 health care provider role a worker role of providing medical care either within or outside the study timeline Person:Jennifer Fostel health care provider health care provider role OBI:0000208 methodology testing objective Methodology_testing_objective is an objective role carried out by a proposition defining the aim of the study is to examine the effect of using different methodologies. Jennifer Fostel methodology testing objective OBI:0000210 analytical cytology data file FCS file, ACS file, foo.fcs, foo.asc A digital entity intended to capture data in analytical cytology domain. person:Chris Stoeckert group:Flow Cytometry community analytical cytology data file OBI:0000211 proxy respondent role Proxy respondent is a worker role of describing patient's symptoms or condition to medical personnel Jennifer Fostel proxy respondent proxy respondent role OBI:0000213 fluorescence compensation matrix ((1.053096, -0.22476), (-0.24877, 1.053096)) A fluorescence compensation matrix is a square matrix which is used as the left multiplier of the vector of fluorescence values while performing digital fluorescence compensation. Also, fluorescence compensation matrix is the inverse of the fluorescence spillover matrix. person:Chris Stoeckert group:Flow Cytometry community fluorescence compensation matrix OBI:0000214 negative reference substance role Saline solution a reference role in which the characteristics or responses elicited by the substance playing the reference substance role are used to establish a "no effect" response Person: Jennifer Fostel negative reference substance negative reference substance role OBI:0000215 role of legally acceptable representative Parent of minor patient; Definition of legally acceptable representative An individual or juridicial or other body authorized under applicable law to consent, on behalf of a prospective subject, to the subject`s participation in the clinical trial. http://www.geneed.com/website/catalog/glossary_search.php?id=2134&search_term=legally%20acceptable%20representative&select=TRUE a role which inheres in a human or organization who are able subject to applicable law to consent, on behalf of a prospective subject, to the subject`s participation in as clinical trial. legally acceptable representative. An individual or juridical or other body authorized under applicable law to consent, on behalf of a prospective subject, to the subject's participation in the clinical trial. [ICH, E6 Glossary] Person: Jennifer Fostel Person:Helen Parkinson legally acceptable representative OBI, CDISC role of legally acceptable representative OBI:0000218 investigation results report An investigation report is a report on the results of an investigation. person:Chris Stoeckert group:OBI investigation results report OBI:0000219 cellular feature identification objective Cellular_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize a biological feature monitored at the cellular level, e.g. stage of cell cycle, stage of differentiation. Jennifer Fostel cellular feature identification objective OBI:0000220 reference subject role Saline treated rat; one of three identically-treated subjects a reference subject role which inheres in an organism or entity of organismal origin so that the characteristics or responses of the participant playing the reference participant role are used for comparison or reference Jennifer Fostel reference participant OBI reference subject role OBI:0000221 vital dye role typtan blue has a vital dye A dye role that is realized when used to detect live cells in an experiment 2009-11-10. Tracker: https://sourceforge.net/tracker/?func=detail&aid=2893048&group_id=177891&atid=886178 Person: Helen Parkinson Person: Jennifer Fostel vital dye vital dye role OBI:0000223 obsolete_blinded medication role 115 patients received ipilimumab and blinded medication Inert pill shaped like aspirin tablet Is a role which inheres in a material entity which is manufactured to be similar in appearance to a test material entity in e.g. a clinical trial to prevent participants from detecting which is the active and inactive substance Will be modelled using a blinding process and specified output blinded medication instead Jennifer Fostel Person:Helen Parkinson obsolete_blinded medication role true OBI:0000224 sub-investigator role a worker role authorized to make study-related decisions and carry out tasks related to the study; this role occurs during the study timeline Person: Jennifer Fostel sub-investigator CDISC definition: Sub-investigator. Any member of the clinical trial team designated and supervised by the investigator at a trial site to perform critical trial-related procedures and/or to make important trial-related decisions (e.g., associates, residents, research fellows) [ICH] See associates, residents, research fellows sub-investigator role OBI:0000227 data encoding storage of measurement results from an assay into a text file, such as a documenting process to encode an information entity into a digital document PlanAndPlannedProcess Branch OBI branch derived We (protocol application branch) placed this term because it kept getting bounced from data transformation and DENRIE data encoding OBI:0000231 enzymatic cleavage Polymorphism R62W results in resistance of CD23 to enzymatic cleavage in cultured cells. Genes Immun. 2007 Apr;8(3):215-23. Epub 2007 Feb 15. PMID: 17301828 enzymatic cleavage is a protocol application to digest the fraction of input material that is susceptible to that enzyme PlanAndPlannedProcess Branch OBI branch derived enzymatic cleavage OBI:0000232 hardware optimization objective Hardware_optimization is a hardware_testing_objective describing a study designed to identify the best hardware. Jennifer Fostel hardware optimization objective OBI:0000233 obsolete_defined_material Place holder class, Utility class to gather the defined classes false Susanna Sansone OBI Biomaterial derived obsolete_defined_material true OBI:0000234 trial statistician role a worker role that analyzes data obtained during a trial or study; this role occurs after the trial or study is completed or terminated. Person:Jennifer Fostel trial statistician CDISC definition: trial statistician. A statistician who has a combination of education/training and experience sufficient to implement the principles in the ICH E9 guidance and who is responsible for the statistical aspects of the trial. [ICH E9] trial statistician role OBI:0000235 standard error A quantitative confidence value which is the standard deviations of the sample in a frequency distribution, obtained by dividing the standard deviation by the total number of cases in the frequency distribution. person:Chris Stoeckert group:OBI see P-Value standard error OBI:0000237 antigen role Antigen is a role played by material which when introduced into an immune-competent organism causes an immune response An antigen is a substance that prompts the generation of antibodies and can cause an immune response. Wikipedia http://en.wikipedia.org/wiki/Antigen. In the strict sense, immunogens are those substances that elicit a response from the immune system, whereas antigens are defined as substances that bind to specific antibodies. Not all antigens produce an immunogenic response, but all immunogens are antigens Role Branch OBI 9Mar09 waiting for discussion with immunology terms antigen role OBI:0000242 software testing objective Software_testing_objective is a hardware_optimization role describing a study designed to examine the effects of using different software or software parameters, e.g. data processing software. Jennifer Fostel software testing objective OBI:0000243 sponsor role a responsible party role involved with any of the following activities: initiating, managing and funding a study Person: Jennifer Fostel sponsor CDISC definition: sponsor. 1. An individual, company, institution, or organization that takes responsibility for the initiation, management, and/or financing of a clinical trial. 2. A corporation or agency whose employees conduct the investigation is considered a sponsor; employees are considered investigators sponsor role OBI:0000245 organization PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods. An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members. BP: The definition summarizes long email discussions on the OBI developer, roles, biomaterial and denrie branches. It leaves open if an organization is a material entity or a dependent continuant, as no consensus was reached on that. The current placement as material is therefore temporary, in order to move forward with development. Here is the entire email summary, on which the definition is based: 1) there are organization_member_roles (president, treasurer, branch editor), with individual persons as bearers 2) there are organization_roles (employer, owner, vendor, patent holder) 3) an organization has a charter / rules / bylaws, which specify what roles there are, how they should be realized, and how to modify the charter/rules/bylaws themselves. It is debatable what the organization itself is (some kind of dependent continuant or an aggregate of people). This also determines who/what the bearer of organization_roles' are. My personal favorite is still to define organization as a kind of 'legal entity', but thinking it through leads to all kinds of questions that are clearly outside the scope of OBI. Interestingly enough, it does not seem to matter much where we place organization itself, as long as we can subclass it (University, Corporation, Government Agency, Hospital), instantiate it (Affymetrix, NCBI, NIH, ISO, W3C, University of Oklahoma), and have it play roles. This leads to my proposal: We define organization through the statements 1 - 3 above, but without an 'is a' statement for now. We can leave it in its current place in the is_a hierarchy (material entity) or move it up to 'continuant'. We leave further clarifications to BFO, and close this issue for now. PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Philippe Rocca-Serra PERSON: Susanna Sansone GROUP: OBI organization OBI:0000248 feed role Purina rat chow; cited use: Control; F = feed (rat chow); W = water; F. g. = feed-ginger concentrate. www.academicjournals.org/AJB/PDF/pdf2007/19Sep/Egwurugwu%20et%20al.pdf - Feb 29, 2008 a role that inheres in a material entity and is realized in the use of that material entity by lab animal to provide all needed nourishment. Person: Jennifer Fostel feed OBI feed role OBI:0000249 technical replicate role Aliquots of a tissue subjected to parallel assays technical replicate role is realized when two portions from one evaluant are used in replicate runs of an assay Person: Jennifer Fostel technical replicate technical replicate role OBI:0000250 dye role A molecular label role which inheres in a material entity and which is realized in the process of detecting a molecular dye that imparts color to some material of interest. Jennifer Fostel dye A substance used to color materials www.answers.com/topic/dye 19feb09 dye role OBI:0000251 cluster Cluster of the lymphocytes population. A data set which is a subset of data that are a similar to each other in some way. person:Allyson person:Chris Stoeckert group:OBI cluster OBI:0000252 cohort role In statistics and demography, a cohort is a group of subjects - most often humans from a given population - defined by experiencing an event (typically birth) in a particular time span. Wikipedia "cohort", Feb 29 2008 a cohort role is a biological replicate role played by a group of study participants who share a common characteristic of interest to the study. Jennifer Fostel WEB:http://www.sceoc.com/glossaryofterms/ # a group of individuals having a statistical factor (as age or class membership) in common in a demographic study, such as a cohort of students. WEB:http://www.thebody.org/content/treat/art2612.html # a group of individuals in a study who share a demographic, clinical, or other statistical characteristic (eg, age, study site). WEB:http://www.uhhospitals.org/tabid/591/Default.aspx # A cohort is a group of people with a common characteristic that is studied over a period of time as part of a scientific or medical investigation. cohort role OBI:0000253 artificially induced nucleic acid hybridization www.ornl.gov/sci/techresources/Human_Genome/publicat/97pr/09gloss.html, http://www.accessexcellence.org/RC/VL/GG/nucleic.html, http://omrf.ouhsc.edu/~frank/HYBNOTES.html. http://en.wikipedia.org/wiki/Nucleic_acid_hybridization,http://www.pnas.org/cgi/reprint/46/8/1044.pdf Is a material transformation in which strands of nucleic acids that are (somewhat) complementary form a double-stranded molecule. Has input at least two single stranded molecules of nucleic acid molecules. PlanAndPlannedProcess Branch OBI branch derived artificially induced nucleic acid hybridization OBI:0000257 DNA extraction A DNA extraction is a nucleic acid extraction where the desired output material is DNA. PlanAndPlannedProcess Branch OBI branch derived DNA extraction OBI:0000260 plan The plan of researcher X to perform an experiment according to a protocol. A plan is a realizable entity that is the inheres in a bearer who is committed to realizing it as a planned process. This class is included to make clear how the plan specification, the plan, and the planned process relate. OBI will however only subclass and work under the 'plan specification', and 'planned process' class, as we want to avoid to get deep into discussions of 'intend' etc. AR, BP, JM, MC, PRS branch derived plan OBI:0000264 obsolete_sample population Patterns of benzylpiperazine/trifluoromethylphenylpiperazine party pill use and adverse effects in a population sample in New Zealand. Drug Alcohol Rev. 2008 Mar 31:1-7. PMID: 18608458 A sample population is an object aggregate that is selected from the population, e.g. the fish in the net that were sampled from the lake, the people that responded to the call for volunteers. 03/21/2010: BP, obsoleting this term, as it is duplicated by 'material sample'. Use that instead term instead, which now also has 'sample population' as an alternative label. PERSON: Jennifer Fostel PERSON: Philippe Rocca-Serra recruited population GROUP: OBI Biomaterial Branch obsolete_sample population true OBI:0000268 organism feature identification objective Organism_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize a biological feature monitored at the level of the organism, e.g. height, weight, stage of development, stage of life cycle. Jennifer Fostel organism feature identification objective OBI:0000269 number of lost events computer 0, 125, 787 events lost due to computer busy. A measurement datum recording the number of measurement events lost due to overloading of the analysis chip in a flow cytometer instrument. The datum has a qualitative role person:Kevin Clancy Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt number of lost events computer OBI:0000272 protocol PCR protocol, has objective specification, amplify DNA fragment of interest, and has action specification describes the amounts of experimental reagents used (e..g. buffers, dNTPS, enzyme), and the temperature and cycle time settings for running the PCR. A plan specification which has sufficient level of detail and quantitative information to communicate it between investigation agents, so that different investigation agents will reliably be able to independently reproduce the process. PlanAndPlannedProcess Branch OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29) study protocol protocol OBI:0000273 role of regulator of consumables and medical devices FDA, EMEA; http://www.fda.gov/; The International Conference of Drug Regulatory Authorities (ICDRAs) provide drug regulatory authorities of WHO Member States with a forum to meet and discuss ways to strengthen collaboration.http://www.who.int/medicines/areas/quality_safety/regulation_legislation/icdra/en/index.html a regulator involved with making and enforcing legislation and governmental orders relevant to the development, testing, manufacture and use of food, drugs and medical devices Person: Jennifer Fostel drug regulatoy authority OBI, CDISC role of regulator of consumables and medical devices OBI:0000274 adding a material entity into a target Injecting a drug into a mouse. Adding IL-2 to a cell culture. Adding NaCl into water. is a process with the objective to place a material entity bearing the 'material to be added role' into a material bearing the 'target of material addition role'. Class was renamed from 'administering substance', as this is commonly used only for additions into organisms. BP branch derived adding a material entity into a target OBI:0000275 analyte role Glucose in blood (measured in an assay to determine the concentration of glucose). A role borne by a molecular entity or an atom and realized in an analyte assay which achieves the objective to measure the magnitude/concentration/amount of the analyte in the entity bearing evaluant role interestingly, an analyte is still an analyte even if it is not detected. for this reason it does not bear a specified input role pH (technically the inverse log of [H+]) may be considered a quality; this remains to be tested. qualities such as weight, color are not assayed but measured, so they do not fall into this category. GROUP: Role Branch OBI Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. analyte role OBI:0000278 disease stage Stage II breast cancer, The timepoint of recovery from a disease a part of an occurrence of a disease process which is associated with position in the normal progression of the disease PERSON: Bjoern peters disease stage OBI:0000281 intraperitoneal injection is the injection of a material entity (bearing the administered substance role) into the peritoneum (bearing the target role) of an organism using a syringe BP intraperitoneal injection OBI:0000286 precipitate Physicochemical properties and antibacterial activity of the precipitate of vancomycin and ceftazidime: implications in the management of endophthalmitis. Retina. 2008 Feb;28(2):320-5. PMID: 18301038 a precipitate is a material entity which is output of a precipitation process PERSON: Philippe Rocca-Serra precipited material GROUP: OBI Biomaterial Branch precipitate OBI:0000288 protein-protein interaction detection An assay with the objective to determine interactions between proteins, such as protein-protein binding. 20091101, Bjoern Peters: This class may be overly broad. Lot's of assays would seem to classify under it, and I have the feeling that the intend would be to limit this to determining protein-protein interactions as they occur within an organism, rather than e.g. peptide:MHC binding assays. protein-protein interaction detection OBI:0000291 transcription factor binding site assay Transcription factor binding site identification in yeast: a comparison of high-density oligonucleotide and PCR-based microarray platforms. Funct Integr Genomics. 2007 Oct;7(4):335-45. Epub 2007 Jul 19. PMID: 17638031 An assay with objective to find DNA region specifically recognized by proteins that function as transcription factors JZ: add equivalent axiom for classification add alternative term 'TF binding' which was used in BCBC database JZ: fixed inconsistency issue and relabel the term see tracker: https://sourceforge.net/p/obi/obi-terms/767/ Philippe Rocca-Serra TF binding OBI transcription factor binding site assay OBI:0000296 obsolete_enrollment Enrollment of patients in a study. Short-term outcome of neuropsychiatric events in systemic lupus erythematosus upon enrollment into an international inception cohort study. Arthritis Rheum. 2008 May 15;59(5):721-9. PMID: 18438902 enrollment is a process of identifying a set of objects for further use in an investigation based on a set of criteria or rules merged with 'enrollment of human subjects Bjoern Peters IEDB obsolete_enrollment true OBI:0000310 adverse event trigger revisit? PERSON:Alan Ruttenberg OBI branch derived adverse event trigger OBI:0000318 eluate Raman spectroscopic detection of haemoproteins in the eluate from high-performance liquid chromatography. J Chromatogr. 1983 Jan 7;254:285-8. PMID: 6298263 a eluate is a material entity which results from an elution, e.g. from a chromatography column. it has as part a material entity with role mobile phase need to add restriction to indicate: has_part some (material entity has_role mobile phase) need to add mobile phase as role PERSON: Philippe Rocca-Serra eluted material OBI Bionaterial eluate OBI:0000319 material to be added role drug added to a buffer contained in a tube; substance injected into an animal; material to be added role is a protocol participant role realized by a material which is added into a material bearing the target of material addition role in a material addition process Role Branch OBI 9 March 09 from discussion with PA branch material to be added role OBI:0000323 obsolete_peritoneum is the serous membrane that forms the lining of the abdominal cavity BP: should be imported in the future, but I need it now to demonstrate how to define intraperitoneal injection obsolete_peritoneum true OBI:0000338 drawing a conclusion based on data Concluding that a gene is upregulated in a tissue sample based on the band intensity in a western blot. Concluding that a patient has a infection based on measurement of an elevated body temperature and reported headache. Concluding that there were problems in an investigation because data from PCR and microarray are conflicting. Concluding that 'defects in gene XYZ cause cancer due to improper DNA repair' based on data from experiments in that study that gene XYZ is involved in DNA repair, and the conclusion of a previous study that cancer patients have an increased number of mutations in this gene. A planned process in which data gathered in an investigation is evaluated in the context of existing knowledge with the objective to generate more general conclusions or to conclude that the data does not allow one to draw general conclusion PERSON: Bjoern Peters PERSON: Jennifer Fostel Bjoern Peters drawing a conclusion based on data OBI:0000339 planning The process of a scientist thinking about and deciding what reagents to use as part of a protocol for an experiment. Note that the scientist could be human or a "robot scientist" executing software. a process of creating or modifying a plan specification 7/18/2011 BP: planning used to itself be a planned process. Barry Smith pointed out that this would lead to an infinite regression, as there would have to be a plan to conduct a planning process, which in itself would be the result of planning etc. Therefore, the restrictions on 'planning' were loosened to allow for informal processes that result in an 'ad hoc plan '. This required changing from 'has_specified_output some plan specifiction' to 'has_participant some plan specification'. Bjoern Peters Bjoern Peters Plans and Planned Processes Branch planning OBI:0000340 obsolete_documenting Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database. 6/11/9: Edited at workshop. Should go into IAO. We need to be able identify a child form of information artifact which corresponds to something enduring (not brain like). This used to be restricted to physical document or digital entity as the output, but that excludes e.g. an audio cassette tape Bjoern Peters wikipedia http://en.wikipedia.org/wiki/Documenting IAO_0000572 obsolete_documenting true OBI:0000341 histological sample preparation histological sample preparation is the preparation of an input tissue via slicing and labeling to make tissue microstructure of interest visible in a future histology assay PERSON:Bjoern Peters OBI branch derived histological sample preparation OBI:0000343 inductive reasoning Based on the observation that all lung cancer patients treated with aspirin in our clinical trial survived longer than the control group, we conclude by inductive reasining that aspirin has a therapeutic effect on lung cancer. a interpreting data that is used to ascribe properties or relations to types based on an observation instance (i.e., on a number of observations or experiences); or to formulate laws based on limited observations of recurring phenomenal patterns. BP: 10/22/122: After changing the parent class to drawing a conclusion *based on data* it is no longer clear that this class is needed; minimally it needs a better definition to distinguish it. Proposal is to obsolete. Bjoern Peters wikipedia: http://en.wikipedia.org/wiki/Inductive_reasoning inductive reasoning OBI:0000345 mass analyzer The mass analyzer of the Voyager-DE(tm) STR Biospectrometry Workstation A Mass analyzer is a device that separates ions according to their mass-to-charge ratio. All mass spectrometers are based on dynamics of charged particles in electric and magnetic fields in vacuum where the two laws of Lorentz force law and Newton's second law of motion apply. Frank Gibson PERSON: Daniel Schober http://en.wikipedia.org/wiki/Mass_spectrometry#Mass_analyzer mass analyzer OBI:0000355 hypothesis driven investigation is an investigation with the goal to test one or more hypothesis PlanAndPlannedProcess Branch OBI branch derived hypothesis driven investigation OBI:0000356 hypothesis generating investigation is an investigation in which data is generated and analyzed with the purpose of generating new hypothesis PlanAndPlannedProcess Branch OBI branch derived hypothesis generating investigation OBI:0000361 ion source The ion source of a Voyager-DE??? STR Biospectrometry Workstation An ion source is a device that is part of a mass spectrometer that ionizes the material under analysis. The ions are then transported by magnetic or electric fields to the mass analyzer. Techniques for ionization have been key to determining what types of samples can be analyzed by mass spectrometry. Electron ionization and chemical ionization are used for gases and vapors. In chemical ionization sources, the material is ionized by chemical ion-molecule reactions during collisions in the source. Two techniques often used with liquid and solid biological samples include electrospray ionization (due to John Fenn PMID 2675315.) and matrix-assisted laser desorption/ionization (MALDI, due to M. Karas and F. Hillenkamp (Measuring Mass: From Positive Rays to Proteins by Michael A. Grayson (Editor) (ISBN 0-941901-31-9))). Frank Gibson http://en.wikipedia.org/wiki/Mass_spectrometry#Ion_source ion source OBI:0000364 ion detector The ion detector of the Voyager-DE(tm) STR Biospectrometry Workstation An ion detector is a device that measures and records the charge induced or current produced when an ion passes by or hits a surface. Example: In a scanning instrument the signal produced in the detector during the course of the scan versus where the instrument is in the scan (at what m/Q) will produce a mass spectrum, a record of ions as a function of m/Q. Frank Gibson http://en.wikipedia.org/wiki/Mass_spectrometry#Detector ion detector OBI:0000366 metabolite profiling Metabolite profiling of human colon carcinoma - deregulation of TCA cycle and amino acid turnover. Mol Cancer. 2008 Sep 18;7(1):72. PMID: 18799019 metabolite profiling is a process which aims at detecting and identifying chemical entities resulting from biochemical and cellular metabolism Philippe Rocca-Serra metabolite assay OBI metabolite profiling OBI:0000367 light emission function A light emission function is an excitation function to excite a material to a specific excitation state that it emits light. Bill Bug Daniel Schober Frank Gibson Melanie Courtot light emission function OBI:0000368 record function A record function is a function that registers or collects information in a particular format on a particular recording medium. For example on paper or a digital representation Bill Bug Daniel Schober Frank Gibson Melanie Courtot record function OBI:0000369 magnify function A magnify function is a function to increase the size of a transmitted object image through the precise arrangement of energy diffraction elements along an imaging path. Bill Bug Daniel Schober Frank Gibson Melanie Courtot magnify function OBI:0000370 contain function A syringe, a beaker A contain function is a function to constrain a material entities location in space Bill Bug Daniel Schober Frank Gibson Melanie Courtot contain function OBI:0000371 heat function A heat function is a function that increases the internal kinetic energy of a material Bill Bug Daniel Schober Frank Gibson Melanie Courtot heat function OBI:0000372 material separation function A material separation function is a function that increases the resolution between two or more material entities. The to distinction between the entities is usually based on some associated physical quality. Bill Bug Daniel Schober Frank Gibson Melanie Courtot material separation function OBI:0000373 ionize process Electrospray ionization in mass spectrometry a physical process of converting an atom or molecule into an ion by adding or removing charged particles such as electrons or other ions. This excludes chemical processes of dissociation. 2009-11-10. Tracker: http://en.wikipedia.org/wiki/Ionize Person:Bjoern Peters ionize process OBI:0000374 excitation function A excitation function is a function to inject energy by bombarding a material with energetic particles (e.g., photons) thereby imbuing internal material components such as electrons with additional energy. These internal, 'excited' particles may lead to the rupturing of covalent chemical bonds or may quickly relax back to there unexcited state with an exponential time course thereby locally emitting energy in the form of photons. Bill Bug Daniel Schober Frank Gibson Melanie Courtot excitation function OBI:0000375 freeze function A freeze function is a function to decrease the internal kinetic energy of a material below the freezing point of that type of material. Bill Bug Daniel Schober Frank Gibson Melanie Courtot freeze function OBI:0000376 synthesizing function A synthesizing function is a function to assemble new output materials from distinct input materials. The output materials typically consist of chemically distinct monomeric objects or object aggregate polymers. Bill Bug Daniel Schober Frank Gibson Melanie Courtot synthesizing function OBI:0000377 perturb function A perturb function is a function that disrupts the normal function of a system induced through either internal or external means. External means of perturbation include: (1) displacement fields in the physical sense - e.g., temperature change, osmotic shock, pressure change; (2) application of small molecules such as drugs or toxins to perturb the function of specific pathways or application of surfactants to perturb the normal function of plasma membrane. Internal means of perturbation include: (1) manipulation of gene function via gene knockout or transcript knockdown via RNAi; (2) directed genetic mutation leading to minimal aa alterations that interfere with peptide function. Bill Bug Daniel Schober Frank Gibson Melanie Courtot http://en.wikipedia.org/wiki/Perturbation_biology perturb function OBI:0000378 filter function A filter function is a function to prevent the flow of certain entities based on a quality or qualities of the entity while allowing entities which have different qualities to pass through Frank Gibson filter function OBI:0000379 mechanical function A mechanical function is a function that is realised via mechanical work (through an certain amount of energy transferred by some force). Bill Bug Daniel Schober Frank Gibson Melanie Courtot http://en.wikipedia.org/wiki/Mechanical_work mechanical function OBI:0000380 gas filter function A gas filter function is a filter function which prevents the flow of solid objects, defined by specific qualities, in a gas-solid mixture Frank Gibson gas filter function OBI:0000381 liquid filter function A liquid filter function is a filter function which prevents the flow of solid objects, defined by specific qualities, in a liquid-solid mixture Frank Gibson liquid filter function OBI:0000383 transfer function A transfer function is a function to displace a material from one location to another. Bill Bug Daniel Schober Frank Gibson Melanie Courtot transfer function OBI:0000384 electricity supply function the function of supplying current during a neuroscience experiment. An electricity supply function is an energy supply function to transfer electricity from one source to another, typically a consumer of the electricity or as a stimulus during a neuroscience experiment. Daniel Schober Frank Gibson Melanie Courtot power supply electricity supply function OBI:0000385 ionization function The ion source in amass spectrometer An ionization function is a function to physically convert an atom or molecule into an ion by adding or removing charged particles such as electrons or other ions. Bill Bug Daniel Schober Frank Gibson Melanie Courtot http://en.wikipedia.org/wiki/Ionization ionization function OBI:0000387 cool function A cool function is a function to decrease the internal kinetic energy of a material below the initial kinetic energy of that type of material. Daniel Schober Frank Gibson Melanie Courtot cool function OBI:0000388 connection function An electricity cable A connection function is a function to couple two or more flow channels so that material or signals can be transported from one set of channels to another. Bill Bug Daniel Schober Frank Gibson Melanie Courtot connection function OBI:0000389 isoelectric focusing device An isoelectric focusing device is a device in which isoelectric focusing can be performed. An isoelectric focussing device had the function to contain and control the contained environment and transfer electrical energy from a power supply to a separation medium and the charged material to be separated. Frank Gibson isoelectric focusing unit sep:00097 isoelectric focusing device OBI:0000390 thermostatic circulator A thermostatic circulator is a device which cools or heats a circulating liquid. It has the function to contain control the contained environment and transfer energy from or to the circulating liquid Frank Gibson sep:00098 thermostatic circulator OBI:0000391 energy supply function An energy supply function is a function to supply or transfer energy from an energy source to a consumer of the energy Frank Gibson energy supply function OBI:0000392 information processor function An information processor function is a function that converts information from one form to another, by a lossless process or an extraction process. Frank Gibson data processor function information processor function OBI:0000393 signal conversion function A signal conversion function is an information processor function which transforms a signal into another type of signal. For example an analog-to-digital_converter, Ac/Ac converter, a synapse converts electrical action potentials into an intermediate chemical signal. The post synapse converts it back into an electric one passed on to the axon. Bill Bug Daniel Schober Frank Gibson Melanie Courtot transduction function signal conversion function OBI:0000394 blot module A blot module is a device which has the function to conatin and facilitate the material transfer process blotting to be realised Frank Gibson sep:00092 blot module OBI:0000395 signal amplification function A signal amplification function is a signal conversion function to inject energy into an input signal so as to produce an output signal with increased differential magnitude while also seeking to minimize increases in the signal to noise ratio. For example, to produce a 0.1 KW output signal from a 1 mW RMS input signal. Bill Bug Daniel Schober Frank Gibson Melanie Courtot signal amplification function OBI:0000397 image acquisition function An image acquisition function is a function to acquire an image of a material Frank Gibson image acquisition function OBI:0000398 image creation device An image creation device is a device which captures a digitized image of an object Frank Gibson image acquisition device sep:00096 image creation device OBI:0000399 solid support function Taped, glued, pinned, dried or molecularly bonded to a solid support A solid support function is a function of a device on which an entity is kept in a defined position and prevented in its movement Daniel Schober Frank Gibson Melanie Courtot solid support function OBI:0000400 display function A display function is a function to present information by translating that information through some lookup process into visual form. Bill Bug Daniel Schober Frank Gibson Melanie Courtot display function OBI:0000401 environment control function An environmental control function is a function that regulates a contained environment within specified parameter ranges. For example the control of light exposure, humidity and temperature. Bill Bug Daniel Schober Frank Gibson Melanie Courtot environment control function OBI:0000403 sort function A sort function is a function to distinguish material components based on some associated physical quality or entity and to partition the separate components into distinct fractions according to a defined order. Daniel Schober Frank Gibson Melanie Courtot sort function OBI:0000404 gel dryer A gel dryer is a device which has the function to contain and to control the contained environment to facilitate the drying of gels Frank Gibson sep:00094 gel dryer OBI:0000405 primer role a complementary nucleotide probe role which inheres in nucleic acid molecular entity and is realized by the use of the entity bearing the role to initiate chain elongation. (cell and molecular biology) A short strand of RNA that is synthesized along single-stranded DNA during replication, initiating DNA polymerase-catalyzed synthesis of the complementary strand. http://www.answers.com/topic/rna-primer primer role OBI:0000406 PCR product PCR products are the results of amplifcation process. Detection of a PCR products is used to detect DNA and RNA. is double stranded DNA that is the specified output of a polymerase chain reaction We are using PCR and not the written out words, as this is the most common used. GROUP: OBI BIomaterial Branch GROUP: OBI BIomaterial Branch PCR product OBI:0000407 viral RNA extraction The AccuPrepTM Viral RNA Extraction Kit is designed for the rapid and convenient extraction of viral RNA from cell-free samples as serum, plasma, CSF, urine, etc - http://www.biokits.com/moreinfos.html?id=2703 The extraction of RNA from an input material that specifically isolates viral RNA Person:Bjoern Peters viral RNA extraction OBI:0000409 nucleic acid template role a model or standard for making comparisons; wordnet.princeton.edu/perl/webwn 19 feb 2009 a reference substance role which inheres in nucleic acid material entity and is realized in the process of using the nucleic acid bearing the template role as a reference during synthesis of a reverse copy. nucleic acid template role OBI:0000410 recombinant plasmid a plasmid in which extraneous DNA has been inserted. PERSON: Bjoern Peters PERSON: Kevin Clancy PERSON: Melanie Courtot GROUP: OBI Biomaterial Branch recombinant plasmid OBI:0000411 cloning vector role pBluescript plays the role of a cloning vector A material to be added role played by a small, self-replicating DNA or RNA molecule - usually a plasmid or chromosome - and realized in a process whereby foreign DNA or RNA is inserted into the vector during the process of cloning. JZ: related tracker: https://sourceforge.net/p/obi/obi-terms/102/ PERSON: Helen Parkinson cloning vector role OBI:0000413 cell cycle synchronization Elimination of serum from the culture medium for about 24 hours results in the accumulation of cells at G1 phase. This effect of nutritional deprivation can be restored by their addition by which time the cell synchrony occurs. a process with the objective to obtain a cell culture in which all cells are in the same stage of the cell cycle OBI PA Bjoern Peters and Nicole Washington cell cycle synchronization OBI:0000415 polymerase chain reaction Opisthorchis viverrini: Detection by polymerase chain reaction (PCR) in human stool samples. Exp Parasitol. 2008 Sep 9. PMID: 18805413 PCR is the process in which a DNA polymerase is used to amplify a piece of DNA by in vitro enzymatic replication. As PCR progresses, the DNA thus generated is itself used as a template for replication. This sets in motion a chain reaction in which the DNA template is exponentially amplified. OBI Plan PCR adapted from wikipedai polymerase chain reaction OBI:0000416 cloning insert role cloning insert role is a role which inheres in DNA or RNA and is realized by the process of being inserted into a cloning vector in a cloning process. Feb 20, 2009. from Wikipedia: cloning of any DNA fragment essentially involves four steps: DNA fragmentation with restriction endonucleases, ligation of DNA fragments to a vector, transfection, and screening/selection. There are multiple processes involved, it is not just "cloning process" GROUP: Role branch OBII and Wikipedia cloning insert role OBI:0000418 measuring glucose concentration in blood serum An assay that determines the concentration of glucose molecules in a blood serum sample Person:Bjoern Peters measuring glucose concentration in blood serum OBI:0000419 reverse transcriptase enzyme and has_function some GO:0003964 (RNA-directed DNA polymerase activity) person:Melanie Courtot group:OBI reverse transcriptase OBI:0000420 obsolete_trypsinized material A trypsinized suspension of cells A material entity that has undergone a process of digestion with trypsin decided to be deprecated on Aug 2, 2010 dev call Person:Bjoern Peters Test Class: to evaluate OBI design pattern obsolete_trypsinized material true OBI:0000422 syringe Accuracy of oral liquid measuring devices: comparison of dosing cup and oral dosing syringe.Ann Pharmacother. 2008 Jan;42(1):46-52. Epub 2007 Dec 4. PMID: 18056832 a processed material which is used to introduce or draw fluids from a material entity. A syringe is made of a piston and body. the movement of the piston in the body determines the amount/volume of fluid to inject or draw Philippe Rocca-Serra OBI Instrument adapted from Wikipedia syringe OBI:0000423 extract Up-regulation of inflammatory signalings by areca nut extract and role of cyclooxygenase-2 -1195G>a polymorphism reveal risk of oral cancer. Cancer Res. 2008 Oct 15;68(20):8489-98. PMID: 18922923 an extract is a material entity which results from an extraction process PERSON: Philippe Rocca-Serra extracted material GROUP: OBI Biomatrial Branch extract OBI:0000424 transcription profiling assay Whole genome transcription profiling of Anaplasma phagocytophilum in human and tick host cells by tiling array analysis. BMC Genomics. 2008 Jul 31;9:364. PMID: 18671858 An assay which aims to provide information about gene expression and transcription activity using ribonucleic acids collected from a material entity using a range of techniques and instrument such as DNA sequencers, DNA microarrays, Northern Blot Philippe Rocca-Serra gene expression profiling OBI transcription profiling transcription profiling assay OBI:0000425 averaging objective A mean calculation which has averaging objective is a descriptive statistics calculation in which the mean is calculated by taking the sum of all of the observations in a data set divided by the total number of observations. It gives a measure of the 'center of gravity' for the data set. It is also known as the first moment. An averaging objective is a data transformation objective where the aim is to perform mean calculations on the input of the data transformation. Elisabetta Manduchi James Malone PERSON: Elisabetta Manduchi averaging objective OBI:0000426 injection Multiple Small-Dose Injections Can Reduce the Passage of Sclerosant Foam into Deep Veins During Foam Sclerotherapy for Varicose Veins. Eur J Vasc Endovasc Surg. 2008 Oct 13. PMID: 18922712 injection is process which aims at introducing a compound or a mixture into a material entity (either biological entity or instrument) by relying on devices such as syringe or injector connection, attached or forced into a vascular system (veins of an organism or tubes of a machine) or in a tissue. Philippe Rocca-Serra OBI Biomaterial injection OBI:0000427 enzyme (protein or rna) or has_part (protein or rna) and has_function some GO:0003824 (catalytic activity) MC: known issue: enzyme doesn't classify under material entity for now as it isn't stated that anything that has_part some material entity is a material entity. If we add as equivalent classes to material entity has_part some material entity and part_of some material entity (each one in his own necessary and sufficient block) Pellet in P3 doesn't classify any more. person: Melanie Courtot GROUP:OBI enzyme OBI:0000429 intraperitoneal administration Rats were injected intraperitoneally with either rrIL-6 (250 ng/0.5 ml) or equal-volume sterile saline twice within an interval of 24 h The administration of a substance into the peritoneum of an organism Person:Bjoern Peters intraperitoneal administration OBI:0000430 plasmid plasmid = DNA and has_quality circular and has_function (is_realized_as some gene expression) GO:0010467 person:Melanie Courtot group:OBI plasmid OBI:0000431 injection into organ section Staining a specimen of human lung tissue with hematoxylin and eosin in order as a preparative step in histology A process in which an input substance is injected into a organ section. Person:Bjoern Peters injection into organ section OBI:0000432 polyacrylamide gel Assessing CMT cell line stability by two dimensional polyacrylamide gel electrophoresis and mass spectrometry based proteome analysis. J Proteomics. 2008 Jul 21;71(2):160-7. PMID: 18617143 a material entity resulting from the polymerization of acrylamide with TEMED in some buffer solution PERSON: Jie Zheng PERSON: Philippe Rocca-Serra GROUP: OBI Biomaterial Branch polyacrylamide gel OBI:0000433 DNA sequence feature detection genotyping using an Affymetrix chip An assay with the objective to determine a sequence feature of DNA should be a defined class where interpretation of data generated by assay qualifies a DNA sequence Person:Bjoern Peters Philippe Rocca-Serra OBI DNA sequence feature detection OBI:0000434 adding material objective creating a mouse infected with LCM virus is the specification of an objective to add a material into a target material. The adding is asymmetric in the sense that the target material largely retains its identity BP adding material objective OBI:0000435 genotyping assay High-throughput genotyping of oncogenic human papilloma viruses with MALDI-TOF mass spectrometry. Clin Chem. 2008 Jan;54(1):86-92. Epub 2007 Nov 2.PMID: 17981923 an assay which generates data about a genotype from a specimen of genomic DNA. A variety of techniques and instruments can be used to produce information about sequence variation at particular genomic positions. Philippe Rocca-Serra genotype profiling, SNP genotyping OBI Biomaterial SNP analysis genotyping assay OBI:0000436 needle Ovarian carcinoma presenting with axillary lymph node metastasis: A case diagnosed by fine-needle aspiration and brief review of the literature. Diagn Cytopathol. 2008 Oct 16. PMID: 18925569 a needle is a sharp, hollow device used to penetrate tissue or soft material. When attached to a syringe. it allows delivery of a specific volume of liquid or gaseous mixture. Philippe Rocca-Serra OBI Instrument needle OBI:0000437 analyte measurement objective The objective to measure the concentration of glucose in a blood sample an assay objective to determine the presence or concentration of an analyte in the evaluant PERSON: Bjoern Peters PPPB branch analyte measurement objective OBI:0000438 DNA sequence variation detection Capturing genomic signatures of DNA sequence variation using a standard anonymous microarray platform. Nucleic Acids Res. 2006;34(18):e121. PMID: 17000641 DNA sequence variation detection is a process which aims at finding changes (expansion, amplification, deletion, mutation) in sequence of DNA molecule. Philippe Rocca-Serra OBI Biomaterial DNA sequence variation detection OBI:0000439 agarose gel Performance comparison of capillary and agarose gel electrophoresis for the identification and characterization of monoclonal immunoglobulins. Am J Clin Pathol. 2008 Mar;129(3):451-8. PMID: 18285269 a material entity resulting from the polymerization of agarose after heating agarose suspended in some buffer solution PERSON: Philippe Rocca-Serra GROUP: OBI Biomaterial Branch agarose gel OBI:0000441 assay objective the objective to determine the weight of a mouse. an objective specification to determine a specified type of information about an evaluated entity (the material entity bearing evaluant role) PPPB branch PPPB branch assay objective OBI:0000442 obsolete_heart Alan Ruttenberg's heart The heart is a muscular organ found in all vertebrates that is responsible for pumping blood throughout the blood vessels by repeated, rhythmic contractions MC: should be imported unused class. decided to be deprecated on Aug 2, 2010 dev call. Will be imported when need. Person:Bjoern Peters http://en.wikipedia.org/wiki/Heart obsolete_heart true OBI:0000443 analyte assay example of usage: In lab test for blood glucose, the test is the assay, the blood bears evaluant_role and glucose bears the analyte role. The evaluant is considered an input to the assay and the information entity that records the measurement of glucose concentration the output An assay with the objective to capture information about the presence, concentration, or amount of an analyte in an evaluant. 2013-09-23: simplify equivalent axiom Note: is_realization of some analyte role isn't always true, for example when there is none of the analyte in the evaluant. For the moment we are writing it this way, but when the information ontology is further worked out this will be replaced with a condition discussing the measurement. logical def modified to remove expression below, as some analyte assays report below the level of detection, and therefore not a scalar measurement datum, replaced by measurement datum and ('has measurement unit label' some 'measurement unit label') and ('is quality measurement of' some 'molecular concentration')) PERSON:Bjoern Peters, Helen Parkinson, Philippe Rocca-Serra, Alan Ruttenberg PERSON:Bjoern Peters PERSON:Helen Parkinson PERSON:Philippe Rocca-Serra PERSON:Alan Ruttenberg GROUP:OBI Planned process branch analyte assay OBI:0000444 target of material addition role peritoneum of an animal receiving an interperitoneal injection; solution in a tube receiving additional material; location of absorbed material following a dermal application. target of material addition role is a role realized by an entity into which a material is added in a material addition process From Branch discussion with BP, AR, MC -- there is a need for the recipient to interact with the administered material. for example, a tooth receiving a filling was not considered to be a target role. GROUP: Role Branch OBI target of material addition role OBI:0000445 mass measurement assay The patients was weighed and mass was determined to be 47 kilograms a process to determine the mass of an evaluant Helen Parkinson OBI Philippe Rocca-Serra mass measurement assay OBI:0000446 obsolete_identification DNA cleavage assay for the identification of topoisomerase I inhibitors. Nat Protoc. 2008;3(11):1736-50. PMID: 18927559 a process by which the identity (what a thing is) of a material entity is established within a certain confidence interval Alan Ruttenberg 2010/11/22: After OBI call. A specific identification objective should be used instead, as necessary See tracker: https://sourceforge.net/tracker/index.php?func=detail&aid=3302925&group_id=177891&atid=886178 Philippe Rocca-Serra obsolete_identification true OBI:0000447 intra cellular electrophysiology recording An intracellular electrophysiology recording is a process where the recording location of the electrode is intracellular PERSON: Frank Gibson PERSON: Frank Gibson intra cellular electrophysiology recording OBI:0000448 packed column A packed column is a chromatography column where the particles of the solid stationary phase or the support coated with a liquid stationary phase may fill the whole inside volume of the tube. PERSON:Daniel Schober WEB:<http:www.iupac.org/publications/pac/1993/pdf/6504x0819.pdf> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01218 packed column OBI:0000449 obsolete_defined_output example of subclass: normalized data set - A normalized data set is a data set that is produced as the output of a normalization data transformation. This is only a placeholder for defined classes, as are its siblings _defined_material and _defined protocol application. Its children should be defined classes constructed as output of a process. PERSON: Alan Ruttenberg PERSON: James Malone PERSON: Melanie Courtot obsolete_defined_output true OBI:0000450 regulatory agency The US Environmental Protection Agency A regulatory agency is a organization that has responsibility over or for the legislation (acts and regulations) for a given sector of the government. GROUP: OBI Biomaterial Branch WEB: en.wikipedia.org/wiki/Regulator regulatory agency OBI:0000451 normalized data set A data set that is produced as the output of a normalization data transformation. PERSON: James Malone PERSON: Melanie Courtot normalized data set OBI:0000453 measure function A glucometer measures blood glucose concentration, the glucometer has a measure function. Measure function is a function that is borne by a processed material and realized in a process in which information about some entity is expressed relative to some reference. PERSON: Daniel Schober PERSON: Helen Parkinson PERSON: Melanie Courtot PERSON:Frank Gibson measure function OBI:0000454 extracellular electrophysiology recording The recording of a spike train in the caudate nucleus of a monkey where the electrodes are extra cellular, i.e. not in the neuron An extracellular electrophysiology recording is process where the recording location of the electrode is extracellular and data PERSON: Frank Gibson, Helen Parkinson PERSON: Frank Gibson extracellular electrophysiology recording OBI:0000455 consume data function Process data function is a function that is borne by in a material entity by virtue of its structure. When realized the material entity consumes data. PERSON: Daniel Schober PERSON: Frank Gibson PERSON: Melanie Courtot consume data function OBI:0000456 material transformation objective The objective to create a mouse infected with LCM virus. The objective to create a defined solution of PBS. an objective specifiction that creates an specific output object from input materials. PERSON: Bjoern Peters PERSON: Frank Gibson PERSON: Jennifer Fostel PERSON: Melanie Courtot PERSON: Philippe Rocca-Serra artifact creation objective GROUP: OBI PlanAndPlannedProcess Branch material transformation objective OBI:0000457 manufacturing Manufacturing is a process with the intent to produce a processed material which will have a function for future use. A person or organization (having manufacturer role) is a participant in this process Manufacturing implies reproducibility and responsibility AR This includes a single scientist making a processed material for personal use. PERSON: Bjoern Peters PERSON: Frank Gibson PERSON: Jennifer Fostel PERSON: Melanie Courtot PERSON: Philippe Rocca-Serra GROUP: OBI PlanAndPlannedProcess Branch manufacturing OBI:0000458 manufacturing objective is the objective to manufacture a material of a certain function (device) PERSON: Bjoern Peters PERSON: Frank Gibson PERSON: Jennifer Fostel PERSON: Melanie Courtot PERSON: Philippe Rocca-Serra GROUP: OBI PlanAndPlannedProcess Branch manufacturing objective OBI:0000463 column chromatography detector There is a wide range of detectors available for both GC and LC each having their own particular areas of application. In general the more catholic the response, the less sensitive the detector and the most sensitive detectors are those that have a specific response. The performance of all detectors should be properly specified so that the user can determine which is most suitable for a specific application. Such specifications are also essential to compare the performance of different detectors supplied by alternative instrument manufactures. Detector specifications should be presented in a standard form and in standard units, so that detectors can be compared that function on widely different principles. PERSON:Daniel Schober WEB:<http://www.chromatography-online.org/Principles/Basic-Chromatograph/Detector/rs56.html> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01077 chromatography detector, defined class/xps column chromatography detector OBI:0000464 Bruker autosampler A Bruker autosampler is an autosampler made by Bruker. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400209 Bruker autosampler OBI:0000465 organic acid column An organic acid column is a chromatography column which enables (reversed-phase) separation of hydrophilic aliphatic and aromatic organic acids with UV detection. Organic acid columns allow retention of polar and apolar organic acids and are hydrolysis resistant. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01099 organic acid column OBI:0000466 thermal conductivity detector The most commonly used detector in preparative GC is the thermal conductivity detector (hot wire detector). Even this detector, however, is often too sensitive and has too high a flow impedance. Under such circumstances, the procedure mentioned above must be employed. The eluent from the preparative column is split and a small portion diverted through the detector (sometimes with further dilution with carrier gas to reduce sensitivity). PERSON:Daniel Schober TCD, hot wire detector WEB:<http://www.chromatography-online.org/Preparative/Apparatus/Detectors/rs27.html> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01084 thermal conductivity detector OBI:0000467 Bruker US 2 NMR magnet An actively-shielded superconducting magnet from Bruker that combines Bruker BioSpin's advanced, proprietary UltraShield active shielding and UltraStabilized sub-cooling technologies. This shielded and stabilized (US2) magnet system delivers high sensitivity and spectral dispersion. PERSON:Daniel Schober WEB:<http://www.bruker-biospin.com/nmr_magnets_950us2.html> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400189 NMR instrument Bruker US 2 NMR magnet OBI:0000468 protein column A protein column is a chromatography column used for the separation of complex protein mixtures. Protein columns enable sample desalting, followed by chromatographic separation or fractionation of complex protein samples, e.g. immunodepleted serum or plasma proteins. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01238 refactor as defined class protein column OBI:0000469 solvent mixer A liquid chromatography device that mixes different solvents, e.g. under high pressure and in differrent volumes ranging from 5 ml to 5 L capacity. Powerful magnetic mixers provide vigorous agitation required for high pressure reaction chemistry. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01072 check on definition ! solvent mixer OBI:0000470 mass spectrometry assay Identification of a proteins cut out from a 2D gel by cleaving it into peptides using trypsin digestion using electrospray ionizatino to ensure the peptides are charged, and accelerating them with an electro magnetic field in which the flight path is determined by the mass / charge ratio of the peptides. Comparing the mass/charge ratio of peptides in the proteins with databases of protein sequences allows to identify which protein gave rise to the peptides. An assay that identifies the amount and type of material entities present in a sample by fragmenting it and measuring the mass-to-charge ratio of the resulting particles. Philippe Rocca-Serra Philippe Rocca-Serra mass spectrometry assay OBI:0000471 study design execution injecting a mouse with PBS solution, weighing it, and recording the weight according to a study design. a planned process that realizes the concretization of a study design removed axiom has_part some (assay or 'data transformation') per discussion on protocol application mailing list to improve reasoner performance. The axiom is still desired. branch derived 6/11/9: edited at workshop. Used to be: study design execution is a process with the objective to generate data according to a concretized study design. The execution of a study design is part of an investigation, and minimally consists of an assay or data transformation. study design execution OBI:0000473 Bruker NMR Case sample changer The NMR Case is an economical NMR sample changer for laboratories with modest automation needs. It expands the maximum number of samples your spectrometer can process during unattended operation to 24. The NMR Case consists of multiple components. The NMR Case exchange module installed atop your cryostat. The two front legs are adjustable, making the NMR Case compatible with many different cryostats. PERSON:Daniel Schober WEB:<http://www.bruker-biospin.com/automation.html> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400203 NMR instrument Bruker NMR Case sample changer OBI:0000474 nano pump system A pump system optimized for nano flow chromatography. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01052 nano pump system OBI:0000475 Bruker AutoClean system NMR tubes are often used once and discarded, creating needless waste. With the Bruker BioSpin Autoclean system you can now recycle 5mm, 3mm, or 5mm/3mm step-down (Wilmad 520-1B) NMR tubes. AutoClean NMR Tube Washing System is a simple way to recoup the substantial investment your organization makes in quality NMR tubes, and cut back on needless waste material. washing system/NMR tube washing system, XPS: device has function washing PERSON:Daniel Schober WEB:<http://www.used-line.com/c5983250s10028-Bruker_Biospin_NMR_Autoclean_Nuclear_Magnetic_Resonance_Organic_Solvents.htm> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400205 Bruker AutoClean system OBI:0000476 manual injection system The traditional hardware system that allows a human to inject a sample into an inlet by hand, using a syringe. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01064 manual injection system OBI:0000477 Varian GEMINI spectrometer An older Varian Broadband NMR spectrometer. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400239 NMR instrument Varian GEMINI spectrometer OBI:0000478 column connector A device that connects two or more columns together in a functional way with leak-tight connection, low dead volume, low thermal mass and high inertness. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01236 chromatography device column connector OBI:0000479 solid NMR probe An NMR probe that is designed to hold a solid sample. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400243 NMR device solid NMR probe OBI:0000480 Bruker high resolution probe BRUKER BIOSPIN's experienced Research & Development group not only delivers top-performance probes for the more common experiments, but also a wealth of special probes for almost any application. For high resolution (HR) NMR we offer probes with a variety of important characteristics and features. PERSON:Daniel Schober HR Probe GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400223 NMR probe Bruker high resolution probe OBI:0000481 chromatography detector A chromatography detector is a device that locates in the dimensions of space and time, the positions of the components of a mixture that has been subjected to a chromatographic process and thus permits the senses to appreciate the nature of the separation. Defining characteristics are Dynamic Range, Response Index or Linearity, Linear Dynamic range, Detector Response, Detector Noise Level, Detector Sensitivity or Minimum Detectable Concentration, Total System Dispersion, Sensor Dimensions, Detector Time Constant, Pressure Sensitivity, Flow Sensitivity, Operating Temperature Range. PERSON:Daniel Schober WEB:<http://www.chromatography-online.org/GC-Detectors/Classification/rs1.html> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01012 chromatography detector OBI:0000482 normal phase column A normal phase column is a chromatography column in which the stationary phase is more polar than the mobile phase. Its counterpart is the reversed phase column. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01097 normal phase column OBI:0000483 APOLLO console The APOLLO is a compact, modular, multiple-DSP, Windows XP Professional-based console that can be equipped with up to 8 DDS-based RF transmitter channels configurable from 2 kHz to 3.5 GHz. Each transmitter channel produces a nominal 1V output and has the most agile frequency, phase and amplitude control of any system on the market. An array of additional options are available including multiple RF transmitters, linear high-power RF amplifiers, digital receiver arrays, low noise figure preamplifiers, a gradient control system, shim unit, MAS spin-speed controller, variable temperature unit, digital lock system and probe/coil interface. With its numerous options, the Apollo can be configured for any NMR, NQR or MRI application. PERSON:Daniel Schober WEB:<http://www.tecmag.com/apollo.htm> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400249 NMR instrument/NMR console APOLLO console OBI:0000484 NMR sample holder An NMR sample holder is the part of an NMR instrument, which carries the NMR probe,sample tube and the nmr sample. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400212 NMR device NMR sample holder OBI:0000485 chromatography instrument Any instrument that is used to carry out a chromatography experiment. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01262 chromatography device, defined class? chromatography instrument OBI:0000486 continuous wave NMR instrument Continuous wave NMR spectrometers are similar to optical spectrometers, but the sample is held in a strong magnetic field, where the frequency of the source is slowly scanned (in some instruments, the source frequency is held constant, and the field is scanned). PERSON:Daniel Schober WEB:<http://teaching.shu.ac.uk/hwb/chemistry/tutorials/molspec/nmr3.htm> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400283 NMR instrument continuous wave NMR instrument OBI:0000487 fourier transformation NMR instrument In fourier transformation NMR, all frequencies in a spectrum are irradiated simultaneously with a radio frequency pulse. Following the pulse, the nuclei return to thermal equilibrium. A time domain emission signal is recorded by the instrument as the nuclei relax. A frequency domain spectrum is obtained by Fourier transformation. PERSON:Daniel Schober GROUP:<http://teaching.shu.ac.uk/hwb/chemistry/tutorials/molspec/nmr3.htm> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400284 NMR instrument fourier transformation NMR instrument OBI:0000489 nitrogen phosphorous detector The nitrogen phosphorus detector (NPD) (sometimes called the thermionic detector) is a very sensitive, specific detector the design of which, is based on the FID. Physically the sensor appears to be very similar to the FID but, in fact, operates on an entirely different principle. The nitrogen phosphorous detector (sometimes called the thermionic detector) is a very sensitive but specific detector that responds almost exclusively to nitrogen and phosphorous compounds. It is based on the flame ionization detector but differs in that it contains a rubidium or cesium silicate (glass) bead situated in a heater coil, a little distance from the hydrogen flame. If the detector is to respond to both nitrogen and phosphorous then the hydrogen flow should be minimal so that the gas does not ignite at the jet. If the detector is to respond to phosphorous only, a large flow of hydrogen is used which is burnt at the jet. The heated bead emits electrons by thermionic emission. These electrons are collected under a potential of a few volts by an appropriately placed anode, and provides a background current. When a solute containing nitrogen or phosphorous is eluted from the column, the partially combusted nitrogen and phosphorous materials are adsorbed on the surface of the bead. The adsorbed material reduces the work function of the surface and, as consequence, the emission of electrons is increased which raises the current collected at the electrode. The sensitivity of the detector to phosphorous is about 10-12 gram per ml and for nitrogen about 10-11 gram per ml at a signal to nose ratio of 2. The alkali bead as a finite life and needs regular replacement. PERSON:Daniel Schober WEB:<http://www.chromatography-online.org/topics/nitrogen/phosphorus/detector.html> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01089 nitrogen phosphorous detector OBI:0000490 cation exchange column A cation exchange column is a chromatography column that is used in cation exchange chromatography. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01096 cation exchange column OBI:0000491 direct detection NMR probe An NMR probe designed to allow the direct detection of acquisition nuclei. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400280 NMR device direct detection NMR probe OBI:0000492 Bruker B-ACS system The Bruker Automatic Sample Changer (B-ACS 60/120), used in conjunction with Bruker DISNMR, UXNMR or XWIN-NMR software, provides dialog-guided facilities which allow the user to easily and effectively perform automatic (continuous) experiments. Features include a 60 or 120 sample capacity, random accessing of samples, positive sample identification with the optional bar code reader, and temperature control of individual samples with the optional sample heater unit. PERSON:Daniel Schober WEB:<http://www.bruker-biospin.com/automation.html> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400210 NMR instrument Bruker B-ACS system OBI:0000493 rapid resolution column A rapid resolution column is a chromatography column as marketed by Agilent, which is used with a rapid resolution cartridge to ensure a fast chromatography process with good separation resolution. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01102 rapid resolution column OBI:0000494 liquid chromatography autosampler Designed to perform capillary LC with injection of sample volumes ranging from nL to L. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01061 liquid chromatography autosampler OBI:0000495 vacuum degasser A degassing system used for degassing solvents in liquid chromatography. Dissolved gasses, usually nitrogen and oxygen from the air, tend to be evolved in the mobile phase as the pressure is reduced when the mobile phase leaves the liquid chromatography column and enters the detector. Gasses in the mobile phase in the detector can produce completely unacceptable noise and, thus, must be removed. The dissolved gasses were originally removed under vacuum but, unfortunately, are soon replaced if the solvent is left in contact with air at atmospheric pressure. For this reason degassing is now usually carried out by bubbling helium through the mobile phase reservoirs. Secondly, vacuum is used in the thermionic detector. This consists of a device, very similar in design to the thermionic valve which is attached to a vacuum and a small quantity of the eluent from a gas chromatography column allowed to bleed through it. Helium is used as the carrier gas. The presence of solute vapor causes the thermionic current to fall. This type of detector tends to become contaminated rather readily. PERSON:Daniel Schober WEB:<http://www.chromatography-online.org/topics/vacuum.html> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01053 vacuum degasser OBI:0000496 capillary column A capillary column is a thin tube with a small inner diameter, usually around 0.5 mm. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01066 capillary column OBI:0000497 sample inlet The column inlet (or injector) provides the means to introduce a sample into a continuous flow of carrier gas. The inlet is a piece of hardware attached to the column head. PERSON:Daniel Schober WEB:<http://en.wikipedia.org/wiki/Gas_chromatography#Inlets> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01044 chromatography device sample inlet OBI:0000498 NMR tube washing system An automatic cleaning system for NMR tubes that removes previous probe and sample residues in order to allow for tube recycling. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400204 NMR instrument NMR tube washing system OBI:0000499 NMR console A component of an NMR instrument that controls the activities of the other components. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400015 NMR instrument, TODO: same as or part of acquisition computer? NMR console OBI:0000500 dual loop autosampler A dual loop autosampler is an autosampler that is designed for handling both analytical (10 mL/min flow rate) to preparative scale sample purification (100 mL/min flow rate). PERSON:Daniel Schober WEB:<http://www.chem.agilent.com/scripts/pds.asp?lpage=17149> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01063 dual loop autosampler OBI:0000501 variable wavelength detector A chromatography detector, that can detect signals within a certain range at user-defined wavelengths. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01079 variable wavelength detector OBI:0000503 Bruker LC-NMR platform The LC-NMR/MS setup was first introduced by Bruker BioSpin in 1999. An LC-NMR system including a Bruker Peak Sampling Unit (BPSU-36) was coupled with a Bruker Daltonics esquire series ion trap mass spectrometer via a Bruker NMR-MS interface (BNMI). Since October 2004 the Bruker Daltonics microTOF-LC time-of-flight mass spectrometer can also be integrated in an LC-NMR setup. PERSON:Daniel Schober WEB:<http://www.bruker-biospin.com/hyphenation_lcnmr_ms.html> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400276 NMR instrument hyphenated NMR instrument platform Bruker LC-NMR platform OBI:0000504 sample injection system An automated chromatography system that injects the sample into the chromatography columns in order to increase speed and minimize human involvement in the purification process for better reproducibility. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01057 chromatography device sample injection system OBI:0000505 multiple wavelength detector A chromatography detector, that can detect many discrete wavelengths in parallel and produces a multiple wavelength chromatographic profile. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01078 multiple wavelength detector OBI:0000506 photoionization detector The selective determination of aromatic hydrocarbons or organo-heteroatom species is the job of the photoionization detector (PID). This device uses ultraviolet light as a means of ionizing an analyte exiting from a GC column. The ions produced by this process are collected by electrodes. The current generated is therefore a measure of the analyte concentration. f the amount of ionization is reproducible for a given compound, pressure, and light source then the current collected at the PID's reaction cell electrodes is reproducibly proportional to the amount of that compound entering the cell. The reason why the compounds that are routinely analyzed are either aromatic hydrocarbons or heteroatom containing compounds (like organosulfur or organophosphorus species) is because these species have ionization potentials (IP) that are within reach of commercially available UV lamps. The available lamp energies range from 8.3 to 11.7 ev, that is, lambda max ranging from 150 nm to 106 nm. Although most PIDs have only one lamp, lamps in the PID are exchanged depending on the compound selectivity required in the analysis. PERSON:Daniel Schober PID WEB:<http://www.chemistry.adelaide.edu.au/external/soc-rel/content/pid.htm> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01090 photoionization detector OBI:0000507 gas generator An instrument that generates gases for use with the gas chromatograph. Previously gas was obtained from gas tanks or gas cylinders. However, over the past decade the use of gas generators have become more popular as it avoids having gases at high pressure in the laboratory which is perceived by some as potentially dangerous. In addition, the use of a hydrogen generator avoids the use of a cylinder of hydrogen at high pressure which is also perceived by some as a serious fire hazard despite the fact that they have been used in laboratories, quite safely for nearly a century. PERSON:Daniel Schober WEB:<http://www.chromatography-online.org/GC/Gas-Supplies/Pure-Air-Generators./rs5.html> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01033 gas chromatography equipment gas generator OBI:0000508 column jacket A column jacket is a piece of column chromatography equipment that covers a column in order to ensure thermoisolation and create a controllable thermostatic microenvironment. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01276 chromatography device column jacket OBI:0000509 electron capture detector The electron capture detector is a GC detector that uses a radioactive Beta emitter (electrons) to ionize some of the carrier gas and produce a current between a biased pair of electrodes. When organic molecules that contain electronegative functional groups, such as halogens, phosphorous, and nitro groups pass by the detector, they capture some of the electrons and reduce the current measured between the electrodes. PERSON:Daniel Schober ECD WEB:<http://homepages.onsnet.nu/%7Ealkema/html/whatisgc.html> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01085 electron capture detector OBI:0000510 reversed phase column A reversed phase column is a chromatography column in which the mobile phase is more polar than the stationary phase. Its counterpart is the normal phase column. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01106 reversed phase column OBI:0000511 injector lubricant A lubricant used in liquid chromatography that eases sample injector penetration. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01118 injector lubricant OBI:0000512 isolation of cell population removing CD4+ cells from PBMCs using magnetic beads. a process in which a population of cells with certain characteristics is isolated from a larger population Person: Bjoern Peters isolation of cell population OBI:0000513 DISCOVERY console The Discovery console is a Windows XP Professional-based, integrated console designed especially for Solid-State NMR. The console includes everything needed to interface to any magnet and solids probe - from computer to cables to duplexing network. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400247 NMR instrument/NMR console DISCOVERY console OBI:0000514 Bruker AMX series NMR instrument A series of older Bruker NMR magnets, now out of production. The Bruker AMX500 has proven an extremely reliable workhorse, with excellent lineshape yielding superior water suppression even without gradients. The Oxford 11.7 Tesla 5.2 cm bore magnet rests on a TMC vibration damping table. Homogeneity is controlled by a BSN-18 and BSN-2 with 19 shim controls. In addition to the 5 mm triple resonance probe, the AMX is equipped with a 10mm broadband observe probe. PERSON:Daniel Schober WEB:<http://www.tufts.edu/med/biochemistry/NMR/amx500.html> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400240 NMR instrument Bruker AMX series NMR instrument OBI:0000515 chromatofocusing column A chromatofocusing column is a chromatography column in which a resin is equilibrated at one pH and eluted at a second pH. The use of a weak ion-exchange resin causes a pH gradient to be formed at the solvent front owing to the buffering action of the resin. This pH gradient in turn leads to an ordering of proteins by isoelectric point. Molecules of charge sign opposite the resin bind; those of charge sign like the resin do not bind. PERSON:Daniel Schober WEB:<http://www.bioprocessintl.com/default.asp?page=glossary&TopicID=1> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01209 chromatofocusing column OBI:0000516 NMR probe Part of an NMR instrument that detects the signals emitted from a sample. No single probe can perform the full range of experiments, and probes that are designed to perform more than one type of measurement usually suffer from performance compromises. The probe represents a rather fragile single point of failure that can render an NMR system completely unusable if the probe is dropped or otherwise damaged. Probes are usually characterised by Sample diameter and Frequency.\n alt The instrument that transmits and receives radiofrequency to and from the NMR sample. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400014 NMR instrument NMR probe OBI:0000517 NMR magnet A magnet which induces a certain frequency (MHz) and which has a certain bore diameter.\n alt The NMR signal is a natural physical property of the certain atomic nuclei but it can only be detected with an external magnetic field. A magnet is a fundamental part of an NMR instrument which induces an electromagnetic force field (RF pulse) and by this excites and aligns the spins of the electrons of the NMR acquisition nucleus. It is usually a big (superconducting) electromagnet which is cooled by liquid helium and can be adjusted to a frequency between 200 and 950 MHz. The magnetic field strength is measured in Tesla or Gauss. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400185 NMR instrument NMR magnet OBI:0000518 trap column A trap column is a chromatography column which is used prior to a, e.g. mass spectrometry, separation to clean up or concentrate controlled amounts of samples prior to elution to a detector. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01261 trap column OBI:0000519 flow probe An NMR probe that allows the automatized flow-through of a sample. The sample is aspirated via a syringe pump into the Flow probe, the NMR spectrum is acquired and when the experiment is complete, the sample is returned to back to an external source (well plate) or flushed to waste. Sometimes pulsed field gradients (PFG) can be established in flow probes. PERSON:Daniel Schober WEB:<http://www.varianinc.com/cgi-bin/nav?products/NMR/accessory/auto_samplers/vast/index&cid=HFIH> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400131 NMR device flow probe OBI:0000520 clinical chemistry assay Influence of hydroxyethyl starch (6% HES 130/0.4) administration on hematology and clinical chemistry parameters. Mueller T, Schimetta W, Dieplinger B, Loeffler P, Rehm M, Kreimeier U, Poelz W, Haltmayer M. Clin Chem Lab Med. 2008;46(4):558-62. PMID: 18605936 a process which uses analytical methods to produce measurements and data on the concentration of a chemical parameters (analytes) present in a bodily fluid collected from an organism. 3/26/09: There needs to be a restriction set that specifies which type of evaluants are used in the assay, somewhere along the lines of 'sample derived of bodily fluid' Person: Philippe Rocca-Serra chemical pathology detection of analyte in blood sample adapted from Wikipedia clinical chemistry clinical chemistry assay OBI:0000521 flame ionization detector A flame ionization detector is a GC detector that consist of a hydrogen/air flame and a collector plate which are normally heated independently of the chromatographic oven. Heating is necessary in order to prevent condensation of water generated by the flame and also to prevent any hold-up of solutes as they pass from the column to the flame. There is an electrode above the flame to collect the ions formed at a hydrogen/air flame. The number of ions hitting the collector is measured and a signal is generated. Flame ionization detectors are most widely used and generally applicable for gas chromatography and hence is used for routine and general purpose analysis. It is easy to use but destructive of the sample. PERSON:Daniel Schober FID WEB:<http://homepages.onsnet.nu/%7Ealkema/html/whatisgc.html> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01197 flame ionization detector OBI:0000522 vial A vial is a cylindrical container often made from glass tubing. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01117 vial OBI:0000523 magic angle spinning rotor A rotor device that holds the NMR sample and enables the adjustment of the orientation of the rotation axis for a sample in a NMR instrument in the magic angle. PERSON:Daniel Schober MAS rotor WEB:<http://www.freepatentsonline.com/4352066.html> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400130 NMR instrument magic angle spinning rotor OBI:0000524 Varian VXR spectrometer A Varian NMR spectrometer. PERSON:Daniel Schober WEB:<http://www.scs.uiuc.edu/NMR/instruments/vxr500.php> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400238 NMR instrument Varian VXR spectrometer OBI:0000525 splitless GC injector Injected sample enters column immediately (while split valve to split vent is closed). Here a sample is introduced into a heated small chamber via a syringe through a septum - the heat facilitates volatilization of the sample and sample matrix. The carrier gas then either sweeps the entirety (splitless mode) or a portion (split mode) of the sample into the column. In split mode, a part of the sample/carrier gas mixture in the injection chamber is exhausted through the split vent. PERSON:Daniel Schober WEB:<http://en.wikipedia.org/wiki/Gas_chromatography> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01060 splitless GC injector OBI:0000526 preparative autosampler For preparative LC with injection of sample volumes ranging from L to mL ranges. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01062 preparative autosampler OBI:0000527 flow high resolution probe Hyphenated analytical techniques combining mass spectrometry and chromatography are well-established laboratory tools. The combination of chromatography and NMR has also made its way into the analytical laboratory. Further developments even combine all three techniques into an LC-NMR/NMR-MS system. The use of solid phase extraction provides an efficient interface between chromatography and NMR with demands for special type of flow probes. PERSON:Daniel Schober flow HR-probe GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400195 NMR probe flow high resolution probe OBI:0000528 liquid chromatography valve A sample valve that must be able to sustain pressures up to 10,000 p.s.i., although it is most likely to operate on a continuous basis, at pressures of 3,000 p.s.i. or less. The higher the operating pressure the tighter the valve seating surfaces must be forced together to eliminate any leak. It follows that any abrasive material, however fine, that passes into the valve can cause the valve seating to become scored each time it is rotated which will ultimately lead to leaks. This will cause the sample size to vary between samples and eventually affect the accuracy of the analysis. It follows that any solid material must be carefully removed from any sample before filling the valve. The sample volume of an internal loop valve is situated in the connecting slot of the valve rotor and can be used only for relatively small sample volumes. Internal sample loop valves provide samples with volumes ranging from 0.1 ml to about 0.5 ml. Valve operation is shown in figure 6. The left-hand side diagram shows the load position. The sample occupies the rotor slot and has been filled by passing the sample from an appropriate syringe through the rotor slot to waste. While loading the sample, the mobile phase supply is passed through the valve directly to the column. To place the sample onto the column, the valve is then rotated and the valve slot containing the sample is now placed between the solvent supply and the column. As a result, the sample is passed into the column by the flow of solvent. PERSON:Daniel Schober WEB:<http://www.chromatography-online.org/EC-Dispersion/HPLC-Sample-Valves/rs16.html> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01110 chromatography device liquid chromatography valve OBI:0000529 JEOL NMR probe An NMR probe that is manufactured by JEOL. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400232 NMR device JEOL NMR probe OBI:0000530 Bruker UltraShield Plus NMR magnet An NMR magnet of which Brukers claims it is the latest and most advanced self-shielding NMR magnet technology ever developed. These magnets are the ultimate advancement in high performance, actively-shielded NMR solutions. They offer unprecedented shielding performance whilst ensuring no compromise in system homogeneity, stability or cryogenic specifications. PERSON:Daniel Schober WEB:<http://www.bruker-biospin.com/nmr_magnets_usplus.html> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400190 NMR instrument Bruker UltraShield Plus NMR magnet OBI:0000531 Bruker CryoProbe The Bruker BioSpin CryoProbe is a high-performance cryogenically cooled probe developed for high-resolution applications. It has improved signal/noise (S/N) ratios obtained by reducing the operating temperature of the coil and the pre-amplifier. As a result, the efficiency of the coil is improved and the noise of the coil and the pre-amplifier are reduced.The dramatic increase in the S/N ratio by a factor of 3-4, as compared to conventional probes, leads to a possible reduction in experiment time of up to 16 or a reduction in required sample concentration by a factor of up to 4. The CryoProbes possess key characteristics for NMR analysis:\n Significant S/N gains (with moderately salty samples also)\n Short pulse widths\n Short ring down times\n Linear behavior in power response\n Gradient capability\n CryoProbes are available as Triple Resonance, Dual, Selective X Detection, MicroImaging, and Quad Nucleus Probes configurations at 400 MHz and higher\n All high resolution probes have a lock circuit\n All high resolution probes have Z-gradient. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400191 NMR probe Bruker CryoProbe OBI:0000532 column cartridge A device that binds the chromatography column and additional connector elements and / or valves or syringes into one physical unity for further processing. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01055 chromatography device, check on definition ! column cartridge OBI:0000533 affinity column An affinity column is a chromatography column that is used in affinity chromatography. Differences in the affinity of molecules to be separated to a stationary phase are used for discriminate retention. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01094 affinity column OBI:0000534 tecmag NMR instrument An NMR instrument that is manufactured by tecmag. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400250 NMR instrument tecmag NMR instrument OBI:0000535 gel filtration column A Gel filtration column is a chromatography column for size-exclusion chromatography, in which the stationary phase is a gel. The main application of gel filtration chromatography is the fractionation of proteins and other water-soluble polymers. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01104 gel filtration column OBI:0000536 fraction collector A fraction detector is a device that allows regular or specified samples to be taken from a column eluate and stored in a retrievable form. The storage vessels are usually small sample tubes or vials that are oriented in a rotating disk or in a moving belt, there movement usually being controlled by a microprocessor. On receiving a signal from the microprocessor, the next vial is placed under the column outlet and the eluate collected until receiving another signal from the computer. Once the properties of the chromatogram that describes the separation has been ascertained, then the collection program can be defined. The fractions can be collected on a basis of time either at regular intervals or a specific times to collect specific peaks. Alternatively the fractions can be collected by monitoring the detector output and when a peak starts to elute the fraction collector is activated and the peak collected in a specific vial. When the peak returns to base line the column eluate is then directed to waste until the next peak starts eluting. Fraction collectors are in common use with most liquid chromatographs. They are used to collect samples for further purification, subsequent examination by spectroscopic techniques or for biological or organoleptic testing. PERSON:Daniel Schober WEB:<http://www.chromatography-online.org/topics/fraction/collector.html> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01073 fraction collector OBI:0000537 copy number variation profiling Profiling of copy number variations (CNVs) in healthy individuals from three ethnic groups using a human genome 32 K BAC-clone-based array. de Ståhl TD, Sandgren J, Piotrowski A, Nord H, Andersson R, Menzel U, Bogdan A, Thuresson AC, Poplawski A, von Tell D, Hansson CM, Elshafie AI, Elghazali G, Imreh S, Nordenskjöld M, Upadhyaya M, Komorowski J, Bruder CE, Dumanski JP. Hum Mutat. 2008 Mar;29(3):398-408. PMID: 18058796 copy number variation profiling is a process which aims to provide information about lost or amplified genomic regions of DNA by comparing genomic DNA originated from tissues from same or different individuals using specific techniques such as CGH, array CGH, SNP genotyping. Philippe Rocca-Serra CNV analysis copy number variation profiling OBI:0000538 in-line filter A solvent filter that sits between the pump and the injection valve that prevents dust particles, general debris and, to some extent, bacteria from entering the chromatography system. Contaminants can interfere with the low-pressure gradient former or the pump and particles entering valves may interfere with the proper function. The result could cause an increased baseline noise, non-repeatable gradient forming, unreliable flow rate or other interferences. Solvent in-line filters are low-pressure filters and will allow a high flow rate due to a large surface area and large porosity. PERSON:Daniel Schober WEB:<http://www.appliedporous.com/frits-chromatography.htm> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01123 in-line filter OBI:0000539 imaging NMR probe An NMR probe that is designed for generating pictures from sample states via NMR imaging. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400244 NMR device imaging NMR probe OBI:0000540 isolation of adherent cells a material separation process in which cells that stick to the container in which they are grown as a cell culture are separated from those in the liquid component of the culture. The output of this process are adherent cells. isolation of adherent cells OBI:0000541 Bruker AC series NMR instrument A series of older Bruker NMR magnets, now out of production. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400241 NMR instrument Bruker AC series NMR instrument OBI:0000542 gas chromatography equipment Any device used in a gas chromatography experiment. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01030 will become defined class/xps gas chromatography equipment OBI:0000543 syringe filter A small membrane filter of defined pore size, that filters samples from a syringe. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01122 syringe filter OBI:0000544 Bruker SampleRail system This Instrument system automatically prepares an NMR sample, inserts it into an NMR magnet, performs NMR experiments on the sample, and transports it back to the preparation system. The SampleRail fulfills the transporting tasks from the preparation system into the NMR magnet and back. PERSON:Daniel Schober WEB:<http://www.bruker-biospin.com/automation.html> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400207 NMR instrument Bruker SampleRail system OBI:0000545 column compartment For chromatography analyses, the ability to maintain a stable column environment regardless of ambient temperature fluctuations is critical for maintaining retention time precision. In order to ensure such stable conditions at different chromatography steps a column compartment can be installed that ensures e.g. stable temperature of the column in a given step. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01068 column compartment OBI:0000546 capillary pump system A pump system optimized for capillary chromatography. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01051 capillary pump system OBI:0000547 evaporative light scattering detector The evaporative light scattering detector, as its name implies, utilizes a spray that continuously atomizes the column eluent into small droplets. These droplets are allowed to evaporate, leaving the solutes as fine particulate matter suspended in the atomizing gas. PERSON:Daniel Schober WEB:<http://www.chromatography-online.org/HPLC-Detectors/Evaporative-Light-Scattering/rs73.html> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01082 evaporative light scattering detector OBI:0000548 isolation of PBMCs cells are extracted from whole blood using ficoll, a hydrophilic polysaccharide that separates layers of blood, with monocytes and lymphocytes forming a buffy coat under a layer of plasma. This buffy coat contains the PBMCs. a process in which cells with a single nucleus are isolated from a blood sample PERSON: bjoern peters wiki http://en.wikipedia.org/wiki/PBMC isolation of PBMCs OBI:0000549 column cartridger A chromatography device where the column cartridge is inserted into and stabilised. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01054 check on definition ! column cartridger OBI:0000550 nitrogen generator A gas generator that generates nitrogen gas. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01034 nitrogen generator OBI:0000551 needle assembly The needle assembly attached to the autosampler, comprises the injector needle that feeds a sample or carrier gas into the inlet PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01065 chromatography device, check on definition ! needle assembly OBI:0000552 reverse transcribed polymerase chain reaction Harmonisation of multi-centre real-time reverse-transcribed PCR results of a candidate prognostic marker in breast cancer: an EU-FP6 supported study of members of the EORTC - PathoBiology Group. Span PN, Sieuwerts AM, Heuvel JJ, Spyratos F, Duffy MJ, Eppenberger-Castori S, Vacher S, O'Brien K, McKiernan E, Pierce A, Vuaroqueaux V, Foekens JA, Sweep FC, Martens JW. Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 reverse transcribe pcr is a process which allow amplification of cDNA during a pcr reaction while the cDNA results from a retrotranscription of messenger RNA isolated from a material entity. 3/21/10, BP:Modified definition to clarify that this is not the assay, but the material transformation Philippe Rocca-Serra RT-PCR reverse transcription polymerase chain reaction reverse transcribed polymerase chain reaction OBI:0000553 Bruker Capillary LC-NMR platform Capillary LC-NMR is a hyphenated technique coupling capillary liquid chromatography and NMR, which increases sensitivity dramatically through the use of miniaturization of the chromatographic techniques and NMR detection volume. LC-NMR hyphenated systems separate a mixture into its pure components and couple the output to NMR for automatic sample analysis. The ever increasing need to measure lower sample amounts and lower level impurities demands the highest NMR sensitivity. Traditional LC-NMR systems with relatively large peak volumes are not optimized for such low levels of detection. Bruker BioSpin, together with Waters and Protasis has developed a Capillary LC-NMR system. The latest capillary LC attributes and highest capillary flow probe sensitivity combine with state of the art NMR systems technology. Greater mass sensitivity and faster spectral analysis with smaller sample volumes is possible. This system is ideal for analysis of metabolites and impurities associated with the drug development process. PERSON:Daniel Schober WEB:<http://www.bruker-biospin.com/hyphenation_caplcnmr.html> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400279 NMR instrument hyphenated NMR instrument platform Bruker Capillary LC-NMR platform OBI:0000554 gas chromatography oven A gas chromatography oven is an oven with a heated connection between the GC and the MS instrument in a GCMS-analysis, that keeps compounds in the gas phase as they leave the GC oven. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01039 gas chromatography equipment gas chromatography oven OBI:0000555 autosampler An optional part of an NMR instrument used to hold samples prior to NMR analysis and that sequentially loads these samples into the analytical part of the NMR instrument. \n alt The autosampler is an automatic sample changer device. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400002 NMR instrument autosampler OBI:0000556 isocratic pump system A pump system optimized for isocratic chromatography. PERSON:Daniel Schober WEB:<http://www.buchi.com/Isocratic-Pump-System.253.0.html> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01049 isocratic pump system OBI:0000557 flash pump system Any pump system used in flash column chromatography to push the solvent through the column. Better flow rates can be achieved by using a pump or by using compressed gas (e.g. air, nitrogen, or argon) to push the solvent through the column (flash column chromatography). PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01048 flash pump system OBI:0000558 Varian UNITY INOVA spectrometer The UNITY INOVA is also the easiest spectrometer to use and is also the choice of those interested in using advanced NMR techniques in their own research, but without becoming, or hiring, an NMR expert. A complete set of turnkey operating environments is available for the UNITY INOVA covering the structure and dynamics of biological macromolecules, small molecules, solids, and imaging. These packages put the combined NMR expertise of the entire Varian NMR community at your fingertips. PERSON:Daniel Schober WEB:<http://www.varianinc.com/cgi-bin/nav?products/NMR/spectromet/inova/index&cid=HFIH> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400236 NMR instrument Varian UNITY INOVA spectrometer OBI:0000559 liquid NMR probe An NMR probe that is designed to hold a liquid sample. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400242 NMR device liquid NMR probe OBI:0000560 ion exchange column An ion exchange column is a chromatography column that is used in ion exchange chromatography and anion or cation exchange resins to enable separation. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01105 ion exchange column OBI:0000561 Bruker NMR probe An NMR probe that is manufactured by Bruker. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400231 NMR device, TODO: May need no definition. Bruker NMR probe OBI:0000562 anion trap column An anion trap column is a trap column and ion-exchange column which contains cationic anion-exchange resins. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01277 anion trap column OBI:0000563 fluorescene detector A single wavelength detector, where the excitation light wavelength is normally a mercury lamp generated high intensity UV light at 253.7 nm. Many substances that fluoresce will be excited by light of this wavelength and hence be detected. PERSON:Daniel Schober WEB:<http://www.chromatography-online.org/HPLC-Detectors/Fluorescence/Single-Wavelength-Excitation/rs57.html> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01080 fluorescene detector OBI:0000564 tecmag EAGLE probe The Eagle is a 4 mm 1H/X solid-state MAS probe with a top spinning speed of 18 kHz. Its simple design is robust, reliable and easy to spin. Configurations are available for 200 to 600 MHz wide bore magnets on Tecmag, Bruker, Chemagnetics, JEOL and Varian spectrometers. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400248 NMR probe tecmag EAGLE probe OBI:0000565 electrical conductivity detector The electrical conductivity detector measures the conductivity of the mobile phase. There is usually background conductivity which must be backed-off by suitable electronic adjustments. If the mobile phase contains buffers, the detector gives a base signal that completely overwhelms that from any solute usually making detection impossible. Thus, the electrical conductivity detector a bulk property detector. and senses all ions whether they are from a solute or from the mobile phase. In order to prevent polarization of the sensing electrodes, AC voltages must be used and so it is the impedance not the resistance of the electrode system that is actually measured. From a physical chemistry stand point the conductivity of a solution is more important than its resistance. However, it is the resistance (impedance) of the electrode system that determines the current across it. The resistance of any conductor varies directly as its length and inversely as its cross sectional area. PERSON:Daniel Schober WEB:<http://www.chromatography-online.org/HPLC-Detectors/Electrical-Conductivity/rs83.html> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01239 electrical conductivity detector OBI:0000566 NMR instrument An Instrument which is used to carry out a NMR analysis of some sample. PERSON:Daniel Schober NMR instrument GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400059 NMR instrument NMR instrument OBI:0000567 Bruker UltraShield NMR magnet An NMR magnet manufactured by Bruker that ensures field homogeneity without amplified effects from vibrations or thermal changes. This magnet technology uses active shielding and optimizes coil design. PERSON:Daniel Schober WEB:<http://www.bruker-biospin.com/nmr_magnets_us.html?&print=http%3A%2Fitsupportunit.com%2Fawstats%2Ficon%2Fnisum%2Fivuj%2F> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400187 NMR instrument Bruker UltraShield NMR magnet OBI:0000568 piston-seal The seal made by a piston in a diaphragm pump. The unique property of the reciprocating diaphragm pump is that the actuating piston does not come into direct contact with the mobile phase and thus, the demands on the piston-cylinder seal are not so great. The diaphragm has a relatively high surface area and thus, the movement of the diaphragm is relatively small and consequently the pump can be operated at a fairly high frequency. High frequency pumping results in a very significant reduction in pulse amplitude and, in addition, high frequency pulses are more readily damped by the column system. Nevertheless, it must be emphasized that diaphragm pumps are not pulseless. PERSON:Daniel Schober WEB:<http://www.chromatography-online.org/HPLC/Basic-HPLC/Pump/Diaphragm/rs15.html> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01116 piston-seal OBI:0000569 mass selective detector A mass selective detector is a GC detector that uses mass spectrometry. It is based upon the ionization of solute molecules in the ion source and the separation of the ions generated on the basis of their mass/charge ratio by an analyzer unit. This may be a magnetic sector analyzer, a quadruple mass filter, or an ion trap. Ions are detected by a dynode electron multiplier. PERSON:Daniel Schober mass spectrometry detector WEB:<http://homepages.onsnet.nu/%7Ealkema/html/whatisgc.html> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01198 mass selective detector OBI:0000570 spin column A spin column is a chromatography column which is suitable for putting it into a centrifuge. A spin column enforces separation through increased G-forces while spinning the column in a centrifuge. It is often used in DNA gel extraction kits. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01232 spin column OBI:0000571 manufacturer role With respect to The Accuri C6 Flow Cytometer System, the organization Accuri bears the role manufacturer role. With respect to a transformed line of tissue culture cells derived by a specific lab, the lab whose personnel isolated the cll line bears the role manufacturer role. With respect to a specific antibody produced by an individual scientist, the scientist who purifies, characterizes and distributes the anitbody bears the role manufacturer role. Manufacturer role is a role which inheres in a person or organization and which is realized by a manufacturing process. GROUP: Role Branch OBI manufacturer role OBI:0000572 transfer line A combination of devices that are used in connection with a sampling head for transferring components of an applied sample to the analyzing part of a chromatography system. PERSON:Daniel Schober WEB:<http://www.freepatentsonline.com/5702671.html> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01235 chromatography device transfer line OBI:0000573 gradient pump system A pump system optimized for gradient chromatography. PERSON:Daniel Schober WEB:<http://www.buchi.com/Gradient-Pump-System.531.0.html> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01050 gradient pump system OBI:0000574 high temperature column A high temperature column is a chromatography column which is suitable for and withstands very high temperatures in chromatography ovens. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01233 high temperature column OBI:0000575 Bruker Ultrastabilized NMR magnet An NMR magnet manufactured by Bruker for Ultra-High Field NMR, available from 750 MHz to 900 MHz, which provides reliable operation at reduced temperature and ambient pressure via being rigidly mounted and stabilized. PERSON:Daniel Schober WEB:<http://www.bruker-biospin.com/nmr_magnets_ultrastabilized.html?&print=http%3A%2Fitsupportunit.com%2Fawstats%2Ficon%2Fnisum%2Fivuj%2F> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400188 NMR instrument Bruker Ultrastabilized NMR magnet OBI:0000576 scattered molecular aggregate the sodium and chloride ions in a glass of salt water a material entity that consists of all the molecules of a specific type that are located in some bounded region and which is part of a more massive material entity that has parts that are other such aggregates PERSON: Alan Ruttenberg Collective Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. With inspiration from the paper Granularity, scale and collectivity: When size does and does not matter, Alan Recto, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349 scattered molecular aggregate OBI:0000577 obsolete_molecular concentration the phosphate concentration should be 0.1M A concentration is a relational quality that inheres in a material entity towards molecular scattered aggregate that is part of it by virtue of some ratio of masses of the two or the counts of the grains of the two or volume occupied by the larger material entity. JZ: Can we replace the term by PATO: http://purl.obolibrary.org/obo/PATO_0000033 If not, we will wait the term available in PATO. Although specified that obsolete reason is 'term imported', the term has not imported yet. Will keep tracking this term until import the replaced term. Term depracted since the object property 'towards' used in the axioms is not avaliable in BFO2. This term represent a quality of molecular concentration. If there is need for some other sort of concentration - e.g. ratio of counts of cells, another term is needed. OBI uses a standard unit for representing concentration qualities but this still needs to be decided on. A relation needs to be defined that relates the quality instance to the representation of its quantitative value in the chosen units. See http://en.wikipedia.org/wiki/Concentration Measurements of concentration may be in any appropriate unit. Note that precise concentrations are virtually never known. Finally, note that there is no such thing as a concentration of 0. A concentration is a *relational* quality and so can't exist unless both entities it inheres in exist. However one map make concentration measurements that turn out not to be about concentrations qualities, if it happens that the scattered molecular aggregate doesn't actually exist. logical definition in OBI: 'quality of related physical entities' ('inheres in' some material_entity) and (towards some 'scattered molecular aggregate') PERSON: Alan Ruttenberg Discussion in Karslruhe, Oct 2008, with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. obsolete_molecular concentration true OBI:0000578 NMR sample tube The sample-tube holds the NMR sample and sits in the nmr probe. It is usually a glass tube of 5-20mm diameter. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400132 NMR device NMR sample tube OBI:0000579 Varian UNITY spectrometer The predecessor series of the Varian UNITY INOVA spectrometer. PERSON:Daniel Schober WEB:<http://www.scs.uiuc.edu/NMR/instruments/u400.php> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400237 NMR instrument Varian UNITY spectrometer OBI:0000580 AVANCE II spectrometer A spectrometer suitable for metabolomics and in vivo NMR studies but structural analysis of small molecules and low molecular weight proteins can also be performed. To accomplish these studies there are six probe-heads available. A successor, the AVANCE III came out recently. PERSON:Daniel Schober WEB:<http://cermax.itqb.unl.pt/mambo/en/index.php?option=com_content&task=view&id=36&Itemid=93> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400197 NMR instrument AVANCE II spectrometer OBI:0000581 y-column connector A column connector that connects one column on one side with two columns at the other side, hence building a Y shaped structure. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01237 y-column connector OBI:0000582 Bruker LC-NMR/MS platform Includes the connection to a high-resolution TOF-LC-MS system. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400277 NMR instrument hyphenated NMR instrument platform Bruker LC-NMR/MS platform OBI:0000583 refractive index detector For analyzing non-UV absorbing substances, such as carbohydrates, lipids and polymers. This is also the detector of choice for gel permeation chromatography. The refractive index detector is one of the least sensitive LC detectors. It is very sensitive to changes in ambient temperature, pressure changes, flow-rate changes and can not be used for gradient elution. Despite these many disadvantages, this detector is extremely useful for detecting those compounds that are nonionic, do not adsorb in the UV, and do not fluoresce. There are many optical systems used in refractive index detectors but one of the most common is the differential refractive index detector. PERSON:Daniel Schober WEB:<http://www.chromatography-online.org/HPLC/Refractive-Index/rs33.html> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01081 refractive index detector OBI:0000584 anion exchange column An anion exchange column is a chromatography column that is used in anion exchange chromatography and which enables the separation of anion mixtures. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01095 anion exchange column OBI:0000586 plunger column A plunger column is a chromatography column with adjustable heigth control. By means of an adjustable endpiece (plunger) the user can adjust the column length without disturbing the packed bed. Plunger columns can equalize volume changes and thus avoids dead volumes within the column. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01108 plunger column OBI:0000588 flame photometric detector The determination of sulfur or phosphorus containing compounds is the job of the flame photometric detector (FPD). This device uses the chemiluminescent reactions of these compounds in a hydrogen/air flame as a source of analytical information that is relatively specific for substances containing these two kinds of atoms. The emitting species for sulfur compounds is excited S2. The lambda max for emission of excited S2 is approximately 394 nm. The emitter for phosphorus compounds in the flame is excited HPO (lambda max = doublet 510-526 nm). In order to selectively detect one or the other family of compounds as it elutes from the GC column, an interference filter is used between the flame and the photomultiplier tube (PMT) to isolate the appropriate emission band. The drawback here being that the filter must be exchanged between chromatographic runs if the other family of compounds is to be detected. PERSON:Daniel Schober FPD WEB:<http://www.shsu.edu/~chemistry/FPD/FPD.html> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01091 flame photometric detector OBI:0000589 chromatography pump system Better flow rates can be achieved by using a pump or by using compressed gas (e.g. air, nitrogen, or argon) to push the solvent through the column (flash column chromatography). PERSON:Daniel Schober WEB:<http://en.wikipedia.org/wiki/Column_chromatography> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01046 chromatography pump system OBI:0000590 Bruker 1mm MicroProbe Over the past few years there has been a significantly growing demand for miniaturization in all areas ofmodern research and development. Evoked by many exciting applications, there is a need for analytical methods which require less amounts of sample. Bruker BioSpin meets this challenge with a revolutionary NMR probe design: The 1mm MicroProbe. It operates with disposable 1mm capillary sample tubes and the sample volume of 5 microliters enables the use of lowest amounts of sample to run all high resolution NMR experiments with outstanding sensitivity and up to 16 times faster measurements. Due to the TXI-type probe design, the z-gradient coil and the automatic matching and tuning accessory, the 1mm MicroProbe can be used for a wide variety of NMR experiments. The key advantages of this probe include:\n up to 4 times higher mass sensitivity than 5mm conventional probes (with respect to the same sample amount)\n excellent solvent suppression properties\n virtually no salt effect\n discrete samples in tubes that can be sealed and stored\n automation accessory for sample preparation and handling available. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400194 NMR probe Bruker 1mm MicroProbe OBI:0000591 Bruker BEST NMR system The introduction of biological screening and combinatorial chemistry for chemical synthesis has also introduced new requirements for NMR automation, e.g., the use of well plates for sample input, increased demands on throughput, and the need for quick and simple interpretation of the acquired NMR data. PERSON:Daniel Schober Bruker Efficient Sample Transfer NMR WEB:<http://www.bruker-biospin.com/automation.html> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400206 NMR instrument Bruker BEST NMR system OBI:0000592 chromatography detector filter An optical filter that is used to obtain monochromatic light of a defined wavelength from detector lamps. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01121 chromatography detector filter OBI:0000593 cation trap column A cation trap column is a trap column and ion-exchange column which contains anionic cation-exchange resins. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01278 cation trap column OBI:0000594 column adapter An Adapter that enabled the connection of a column to additional devices. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01113 chromatography device column adapter OBI:0000595 pulsed amperometric detector A chromatography detector as used by high-performance anion exchange chromatography that provides sensitive and specific detection of carbohydrates. Pulsed Electrochemical Detection (PED) allows simple, sensitive, and direct detection of numerous polar aliphatic compounds, especially carbohydrates. This technique exploits the electrocatalytic activity of noble metal electrode surfaces to oxidize various polar functional groups. In PED, multi-step potential-time waveforms at Au and Pt electrodes realize amperometric/coulometric detection while maintaining uniform and reproducible electrode activity. The response mechanisms in PED are dominated by the surface properties of the electrode, and, as a consequence, members of each chemical class of compounds produce virtually identical voltammetric responses. Thus, the full potential is realized when combined with high performance liquid chromatography (HPLC). PERSON:Daniel Schober PAD WEB:<http://adsabs.harvard.edu/abs/2004SPIE.5261..103L> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01240 pulsed amperometric detector OBI:0000596 Bruker NMR instrument An NMR instrument that is manufactured by Bruker. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400198 NMR instrument Bruker NMR instrument OBI:0000597 Bruker NMR magnet An NMR magnet that is manufactured by Bruker. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400186 NMR instrument Bruker NMR magnet OBI:0000598 ozone-induced chemiluminescence detector Although there are many direct ozone chemiluminescent reactions with various gaseous molecules, the incorporation of a conversion step to convert various non-chemiluminescent analytes to a species capable of reacting with ozone to produce chemiluminescence broadens the horizon of this technique tremendously. The conversion of nearly all nitrogen- and sulfur-containing compounds to their respective chemiluminescent species for universal nitrogen and sulfur detection has made nitrogen/sulfur chemiluminescence detection the most widely used analytical methods based upon ozone-induced chemiluminescence. In addition to non-chromatographic applications, nitrogen/sulfur chemiluminescence detection has been adapted to various chromatographic techniques from gas chromatography to liquid and supercritical fluid chromatography as specialized element-specific detectors. The characteristics of these detectors are evaluated and compared to other element-selective detection techniques. The unique features of the chemiluminescence detectors have made them powerful tools in many diverse fields of analytical chemistry. PERSON:Daniel Schober WEB:<http://sangerhinxtongbr.library.ingentaconnect.com/content/els/00219673/1999/00000842/00000001/art00177> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01088 ozone-induced chemiluminescence detector OBI:0000599 tecmag NMR console An NMR console manufactured by tecmac. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400246 NMR instrument tecmag NMR console OBI:0000600 JEOL NMR instrument An NMR instrument that is manufactured by JEOL. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400226 NMR instrument JEOL NMR instrument OBI:0000601 chromatography consumable A chromatography consumable is a consumable that is used in a chromatography experiment. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01115 chromatography device chromatography consumable OBI:0000602 column frit A part of the column content that separates column packing compartments. In radial columns the packing is supported between two cylindrical frits and the gap between represents the bed height or column length. The outer frit is the column inlet and consequently the sample initially has a large area of stationary phase with which to interact. Frits are porous metal products to prevent unwanted particles from entering the chromatography system. These particles may come from the sample, the solvent or debris generated by the chromatography system itself. Such particles entering the system may lead to clogging of capillaries, interference with the chromatography by changing chromatographic parameters or disturbance of the detector function. Characteristics of a frit, besides the diameter and the thickness, is the porosity (pore distribution, density). PERSON:Daniel Schober WEB:<http://www.chromatography-online.org/topics/radial/columns.html> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01070 chromatography device column frit OBI:0000603 liquid chromatography column A liquid chromatography column is a chromatography column that is used in liquid chromatography, i.e. a column that is provided with a liquid sample mix. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01227 liquid chromatography column OBI:0000604 detector lamp A lamp used in a chromatography detector that excites sample molecules at certain frequencies / emission wavelengths, e.g. Mercury Vapor Lamp (253.7 nm), Zinc Vapor Lamp (2123.9 nm and 307.6 nm), Cadmium Vapor Lamp (228.8, 326.1,340.3, and 346.6 nm). To obtain monochromatic light an appropriate light filter would be needed. PERSON:Daniel Schober WEB:<http://www.chromatography-online.org/HPLC/UV-Detectors/Fixed-Wavelength/rs23.html> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01119 detector lamp OBI:0000605 chart recorder The chart recorder is a device that transduces signal-intensities into a graphical peak output: As the separated components of the gas sample emerge into the detector, the change in voltage in the detecting bridge circuit causes a representative peak to be drawn on a chart recorder. The position of the peak along the time axis of the chart measures the component's retention time, which identifies the component. This is directly related to carrier gas flow rate, temperature and column packing and dimensions. The area under each peak is proportional to the concentration of the component of the sample. The area of the peaks inscribed on the chart recorder can be determined by multiplying the height of the peak in mm, by the width of the peak in mm at 1/2 the peak height. The calibration curves for use with the chart recorder are therefore peak area plotted against concentration. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01069 chromatography device chart recorder OBI:0000606 open tubular column An open tubular column is a chromatography column in which the particles of the solid stationary phase or the support coated with a liquid stationary phase are concentrated on or along the inside tube wall leaving an open, unrestricted path for the mobile phase in the middle part of the tube. PERSON:Daniel Schober WEB:<http:www.iupac.org/publications/pac/1993/pdf/6504x0819.pdf> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01219 open tubular column OBI:0000607 high resolution magic angle spin probe Samples that are neither solid nor liquid, being of biological, chemical, or pharmaceutical interest, reveal highly resolved spectra when magic angle spinning is applied. The correct solution is a gradient, such that the field varies along the spinner axis. This so-called Magic Angle Gradient is employed in Brukers high resolution Magic Angle Spinning (hr-MAS) probes, and is implemented in such a way that it is compatible with the stator and does not interfere with the sample eject or insert. Bruker BioSpin has developed a series of dedicated probes for standard bore magnets to accommodate the rapidly expanding field of hr-MAS. These probes are available in double (e.g. 1H and 13C) and triple resonance (e.g. 1H, 13C, 15N) modes and come equipped with a deuterium lock channel. The probes have automatic sample ejection and insertion capability, with the availability of an optional sample changer, enabling fully automated sample runs. Probes can be equipped with an optional B0 gradient, directed along the magic angle, so that gradient spectroscopy can be done used. PERSON:Daniel Schober high resolution MAS, hr-MAS GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400192 NMR probe high resolution magic angle spin probe OBI:0000608 hydrogen generator A gas generator that generates hydrogen gas. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01035 hydrogen generator OBI:0000609 glass column A glass column is a chromatography column made out of glass that is usually used for larger scale and preparative liquid chromatography separations. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01101 glass column OBI:0000610 auto injector A gas chromatography device that can auto-inject a small number of samples an inlet. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01058 auto injector OBI:0000611 Varian NMR instrument An NMR instrument that is manufactured by Varian. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400234 NMR instrument Varian NMR instrument OBI:0000612 Bruker MATCH tube holder system The Bruker Multiple Adjustable Tube Clamp Holder MATCH system is a holder for 100 mm long NMR sample tubes with diameters ranging from micro tubes up to 5 mm NMR tubes. The MATCH insert fits into a standard 10 mm Bruker spinner and is suitable for all non-spinning applications.\n The MATCH system provides an easy and cost efficient means of optimizing the signal-to-noise ratio of each sample. By matching the NMR tube diameter to the size of the sample, most of the sample can be placed in the active column of the NMR coil. This leads to an enhanced signal detection compared to diluting the same sample quantity in a larger tube. PERSON:Daniel Schober Bruker Multiple Adjustable Tube Clamp Holder GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400211 NMR instrument Bruker MATCH tube holder system OBI:0000613 Bruker SPE-NMR platform A Solid Phase Extraction (SPE) system provides an interface between liquid chromatography (LC) and NMR. For the process of LC-SPE NMR a chromatographic separation is done and the peaks of interest are trapped on an individual SPE cartridge after the column. The peak selection is done either by UV detection or by evaluation of the on-line registered MS or MSn spectra. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400278 NMR instrument hyphenated NMR instrument platform Bruker SPE-NMR platform OBI:0000614 guard column Guard columns are installed between the injection valve and the analytical or preparative column and here will remove contaminants and prolong the lifetime of the columns. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01111 chromatography device guard column OBI:0000615 protein expression profiling Protein Expression Profiling During Chick Retinal Maturation: A Proteomics-based approach. Finnegan S, Robson JL, Wylie M, Healy A, Stitt AW, Curry WJ. Proteome Sci. 2008 Dec 10;6(1):34.PMID: 19077203 a planned process which aims to provide information about protein expression and translation activity using protein extracts collected from a material entity using a range of techniques and instrument such as Mass spectrometers, Gel electrophoresis, Western Blots, Protein microarrays Phlippe Rocca-Serra proteomic analysis OBI branch derived protein expression profiling OBI:0000616 high resolution probe with automatic tuning and matching The Automatic Tuning and Matching (ATM) option for AVANCE spectrometers is available for double resonance probes in fixed-frequency and broadband tunable configurations with either direct or indirect detection. Thus, for multinuclear operation, as often required for applications in inorganic chemistry, ATM facilitates the accurate setting of 90 degree pulse widths on both observe and decoupling channels for each chosen nucleus and each individual sample - even with full automation. Triple resonance probes in fixed-frequency configurations, as typically used for inverse detection with high-field systems. PERSON:Daniel Schober High Resolution Probes with Automatic Tuning and Matching, HR_probe_with_ATM GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400224 NMR probe high resolution probe with automatic tuning and matching OBI:0000617 fluorine-induced chemiluminescence detector A gas chromatographic detection system based on the low pressure, gas phase chemiluminescence of the reaction mixture of molecular fluorine with organo-sulfur, -selenium, and -tellurium compounds separated from (gas phase) headspace samples. This detector was originally developed in the research group of John Birks at the University of Colorado, USA and was manufactured and sold by Sievers Instruments (Boulder Colorado, USA). This system can be divided up into three parts: the chromatograph, transfer line, and reaction cell; PMT and photon counting electronics; and the molecular fluorine generator. PERSON:Daniel Schober WEB:<http://www.shsu.edu/~chm_tgc/publications/JPP/chasteen.htm> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01087 fluorine-induced chemiluminescence detector OBI:0000618 size exclusion column A size exclusion column is a chromatography column as used in size exclusion chromatography and which enables the separation of mixtures according to differrences in molecular size. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01100 size exclusion column OBI:0000619 chromatography splitter An adjustable restriction that is placed in the waste outlet to allow the necessary pressure to develop at the column inlet to force a flow (q ml/min) through the column. If the flow of mobile phase is Q ml/min then the waste flow will be (Q-q) ml/min. by adjusting the waste flow, the proportion of the sample entering the capillary column can be varied over a wide range of values and the necessary minimum permissible volume for the particular column in use can be selected for analysis. Unfortunately, the fraction taken in this way may not be representative of the original sample. This is due to the individual solutes in the mixture having different diffusivities and, thus, they distribute themselves across the sampling tube in an irregular manner. In general, the components with higher diffusivities (e.g., those solutes of lower molecular weight) will diffuse away from the bulk sample more quickly than those having lower diffusivities. PERSON:Daniel Schober WEB:<http://www.chromatography-online.org/EC-Dispersion/GC-Capillary-Columns/rs13.html> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01041 chromatography device chromatography splitter OBI:0000620 Bruker micro imaging probe For medical, biological and material sciences research, avance imaging systems provide optimal object handling and performance with a variety of samples types. Two classes of imaging probes are available: in vivo probes for handling and sustaining live objects such as animals and plants, and conventional imaging probes for materials samples. PERSON:Daniel Schober WEB:<http://www.bruker-biospin.com/probes_microimaging.html> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400225 NMR probe Bruker micro imaging probe OBI:0000621 custom made column A custom made column ia a chromatography column which is specifically tailored according to the needs of the separation as requested by a scientist or working group. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01234 custom made column OBI:0000622 gel permeation column A gel permeation column is a chromatography column which is used in gel permeation chromatography and which employs as the stationary phase a swollen gel made by polymerizing and cross-linking styrene in the presence of a diluent which is a nonsolvent for the styrene polymer. The polymer to be analyzed is introduced at the top of the column and then is elutriated with a solvent. The polymer molecules diffuse through the gel at rates depending on their molecular size. PERSON:Daniel Schober WEB:<http://composite.about.com/od/glossaries/l/bldef_g2419.htm> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01103 gel permeation column OBI:0000623 NMR spectroscopy Metabolic profiling studies on the toxicological effects of realgar in rats by (1)H NMR spectroscopy. Wei L, Liao P, Wu H, Li X, Pei F, Li W, Wu Y. Toxicol Appl Pharmacol. 2008 Nov 25. PMID: 19073202 NMR spectroscopy is a process which exploits the magnetic properties of certain nuclei (those with a spin) to resonate when placed in particular magnetic field conditions. Instruments recording NMR spectrum and sets of analysis can be used to deduce identity of chemical as well as composition of complex chemical mixtures. Philippe Rocca-Serra Nuclear magnetic resonance spectroscopy adapted from Wikipedia NMR spectroscopy OBI:0000624 Bruker SampleJet system Bruker BioSpin introduces the SampleJet, a robot for NMR tube automation. The SampleJet has been consciously designed to meet the growing customer demand for simplicity, versatility and higher throughput in NMR sample tube automation.\n The SampleJet utilizes the modern-day industry standard for sample arrangements-the 96 well plate array. Therefore, the samples may be handled by standard lab automation devices before or after the NMR measurement. PERSON:Daniel Schober WEB:<http://www.bruker-biospin.com/automation.html> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400208 NMR instrument Bruker SampleJet system OBI:0000625 JEOL ECX NMR spectrometer The ECX series of NMR spectrometers is designed for any laboratory needing an easy-to-use, reliable, routine NMR system. The ECX NMR series is available from 300 to 500 MHz. The console is designed around a modular, digital NMR electronics chassis controlled by an intelligent acquisition computer. For unprecedented flexibility, the JEOL NMR system offers a Windows XP, Mac OSX or LINUX. Both the workstation and spectrometer may be connected to a standard network, allowing seamless remote operation anywhere in the world. PERSON:Daniel Schober WEB:<http://www.jeol.com/PRODUCTS/AnalyticalInstruments/NuclearMagneticResonance/ECX/tabid/145/Default.aspx> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400227 NMR instrument JEOL ECX NMR spectrometer OBI:0000626 DNA sequencing Genomic deletions of OFD1 account for 23% of oral-facial-digital type 1 syndrome after negative DNA sequencing. Thauvin-Robinet C, Franco B, Saugier-Veber P, Aral B, Gigot N, Donzel A, Van Maldergem L, Bieth E, Layet V, Mathieu M, Teebi A, Lespinasse J, Callier P, Mugneret F, Masurel-Paulet A, Gautier E, Huet F, Teyssier JR, Tosi M, Frébourg T, Faivre L. Hum Mutat. 2008 Nov 19. PMID: 19023858 DNA sequencing is a sequencing process which uses deoxyribonucleic acid as input and results in a the creation of DNA sequence information artifact using a DNA sequencer instrument. Philippe Rocca-Serra OBI Branch derived nucleotide sequencing DNA sequencing OBI:0000627 quaternary pump system A pump system that pump and mix up to four different solvents in parallel. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01047 quaternary pump system OBI:0000628 carbon nanotube column Carbon nanotubes (CNTs) are known to have high thermal and mechanical stability and have the potential to be high-performance separation media that utilize the nanoscale interactions. CNT can be applied in long capillary tubes for the development of gas chromatography columns. A film of CNTs can be deposited by chemical vapor deposition (CVD) to form the stationary phase in the open tubular format. Altering the CVD conditions can vary the thickness and the morphology of the CNT film, which opens the possibility of selectivity tuning. The ability to fabricate long tubes coated with CNTs can be readily employed in other gas- and liquid-phase separations as well. PERSON:Daniel Schober WEB:<http://pubs.acs.org/cgi-bin/abstract.cgi/ancham/2005/77/i21/abs/ac050812j.html> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01107 carbon nanotube column OBI:0000629 Bruker solid magic angle spinning probe Magic angle spinning, nowadays a routine technique for solids NMR, still offers the capability of innovation. The high mechanical performance of MAS probes in conjunction with efficient rf pulse techniques open new exciting fields in solids NMR of biological samples and in the field of quadrupolar nuclei. PERSON:Daniel Schober solid MAS probe GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400193 NMR probe Bruker solid magic angle spinning probe OBI:0000630 hematology Co-associations between insulin sensitivity and measures of liver function, subclinical inflammation, and hematology. Godsland IF, Johnston DG. Metabolism. 2008 Sep;57(9):1190-7. PMID: 18702943 hematology is a process studying blood and blood producing organs relying on a variety of techniques and instruments Philippe Rocca-Serra blood analysis, haematology OBI branch derived hematology OBI:0000631 Varian MERCURY spectrometer MERCURYplus spectrometers provide superior control, stability, and performance for high-productivity environments. Surface-mount electronics enable a small footprint without compromising data quality. Modular design allows flexible configuration. Direct digital synthesis, linear amplifiers, and other innovative RF and digital technologies enable push-button operation. PERSON:Daniel Schober WEB:<http://www.varianinc.com/cgi-bin/nav?varinc/docs/products/NMR/spectromet/mercury/index&cid=975JINLIKLRMPGLMNOILJ> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400235 NMR instrument Varian MERCURY spectrometer OBI:0000632 Bruker Metabolic Profiler An NMR platform for conducting metabonomics studies, traditional metabolism studies, and analysis of complex mixtures, featuring an Avance NMR spectrometer and a microTOF from Bruker Daltonics. By combining the structural resolving power of NMR with mass accuracy of the microTOF Bruker offers a complete system for metabolic research. The Metabolic Profiler provides a simple, easy to use and inexpensive base-system to acquire the spectroscopic data, needed to do basic metabolic profiling including metabonomic statistical analysis. PERSON:Daniel Schober WEB:<http://www.bruker-biospin.com/metabolicprofiler.html> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400199 NMR instrument hyphenated NMR instrument platform Bruker Metabolic Profiler OBI:0000633 column heater The glass liner can be fitted with a separate heater and the volatilization temperature can, thus, be controlled. This flash heater system is available in most chromatographs. By using a syringe with a long needle, the tip can be made to penetrate past the liner and discharge its contents directly into the column packing. This procedure is called 'on-column injection' and, as it reduces peak dispersion on injection and thus, provides higher column efficiencies, is often the preferred procedure. PERSON:Daniel Schober WEB:<http://www.chromatography-online.org/GC/Injection-Devices/Open-Tubular-Column/rs15.html> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01040 column heater OBI:0000634 DNA methylation profiling assay Genome-wide, high-resolution DNA methylation profiling using bisulfite-mediated cytosine conversion. Reinders J, Delucinge Vivier C, Theiler G, Chollet D, Descombes P, Paszkowski J. Genome Res. 2008 Mar;18(3):469-76. Epub 2008 Jan 24. PMID: 18218979 an assay which aims to provide information about state of methylation of DNA molecules using genomic DNA collected from a material entity using a range of techniques and instrument such as DNA sequencers and often relying on treatment with bisulfites to ensure cytosine conversion. Philippe Rocca-Serra OBI branch derived DNA methylation profiling DNA methylation profiling assay OBI:0000635 JEOL CapNMR probe The JEOL ECA and ECX NMR spectrometers now support the MRM/Protasis CapNMR Probe for well plate-based and microvial-based NMR analysis. The CapNMR probe is available at proton frequencies ranging from 300 MHz to 800 MHz in both indirect configurations (e.g. 1H{13C} and 1H {31P}) and also in triple resonance configurations (e.g. 1H{13C, 15N}, 1H{31P, 15N}). Both employ a high-strength z-directed field gradient. The flowprobes come with the choice of two flowcell volumes: a 5 μl flowcell with an NMR active volume of 2.5 μl, and a 10 μl flowcell with an NMR active volume of 5 μl. The fluidic connections are 75 μm i.d. and 1/32 o.d. FEP Teflon with hastelloy unions for exceptional solvent compatibility. PERSON:Daniel Schober WEB:<http://www.jeol.com/PRODUCTS/AnalyticalInstruments/NuclearMagneticResonance/CapNMRProbe/tabid/396/Default.aspx> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400233 NMR probe JEOL CapNMR probe OBI:0000636 acquisition computer A Computer used for NMR, can be divided into central processing unit (CPU), consisting of instruction, interpretation and arithmetic unit plus fast access memory, and peripheral devices such as bulk data storage and input and output devices (including, via the interface, the spectrometer). Under software control, the computer controls the RF pulses and gradients necessary to acquire data, and process the data to produce spectra or images. Note that devices such as the spectrometer may themselves incorporate small computers. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400013 NMR instrument acquisition computer OBI:0000637 gas chromatography detector A gas chromatography detector is a chromatography detector that locates in the dimensions of space and time, the positions of the components of a mixture that has been subjected to a gas chromatographic process and thus permits the senses to appreciate the nature of the separation. There is no LC detector that has an equivalent performance to the flame ionization detector (FID) used in GC. In general, LC detectors have sensitivities of two to three orders of magnitude less than their GC counterparts and linear dynamic ranges one to two orders of magnitude lower. Only highly specific LC detectors have sensitivities that can approach those of GC detectors. PERSON:Daniel Schober FID WEB:<http://www.chromatography-online.org/GC-Detectors/Classification/rs1.html> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01083 chromatography detector, defined class/xps gas chromatography detector OBI:0000638 gas purifier Gas purifiers are instruments used for the removal of gas impurities like hydrocarbons, oxygen, and moisture from carrier gas and fuel gases for GC or GC-MS systems. PERSON:Daniel Schober WEB:<http://www.sigmaaldrich.com/Area_of_Interest/Analytical__Chromatography/Gas_Chromatography/Accessories/SGT_Gas_Purifier.html> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01036 gas chromatography equipment gas purifier OBI:0000639 material separation objective The objective to obtain multiple aliquots of an enzyme preparation. The objective to obtain cells contained in a sample of blood. is an objective to transform a material entity into spatially separated components. PPPB branch PPPB branch material separation objective OBI:0000640 indirect detection probe An NMR probe designed to allow the indirect detection of acquisition nuclei. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400281 NMR device indirect detection probe OBI:0000641 JEOL ECA NMR spectrometer The ECA series of NMR spectrometers is a high performance, research grade NMR system configurable to a wide range off applications. The ECA NMR is available from 300 to 930 MHz field strengths and is 1GHz ready. The system is designed around a modular, digital NMR electronics chassis controlled from a UNIX or Windows workstation and acquisition system. Both the workstation and spectrometer may be connected to a standard network, allowing seamless remote operation anywhere in the world. PERSON:Daniel Schober WEB:<http://www.jeol.com/PRODUCTS/AnalyticalInstruments/NuclearMagneticResonance/ECA/tabid/146/Default.aspx> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400228 NMR instrument JEOL ECA NMR spectrometer OBI:0000642 atomic emission detector Instead of measuring simple gas phase (carbon containing) ions created in a flame as with the flame ionization detector, or the change in background current because of electronegative element capture of thermal electrons as with the electron capture detector, the AED has a much wider applicability because it is based on the detection of atomic emissions. The strength of the AED lies in the detector's ability to simultaneously determine the atomic emissions of many of the elements in analytes that elute from a GC capillary column (called eluants or solutes in some books). As eluants come off the capillary column they are fed into a microwave powered plasma (or discharge) cavity where the compounds are destroyed and their atoms are excited by the energy of the plasma. The light that is emitted by the excited particles is separated into individual lines via a photodiode array. The associated computer then sorts out the individual emission lines and can produce chromatograms made up of peaks from eluants that contain only a specific element. PERSON:Daniel Schober AED WEB:<http://elchem.kaist.ac.kr/vt/chem-ed/sep/gc/detector/aed.htmt> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01086 atomic emission detector OBI:0000648 clustered data set A clustered data set is the output of a K means clustering data transformation A data set that is produced as the output of a class discovery data transformation and consists of a data set with assigned discovered class labels. PERSON: James Malone PERSON: Monnie McGee data set with assigned discovered class labels AR thinks could be a data item instead clustered data set OBI:0000649 data set of features A data set that is produced as the output of a descriptive statistical calculation data transformation and consists of producing a data set that represents one or more features of interest about the input data set. PERSON: James Malone PERSON: Monnie McGee data set of features OBI:0000650 differential expression analysis data transformation A differential expression analysis data transformation is a data transformation that has objective differential expression analysis and that consists of James Malone Melanie Courtot Monnie McGee WEB: differential expression analysis data transformation OBI:0000651 urine specimen a portion of urine collected from an organism 4/10/2011BP: It seems to me that the editor notes refer to a previous version, and are no longer relevant. This could be instead a kind of collection of secreted stuff. Among secreted stuff there is passive, and active. urine is secreted, passiv. lavage is secreted, active are we happy calling collection of urine a material separation? urine specimen OBI:0000652 material combination Mixing two fluids. Adding salt into water. Injecting a mouse with PBS. is a material processing with the objective to combine two or more material entities as input into a single material entity as output. created at workshop as parent class for 'adding material into target', which is asymmetric, while combination encompasses all addition processes. bp bp material combination OBI:0000653 fuzzy clustering objective A fuzzy clustering objective is a data transformation objective where the aim is to assign input objects (typically vectors of attributes) a probability that a point belongs to a class, where the number of class and their specifications are not known a priori. James Malone PERSON: James Malone PERSON: Ryan Brinkman fuzzy clustering objective OBI:0000654 device setting Examples, 300V for 4 hours, 200mvolts, 37degrees.A knob set a 300 V is the device setting, the protocol stating to set the instrument to 300V is a device setting specification a quality inheres_in some device and is concretization of some (device_setting_specification and is_about a quality of the device PERSON: Frank Gibson device setting OBI:0000655 blood specimen blood drawn from a human for glucose assay a material entity derived from a portion of blood collected from an organism Bjoern Peters Bjoern Peters blood specimen OBI:0000656 data set of predicted values according to fitted curve A data set which is the output of a curve fitting data transformation in which the aim is to find a curve which matches a series of data points and possibly other constraints. PERSON: James Malone PERSON: Monnie McGee data set of predicted values according to fitted curve OBI:0000658 data representational model gene regulatory graph model phylogenetic tree protein interaction network Data representational model is an information content entity of the relationships between data items. A data representational model is encoded in a data format specification such as for cytoscape or biopax. Melanie Courtot data structure data structure specification GROUP: OBI 2009-02-28: work on this term has been finalized during the OBI workshop winter 2009 data representational model OBI:0000659 specimen collection process drawing blood from a patient for analysis, collecting a piece of a plant for depositing in a herbarium, buying meat from a butcher in order to measure its protein content in an investigation A planned process with the objective of collecting a specimen. Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. Philly2013: A specimen collection can have as part a material entity acquisition, such as ordering from a bank. The distinction is that specimen collection necessarily involves the creation of a specimen role. However ordering cell lines cells from ATCC for use in an investigation is NOT a specimen collection, because the cell lines already have a specimen role. Philly2013: The specimen_role for the specimen is created during the specimen collection process. label changed to 'specimen collection process' on 10/27/2014, details see tracker: http://sourceforge.net/p/obi/obi-terms/716/ Bjoern Peters specimen collection 5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession 6/9/09: used at workshop specimen collection process OBI:0000660 background corrected data set A data set that is produced as the output of a background correction data transformation. PERSON: James Malone PERSON: Melanie Courtot background corrected data set OBI:0000661 enzyme-linked immunosorbent assay 1) Detection of IL-2 (analyte) in a cell supernatant (evaluant), using plate bound anti IL-2 antibodies, and a reporter enzyme-linked reporter antibody. 2) Measurement of IgG antibody (analyte) titer in a serum sample (evaluant) using plate bound antigen and a reporter anti-IgG antibody. An analyte assay where binding of an enzyme linked antibody to a material entity that is immobilized on solid support is detected utilizing a chemiluminescent reaction. Depending on the setup, the enzyme-linked antibody could be binding directly to the analyte, or it serves as a secondary antibody detecting binding of the primary antibody to the analyte. IEDB ELISA IEDB enzyme-linked immunosorbent assay OBI:0000662 error corrected data set A data set that is produced as the output of an error correction data transformation and consists of producing a data set which has had erroneous contributions from the input to the data transformation removed (corrected for). PERSON: James Malone PERSON: Monnie McGee error corrected data set OBI:0000663 class prediction data transformation A class prediction data transformation (sometimes called supervised classification) is a data transformation that has objective class prediction. James Malone supervised classification data transformation PERSON: James Malone class prediction data transformation OBI:0000664 BrdU incorporation assay The measurement of T cell proliferation as a response to a viral peptide by culturing T cells stimulated with APCs and peptide in the presence of BrdU. A cell proliferation assay in which cells are cultured in the presence of BrdU which is incorporated into newly synthesized DNA of replicating cells (during the S phase of the cell cycle), substituting for thymidine during DNA replication, which can be quantified by BrdU specific antibodies. IEDB IEDB BrdU incorporation assay OBI:0000665 obsolete intracellular cytokine staining assay Permeabilizing T cells and staining them with fluorescent labeled anti-IFN-gamma antibodies The measurement of cytokines within the cytoplasm of a cell by permeabilizing the cell membrane to allow entry of specific antibodies, and counting the stained cells using a flow cytometer. IEDB ICS ICCS IEDB intracellular cytokine staining (ICS) obsolete intracellular cytokine staining assay true OBI:0000666 background correction data transformation A background correction data transformation (sometimes called supervised classification) is a data transformation that has the objective background correction. James Malone PERSON: James Malone background correction data transformation OBI:0000667 obsolete MHC multimer staining assay Measuring T cells that are specific for the SYFPEITHI peptide when presented by the murine MHC molecule H-2 Kd by staining them with a tetramer of peptide loaded MHC complexes. An MHC multimer assay is an assay that detects T cells capable of binding the MHC:ligand complexes present in the multimer. The multimer is fluorescently labelled. The T cells bound to multimers are counted in a flow cytometer IEDB MHC tetramer assay IEDB MHC tetramer/multimer staining obsolete MHC multimer staining assay true OBI:0000668 error correction data transformation An error correction data transformation is a data transformation that has the objective of error correction, where the aim is to remove (correct for) erroneous contributions from the input to the data transformation. James Malone Monnie McGee EDITORS error correction data transformation OBI:0000669 tritiated thymidine incorporation assay The measurement of T cell proliferation as a response to a viral peptide by culturing T cells stimulated with APCs and peptide in the presence of tritiated thymidine, and using a scintillation counter to detect the radioactivity. A cell proliferation assay in which cells are cultured in the presence of tritiated thymidine which is incorporated into newly synthesized DNA of replicating cells (during the S phase of the cell cycle). The radioactivity of tritiated thymidine in a cell is a proxy for cells that were actively replicating. IEDB IEDB tritiated thymidine incorporation assay OBI:0000671 sample from organism a material obtained from an organism in order to be a representative of the whole 5/29: This is a helper class for now we need to work on this: Is taking a urine sample a material separation process? If not, we will need to specify what 'taking a sample from organism' entails. We can argue that the objective to obtain a urine sample from a patient is enough to call it a material separation process, but it could dilute what material separation was supposed to be about. sample from organism OBI:0000673 statistical hypothesis test A statistical hypothesis test data transformation is a data transformation that has objective statistical hypothesis test. James Malone PERSON: James Malone statistical hypothesis test OBI:0000674 center value A data item that is produced as the output of a center calculation data transformation and represents the center value of the input data. PERSON: James Malone PERSON: Monnie McGee median center value OBI:0000675 statistical hypothesis test objective is a data transformation objective where the aim is to estimate statistical significance with the aim of proving or disproving a hypothesis by means of some data transformation James Malone Person:Helen Parkinson hypothesis test objective WEB: http://en.wikipedia.org/wiki/Statistical_hypothesis_testing statistical hypothesis test objective OBI:0000676 reduced dimension data set A data set that is produced as the output of a data vector reduction data transformation and consists of producing a data set which has fewer vectors than the input data set. PERSON: James Malone PERSON: Monnie McGee reduced dimension data set OBI:0000678 portioning objective The objective to obtain multiple aliquots of an enzyme preparation. A material separation objective aiming to separate material into multiple portions, each of which contains a similar composition of the input material. portioning objective OBI:0000679 average value A data item that is produced as the output of an averaging data transformation and represents the average value of the input data. PERSON: James Malone PERSON: Monnie McGee arithmetic mean average value OBI:0000680 whole organism preparation putting a mouse in the blender. Not: putting a mouse on a scale A material entity which is the output of a process in which one or more whole organisms are prepared in a way to make it easier to study them, and in which the great majority of organismal parts are maintained does this include injecting a dye to a patient to be able to visualize parts of his brain? If not, we should state that the components of the organism are substantially re-arranged. whole organism preparation OBI:0000681 separation into different composition objective The objective to obtain cells contained in a sample of blood. A material separation objective aiming to separate a material entity that has parts of different types, and end with at least one output that is a material with parts of fewer types (modulo impurities). We should be using has the grain relations or concentrations to distinguish the portioning and other sub-objectives separation into different composition objective OBI:0000682 obsolete_study result Study result is an information content entity that is a specified data output of a study. GROUP: OBI 2009-02-28: work on this term has been finalized during the OBI workshop winter 2009 obsolete_study result true OBI:0000684 specimen collection objective The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient. A objective specification to obtain a material entity for potential use as an input during an investigation. Bjoern Peters Bjoern Peters specimen collection objective OBI:0000685 creating a mixture of molecules in solution The production of PBS is a process with the objective to prepare a liquid solution of one or more chemicals at desired concentrations. Bjoern Peters PERSON: Helen Parkinson creating a mixture of molecules in solution OBI:0000686 material combination objective is an objective to obtain an output material that contains several input materials. PPPB branch bp material combination objective OBI:0000687 nucleotide overhang cloning Cloning vectors are commercially available and supplied in linearized form with 3' dT overhangs Nucleotide overhang cloning is the process of inserting nucleic acid into a vector using nucleotide overhangs used to prevent self ligation Helen Parkinson nucleotide overhang cloning OBI:0000688 rodent care protocol Keeping mice in the UCSD animals facility at 20 - 25 degrees celsius, in cages of 4 animals each and providing food twice daily. A rodent care protocol is an animal protocol in which the animals being taken care of are rodents. Bjoern Peters Bjoern Peters rodent care protocol OBI:0000689 454 Genome Sequence 20 PMID: 18946007.Pyrosequencing analysis of the oral microflora of healthy adults. Keijser BJ, Zaura E, Huse SM, van der Vossen JM, Schuren FH, Montijn RC, ten Cate JM, Crielaard W. J Dent Res. 2008 Nov;87(11):1016-20. is a DNA sequencer which is manufactured by 454 Life Science Corporation and enables pyrosequencing to be performed. It comprises both optics and fluidics subsystems, which are controlled by a computer subsystem. The fluidics subsystem ensures accurate reagent dispensing. It consists of a reagents cassette (which holds the reagent containers), a sipper manifold, pumps, valves, and debubblers. The fluidics subsystem flows the sequencing reagents across the wells of the PicoTiterPlate device, and moves the spent reagents from the PicoTiterPlate device to the waste receptacle. The optics subsystem consists of a CCD camera and a camera controller. The camera captures the light emitted in the wells of the PicoTiterPlate device during each step of the sequencing cycle, and sends the digital images to the computer subsystem for processing. The computer controls the other Sequencer subsystems, and processes the digital images sent by the camera to extract the DNA sequence information. Philippe Rocca-Serra GS 20 454 Genome Sequence 20 OBI:0000690 immunoprecipitation PMID: 19419533. Arabidopsis RNA immunoprecipitation. Terzi LC, Simpson GG. Plant J. 2009 Jul;59(1):163-8. is a process which realizes a material separation objective by relying on antibodies to specifically binding to material entity Philippe Rocca-Serra OBI plan and planned process branch immunoprecipitation OBI:0000691 ABI 377 automated sequencer is a DNA sequencer which is manufactured by Applied Biosystems corporation (formerly Perkin-Elmer). It allows automated chain termination DNA sequencing. It has part polyacrylamide gel electrophoresis system and a laser -based detection system to detect fluorescence intensity emitted by the dyes attached to the dideoxyterminator nucleotides or to the primers. Philippe Rocca-Serra Applied Biosystems ABI 377 automated sequencer OBI:0000692 recombination enzyme based cloning a recombination enzyme based cloning is a recombinant vector cloning process that uses complementary nucleotide sequences in both the insert genetic material and the cloning vector with a recombination enzyme to directly create a recombinant vector recombination enzyme based cloning OBI:0000693 MeDIP-seq assay PMID: 18612301. A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Down TA, Rakyan VK, Turner DJ, Flicek P, Li H, Kulesha E, Gräf S, Johnson N, Herrero J, Tomazou EM, Thorne NP, Bäckdahl L, Herberth M, Howe KL, Jackson DK, Miretti MM, Marioni JC, Birney E, Hubbard TJ, Durbin R, Tavaré S, Beck S. Nat Biotechnol. 2008 Jul;26(7):779-85. is an assay which aims at identifying methylated sites in genomic DNA and determining methylation pattern that affect gene transcription by relying on immunoprecipitation of methylated genomic DNA, creation of a library of corresponding DNA fragments (either single or paired-end fragments) and subsequent sequencing using parallelized sequencing methods. Philippe Rocca-Serra Methylated DNA immunoprecipitation sequencing assay adapted from wikipedia MeDIP-seq assay OBI:0000694 animal feeding giving crickets to a snake. animal feeding is a process in which animals are provided with food In an investigation, this will typically be part of an animal care process Bjoern Peters branch derived animal feeding OBI:0000695 chain termination sequencing PMID: 271968. DNA sequencing with chain-terminating inhibitors. Sanger F, Nicklen S, Coulson AR. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463-7. is a DNA sequencing which rely on the use of dideoxynucleotides used in 4 distinct sequencing reaction on the same DNA sample. The dideoxynucleotides, once incorporated in the complementary DNA strand being synthesized by the DNA polymerase prevent any further chain elongation. The newly generated sequences are resolved on a polyacrylamide gel using electrophoresis and labels (either fluorochrome or radioactivity) are used to determine the nucleotide present at a given position Philippe Rocca-Serra Sanger sequencing dye terminator sequencing adapted from wikipedia chain termination sequencing OBI:0000696 AB SOLiD System PMID: 19336255. RNA-Seq-quantitative measurement of expression through massively parallel RNA-sequencing. Wilhelm BT, Landry JR. Methods. 2009 Jul;48(3):249-57. is a DNA sequencer which is manufactured by Applied Biosystems and which enable DNA sequencing by ligation Philippe Rocca-Serra Applied Biosystems AB SOLiD System OBI:0000697 Helicos sequencing PMID: 18388294. Single-molecule DNA sequencing of a viral genome. Harris TD, Buzby PR, Babcock H, Beer E, Bowers J, Braslavsky I, Causey M, Colonell J, Dimeo J, Efcavitch JW, Giladi E, Gill J, Healy J, Jarosz M, Lapen D, Moulton K, Quake SR, Steinmann K, Thayer E, Tyurina A, Ward R, Weiss H, Xie Z. Science. 2008 Apr 4;320(5872):106-9. is a DNA sequencing which allows sequence identification of billions of DNA molecules immobilized to a surface by using DNA polymerase and fluorescently labeled nucleotides added one at a time. The sequencing process does not requires amplification step and is typically able to produce reads of 25 base pair length. Philippe Rocca-Serra true single molecule sequencing adapted from wikipedia Helicos sequencing OBI:0000698 obsolete_DNA ligase A DNA ligase is an enzyme that covalently joins two compatible pieces of DNA through the cleavage of an ATP molecule 5/22 Need to explore if there are GO / other classes exist that capture this. We need it now for cloning experiments replaced by imported PRO: DNA ligase Kevin Clancy, Bjoern Peters ligase obsolete_DNA ligase true OBI:0000699 survival assessment Survival assessment is an assay that measures the occurrence of death events in one or more organisms that are monitored over time Need to point out more specifically that survival / death is measured. survival assessment OBI:0000700 support vector machine A support vector machine is a data transformation with a class prediction objective based on the construction of a separating hyperplane that maximizes the margin between two data sets of vectors in n-dimensional space. James Malone Ryan Brinkman SVM PERSON: Ryan Brinkman support vector machine OBI:0000701 self-organizing map A self-organizing map (SOM) is an artificial neural network with objective class discovery that uses a neighborhood function to preserve the topological properties of a dataset to produce low-dimensional (typically 2) discretized representation of the training data set. A set of artificial neurons learn to map points in an input space to coordinates in an output space. The input space can have different dimensions and topology from the output space, and the SOM will attempt to preserve these. James Malone Ryan Brinkman SOM PERSON: Ryan Brinkman self-organizing map OBI:0000702 454 Genome Sequencer FLX PMID: 18616967. The Genome Sequencer FLX System--longer reads, more applications, straight forward bioinformatics and more complete data sets. Droege M, Hill B. J Biotechnol. 2008 Aug 31;136(1-2):3-10. is a DNA sequencer which is manufactured by 454 Life Science Corporation and enables pyrosequencing to be performed. It comprises both optics and fluidics subsystems, which are controlled by a computer subsystem. The fluidics subsystem ensures accurate reagent dispensing. It consists of a reagents cassette (which holds the reagent containers), a sipper manifold, pumps, valves, and debubblers. The fluidics subsystem flows the sequencing reagents across the wells of the PicoTiterPlate device, and moves the spent reagents from the PicoTiterPlate device to the waste receptacle. The optics subsystem consists of a CCD camera and a camera controller. The camera captures the light emitted in the wells of the PicoTiterPlate device during each step of the sequencing cycle, and sends the digital images to the computer subsystem for processing. The computer controls the other Sequencer subsystems, and processes the digital images sent by the camera to extract the DNA sequence information. Philippe Rocca-Serra 454 GS FLX GS-FLX adapted from https://www.roche-applied-science.com/servlet/RCProductDisplay?langId=-1&storeId=10202&productId=3.8.8.1.1.3&catalogId=10202&krypto=mgV8a0Sdps6%2BCXU8IoddmzNEyGgjde9j8MOFCiMzRsduELeenAlVZ%2FE1QR%2BxLpzNlqMZPLRHqaI%3D&ddkey=https:RCProductDisplay 454 Genome Sequencer FLX OBI:0000703 Illumina Genome Analyzer II PMID: 19336255. RNA-Seq-quantitative measurement of expression through massively parallel RNA-sequencing. Wilhelm BT, Landry JR.Methods. 2009 Jul;48(3):249-57. is a DNA sequence which is manufactured by Illumina (Solexa) corporation. it support sequencing of single or paired end clone libraries relying on sequencing by synthesis technology Philippe Rocca-Serra Illumina Corporation Illumina Genome Analyzer II OBI:0000704 decision tree induction objective A decision tree induction objective is a data transformation objective in which a tree-like graph of edges and nodes is created and from which the selection of each branch requires that some type of logical decision is made. James Malone decision tree induction objective OBI:0000705 Edman degradation Determination of the amino acid sequence of a peptide eluted from HLA-DRB1*04:01 to be VYPEVTVYPAKT. A sequencing assay in which the amino acid sequence of input peptides or proteins is determined by iteratively cleaving of the amino-terminal (N-terminal) residue without disrupting the peptide bonds and identifying it by e.g. chromatography or electropheresis. IEDB IEDB Edman degradation OBI:0000706 SOLiD sequencing PMID: 19119315. High-resolution analysis of the 5'-end transcriptome using a next generation DNA sequencer. Hashimoto S, Qu W, Ahsan B, Ogoshi K, Sasaki A, Nakatani Y, Lee Y, Ogawa M, Ametani A, Suzuki Y, Sugano S, Lee CC, Nutter RC, Morishita S, Matsushima K. PLoS One. 2009;4(1):e4108. is a DNA sequencing which allows sequence identification by relying on the following steps: 1. Primers hybridize to the P1 adapter sequence within the library template. 2. A set of four fluorescently labeled di-base probes compete for ligation to the sequencing primer. Specificity of the di-base probe is achieved by interrogating every 1st and 2nd base in each ligation reaction. 3. Multiple cycles of ligation, detection and cleavage are performed with the number of cycles determining the eventual read length. 4. Following a series of ligation cycles, the extension product is removed and the template is reset with a primer complementary to the n-1 position for a second round of ligation cycles Philippe Rocca-Serra adapted from Wikipedia and Applied Biosystems web site SOLiD sequencing OBI:0000707 decision tree building data transformation A decision tree building data transformation is a data transformation that has objective decision tree induction. James Malone PERSON: James Malone decision tree building data transformation OBI:0000708 laboratory animal care a process that realizes an animal care protocol that specifies how animals are kept and maintained laboratory animal care OBI:0000709 yeast artificial chromosome vector a double-stranded DNA that was engineered to contain a yeast origin of replication, encodes for a selectable gene product, contains a cloning site, and has yeast telomerase sequences this should be a child of 'chromosome' if we import that from another source Kevin Clancy, Bjoern Peters YAC yeast artificial chromosome vector OBI:0000710 Li-Cor 4300 DNA Analysis System is a DNA sequencer which is manufactured by Li-Cor corporation and enable automated chain termination based DNA sequencing Philippe Rocca-Serra OBI and Li-Cor Li-Cor 4300 DNA Analysis System OBI:0000711 library preparation PMID: 19570239. Construction and analysis of cotton (Gossypium arboreum L.) drought-related cDNA library. Zhang L, Li FG, Liu CL, Zhang CJ, Zhang XY. BMC Res Notes. 2009 Jul 2;2:120. is a process which results in the creation of a library from fragments of DNA using cloning vectors or oligonucleotides with the role of adaptors. Philippe Rocca-Serra library construction library preparation OBI:0000712 pathogen challenge A pathogen challenge is the administration of a live pathogenic organism to a host pathogen challenge OBI:0000713 GenePattern software a software that provides access to more than 100 tools for gene expression analysis, proteomics, SNP analysis and common data processing tasks. James Malone Person:Helen Parkinson WEB: http://www.broadinstitute.org/cancer/software/genepattern/ GenePattern software OBI:0000714 graph of vertices For example, if the nodes are cities, then the edges may have numerical values that correspond to the distances between the cities. A construct that consists of many nodes connected with edges. The edges represent a relationship between the objects represented by the nodes. A graph can be equivalently represented as a matrix. Bjoern Peters Chris Stoeckert James Malone WEB: http://mitpress.mit.edu/books/FLAOH/cbnhtml/glossary-G.html graph of vertices OBI:0000715 animal care protocol Keeping mice in the UCSD animals facility at 20 - 25 degrees celsius, in cages of 4 animals each and providing food twice daily. An animal care protocol is a protocol which specifies the environment in which animals are being kept in captivity for research purposes Bjoern Peters Bjoern Peters animal care protocol OBI:0000716 ChIP-seq assay PMID: 19275939 ChIP-seq: using high-throughput sequencing to discover protein-DNA interactions. Schmidt D, Wilson MD, Spyrou C, Brown GD, Hadfield J, Odom DT. Methods. 2009 Jul;48(3):240-8. Epub 2009 Mar 9. an assay which aims at identifying protein binding sites in genomic DNA and determining how protein may regulate gene transcription by relying on immunoprecipitation of DNA bound protein, creation of a library of corresponding DNA fragments (either single or paired-end fragments) and subsequent sequencing using parallelized sequencing methods. Philippe Rocca-Serra chromatin immunoprecipitation sequencing assay adapted from Wikipedia made some modification based on the discussion on 2011/4/4 obi dev call, using DNA sequencing instead of union of some specific DNA sequencing processes ChIP-seq assay OBI:0000717 HeliScope Single Molecule Sequencer is a DNA sequencer manufacturer by Helicos Corporation to carry out Single Molecule sequencing using reversible termination chemistry Philippe Rocca-Serra HeliScope Single Molecule Sequencer OBI:0000718 pathogen role Pathogen: An agent of disease. A disease producer. The term pathogen most commonly is used to refer to infectious organisms. These include bacteria (such as staph), viruses (such as HIV), and fungi (such as yeast). Less commonly, pathogen refers to a noninfectious agent of disease such as a chemical. http://www.medterms.com/script/main/art.asp?articlekey=6383 pathogen role is a role which inheres in an organism and realized in the process of disease course in the organism bearing host role caused by the organism bearing pathogen role GROUP: Role Branch OBI 6 April 2009: from the Vaccine Community pathogen role OBI:0000719 vaccine preparation The production of B. pertussis vaccine. vaccine preparation is a planned process with specified output a vaccine OBI vaccine preparation OBI:0000720 immunologic adjuvant role Adjuvants are pharmacological or immunological agents that modify the effect of other agents (e.g., drugs, vaccines) while having few if any direct effects when given by themselves. http://en.wikipedia.org/wiki/Adjuvant The role a material entity plays when it is co-administered with an immunogen in order to enhance the immune response to the immunogen. 11Feb09:Vaccine Ontology Definition: Adjuvant boosts immune response of a vaccine or antigen in the host. the role 'adjuvant role' inheres in some 'material entity' and is realized by some 'immune response assay'. GROUP: Role branch Vaccine Ontology, Wikipedia, OBI Renamed from adjuvent role, to be a more specific useage for immunology, tracker https://sourceforge.net/tracker/?func=detail&atid=886178&aid=2887909&group_id=177891 immunologic adjuvant role OBI:0000721 glucose tolerance test PMID: 19527607 Using the 100-g Oral Glucose Tolerance Test to Predict Fetal and Maternal Outcomes in Women with Gestational Diabetes Mellitus. Lin CH, Wen SF, Wu YH, Huang MJ. Chang Gung Med J. 2009 May-Jun;32(3):283-9. is a process in which following administration of a bolus a glucose in-vivo, glucose clearance from blood plasma is monitored over time by repeated glucose measurement in blood serum. the output of a process is a measure which can be used to evaluate the severity of insulin resistance or the efficiency of glucose clearance. 30-10-2013:[author: PRS] removing "realizes some (concretizes some 'time series design')" axiom as it causes 'gtt' to be classified under study design execution instead of assay Philippe Rocca-Serra NuGO OBI plan branch glucose tolerance test OBI:0000722 paired-end library PMID: 19339662. Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses. Genome Res. 2009 Apr;19(4):521-32. Fullwood MJ, Wei CL, Liu ET, Ruan Y. is a collection of short paired tags from the two ends of DNA fragments are extracted and covalently linked as ditag constructs Philippe Rocca-Serra mate-paired library paired-end tag (PET) library adapted from information provided by Solid web site paired-end library OBI:0000723 DNA sequencing by ligation PMID: 19546169. Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two base encoding. McKernan KJ, Peckham HE, Costa G, McLaughlin S, Tsung E, Fu Y, Clouser C, Dunkan C, Ichikawa J, Lee C, Zhang Z, Sheridan A, Fu H, Ranade S, Dimilanta E, Sokolsky T, Zhang L, Hendrickson C, Li B, Kotler L, Stuart J, Malek J, Manning J, Antipova A, Perez D, Moore M, Hayashibara K, Lyons M, Beaudoin R, Coleman B, Laptewicz M, Sanicandro A, Rhodes M, De La Vega F, Gottimukkala RK, Hyland F, Reese M, Yang S, Bafna V, Bashir A, Macbride A, Aklan C, Kidd JM, Eichler EE, Blanchard AP. Genome Res. 2009 Jun 22. is a DNA sequencing which relies on DNA ligase activity to perform chain extension during the sequencing reaction step. PERSON: Philippe Rocca-Serra DNA sequencing by ligation OBI:0000724 Solexa sequencing PMID: 18987734 Accurate whole human genome sequencing using reversible terminator chemistry. Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, Brown CG, Hall KP, Evers DJ, Barnes CL, Bignell HR, Boutell JM, Bryant J, Carter RJ, Keira Cheetham R, Cox AJ, Ellis DJ, Flatbush MR, Gormley NA, Humphray SJ, Irving LJ, Karbelashvili MS, Kirk SM, Li H, Liu X, Maisinger KS, Murray LJ, Obradovic B, Ost T, Parkinson ML, Pratt MR, Rasolonjatovo IM, Reed MT, Rigatti R, Rodighiero C, Ross MT, Sabot A, Sankar SV, Scally A, Schroth GP, Smith ME, Smith VP, Spiridou A, Torrance PE, Tzonev SS, Vermaas EH, Walter K, Wu X, Zhang L, Alam MD, Anastasi C, Aniebo IC, Bailey DM, Bancarz IR, Banerjee S, Barbour SG, Baybayan PA, Benoit VA, Benson KF, Bevis C, Black PJ, Boodhun A, Brennan JS, Bridgham JA, Brown RC, Brown AA, Buermann DH, Bundu AA, Burrows JC, Carter NP, Castillo N, Chiara E Catenazzi M, Chang S, Neil Cooley R, Crake NR, Dada OO, Diakoumakos KD, Dominguez-Fernandez B, Earnshaw DJ, Egbujor UC, Elmore DW, Etchin SS, Ewan MR, Fedurco M, Fraser LJ, Fuentes Fajardo KV, Scott Furey W, George D, Gietzen KJ, Goddard CP, Golda GS, Granieri PA, Green DE, Gustafson DL, Hansen NF, Harnish K, Haudenschild CD, Heyer NI, Hims MM, Ho JT, Horgan AM, Hoschler K, Hurwitz S, Ivanov DV, Johnson MQ, James T, Huw Jones TA, Kang GD, Kerelska TH, Kersey AD, Khrebtukova I, Kindwall AP, Kingsbury Z, Kokko-Gonzales PI, Kumar A, Laurent MA, Lawley CT, Lee SE, Lee X, Liao AK, Loch JA, Lok M, Luo S, Mammen RM, Martin JW, McCauley PG, McNitt P, Mehta P, Moon KW, Mullens JW, Newington T, Ning Z, Ling Ng B, Novo SM, O'Neill MJ, Osborne MA, Osnowski A, Ostadan O, Paraschos LL, Pickering L, Pike AC, Pike AC, Chris Pinkard D, Pliskin DP, Podhasky J, Quijano VJ, Raczy C, Rae VH, Rawlings SR, Chiva Rodriguez A, Roe PM, Rogers J, Rogert Bacigalupo MC, Romanov N, Romieu A, Roth RK, Rourke NJ, Ruediger ST, Rusman E, Sanches-Kuiper RM, Schenker MR, Seoane JM, Shaw RJ, Shiver MK, Short SW, Sizto NL, Sluis JP, Smith MA, Ernest Sohna Sohna J, Spence EJ, Stevens K, Sutton N, Szajkowski L, Tregidgo CL, Turcatti G, Vandevondele S, Verhovsky Y, Virk SM, Wakelin S, Walcott GC, Wang J, Worsley GJ, Yan J, Yau L, Zuerlein M, Rogers J, Mullikin JC, Hurles ME, McCooke NJ, West JS, Oaks FL, Lundberg PL, Klenerman D, Durbin R, Smith AJ. Nature. 2008 Nov 6;456(7218):53-9. is a DNA sequencing which allows sequence identification by relying on use of DNA polymerase and reversible terminator. The methods requires immobilization of genomic DNA fragment onto a surface and a specific clonal amplification step known as bridge PCR. Reliance on reversible terminator allow cycles of DNA chain extension by DNA polymerase and imaging without the need of electrophoretic separation of newly synthesized DNA fragment as with Sanger sequencing. Philippe Rocca-Serra reversible terminator sequencing adapted from Wikipedia and Illumina / Solexa web site (SS_DNAsequencing.pdf document available on july 2009) Solexa sequencing OBI:0000725 host role In biology, a host is an organism that harbors a virus or parasite, or a mutual or commensal symbiont, typically providing nourishment and shelter. http://en.wikipedia.org/wiki/Host_(biology) 30 March 09 host role is a role played by an organism and realized by providing nourishment, shelter or a means of reproduction to another organism within the organism playing the host role 30Mar09 virus reproducing inside a cell; bacteria causing a disease, host can be harmed or not. we want to avoid a cat sitting on my lap and an animal care technician; these are not examples or hosts; dental cares = on tooth, but part of outer layer of tooth, so covered by "within" in the definition GROUP: Role Branch 30 Mar09 submitted by vaccine community OBI http://en.wikipedia.org/wiki/Host_(biology) host role OBI:0000726 peak matching Peak matching is a data transformation performed on a dataset of a graph of ordered data points (e.g. a spectrum) with the objective of pattern matching local maxima above a noise threshold James Malone Ryan Brinkman PERSON: Ryan Brinkman peak matching OBI:0000727 k-nearest neighbors A k-nearest neighbors is a data transformation which achieves a class discovery or partitioning objective, in which an input data object with vector y is assigned to a class label based upon the k closest training data set points to y; where k is the largest value that class label is assigned. James Malone k-NN PERSON: James Malone k-nearest neighbors OBI:0000728 rodent care keeping animal rodent care is the process by which rodents are being provided with a controlled living environment while kept in captivity for the purpose of research. PPPB branch PPPB branch rodent care OBI:0000729 cloning plasmid A cloning plasmid is a plasmid that was engineered to contain a bacterial origin of replication, encodes for a selectable gene product and contains a cloning site. Note: 'cloning vector role' is really a function. Should be dealt with globally cloning plasmid OBI:0000730 pyrosequencing Pyrosequencing sheds light on DNA sequencing. PMID: 1115661. Ronaghi M. Genome Res. 2001 Jan;11(1):3-11. Review. is a DNA sequencing which allows sequencing of a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step. The template DNA is immobilized, and solutions of A, C, G, and T nucleotides are added and removed after the reaction, sequentially. Light is produced only when the nucleotide solution complements the first unpaired base of the template. The sequence of solutions which produce chemiluminescent signals allows the determination of the sequence of the template. ssDNA template is hybridized to a sequencing primer and incubated with the enzymes DNA polymerase, ATP sulfurylase, luciferase and apyrase, and with the substrates adenosine 5-prime phosphosulfate (APS) and luciferin. Philippe Rocca-Serra Wikipedia (http://en.wikipedia.org/wiki/Pyrosequencing) and Roche 454 life science web site pyrosequencing OBI:0000731 recombinant vector A recombinant vector is created by a recombinant vector cloning process, and contains nucleic acids that can be amplified. It retains functions of the original cloning vector. recombinant vector OBI:0000732 restriction enzyme The enzyme EcoR1 cuts DNA at the canonical cleavage site CAATTG an enzyme that has a specific target cleavage sites within nucleic acids Kevin Clancy, Bjoern Peters 5/22 Need to explore if there are GO / other classes exist that capture this. We need it now for cloning experiments restriction enzyme OBI:0000734 DNA sequencing by synthesis PMID: 18263613. A new class of cleavable fluorescent nucleotides: synthesis and optimization as reversible terminators for DNA sequencing by synthesis. Turcatti G, Romieu A, Fedurco M, Tairi AP. Nucleic Acids Res. 2008 Mar;36(4):e25. is a DNA sequencing which relies on DNA polymerase activity to perform chain extension during the sequencing reaction step. PERSON: Philippe Rocca-Serra DNA sequencing by synthesis OBI:0000735 NTP-2000 a material consisting of 14.5% protein, 8.5% fat and 9.5% fiber produced to feed rodents Jennifer Fostel, Bjoern Peters NTP-2000 OBI:0000736 single fragment library is a collection of short tags from DNA fragments, are extracted and covalently linked as single tag constructs Philippe Rocca-Serra fragment library single fragment library OBI:0000737 cloning vector A cloning vector is an engineered material that is used as an input material for a recombinant vector cloning process to carry inserted nucleic acids. It contains an origin of replication for a specific destination host organism, encodes for a selectable gene product and contains a cloning site. cloning vector OBI:0000738 restriction enzyme based cloning restriction enzyme based cloning is a recombinant vector cloning process that has as an input genetic material that was cleaved with restriction enzymes, and a cloning vector that was cleaved with complementary restriction enzymes. It uses ligase to chemically join the input genetic material and the cloning vector to create a recombinant vector. Kevin Clancy, Bjoern Peters restriction enzyme based cloning OBI:0000739 Student's t-test Studen't t-test is a data transformation with the objective of a statistical hypothesis test in which the test statistic has a Student's t distribution if the null hypothesis is true. It is applied when the population is assumed to be normally distributed but the sample sizes are small enough that the statistic on which inference is based is not normally distributed because it relies on an uncertain estimate of standard deviation rather than on a precisely known value. James Malone WEB: http://en.wikipedia.org/wiki/T-test Student's t-test OBI:0000740 material sample role a role borne by a portion of blood taken to represent all the blood in an organism; the role borne by a population of humans with HIV enrolled in a study taken to represent patients with HIV in general. A material sample role is a specimen role borne by a material entity that is the output of a material sampling process. 7/13/09: Note that this is a relational role: between the sample taken and the 'sampled' material of which the sample is thought to be representative off. material sample role OBI:0000741 topologically preserved clustered data set the output data set generated from a self-organizing map. A clustered data set in which the topology, i.e. the spatial properties between data points, is preserved from the original input data from which it was derived. James Malone PERSON: James Malone topologically preserved clustered data set OBI:0000742 nucleic acid restriction enzyme digest A nucleic acid digest is a material that is the output of a process in which nucleic acids are combined with a restriction enzyme resulting in digested fragments with defined ends based on the enzymes cleavage site Kevin Clancy, Bjoern Peters nucleic acid restriction enzyme digest OBI:0000743 immune response assay an assay with the objective to determine information about an immune response immune response assay OBI:0000744 material sampling process A specimen gathering process with the objective to obtain a specimen that is representative of the input material entity material sampling process OBI:0000747 material sample blood drawn from patient to measure his systemic glucose level. A population of humans with HIV enrolled in a study taken to represent patients with HIV in general. A material entity that has the material sample role OBI: workshop sample population sample material sample OBI:0000748 bisulfite sequencing PMID: 19581485. High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing. Hodges E, Smith A, Kendall J, Xuan Z, Ravi K, Rooks M, Zhang M, Ye K, Battacharjee A, Brizuela L, McCombie WR, Wigler M, Hannon GJ, Hicks J. Genome Res. 2009 Jul 6. An assay which allows to determine the methylation status of genomic DNA using DNA sequencing techniques preceded by a bisulfite based chemical modification of genomic DNA at CpG island location. 8/19/09: Chris says that there may used to be a way of doing bisulfite sequencing comparing lengths of restriction fragments, which implies that it is possible to do without DNA sequencing. Philippe Rocca-Serra adapted from Wikipedia bisulfite sequencing OBI:0000749 CART A CART (classification and regression trees) is a data transformation method for producing a classification or regression model with a tree-based structure. James Malone classification and regression trees BOOK: David J. Hand, Heikki Mannila and Padhraic Smyth (2001) Principles of Data Mining. CART OBI:0000750 study design independent variable In a study in which gene expression is measured in patients between 8 month to 4 years old that have mild or severe malaria and in which the hypothesis is that gene expression in that age group is a function of disease status, disease status is the independent variable. a directive information entity that is part of a study design. Independent variables are entities whose values are selected to determine its relationship to an observed phenomenon (the dependent variable). In such an experiment, an attempt is made to find evidence that the values of the independent variable determine the values of the dependent variable (that which is being measured). The independent variable can be changed as required, and its values do not represent a problem requiring explanation in an analysis, but are taken simply as given. The dependent variable on the other hand, usually cannot be directly controlled 2/2/2009 Original definition - In the design of experiments, independent variables are those whose values are controlled or selected by the person experimenting (experimenter) to determine its relationship to an observed phenomenon (the dependent variable). In such an experiment, an attempt is made to find evidence that the values of the independent variable determine the values of the dependent variable (that which is being measured). The independent variable can be changed as required, and its values do not represent a problem requiring explanation in an analysis, but are taken simply as given. The dependent variable on the other hand, usually cannot be directly controlled. In the Philly 2013 workshop the label was chosen to distinguish it from "dependent variable" as used in statistical modelling. See: http://en.wikipedia.org/wiki/Statistical_modeling PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Chris Stoeckert experimental factor independent variable Web: http://en.wikipedia.org/wiki/Dependent_and_independent_variables 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify thisdefinition please notify OBI. study factor study design independent variable OBI:0000751 study design dependent variable In a study in which gene expression is measured in patients between 8 month to 4 years old that have mild or severe malaria and in which the hypothesis is that gene expression in that age group is a function of disease status, the gene expression is the dependent variable. dependent variable specification is part of a study design. The dependent variable is the event studied and expected to change when the independent variable varies. 2/2/2009 In the design of experiments, independent variables are those whose values are controlled or selected by the person experimenting (experimenter) to determine its relationship to an observed phenomenon (the dependent variable). In such an experiment, an attempt is made to find evidence that the values of the independent variable determine the values of the dependent variable (that which is being measured). The independent variable can be changed as required, and its values do not represent a problem requiring explanation in an analysis, but are taken simply as given. The dependent variable on the other hand, usually cannot be directly controlled. In the Philly 2013 workshop the label was chosen to distinguish it from "dependent variable" as used in statistical modelling. See: http://en.wikipedia.org/wiki/Statistical_modeling PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Chris Stoeckert dependent variable WEB: http://en.wikipedia.org/wiki/Dependent_and_independent_variables 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify thisdefinition please notify OBI. study design dependent variable OBI:0000784 anticoagulant-containing test tube A 'blue top' test tube that contains anticoagulant for storing blood specimens' Person:Alan Ruttenberg 2009/09/28 Alan Ruttenberg. Fucoidan-use-case anticoagulant-containing test tube OBI:0000785 study design controlled variable In a study in which gene expression is measured in patients between 8 month to 4 years old that have mild or severe malaria and in which the hypothesis is that gene expression in that age group is a function of disease status, age is a controlled variable. Controlled variable specification is a part of a study design. They are the entities that could vary, but are kept constant to prevent their influence on the effect of the independent variable on the dependent. 2/2/2009 Original definition: Controlled variables are also important to identify in experiments. They are the variables that are kept constant to prevent their influence on the effect of the independent variable on the dependent. Every experiment has a controlling variable, and it is necessary to not change it, or the results of the experiment won't be valid In the Philly 2013 workshop the label was chosen to distinguish it from "controlled variable" as used in statistical modelling PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Chris Stoeckert controlled variable WEB: http://en.wikipedia.org/wiki/Control_variable 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify thisdefinition please notify OBI. study design controlled variable OBI:0000787 human antithrombin-III (AT-III) in blood assay PMID:19696660#The antithrombin-III (AT-III) was determined using a Berichrom(r) Antithrombin-III (A) kit. An assay to measure the amount of antithrombin III in blood. Person:Alan Ruttenberg WEB:http://www.muschealth.com/lab/content.aspx?id=150006@2009/08/06 human antithrombin-III (AT-III) in blood assay OBI:0000788 fluorescently labeled MHC multimer A complex of two or more linked MHC molecules including a fluorescent label that can be loaded with a ligand, and is used in flow cytometry assay to bind to T cell receptors of T cells specific for the ligand fluorescently labeled MHC multimer OBI:0000789 survival rate A measurement data that represents the percentage of people or animals in a study or treatment group who are alive for a given period of time after diagnosis or initiation of monitoring. Oliver He adapted from wikipedia http://en.wikipedia.org/wiki/Survival_rate survival rate OBI:0000790 recombinant BAC cloning Recombinant BAC cloning is a process with the objective to insert genetic material into an F plasmid based bacterial artificial chromosome for future replication of the inserted material http://en.wikipedia.org/wiki/Bacterial_artificial_chromosome recombinant BAC cloning OBI:0000791 multiple testing correction objective Application of the Bonferroni correction A multiple testing correction objectives is a data transformation objective where the aim is to correct for a set of statistical inferences considered simultaneously multiple comparison correction objective http://en.wikipedia.org/wiki/Multiple_Testing_Correction multiple testing correction objective OBI:0000792 statistical model validation Using the expression levels of 20 proteins to predict whether a cancer patient will respond to a drug. A practical goal would be to determine which subset of the 20 features should be used to produce the best predictive model. - wikipedia A data transformation which assesses how the results of a statistical analysis will generalize to an independent data set. Helen Parkinson http://en.wikipedia.org/wiki/Cross-validation_%28statistics%29 statistical model validation OBI:0000793 double blind study execution A double blind study execution is defined as any study execution in which neither the subjects nor the investigators are informed of which study arm the subjects are part of during the portion of the trial when the subjects are being treated Person:Alan Ruttenberg http://clinicaltrials.gov/ct2/info/glossary#double 2009/09/28 Alan Ruttenberg. Fucoidan-use-case double blind study execution OBI:0000794 transcription factor binding site SO:0000235 PLace_holder for sequence ontology term transcription factor binding site OBI:0000795 glucometer Diabetic patients use glucometers to determine their glucose levels A measurement device with the function to measure and record the level/amount of glucose in a blood sample PERSON:Frank Gibson PERSON:Helen Parkinson glucose meter http://en.wikipedia.org/wiki/Glucose_meter glucometer OBI:0000796 purification objective the objective to obtain a pure fraction of a specific peptide when running an HPLC on a crude synthesis of peptides. The objective to separate a material entity into different compositions of which one or more have are purified fractions that contain higher concentration of a desired component, while others contain impurities and are not of interest PERSON:Bjoern Peters isolation objective BP 10/14/09, BP: This should be linked to the 'purified' 'currently conferred quality purification objective OBI:0000797 obsolete_primary structure of protein SIINFEKL' is the primary structure of a peptide The primary structure of a protein that is completely defined by the set of its amino acid residue parts and the linear order induced by the peptide bonds that hold them together Person:Bjoern Peters replaced by SO_0000104 polypeptide obsolete_primary structure of protein true OBI:0000798 capsule shell a small rounded gelatinous container Person:Alan Ruttenberg http://www.golovchenko.org/cgi-bin/wnsearch?q=capsule#2n 2009/09/28 Alan Ruttenberg. Fucoidan-use-case capsule shell OBI:0000799 recombinant phage cloning Insert selection by BamHI methyltransferase protection in P1 phage-based cloning Recombinant phage cloning is the process of using a phage plus some insert nucleic acid for the purposes of amplification of the insert material achieved by phage assembly in vitro. Helen Parkinson http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mcb.section.1611 recombinant phage cloning OBI:0000800 cross linking cross linking can be used as a probe to link proteins together, to check protein protein interactions A process in which bonds are created that link one polymer to another PERSON: Chris Stoeckert http://en.wikipedia.org/wiki/Cross-link cross linking OBI:0000801 spike train datum Measurement of temporal regularity of spike train responses in auditory nerve fibers of the green treefrog A measurement datum which represents information about an ordered series of action potentials in an organism's CNS measured over time. needs more work to see exactly what the data set looks like - HP Helen Parkinson, Alan Ruttenberg spike train measurement Jessica Turner, NIF spike train datum OBI:0000802 prothrombin time assay PMID:19696660#The prothrombin time (PT) was quantitatively determined using RecombiPlasTin (Instrumentation Laboratory Company, Lexington, Massachusetts, USA). The prothrombin time is an assay most commonly measured using blood plasma. Blood is drawn into a test tube containing liquid citrate, which acts as an anticoagulant by binding the calcium in a sample. The blood is mixed, then centrifuged to separate blood cells from plasma. In newborns, whole blood is used. The plasma is analyzed by a biomedical scientist on an automated instrument at 37 degrees C, which takes a sample of the plasma. An excess of calcium is added (thereby reversing the effects of citrate), which enables the blood to clot again. For an accurate measurement the proportion of blood to citrate needs to be fixed; many laboratories will not perform the assay if the tube is underfilled and contains a relatively high concentration of citrate. If the tube is underfilled or overfilled with blood, the standardized dilution of 1 part anticoagulant to 9 parts whole blood is no longer valid. For the prothrombin time test the appropriate sample is the blue top tube, or sodium citrate tube, which is a liquid anticoagulant. Tissue factor (also known as factor III or thromboplastin) is added, and the time the sample takes to clot is measured optically. Some laboratories use a mechanical measurement, which eliminates interferences from lipemic and icteric samples. The prothrombin ratio is the prothrombin time for a patient, divided by the result for control plasma. 2009/10/18 Alan Ruttenberg. This assay was added during the fucoidan use case exercise but still needs to be fleshed out. Only the AT-III assay has more carefully specified inputs and outputs Person:Alan Ruttenberg WEB:http://en.wikipedia.org/wiki/Prothrombin_time@2009/10/06 2009/09/28 Alan Ruttenberg. Fucoidan-use-case prothrombin time assay OBI:0000803 denaturing Denaturing DNA in alcohol Is a process in which the tertiary or secondary structure of a polymer is disrupted http://en.wikipedia.org/wiki/Denaturation_%28biochemistry%29 denaturing OBI:0000804 informing investigator of subject study arm A process in which an investigator is made aware of which study arm that a patient is participating in, for example whether they are receiving a placebo or a treatment with an investigational compound. 09/28/2009 Alan Ruttenberg. This and the class informing-subject-of-study-arm are defined in order to solve the question of how to represent single and double blind experiments. To represent the aspect of double blinding pertaining to investigators, we say that the study execution doesn't include any processes of this sort Person:Alan Ruttenberg 2009/09/28 Alan Ruttenberg. Fucoidan-use-case informing investigator of subject study arm 1 OBI:0000805 antithrombin-III (AT-III) berichrome assay An antithrombin-III (AT-III) assay in which exogenous bovine thrombin and heparin are added to test plasma to form a thrombin-heparin-AT complex. The residual thrombin not bound then hydrolyzes the p-nitroalanine substrate to produce a yellow color, which is read at 405 nm. The intensity of color produced is inversely proportional to the AT present. A calibration is done with standard human plasma reagent and results for a given specimen are reported as a percentage relative to the standard todo Reagents from Berichrom(r) Antithrombin III (A) and standard human plasma WEB:http://www.clinchem.org/cgi/content/full/43/9/1783@2009/08/06 2009/09/28 Alan Ruttenberg. Fucoidan-use-case antithrombin-III (AT-III) berichrome assay OBI:0000806 material maintenance objective An objective specification maintains some or all of the qualities of a material over time. PERSON: Bjoern Peters PERSON: Bjoern Peters material maintenance objective OBI:0000807 presentation of stimulus The presentation of a flashing light to a monkey during reward training a planned process in which an organism is exposed to some stimulus with the intent to invoke an action Helen Parkinson, Jessica Turner, Dirk Derom stimulation of organism Helen Parkinson, Jessica Turner, Dirk Derom presentation of stimulus OBI:0000808 spectrolyse heparin antifactor-Xa assay PMID:19696660#Antifactor-Xa (anti-Xa) was determined using spectrolyse heparin (Xa) (Trinity Biotech plc, Bray, County Wicklow, Ireland). A Spectrolyse Heparin (Xa) assay is intended for the quantitative determination of therapeutic Heparin in human plasma. The principle inhibitor of Thrombin, Factor Xa and other coagulation serine proteases in plasma is Antithrombin III. The rate of inhibition, under normal conditions, is slow, but can be increased several thousand-fold by Heparin. This mechanism accounts for the anticoagulant effect of Heparin. Low Molecular Weight Therapeutic Heparin (LMWH) preparations appear to catalyze the reaction between Factor Xa and Antithrombin III more readily than the reaction between Thrombin and Antithrombin III while standard Heparin catalyzes both reactions equally. The Factor Xa inhibition test is the most useful test for assaying the widest variety of therapeutic Heparin preparations. In this method, when both Factor Xa and Antithrombin III are present in excess, the rate of Factor Xa inhibition is directly proportional to the Heparin concentration. The residual Factor Xa activity, measured with a Factor Xa-specific chromogenic substrate, is inversely proportional to the Heparin concentration. 2009/10/18 Alan Ruttenberg. This assay was added during the fucoidan use case exercise but still needs to be fleshed out. Only the AT-III assay has more carefully specified inputs and outputs Person:Alan Ruttenberg WEB:http://www.kordia.nl/en/product/hemostasis/specialty_kits__reagens/598/spectrolyse_heparin_anti_xa@2009/08/06 2009/09/28 Alan Ruttenberg. Fucoidan-use-case spectrolyse heparin antifactor-Xa assay OBI:0000809 amplified DNA Amplied DNA created by PCR DNA that has been produced in an enzymatic amplification process PERSON: Alan Ruttenberg Alan Ruttenberg amplified DNA OBI:0000810 informed consent process A planned process in which a person or their legal representative is informed about key facts about potential risks and benefits of a process and makes a documented decision as to whether the person in question will participate. 09/28/2009 Alan Ruttenberg: This is made a subclass of the higher level processual entity in BFO because I don't want to take a stand on whether it is a process aggregate. Analogous to the situation with Material entity. Person:Alan Ruttenberg http://clinicaltrials.gov/ct2/info/glossary#informed 2009/09/28 Alan Ruttenberg. Fucoidan-use-case informed consent process OBI:0000811 primary structure of DNA macromolecule a quality of a DNA molecule that inheres in its bearer due to the order of its DNA nucleotide residues. placeholder for SO BP et al primary structure of DNA macromolecule OBI:0000812 measuring neural activity in the caudate nucleus An SU micro-electrode was used to measure neural activity in the form of spike trains in the caudate nucleus of monkeys in response to a flashing light stimulus The process of measuring neural activity in the caudate nucleus Helen Parkinson Jessica Turner, NIF, Dirk Derom, OBI measuring neural activity in the caudate nucleus OBI:0000813 to be treated with active ingredient role Role of a patient in a group treated with an active substance in a clinical trial A study subject role which begins to exist when a subject is assigned to be one of those who will receive active ingredient, and is realized in a study execution in which they receive the active ingredient Person:Alan Ruttenberg PERSON: Helen Parkinson 2009/09/28 Alan Ruttenberg. Fucoidan-use-case to be treated with active ingredient role OBI:0000814 guar gum Guar gum, also called guaran, is a galactomannan. It is primarily the ground endosperm of guar beans. The guar seeds are dehusked, milled and screened to obtain the guar gum.[1] It is typically produced as a free flowing, pale, off-white colored, coarse to fine ground powder. Helen Parkinson http://en.wikipedia.org/wiki/Guar_gum guar gum OBI:0000815 Berichrom(r) Antithrombin III (A) Kit For the chromogenic determination of antithrombin III. Autoanalyzer method for undiluted samples. For the quantitative chromogenic determination of the functional activity of antithrombin III in plasma on autoanalyzers for the diagnosis of diminished AT III synthesis, increased consumption, and for monitoring substitution therapy. Berichrom(r) Antithrombin III (A) is used for the rapid determination of the physiologically active antithrombin III and permits the diagnosis of congenital and acquired antithrombin III deficiency, a condition frequently associated with an increased risk of thrombosis. Acquired antithrombin III deficiencies frequently occur due to consumption following major operations or due to disseminated intravascular coagulation (DIC) in cases of septicaemia, nephroses, liver parenchymal damage (hepatitis, drug intoxication, alcoholism) and estrogen-containing contraceptives. The test permits early detection of patients at increased risk for thrombosis. Kit contains: 6 x for 5.0 mL Thrombin (bovine), 3 x for 3.0 mL Substrate Reagent, 1 x 30.0 mL Buffer Solution Person:Alan Ruttenberg WEB:http://www.dadebehring.com/edbna2/ebusiness/products/productDetail.jsp?sDiscipline=Hemostasis&FirstLevelOID=-13075&sCategory_Name=BCS&SecondLevelOID=-13895&ThirdLevelOID=-13904&selectedProductType=H-Assays+-+non+US&sProductName=OWWR15&PROD_OID=44198@2009/08/06 2009/09/28 Alan Ruttenberg. Fucoidan-use-case Berichrom(r) Antithrombin III (A) Kit OBI:0000816 micro electrode A micro-electrode recording device used to record extracellular action potentialsin monkey caudate nucleus An electrode of very fine caliber consisting usually of a fine wire or a glass tube of capillary diameter drawn to a fine point and filled with saline or a metal used in physiological experiments to stimulate or record action currents of extracellular or intracellular origin in the nervous system. Helen Parkinson, Jessica Turner, Dirk Derom micro electrode measuring device Jessica Turner, Dirk Derom micro electrode OBI:0000817 fucoidan Fucoidan is a sulfated polysaccharide (MW: average 20,000) found mainly in various species of brown seaweed such as kombu, limu moui,bladderwrack, wakame, mozuku, and hijiki (variant forms of fucoidan have also been found in animal species, including the sea cucumber). Helen Parkinson http://en.wikipedia.org/wiki/Fucoidan fucoidan OBI:0000818 calibration the process of using pH buffer adjust a pH meter A planned process with the objective to establish the relationship between data produced by a measurement device and physical qualities. This is done by using the measurement device under defined conditions, and either tuning it to adjust the measured output, or record the output and use it as a reference in future measurements. GROUP: OBI Philly workshop WEB:http://en.wikipedia.org/wiki/calibration calibration OBI:0000819 anticoagulant tube storage of blood specimen Storage of a blood specimen in a tube with anticoagulant Person:Alan Ruttenberg 2009/09/28 Alan Ruttenberg. Fucoidan-use-case anticoagulant tube storage of blood specimen OBI:0000820 activated partial thromboplastin time (aPTT) assay PMID:19696660#The activated partial thromboplastin time (aPTT) was determined using Dade Actin FSL activated PTT reagent. An activated partial thromboplastin time (aPTT) assay is a an assay measuring the efficacy of both the 'intrinsic' (now referred to as the contact activation pathway) and the common coagulation pathways. In order to activate the intrinsic pathway, phospholipid, an activator (such as silica, celite, kaolin, ellagic acid), and calcium (to reverse the anticoagulant effect of the oxalate) are mixed into the plasma sample . The time is measured until a thrombus (clot) forms. 2009/10/18 Alan Ruttenberg. This assay was added during the fucoidan use case exercise but still needs to be fleshed out. Only the AT-III assay has more carefully specified inputs and outputs Person:Alan Ruttenberg WEB:http://en.wikipedia.org/wiki/Partial_thromboplastin_time@2008/10/06 2009/09/28 Alan Ruttenberg. Fucoidan-use-case activated partial thromboplastin time (aPTT) assay OBI:0000821 filled capsule A pill in the form of a small rounded gelatinous container with medicine inside. Person:Alan Ruttenberg http://www.golovchenko.org/cgi-bin/wnsearch?q=capsule#2n 2009/09/28 Alan Ruttenberg. Fucoidan-use-case filled capsule OBI:0000822 single blind study execution A single blind study execution is defined as any study execution in which the subjects are not informed of which study arm they are part of during the portion of the trial when the subjects are being treated Person:Alan Ruttenberg http://clinicaltrials.gov/ct2/info/glossary#single 2009/09/28 Alan Ruttenberg. Fucoidan-use-case single blind study execution OBI:0000823 thrombin time assay PMID:19696660#The thrombin time was determined using thromboclotin assay kit. A thrombin time assay is on in which after liberating the plasma from whole blood by centrifugation, bovine Thrombin is added to the sample of plasma. The clot is formed and is detected optically or mechanically by a coagulation instrument. The time between the addition of the thrombin and the clot formation is recorded as the thrombin clotting time 2009/10/18 Alan Ruttenberg. This assay was added during the fucoidan use case exercise but still needs to be fleshed out. Only the AT-III assay has more carefully specified inputs and outputs Person:Alan Ruttenberg WEB:http://en.wikipedia.org/wiki/Thrombin_time@2009/10/06 2009/09/28 Alan Ruttenberg. Fucoidan-use-case thrombin time assay OBI:0000824 recombinant YAC cloning Isolation of a YAC clone covering a cluster of nine S100 genes on human chromosome 1q21 Recombinant YAC cloning is a process with the objective to insert genetic material into a yeast artificial chromosome vector for future replication of the inserted material Helen Parkinson http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mcb.section.1611 recombinant YAC cloning OBI:0000825 to be treated with placebo role A study subject role which begins to exist when a subject is assigned to be one of those who will receive a placebo, and realized in a study execution in which they receive the placebo Person:Alan Ruttenberg 2009/09/28 Alan Ruttenberg. Fucoidan-use-case to be treated with placebo role OBI:0000826 treatment portion of study execution A planned process, part of a study design execution, during which the treatment of subjects is ongoing 09/28/2009 Alan Ruttenberg. Needed because we have to have a process to scope blinding over Person:Alan Ruttenberg 2009/09/28 Alan Ruttenberg. Fucoidan-use-case treatment portion of study execution OBI:0000827 pill A dose of medicine or placebo in the form of a small pellet. Person:Alan Ruttenberg http://www.golovchenko.org/cgi-bin/wnsearch?q=pill#2n 2009/09/28 Alan Ruttenberg. Fucoidan-use-case pill OBI:0000828 research organization The SALK institute is a research organization. An organization formed with a goal to have its members conduct investigations Person:Bjoern Peters research organization OBI:0000830 obsolete_primary structure of sequence macromolecule A quality inhering in a molecule that is completely defined by the linear sequence of a set of residues which are connected by directional, linear bonds 2010-06-28 Alan Ruttenberg. This term and its children to be replaced by sequence ontology terms once we figure out what the right terms are . These are all placeholders and should be replaced by SO terms Person:Bjoern Peters these are not in great shape yet; need to clarify how what a 'sequence macromolecule is' and how it differes from molecules in general (directivity of certain bonds, linear connectivity along that type of bond etc.) replaced by SO_0000001 region obsolete_primary structure of sequence macromolecule true OBI:0000831 DNA residue methylation a quality of a DNA residue that has a methyl group attached to it DNA residue methylation OBI:0000832 measurement device A ruler, a microarray scanner, a Geiger counter. A device in which a measure function inheres. GROUP:OBI Philly workshop OBI measurement device OBI:0000834 high molecular weight DNA extract Extraction of chromosomal DNA from mammalian cells by first isolating nucei The output of an extraction process in which DNA molecules above a molecular weight cutoff are purified in order to exclude DNA from organellas. PERSON:Chris Stoeckert OBI high molecular weight DNA extract OBI:0000835 manufacturer A person or organization that has a manufacturer role manufacturer OBI:0000836 test tube A test tube is a device consisting of a glass or plastic tubing, open at the top, usually with a rounded U-shaped bottom which has the function to contain material Bjoern Peters collection tube sample tube http://en.wikipedia.org/wiki/Test_tube test tube OBI:0000837 oral ingestion of pill An adding a material entity to target with the entity is a pill and the target is the mouth Person:Alan Ruttenberg 2009/09/28 Alan Ruttenberg. Fucoidan-use-case oral ingestion of pill OBI:0000838 material maintenance a process with that achieves the objective to maintain some or all of the characteristics of an input material over time material maintenance OBI:0000839 labeled oligonucleotide a labeled oligonucleotide is a short nucleic acid which underwent a labeling process resulting in a radioactive isotope such as P32 or P33 added to its backbone for instance by end labeling with polynucleotide kinase which added radiolabeled ATP to the 5' end of oligonucleotide 2010-01-31: Philippe Rocca-Serra placeholder Person: Philippe Rocca-Serra labeled oligonucleotide OBI:0000840 unblinding process The part of the study execution in which the subjects are told what study arm they are in and in which the investigators are told which subjects are in which trials Person:Alan Ruttenberg 2009/09/28 Alan Ruttenberg. Fucoidan-use-case unblinding process OBI:0000841 subject agrees they understand informed consent document A process in which a subject receives an informed consent document and agrees that they have understood it 09/28/2009 Alan Ruttenberg. There's a need for a general process like this in IAO - document and person in, signed document (and associated obligations, rights, out Person:Alan Ruttenberg 2009/09/28 Alan Ruttenberg. Fucoidan-use-case subject agrees they understand informed consent document OBI:0000842 informing subject of study arm A process in which the subject is made aware of which study arm they are participating in, for example whether they are receiving a placebo or a treatment with an investigational compound. 09/28/2009 Alan Ruttenberg. This and the class informing-investigator-of-study-arm are defined in order to solve the question of how to represent single and double blind experiments. To represent the aspect of blinding pertaining to subjects (happens in single and double blinding) we say that that the study execution doesn't include any processes of this sort Person:Alan Ruttenberg 2009/09/28 Alan Ruttenberg. Fucoidan-use-case informing subject of study arm OBI:0000843 Sysmex CA-6000 Coagulation Analyzer The Sysmex CA-6000 automated coagulation analyzer is a random access instrument that is capable of performing 20 clot-based and chromogenic assays Person:Alan Ruttenberg web:http://www.clinchem.org/cgi/content/full/43/9/1783@2009/08/06 2009/09/28 Alan Ruttenberg. Fucoidan-use-case Sysmex CA-6000 Coagulation Analyzer OBI:0000844 hospital human ethics approval was obtained from the Southern Tasmania Health & Medical Human Research Ethics Committee and the Royal Hobart Hospital Research Ethics Committee [pmid:19696660] A medical organization at which sick or injured people are given clinical care Person:Alan Ruttenberg Person:Helen Parkinson http://www.golovchenko.org/cgi-bin/wnsearch?q=hospital#2n modified from the wording of the wordnet definition 2009/09/28 Alan Ruttenberg. Fucoidan-use-case hospital OBI:0000845 primary structure of RNA molecule The primary structure of an RNA molecule that is completely defined by the set of its nucleic residue parts and the linear order induced by the peptide bonds that hold them together Person:Bjoern Peters primary structure of RNA molecule OBI:0000847 test substance role fucoidan bears a test substance role in a study to test safety taking a certain dosage of it orally A role born by a material entity and realized in a process where the substance is used as specified as the independent variable for an investigation Person:Alan Ruttenberg Group:OBI test substance role OBI:0000848 polyA RNA extraction A RNA extraction process typically involving the use of poly dT oligomers in which the desired output material is polyA RNA. Person: Chris Stoeckert Person: Jie Zheng UPenn Group polyA RNA extraction OBI:0000849 organellar RNA extraction A RNA extraction process in which the desired output material is RNA in the organelle(s). Person: Chris Stoeckert Person: Jie Zheng UPenn Group organellar RNA extraction OBI:0000851 obsolete_diethyl pyrocarbonate Replaced by CHEBI_59051 Diethylpyrocarbonate obsolete_diethyl pyrocarbonate true OBI:0000852 record of missing knowledge A statement in a journal article indicating that the age of a patient at the onset of disease is not known. A statement indicating that the weight of a mouse was not measured. a information content entity created to indicate that information about something is not available to the person recording it. This class should probably end up in IAO. It could be further breaken down to indicate different kinds of lack of knowledge, e.g. inability to determine something vs. no attempt made to determine something vs. no informatino available if it was even attempted to determine something. The design pattern should be generalizable. 'unknown sex' is the first example, and needed immediately. Bjoern Peters record of missing knowledge OBI:0000854 western blot analysis Running a cell lysate on an acrylamide gel in a western blot aparatus to separate the constituent proteins, followed by transfer of the proteins from the gel to a nitrocellulose membrane. Staining this membrane with specific antibodies to detect the presence of specific proteins of interest. An analyte assay that detects specific peptides in an input material by separating it using gel electrophoresis, transfering the separated molecules to a membrane, and staining them with  antibodies specific to the analyte molecules. Philippe Rocca-Serra, IEDB Philippe Rocca-Serra, IEDB western blot analysis OBI:0000855 total RNA extraction A RNA extraction process in which total cellular and organelle RNA are extracted. Person: Chris Stoeckert Person: Jie Zheng UPenn Group total RNA extraction OBI:0000856 obsolete intracellular material detection by flow cytometry assay An assay in which the presence of a material inside a cell is measured by permeabilizing the cell membrane to allow entry of specific antibodies, and counting the stained cells using a flow cytometer. intracellular staining obsolete intracellular material detection by flow cytometry assay true OBI:0000857 complementary nucleotide probe role A primer in a PCR reaction. A probe on an Affymetrix chip. A role played by a nucleic acid molecule that is used in a planned process for its ability to bind a nucleic acid molecules with complementary nucleotide sequence PERSON:Bjoern Peters complementary nucleotide probe role OBI:0000858 record of unknown sex A database record indicating that the tissue sample in a microarray experiment came from an organism for which the biological sex is not known to the person who created the record. a record indicating that the biological sex of an organism is not known. I think the statement is still about the instance of the biological sex quality of an organism. It is also about information available to the person making the statement. Bjoern Peters record of unknown sex OBI:0000859 cytoplasmic RNA extraction A RNA extraction process in which the desired output material is RNA in the cytoplasm. Person: Chris Stoeckert Person: Jie Zheng UPenn Group cytoplasmic RNA extraction OBI:0000860 northern blot analysis PMID: 18428227. Analysis of RNA by northern blot hybridization. Brown T, Mackey K. Curr Protoc Hum Genet. 2001 Nov;Appendix 3:Appendix 3K. a northern blot analysis is an assay allowing monitoring presence of gene transcripts by hybridizing labeled RNA or DNA probes against messenger RNAs isolated from tissue or cell cultures, resolved on denaturing agarose gel, transfered by blotting procedure to a nitrocellulose or nylon membrane and immobilized by cross linking or baking to the membrane. Detection of hybridization signals is carried out by immunofluorescence or radioactivity measurements using photographic films or digital imaging devices such as Phosphor Imager 2010-01-31: Philippe Rocca-Serra: Need to add a restriction taking into account probe and transcript information Person: Philippe Rocca-Serra northern blot northern blot analysis OBI:0000861 Likelihood-ratio test Likelihood-ratio is a data transformation which tests whether there is evidence of the need to move from a simple model to a more complicated one (where the simple model is nested within the complicated one); tests of the goodness-of-fit between two models. Tina Boussard Likelihood-ratio test OBI:0000862 nuclear RNA extract Isolation and purification of nuclear RNA from animal cells using Norgen Bioteck corp. cytoplasmic and nuclear RNA purification kit (http://www.norgenbiotek.com/display-product.php?ID=30) A RNA extract that is the output of an extraction process in which RNA molecules found in the nucleus, including mRNA precursors (pre-mRNA), are extracted. PERSON: Chris Stoeckert PERSON: Jie Zheng UPenn Group nuclear RNA extract OBI:0000865 96-well neutralization assay A serum neutralization of viral infectivity assay which done in a 96-well plate. person: Bjoern Peters person: Melanie Courtot microneutralization assay MC: 20100217: microneutralization is used by the influenza community, to refer to a nutralizationassay at a smaller scale. However smaller is difficult to define accurately, and we therefore chose a label being more specific. 96-well neutralization assay OBI:0000867 establishing cancer cell line Establishment of HeLa immortal cell line is a planned process in which the objective is to generate a cell line from a natural population of cancer cells which are already immortal Helen Parkinson establishing cancer cell line OBI:0000868 pattern matching objective A pattern matching objective aims to detect the presence of the constituents of a given pattern. In contrast to pattern recognition, the pattern is rigidly specified. Patterns are typicall sequences or trees. Tina Boussard http://en.wikipedia.org/wiki/Pattern_matching pattern matching objective OBI:0000869 polyA RNA extract Preparation of polyA RNA by cellulose-bound oligo-dT (Aviv, H., Leder, P. 1972. Purification of biologically active globin messenger RNA by chromatography on oligothymidylic acid-cellulose. Proc. Nat. Acad. Sci. USA 69, 1408-1412.) A RNA extract that is the output of an extraction process in which RNA molecules with poly A tail at its 3' end are purified. PERSON: Chris Stoeckert PERSON: Jie Zheng UPenn Group polyA RNA extract OBI:0000870 single-nucleotide-resolution nucleic acid structure mapping assay is an assay which aims to provide information about the secondary structure of nucleic acids using chemical or enzymatic probing to establish the extent of base-pairing or solvent accessiblity. 2010-01-31: Philippe Rocca-Serra: OBI needs to review 'structure assay' as currently defined. Need to get feedback from Kevin Clancy. Person: Philippe Rocca-Serra RNAO single-nucleotide-resolution nucleic acid structure mapping assay OBI:0000871 viral hemagglutination assay The viral hemagglutination assay (HA) is a quantification of viruses by hemagglutination. person: Bjoern Peters person: Melanie Courtot HA HI viral hemeagglutination assay WEB: http://en.wikipedia.org/wiki/Hemagglutination_assay viral hemagglutination assay OBI:0000872 serum neutralization of viral infectivity assay A quantitative assay where different dilutions of serum are mixed with virus and used to infect cells. At the lower dilutions, antibodies will block infection, but at higher dilutions, there will be too few antibodies to have an effect. The simple process of dilution provides a way to compare the virus- neutralizing abilities of different sera. The neutralization titer is expressed as the reciprocal of the highest dilution at which virus infection is blocked. person: Bjoern Peters person: Melanie Courtot influenza neutralization assay WEB: http://www.virology.ws/2009/05/28/influenza-microneutralization-assay/ MC, 20100217: I added influenza neutralization assay as alternative term. This should be tagged with a community specific value, eg "influenza ontology" or else. serum neutralization of viral infectivity assay OBI:0000873 pre-mortem specimen material obtained through a liver biopsy from a human patient a specimen that was taken from a live organism Bjoern Peters MO_705 premortem pre-mortem specimen OBI:0000874 detection of specific nucleic acid polymers with complementary probes Primer based PCR assay, Norther blot, Southern Blot, and RNAse protection assays. An analyte assay in which a specified input material (the evaluant) is examined for the presence or quantity of specified nucleic acid polymers, which are identified based on the use of complementary nucleic acid probes. IEDB IEDB detection of specific nucleic acid polymers with complementary probes OBI:0000875 viral hemagglutination inhibition assay Examining the ability of a monoclonal antibody to inhibit hemagglutination by Influenza A virus by comparing the levels of hemagglutination with and without the presence of the antibody. An assay that measures the ability of an evaluant to inhibit hemagglutination by a virus. Hemagglutinin is a viral protein which binds to sialic acid receptors on cells or to erythrocytes, causing the cells to clump. Loss of clumping indicates hemagglutination inhibition by the antibody. Bjoern and Melanie Bjoern and Melanie viral hemagglutination inhibition assay OBI:0000876 cytoplasmic RNA extract Cytoplasmic RNA extraction from mammalian tissues to create cDNA library (Carninci P, Nakamura M, Sato K, Hayashizaki Y, Brownstein MJ. Cytoplasmic RNA extraction from fresh and frozen mammalian tissues. Biotechniques. 2002;33:306–309.) A RNA extract that is the output of a RNA extraction process in which RNA molecules found in the cytoplasm are extracted. PERSON: Chris Stoeckert PERSON: Jie Zheng UPenn Group cytoplasmic RNA extract OBI:0000877 cell line immortalization Production of a cell line for the purposes of experimentation e.g. EBV transformation of PBMs an establishing cell line process whereby a mortal cell line is intentionally genetically modified to be capable of indefinite propagation and re-established as a new immortal cell line 4-20-13 MHB: This class was repositioned as a child of 'establishing cell line', based on the existing definition ("the planned process of experimentally creating a cell line which is capable of dividing indefinitely in vitro"), and examples and other annotations indicating the intent to describe a process through which a new immortal cell line is established from an existing mortal cell line using genetic modification techniques. The definition above was modified to clarify this perspective. Bjoern Peters 'establishing immortal cell line through directed genetic modification' OBI A immortalizing genetic transformation of an existing population of cell line cells is required as part of this process, as are additional steps for selecting and propagating the cells output form this process into a cell line. cell line immortalization OBI:0000879 random primed DNA labeling PMID: 8713846. Random primed 32P-labeling of DNA. Smith DR. Methods Mol Biol. 1996;58:27-9. a labeling in which random primers are used to uniformly label input DNA need to add Klenow subunit of DNA polymerase I under material entity Person: Bjoern Peters Person: Chris Stoeckert Person: Philippe Rocca-Serra PMID: 6312838. A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity. Feinberg AP, Vogelstein B. Anal Biochem. 1983 Jul 1;132(1):6-13. random primed DNA labeling OBI:0000880 RNA extract an extract which is the output of an extraction process in which RNA molecules are isolated from a specimen. PERSON: Chris Stoeckert PERSON: Jie Zheng Group: UPenn Group RNA extract OBI:0000882 cell-cell killing assay Autologous EBV-transformed B-LCL were used as target cells for the influenza virus-specific CTL assays. Equal volumes of target and effector cells were added to tissue culture plates, and 1:2 serial dilutions of effectors were made. After a 4-h incubation of the effector cells with the target cells, supernatants were collected and counted with the LKB 1272 Clinigamma counter. Percent specific killing was determined with the following equation: (experimental 51Cr release - spontaneous 51Cr release)/(maximum 51Cr release - spontaneous 51Cr release) x 100. A cytometry assay that monitors a cell population to track how many are killed by other cells. IEDB IEDB cell-cell killing assay OBI:0000883 in vivo cell killing assay Labeling two populations of cells with different levels of CFSE, pusling one population with an influenza peptide, injecting the cells into a mouse, and recoving cells 24 hours later. By comparing the recovery rate of cells with different CFSE labeling, it is possible to determine if there was specific killing of peptide pulsed target cells. A cell killing assay that measures if and how many target cells are killed within an organism. IEDB IEDB in vivo cell killing assay OBI:0000885 secondary structure of sequence macromolecule A quality inhering in a molecule that refers to general three-dimensional form of local segments of biopolymers such as proteins and nucleic acids (DNA/RNA). It does not, however, describe specific atomic positions in three-dimensional space, which are considered to be tertiary structure. Secondary structure was introduced by Kaj Ulrik Linderstrøm-Lang in the 1952 Lane medical lectures at Stanford. 2010-01-31: Philippe Rocca-Serra: This is a placeholder to allow work on 'nucleic acid mapping assay' in collaboration with RNAOntology group. Need to liaise with SO Person: Philippe Rocca-Serra Wikipedia secondary structure of sequence macromolecule OBI:0000888 nuclear RNA extraction A RNA extraction process in which the desired output material is RNA in the nucleus. Person: Chris Stoeckert Person: Jie Zheng UPenn Group nuclear RNA extraction OBI:0000889 survival curve A survival curve is a report graph which is a graphical representation of data where the percentage of survival is plotted as a function of time. PERSON:Chris Stoeckert PERSON:James Malone PERSON:Melanie Courtot WEB: http://www.graphpad.com/www/book/survive.htm survival curve OBI:0000891 cell proliferation assay Measuring the amount of tritiated thymidine incorporated by dividing cells as a proxy for cell proliferation. A cytometry assay which measures the degreee to which input cells are replicating. IEDB IEDB cell proliferation assay OBI:0000892 Southern blot analysis PMID: 9452032. Germline mutations detected in the von Hippel-Lindau disease tumor suppressor gene by Southern blot and direct genomic DNA sequencing. Li C, Weber G, Ekman P, Lagercrantz J, Norlen BJ, Akerström G, Nordenskjöld M, Bergerheim US. Hum Mutat. 1998;Suppl 1:S31-3. Southern blot analysis is a an assay used in molecular biology to assert the presence/absence status of a specific DNA sequence in DNA samples. DNA samples to be assayed are first digested by restriction enzymes, fragments are then resolved by gel electrophoresis following by a blotting ensuring transfer to nitrocellulose or nylon membrane. Immobilization of DNA fragments to the membrane is achieved by UV crosslinking and/or baking. Probes raised against the specific sequences are then hybridized to the membrane. Detection of hybridization signals is carried out by immunofluorescence or radioactivity measurements using photographic films or digital imaging devices such as Phosphor Imager. 2010-01-31: Philippe Rocca-Serra: need extra work on 'labeled probe' 2010-01-31: Philippe Rocca-Serra: departure from naming convention as the assay is named after Edwin Southern. Person: Philippe Rocca-Serra Southern blot OBI & Wikipedia Southern blot analysis OBI:0000893 real time polymerase chain reaction assay A laboratory technique based on the PCR, which is used to amplify and simultaneously quantify a specific DNA molecule based on the use of complementary probes/primers. It enables both detection and quantification (as absolute number of copies or relative amount when normalized to DNA input or additional normalizing genes) of one or more specific sequences in a DNA sample. person: Bjoern Peters person: Melanie Courtot Q-PCR kinetic polymerase chain reaction qPCR quantitative real time polymerase chain reaction WEB: http://en.wikipedia.org/wiki/Real-time_polymerase_chain_reaction real time PCR real time polymerase chain reaction assay OBI:0000894 protein extract PMID: 20032479. A bovine whey protein extract stimulates human neutrophils to generate bioactive IL-1Ra through a NF-kappaB- and MAPK-dependent mechanism. Rusu D, Drouin R, Pouliot Y, Gauthier S, Poubelle PE. J Nutr. 2010 Feb;140(2):382-91. Epub 2009 Dec 23. a protein extract is the output of an extraction process from tissues or cell cultures resulting in a solution of cellular and/or organellar proteins in buffer solution used to prevent degradation, Person: Philippe Rocca-Serra OBI & wikipedia protein extract OBI:0000895 total RNA extract Extraction of total RNA from cells with Qiagen mini RNeasy kit. A RNA extract that is the output of an extraction process in which total celluar and organelle RNA molecules are isolated from a specimen. PERSON: Chris Stoeckert PERSON: Jie Zheng UPenn Group total RNA extract OBI:0000896 secondary structure of RNA molecule PMID: 15630685: Single molecule studies of RNA secondary structure: AFM of TYMV viral RNA. 2010-01-31: Philippe Rocca-Serra: This is a placeholder to allow work on 'nucleic acid mapping assay' in collaboration with RNAOntology group. Need to liaise with SO Person: Philippe Rocca-Serra secondary structure of RNA molecule OBI:0000897 DEPC structure mapping assay PMID:2446263. Probing the structure of RNAs in solution. Nucleic Acids Res. 1987 Nov 25;15(22):9109-28. is a single-nucleotide-resolution nucleic acid structure mapping assay which uses DEPC as reagent and chemical probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure Person: Philippe Rocca-Serra RNA ontology DEPC structure mapping assay OBI:0000899 organellar RNA extract Extraction of organellar RNA from plant cells using organellar RNA binding protein. A RNA extract that is the output of an extraction process in which RNA molecules found in an organelle, e.g., mitochondrion, ER, or chloroplast, excluding the nucleus, are extracted. PERSON: Chris Stoeckert PERSON: Jie Zheng UPenn Group organellar RNA extract OBI:0000902 post mortem specimen the spleen taken from a dead mouse a specimen that was taken from a dead organism Bjoern Peters MO_416 postmortem post mortem specimen OBI:0000903 in vitro cell killing assay Autologous EBV-transformed B-LCL were used as target cells for the influenza virus-specific CTL assays. Equal volumes of target and effector cells were added to tissue culture plates, and 1:2 serial dilutions of effectors were made. After a 4-h incubation of the effector cells with the target cells, supernatants were collected and counted with the LKB 1272 Clinigamma counter. Percent specific killing was determined with the following equation: (experimental 51Cr release - spontaneous 51Cr release)/(maximum 51Cr release - spontaneous 51Cr release) x 100. A cell killing assay that measures if and how many target cells are actively killed by other cells in a cell culture. IEDB IEDB in vitro cell killing assay OBI:0000904 reporter cell line analyte detection bioassay CTLL-2 cells were grown in the presence of hybridoma supernatants and their growth was monitored by a 3H-thymidine incorporation cell proliferation assay in order to detect IL-2 in the hybridoma supernatant. An analyte assay in which a cell line whose growth is known to be affected by the presence of a specific type of material (the anlyte) is cultured in the presence of an input material (the evaluant) in order to detect presence of the analyte in the evaluant. IEDB IEDB reporter cell line analyte detection bioassay OBI:0000905 sequence feature annotation Information about a sequence region Bjoern Peters Bjoern Peters place holder for sequence ontology term sequence feature annotation OBI:0000906 induced hemagglutination The clumping or clustering of red blood cells caused by certain viruses, antibodies, or other substances MC, 20100217: This term was originally submitted to GO, see discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=2947975&group_id=36855&atid=440764. After discussion it was agreed that this isn't a natural in vivo process and therefore out of scope for GO. Dev call Nov 22, 2010: To reflect this, the term's label has been updated to 'induced hemagglutination'. person: Bjoern Peters person: Melanie Courtot hemeagglutination WEB: http://medical-dictionary.thefreedictionary.com/hemagglutination induced hemagglutination OBI:0000907 supplying Jackson Labs supplies mouse strains. The planned process of providing material entities to be used in an investigation. Jennifer Fostel Jennifer Fostel 5/31/2012: A supplying process implies that there is an acquisition process. These may need to be tied together, so that modeling either way is reciprocal. supplying OBI:0000908 labeled DNA extract a labeled specimen that is the output of a labeling process and has grain labeled DNA to be able to detect DNA in future experiments. Need to find out if we consider labeled nucleotides still nucleotides. It is after consulting with ChEBI group. Added duirng Mar 1, 2010 dev call Group: OBI group Group: OBI group labeled DNA extract OBI:0000909 cloacal specimen type of sample used in the PCIRN influenza network A specimen obtained by inserting a swab deeply into the vent of the cloaca of an organism and vigorously swabbing the wall. The swab should be deeply stained with fecal material and is then placed in transport medium. PERSON: Melanie Courtot WEB: http://www.wpro.who.int/NR/rdonlyres/EFD2B9A7-2265-4AD0-BC98-97937B4FA83C/0/manualonanimalaidiagnosisandsurveillance.pdf cloacal specimen OBI:0000910 radio immuno assay To evaluate the specificity of antibody binding to 35S-labeled IA-2(256–760) in comparison with 35S-labeled IA-2IC construct, the mutual inhibition activity of different concentrations of unlabeled IA-2IC and/or IA-2(256–760) fragments were tested. Unlabeled recombinant IA-2(256–760) and/or IA-2IC (0.5-, 1-, 2-, and 4-fold the amount of 35S-labeled protein) were added to each tube and incubated overnight at 4°C with patient sera. The following day, after incubation with radiolabeled 35S–IA-2(256–760) or 35S–IA-2IC proteins, samples were processed with the usual radioimmunoprecipitation assay. An assay in which a radioactive labeled antigen or antibody is used to determine the interaction between an antigen and its receptor. This can be used to detect the presence of an antigen of interest in an input sample or determine the specificity of an input antibody. IEDB IEDB radio immuno assay OBI:0000911 real time reverse-transcription polymerase chain reaction assay Is_a PCR real time preceded by a reverse transcription step (reverse transcription step = an RNA strand is reverse transcribed into its DNA complement using the enzyme reverse transcriptase) PERSON: Bjoern Peters PERSON: Melanie Courtot RRT-PCR RT-rt PCR qRT-PCR real time reverse-transcription polymerase chain reaction assay OBI:0000912 X-ray crystallography assay Crystallizing an antibody:antigen complex, and recording the diffraction pattern of a synchrotron beam, and assembling the 3d complex structure based on homologous complexes. A 3D structure determination assay in which the diffraction of pattern of X-ray beams in a crystal of purified material entities is used to resolve the 3-dimensional structure of the material entity of interest. IEDB IEDB X-ray crystallography assay OBI:0000913 promoter activity detection by reporter gene assay A T cell hybridoma in which the beta-galactosidase gene (lacZ) was inserted under the control of the IL-2 promoter, is detected by adding the X-gal substrate which when cleaved by lacZ results in detectable blue color. An assay in which the activity of a promoter in a cell is monitored by using a reporter gene that was inserted in a genomic location under control of the promoter and whose expression can be easily detected based on qualities or functions of the gene. IEDB IEDB promoter activity detection by reporter gene assay OBI:0000914 nasopharyngeal aspirate specimen type of sample used in the PCIRN influenza network A speciemn which derives from nasopharyngeal mucosa after aspiration. PERSON: Melanie Courtot WEB: http://www.wpro.who.int/NR/rdonlyres/EFD2B9A7-2265-4AD0-BC98-97937B4FA83C/0/manualonanimalaidiagnosisandsurveillance.pdf nasopharyngeal aspirate specimen OBI:0000915 freezing storage a fozen pellet used for later assay A storage process in temperature that maintenance the frozen status of the stored entities. 2010/3/3 Alan Ruttenberg: There is a question of whether we should have a separate objective to "prepare for maintenance" 2014/2/3 OBI dev call: "prepare for maintenance" is a separate process. For example, 'freezing' and 'flash freezing' are defined and can be used to produce frozen material for storage. Updated both textual and logical definition. Both input and output material of freezing storage have quality frozen. Person: Alan Ruttenberg, Mathias Brochhausen MO_481 frozen_storage OBI freezing storage OBI:0000916 flow cytometry assay Using a flow cytometer to quantitate the percent of CD3 positive cells in a population by labeling them with a FITC tagged anti-CD3 antibody. A cytometry assay in which an input cell population is put in solution, is passed by a laser, and optical sensors are used to detect scattering of the laser light and/or fluorescence of specific markers to count and characterize the particles in solution. IEDB IEDB flow cytometry assay OBI:0000917 nasal swab specimen type of sample used in the PCIRN influenza network A specimen obtained using a cotton swab on a stick, passed up the nostril to obtain a sample of exudate and epithelial debris for microbiological or cellular examination. PERSON: Melanie Courtot WEB: http://www.wpro.who.int/NR/rdonlyres/EFD2B9A7-2265-4AD0-BC98-97937B4FA83C/0/manualonanimalaidiagnosisandsurveillance.pdf nasal swab specimen OBI:0000918 Dulbecco's modified Eagle medium A culture medium containing iron, phenol red, amino acids, salts, glucose and vitamins. Logical definition should contain all components listed in textual definition at some point. PERSON:Bjoern Peters D-MEM DMEM Dulbecco's modified Eagle medium OBI:0000919 animal euthanization Rats were euthanized with CO2 A process in which is the end of life of animal is brought about in accordance with local regulations on treatment of animal subjects and using a method which causes minimal pain and distress to the animal subject Helen Parkinson and Melissa Haendel animal sacrifice Melissa Haendel may later be refined with more specific list of organisms animal euthanization OBI:0000920 cytometric bead array assay Using a Luminex machine to detect IFN-gamma and IL-10 in the supernatant of a cell culture. An analyte assay in which a series of beads coated with antibodies specific for different analytes and marked with discrete fluorescent labels are used to simultaneously capture and quantitate soluble analytes. IEDB Luminex assay IEDB cytometric bead array assay OBI:0000921 labeled RNA extract a labeled specimen that is the output of a labeling process and has grain labeled RNA to be able to detect RNA in future experiments. Need to find out if we consider labeled nucleotides still nucleotides. It is after consulting with ChEBI group. Added duirng Mar 1, 2010 dev call Group: OBI group Group: OBI group labeled RNA extract OBI:0000922 frozen specimen Frozen blood plasma A specimen that has been frozen in order to store it. Person:Alan Ruttenberg MO_610 frozen_sample frozen specimen OBI:0000923 surface plasmon resonance binding assay Running a Biacore instrument to measure the affinity, on and off rates of binding of a plate bound antibody to a antigen passing by in flow. A binding assay that uses the detection of electromagnetic waves in a surface to detect material entities adsorbed to the surface, which change the local optical index of refraction. IEDB IEDB surface plasmon resonance binding assay OBI:0000924 labeled specimen A specimen that has been modified in order to be able to detect it in future experiments added during call 3/1/2010 OBI group labeled specimen OBI:0000925 infectious agent is a material entity bearing the disposition to infect an organism IEDB IEDB infectious agent OBI:0000926 obsolete_ambidexterious handedness obsolete_ambidexterious handedness true OBI:0000927 lyophilization storage a storage process with input material entity and output freeze dried material for long time storage PERSON: Chris Stoeckert PERSON: Jie Zheng can link to freezing-dying equipment, such as freeze-dryer, rotary evaporator, if needed lyophilization storage OBI:0000928 material combination function A stirrer has a material combination function A material separation function is a function that decreases the resolution between two or more material entities. Helen Parkinson OBI material combination function OBI:0000929 obsolete_training service provider role EBI provides training on databases and tools and has a training service provider role a service provider role which is realized by a servicer provider organization performing some training obsolete during the San Diego workshop, March 2011 The reason is that we decided to pursue a different modeling approach for services keeping just the 'service consumer' and 'service provider' roles and differentiate just at the level of planned process offered a s service. PERSON:Helen Parkinson OBI obsolete_training service provider role true OBI:0000930 calorimeter A measurement device that is used to calculate the heat flow of a chemical reaction or physical change. PERSON:Bjoern Peters calorimetry instrument? http://chemistry.about.com/od/chemistryglossary/a/calorimeterdef.htm calorimeter OBI:0000931 study intervention the part of the execution of an intervention design study which is varied between two or more subjects in the study PERSON: Bjoern Peters GROUP: OBI study intervention OBI:0000932 material separation device flow cytometer A device with a separation function realized in a planed process material separation device OBI:0000933 positron emission tomography scanner A device that produces a three-dimensional image or picture of functional processes in the body. It detects pairs of gamma rays emitted indirectly by a positron-emitting radionuclide (tracer), which is introduced into the body on a biologically active molecule. PERSON:Bjoern Peters PET scanner? http://en.wikipedia.org/wiki/Positron_emission_tomography positron emission tomography scanner OBI:0000934 intramuscular injection is the injection of a material entity (bearing the administered substance role) into the muscle (bearing the target role) of an organism using a syringe intramuscular injection OBI:0000935 micromanipulator A device that is used to physically interact with a sample under a microscope, where a level of precision of movement is necessary that cannot be achieved by the unaided human hand. PERSON:Bjoern Peters http://en.wikipedia.org/wiki/Micromanipulator micromanipulator OBI:0000936 obsolete_material access provider role A person or organization who provides access to a DNA sequencer. a service provider role which is realized by a servicer provider organization performing access to some material obsolete during the San Diego workshop, March 2011 The reason is that we decided to pursue a different modeling approach for services keeping just the 'service consumer' and 'service provider' roles and differentiate just at the level of planned process offered a s service. PERSON:Helen Parkinson OBI obsolete_material access provider role true OBI:0000937 obsolete_left handedness obsolete_left handedness true OBI:0000938 categorical measurement datum A measurement datum that is reported on a categorical scale Bjoern Peters nominal mesurement datum Bjoern Peters categorical measurement datum OBI:0000939 training process e.g. a training course run by a vendor on their instrument, a training service on a assay by a core facility a process that achieves a training objective training process OBI:0000940 optical microscope A microscope that produces an image of an object by targeting it with an electro-magnetic beam in the visible frequency range PERSON:Bjoern Peters optical microscope OBI:0000941 service consumer role A biologist who uses a sequencing services fulfills the role of a service consumer a role which inheres in a person who uses a service Person:Helen Parkinson OBI service consumer role OBI:0000942 intradermal injection is the injection of a material entity (bearing the administered substance role) into the dermis (bearing the target role) of an organism using a syringe PERSON: Melanie Courtot intradermal injection OBI:0000943 chemical cleavage PMID: 20171258. Comparative reactivity of mismatched and unpaired bases in relation to their type and surroundings. Chemical cleavage of DNA mismatches in mutation detection analysis.Yakubovskaya MG, Belyakova AA, Gasanova VK, Belitsky GA, Dolinnaya NG. Biochimie. 2010 Feb 18. chemical cleavage is a protocol application relying on a chemical compound to cause the fragmentation of an input material that is susceptible to that chemical agent PERSON:Philippe Rocca-Serra RNA ontology group chemical cleavage OBI:0000944 handedness assay The Edinburgh handedness assay is a specific method of determing handedness A handedness assay measures the unequal distribution of fine motor skill between the left and right hands typically in human subjects by means of some questionnaire and scoring procedure. Helen Parkinson handedness test http://en.wikipedia.org/wiki/Handedness handedness assay OBI:0000945 vibration isolation table A device that supports another device such as a precision instrument by isolating it from vibration that is transmitted from the floor. PERSON:Bjoern Peters United States Patent 6877711 vibration isolation table OBI:0000946 sterilization function a function to remove viable organisms from an input material sterilization function OBI:0000947 service provider role Jackson Lab provides experimental animals, EBI provides training on databases, a core facility provides access to a DNA sequencer. is a role which inheres in a person or organization and is realized in in a planned process which provides access to training, materials or execution of protocols for an organization or person PERSON:Helen Parkinson service provider role OBI:0000948 oscilloscope A device that measures and displayes signal voltages, usually as a two-dimensional graph of one or more electrical potential differences (vertical axis) plotted as a function of time or of some other voltage (horizontal axis). PERSON:Bjoern Peters http://en.wikipedia.org/wiki/Oscilloscope oscilloscope OBI:0000949 accessed material role the role of the DNA sequencer to which someone gets access to a period of time, e.g. by payment, or other mechanism is realized in a planned process where the bearer participates AR: rent a DNA sequencer for a period of time. two realizations, payment for the service and also when the person who pays for the service uses it accessed material role OBI:0000950 paraffin specimen liver tissue embedded in paraffin a specimen that is output of a paraffin storage process in which specimen is embedded in paraffin PERSON: Chris Stoeckert PERSON: Jie Zheng MO_990 paraffin_sample paraffin specimen OBI:0000951 compound treatment design an intervention design in which the treatment is the administration of a compound This is meant to include all kinds of material administrations, including vaccinations, chemical compounds etc. PERSON: Bjoern Peters MO_555 compound_treatment_design compound treatment design OBI:0000952 oral administration The administration of a substance into the mouth of an organism PERSON: Melanie Courtot oral administration OBI:0000953 processed specimen A tissue sample that has been sliced and stained for a histology study. A blood specimen that has been centrifuged to obtain the white blood cells. A specimen that has been intentionally physically modified. Bjoern Peters Bjoern Peters A tissue sample that has been sliced and stained for a histology study. processed specimen OBI:0000954 subcutaneous injection is the injection of a material entity (bearing the administered substance role) into the hypodermis (bearing the target role) of an organism using a syringe PERSON: Melanie Courtot subcutaneous injection OBI:0000955 electrode puller A device used in the first step in making electrodes, that applies constant tension on a glass capillary tube and eventually breaks it while heating it; this produces a very fine point on the capillary tube. PERSON:Bjoern Peters http://faculty.plattsburgh.edu/donald.slish/Puller1.html electrode puller OBI:0000956 obsolete_handedness http://purl.obolibrary.org/obo/PATO_0002201 obsolete_handedness true OBI:0000957 self reported handedness assessment An assay in which a person makes a statement that indicates what handedness he has from a choice of different categories. self reported handedness assessment OBI:0000959 vibrotome A preparation device that uses a vibrating razor blade to cut through tissue. vibrotome OBI:0000960 reagent application function An automatic tissue processor automatically applies antibodies and buffers to histological tissue preparations. A function that is realized when a reagent is automatically added to some research material. PERSON: Nicole Vasilevsky, Matthew Brush PERSON: Nicole Vasilevsky, Matthew Brush 4/10/2011: It is unclear if we need / want this, or what this is supposed to be for. Lots of the functions we have are reagent specific. Will this only confuse people? reagent application function OBI:0000961 addition of molecular tracer function Immunohistochemical labeling of tissue sections by an autostainer staining system. A reagent application function that is realized when a molecular tracer, such as an antibody or probe is automatically transferred to a biological specimen. PERSON: Nicole Vasilevsky, Matthew Brush PERSON: Nicole Vasilevsky, Matthew Brush addition of molecular tracer function OBI:0000962 training objective A training objective is fulfilled by e.f. a bioconductor tutorial which instructs the user in the use of a package An training objective which is fulfilled by the provision of some training Helen Parkinson OBI training objective OBI:0000963 categorical label The labels 'positive' vs. 'negative', or 'left handed', 'right handed', 'ambidexterous', or 'strongly binding', 'weakly binding' , 'not binding', or '+++', '++', '+', '-' etc. form scales of categorical labels. A label that is part of a categorical datum and that indicates the value of the data item on the categorical scale. Bjoern Peters Bjoern Peters categorical label OBI:0000964 in live cell assay An assay in which a measurement is made by observing entities located in a live cell. in live cell assay OBI:0000965 lyophilized specimen freezing dried DNA a specimen that is output of a lyophilization storage process in which specimen is lyophilized for storage. PERSON: Chris Stoeckert PERSON: Jie Zheng MO_589 freeze_dried_sample lyophilized specimen OBI:0000966 in live organism assay Measuring the rate in which cells that are pulsed with a peptide are killed inside a mouse by peptide specific cytotoxic T cells. An assay in which a measurement is made by observing entities located in an organism. PERSON:Bjoern Peters in vivo assay in live organism assay OBI:0000967 container A device that can be used to restrict the location of material entities over time 03/21/2010: Added to allow classification of children (similar to what we want to do for 'measurement device'. Lookint at what classifies here, we may want to reconsider a contain function assigned to a part of an entity is necessarily also a function of the whole (e.g. is a centrifuge a container because it has test tubes as parts?) PERSON: Bjoern Peters container OBI:0000968 device A voltmeter is a measurement device which is intended to perform some measure function. An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure. A material entity that is designed to perform a function in a scientific investigation, but is not a reagent. 2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of "device", and are enumerating the types of roles that a reagent can perform. 2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example: (1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part. (2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay. (3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel. In the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent role is not transitive across the part_of relation). In this way, the asserted disjointness between a reagent and device holds, as both roles are never realized in the same bearer during execution of an assay. PERSON: Helen Parkinson instrument OBI development call 2012-12-17. device OBI:0000969 dose specification a protocol specifying to administer 1 ml of vaccine to a mouse a directive information entity that describes the dose that will be administered to a target dose specification 1 OBI:0000970 scalar score from composite inputs A measurement datum which is the result of combining multiple datum. For example, a mean or summary score. JT: We included this because we wanted to talk about an output from a questionnaire that summarized the answers to the questionnaire, but which was not actually the answer to any single question. Person: Jessica Turner questionaire score Person: Jessica Turner JZ: can we defined it logically as the output of some data transformation, like aggragate data transformation? scalar score from composite inputs OBI:0000971 fresh specimen a liver freshly removed from a rat a specimen that is output of a specimen creation process used for an investigation without storage. PERSON: Chris Stoeckert PERSON: Jie Zheng MO_730 fresh_sample fresh specimen OBI:0000972 obsolete_electrically powered device a processed material created to have a function and which requires electrical power to execute obsolete_electrically powered device true OBI:0000973 sequence data example of usage: the representation of a nucleotide sequence in FASTA format used for a sequence similarity search. A measurement datum that representing the primary structure of a macromolecule(it's sequence) sometimes associated with an indicator of confidence of that measurement. Person:Chris Stoeckert GROUP: OBI sequence data OBI:0000974 obsolete_right handedness obsolete_right handedness true OBI:0000975 cell-cell binding detection by flow cytometry assay Staining a B cell with PE and staining a T cell with FITC, incubating them together with a peptide, and counting the number of co-stained conjugates. A binding assay which uses a flow cytometer to detect pairs of cells that are bound to each other by staining them with different fluorescent labels. IEDB IEDB cell-cell binding detection by flow cytometry assay OBI:0000976 handedness categorical measurement datum A datum used to record the answer to a self assessment of whether a person uses their left hand, right hand primarily or each hand equally PERSON:Alan Ruttenberg PERSON:Jessica Turner handedness categorical measurement datum OBI:0000977 paraffin storage a storage process with input organism or anatomical entity and paraffin and output material embedded in paraffin for long term storage PERSON: Chris Stoeckert PERSON: Jie Zheng UPenn Group need to specify paraffin or wax is one of specified input of the process paraffin storage OBI:0000978 in container assay an assay in which a measurement is made by observing entities located in a container. in container assay OBI:0000980 obsolete_protocol service provider role DNA sequencing of a sample by a core lab which returns data to the consumer a service provider role which is realized by a servicer provider organization performing a protocol execution obsolete during the San Diego workshop, March 2011 The reason is that we decided to pursue a different modeling approach for services keeping just the 'service consumer' and 'service provider' roles and differentiate just at the level of planned process offered a s service. PERSON:Helen Parkinson obsolete_protocol service provider role true OBI:0000981 agar stab specimen a specimen that is output of a process that cell culture inoculated into agar for long term storage. PERSON: Chris Stoeckert PERSON: Jie Zheng MO_971 agar_stab agar stab specimen OBI:0000982 computed tomography scanner An image acquisition device that generates a three-dimensional image of the inside of an object from a large series of two-dimensional X-ray images taken around a single axis of rotation. PERSON:Bjoern Peters CT scanner X-ray computed tomography scanner http://en.wikipedia.org/wiki/X-ray_computed_tomography computed tomography scanner OBI:0000983 intranasal mucosal administration The administration of a substance into the intranasal mucosis of an organism PERSON: Melanie Courtot intranasal mucosal administration OBI:0000984 dose An organism has been injected 1ml of vaccine A measurement datum that measures the quantity of something that may be administered to an organism or that an organism may be exposed to. Quantities of nutrients, drugs, vaccines and toxins are referred to as doses. dose OBI:0000985 growth condition intervention design A study design in which the independent variable is the environmental condition in which the specimen is growing PERSON: Bjoern Peters MO_588 growth_condition_design growth condition intervention design OBI:0000986 obsolete_DNA sequencing training service A training process with the objective to provide a trainee with the skill to run DNA sequencing experiments 03/22/2010:workshop: there is a user requirement that not in all cases of the training the trainee gains the skills. obsolete_DNA sequencing training service true OBI:0000987 obsolete_general scalar measurement datum 4/10/2011 BP: It is unclear to me why we need this, and don't just use the scalar measurement datum. See tracker: https://sourceforge.net/tracker/index.php?func=detail&aid=3302925&group_id=177891&atid=886178 obsolete_general scalar measurement datum true OBI:0000988 performing a diagnosis Diagnosing that a patient has pneumonia based on information on measurements of temperature, sound of breathing, and patient complaining about a headache. The interpretation of the information available about bodily features (clinical picture) of a patient resulting in a diagnosis performing a diagnosis OBI:0000989 PCR instrument A device that is used to amplify a single or few copies of a piece of DNA across several orders of magnitude, generating thousands to millions of copies of a particular DNA sequence. 03/21/2010: Added because it is unclear if the thermal cycler definition is intentionally broader than PCR instrument. Contacted Melanie and Trish about this. Definitions and use of alternative terms need to be made consistent. PCR instrument OBI:0000990 electron microscope A microscope that produces an image of an object by targeting it with an electron beam electron microscope 1 OBI:0000991 Edinburgh score A score that measures the dominance of a person's right or left hand in everyday activities. Person: Alan Ruttenberg Person:Jessica Turner PMID:5146491#Oldfield, R.C. (1971). The assessment and analysis of handedness: The Edinburgh inventory. Neuropsychologia, 9, 97-113 WEB:http://www.cse.yorku.ca/course_archive/2006-07/W/4441/EdinburghInventory.html Edinburgh score OBI:0000992 DNA sequencing service A DNA sequencing process provided as a service - which is the realization of some DNA sequencing in which the service provider role is realized. Eagle-i will supply better English definition DNA sequencing service OBI:0000993 service provision objective A sequencing centre has a service provision objective An objective which is fulfilled by the provision of some service e.g. a training service Helen Parkinson OBI service provision objective OBI:0000994 intravenous injection is the injection of a material entity (bearing the administered substance role) into the vein (bearing the target role) of an organism using a syringe PERSON: Melanie Courtot intravenous injection OBI:0000995 administration of material to specimen Staining cells in a tissue slice with a dye. The directed combination of a material entity with a specimen. Bjoern Peters Bjoern Peters administration of material to specimen OBI:0000996 device creation objective an objective which aims to create a device with a specified function PERSON: Helen Parkinson OBI device creation objective OBI:0000997 growth environment The collection of material entities and their qualities that are located near a live organism, tissue or cell and can influence its growth. Right now this may be incomplete. Should also cover e.g. sound, light as well. PERSON:Richard Scheuermann, Jie Zheng, Bjoern Peters OBI group growth environment OBI:0001000 questionnaire A document with a set of printed or written questions with a choice of answers, devised for the purposes of a survey or statistical study. JT: It plays a role in collecting data that could be fleshed out more; but I'm thinking it is, in itself, an edited document. JZ: based on textual definition of edited document, it can be defined as N&S. I prefer to leave questionnaire as a document now. We can add more restrictions in the future and use that to determine it is an edited document or not. Need to clarify if this is a document or a directive information entity (or what their connection is)) PERSON: Jessica Turner Merriam-Webster questionnaire OBI:0001001 Edinburgh handedness assay The Edinburgh Handedness assay is an assay in which a set of questions = the Edinburgh Handedness inventory - is asked and the answers to these questions are turned into a score, used to assess the dominance of a person's right or left hand in everyday activities. The inventory can be used by an observer assessing the person, or by a person self-reporting hand use. The latter method tends to be less reliable due to a person over-attributing tasks to the dominant hand. PERSON:Jessica Turner Person:Alan Ruttenberg WEB:http://en.wikipedia.org/wiki/Edinburgh_Handedness_Inventory Edinburgh handedness assay OBI:0001002 Faraday cage A device formed by conducting material or by a mesh of such material, that blocks out external static electric fields. PERSON:Bjoern Peters Faraday shield Wikipedia http://en.wikipedia.org/wiki/Faraday_cage isolation function? HP Faraday cage OBI:0001003 agar stab storage a storage process with input cell culture and agar and output agar stab for long time storage PERSON: Chris Stoeckert PERSON: Jie Zheng UPenn Group need to specify that agar is one of input for this process agar stab storage OBI:0001005 RNASE CL3 structure mapping assay PMID:16453415 a single-nucleotide-resolution ribonucleic acid structure mapping assay which uses RNAse CL3 as reagent and enzymatic probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure Person:Philippe Rocca-Serra single nucleotide resolution mapping assay using RNAse CL3 RNA ontology RNASE CL3 structure mapping assay OBI:0001006 CMCT structure mapping assay PMID:2422386 and PMID:2446263 a single-nucleotide-resolution nucleic acid structure mapping assay which uses CMCT as reagent and chemical probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure Person: Philippe Rocca-Serra single nucleotide resolution mapping assay using CMCT probe RNA ontology CMCT structure mapping assay OBI:0001007 image creation Taking a polaroid picture of a patients skin lesion; Using a digital camera to take a picture of a gel A planned process that captures an image of an object. PERSON: Jie Zheng image acquisition image creation OBI:0001008 MPE-Fe(II) structure mapping assay PMID:6209709 a single-nucleotide-resolution ribonucleic acid structure mapping assay which uses Fe-MP as reagent and chemical probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure Person: Philippe Rocca-Serra single nucleotide resolution mapping assay using Fe-MP probe RNA ontology MPE-Fe(II) structure mapping assay OBI:0001009 obsolete_qualitative binding detection assay A binding assay where the specified output determines if two or more material entities do or do not have the disposition to form a complex above a threshold level of significance. The threshold can be defined through detection limits of the instrument, the use of experimental controls that establish what is considered significant binding, or a predefined cutoff based on what binding is considered significant in a certain context. PERSON: Bjoern Peters, Randi Vita, Jason Greenbaum obsolete_qualitative binding detection assay true OBI:0001010 nucleic acid extract An extract that is the output of an extraction process in which nucleic acid molecules are isolated from a specimen. PERSON: Jie Zheng UPenn Group nucleic acid extract OBI:0001011 ENU structure mapping assay PMID:7002606 and PMID:2446263 a single-nucleotide-resolution nucleic acid structure mapping assay which uses ENU as reagent and chemical probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure Person: Philippe Rocca-Serra single nucleotide resolution mapping assay using ENU probe RNA ontology ENU structure mapping assay OBI:0001012 RNASE V1 structure mapping assay PMID:7031604 a single-nucleotide-resolution ribonucleic acid structure mapping assay which uses RNAse V1 as reagent and enzymatic probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure Person:Philippe Rocca-Serra single nucleotide resolution mapping assay using RNAse V1 RNA ontology RNASE V1 structure mapping assay OBI:0001013 kethoxal structure mapping assay single nucleotide resolution mapping assay using Kethoxal probe is a single-nucleotide-resolution nucleic acid structure mapping assay which uses kethoxal as reagent and chemical probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure Person: Philippe Rocca-Serra RNA ontology kethoxal structure mapping assay OBI:0001014 single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing a single-nucleotide-resolution nucleic acid structure mapping assay which relies on proteins acting as enzymatic probes in order to produce measurement information which one interpreted provide structural information about the RNA species under study. Person: Philippe Rocca-Serra RNAO and OBI single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing OBI:0001015 DMS structure mapping assay PMID:6159633 and PMID:2446263 a single-nucleotide-resolution nucleic acid structure mapping assay which uses DMS as reagent and chemical probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure Person: Philippe Rocca-Serra single nucleotide resolution mapping assay using DMS probe RNA Ontology DMS structure mapping assay OBI:0001016 DNASE 1 structure mapping assay PMID:3773731 a single-nucleotide-resolution deoxyribonucleic acid structure mapping assay which uses DNAse 1 as reagent and enzymatic probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure Person:Philippe Rocca-Serra DNAse footprinting assay single nucleotide resolution mapping assay using DNAse I RNA ontology DNASE 1 structure mapping assay OBI:0001017 single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing a single-nucleotide-resolution nucleic acid structure mapping assay which relies on small chemical compounds acting as chemical probes in order to produce measurement information which one interpreted provide structural information about the RNA species under study. Person: Philippe Rocca-Serra RNAO and OBI single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing OBI:0001018 Rhodium DNA structure mapping assay PMID:2843807 a single-nucleotide-resolution nucleic acid structure mapping assay which uses Rhodium as reagent and chemical probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure Person:Philippe Rocca-Serra single nucleotide resolution mapping assay using Rhodium probe RNA ontology Rhodium DNA structure mapping assay OBI:0001019 RNA ADA I RNA structure mapping assay PMID:7527340 a single-nucleotide-resolution ribonucleic acid structure mapping assay which uses RNA adenosine deaminase I as reagent and enzymatic probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure Person: Philippe Rocca-Serra single nucleotide resolution mapping assay using RNA adenosine deaminase I RNA ontology RNA ADA I RNA structure mapping assay OBI:0001020 Lead structure mapping assay PMID:2686708 a single-nucleotide-resolution nucleic acid structure mapping assay which uses lead as reagent and chemical probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure Person:Philippe Rocca-Serra single nucleotide resolution mapping assay using Lead probe RNA ontology Lead structure mapping assay OBI:0001021 RNASE T2 structure mapping assay PMID:6207483 a single-nucleotide-resolution ribonucleic acid structure mapping assay which uses RNAse T2 as reagent and enzymatic probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure Person:Philippe Rocca-Serra single nucleotide resolution mapping assay using RNAse T2 RNA ontology RNASE T2 structure mapping assay OBI:0001022 gene dosage assay an assay of changes in phenotype due to increased or decreased dosage of a single allele of a gene. PERSON: Bjoern Peters David Osumi Sutherland gene dosage assay OBI:0001023 Fe-BABE RNA structure mapping assay PMID: 7862644 a single-nucleotide-resolution ribonucleic acid structure mapping assay which uses Fe-BABE as reagent and chemical probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure Person:Philippe Rocca-Serra single nucleotide resolution mapping assay using Fe-BABE probe RNA ontology Fe-BABE RNA structure mapping assay OBI:0001024 RNASE U2 structure mapping assay PMID:409999 a single-nucleotide-resolution ribonucleic acid structure mapping assay which uses RNAase U2 as reagent and enzymatic probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure Person:Philippe Rocca-Serra single nucleotide resolution mapping assay using RNAse U2 RNA ontology RNASE U2 structure mapping assay OBI:0001025 binding constant determination assay Determination of KD value for an antibody binding a protein using a BIACORE assay. A binding assay where the specified output is a binding constant PERSON: Bjoern Peters, Randi Vita, Jason Greenbaum binding constant determination assay OBI:0001026 NMIA RNA structure mapping assay PMID: 15796531 a single-nucleotide-resolution ribonucleic acid structure mapping assay which uses NMIA as reagent and chemical probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure Person:Philippe Rocca-Serra SHAPE mapping assay single nucleotide resolution mapping assay using NMIA probe RNA ontology NMIA RNA structure mapping assay OBI:0001027 Terbium RNA structure mapping assay PMID:10772868 a single-nucleotide-resolution nucleic acid structure mapping assay which uses Terbium as reagent and chemical probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure Person:Philippe Rocca-Serra single nucleotide resolution mapping assay using Terbium probe RNA ontology Terbium RNA structure mapping assay OBI:0001028 feature extraction A planed process with objective of obtaining quantified values from an image. PERSON: Jie Zheng MO_928: feature_extraction feature extraction OBI:0001029 OH-radical structure mapping assay PMID:2501870 a single-nucleotide-resolution nucleic acid structure mapping assay which uses hydroxyl radical as reagent and chemical probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure Person:Philippe Rocca-Serra MOHCA assay OH footprinting assay single nucleotide resolution mapping assay using OH-radical probe RNA ontology OH-radical structure mapping assay OBI:0001030 RNASE T1 structure mapping assay PMID:114514 a single-nucleotide-resolution ribonucleic acid structure mapping assay which uses RNAse T1 as reagent and enzymatic probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure Person:Philippe Rocca-Serra single nucleotide resolution mapping assay using RNAse T1 RNA ontology RNASE T1 structure mapping assay OBI:0001031 array image creation An image creation process that generate an image from the array. PERSON: Jie Zheng array image acquisition MO_929: image_acquisition array image creation OBI:0001032 light emission device A light source is an optical subsystem that provides light for use in a distant area using a delivery system (e.g., fiber optics) a device which has a function to emit light. Person:Helen Parkinson OBI light emission device OBI:0001033 perturbation device A homogenizer is a perturbation device. A perturbation device is a device which is designed to perform a perturb function Helen Parkinson OBI Vancouver workshop 2010 PERSON: Helen Parkinson perturbation device OBI:0001034 environmental control device A growth chamber is an environmental control device. An environmental control device is a device which has the function to control some aspect of the environment such as temperature, or humidity. Helen Parkinson OBI environmental control device OBI:0001035 Nuclease S1 structure mapping assay PMID:363143 a single-nucleotide-resolution deoxyribonucleic acid structure mapping assay which uses DNAse 1 as reagent and enzymatic probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure Person: Philippe Rocca-Serra single nucleotide resolution mapping assay using Nuclease S1 RNA ontology Nuclease S1 structure mapping assay OBI:0001036 specimen fixation function e.g the function of a bar code reader used to read slide bar codes a function that allows specific identification of individual speciment from one another. EAGLE-I specimen fixation function OBI:0001037 obsolete_specimen fixation function A specimen fixation function is a function that holds or fastens an entity in a fixed position. EAGLE-I duplicate term obsolete_specimen fixation function true OBI:0001038 Ruthenium structure mapping assay PMID:3016894 is a single-nucleotide-resolution nucleic acid structure mapping assay which uses Rhutenium as reagent and chemical probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure Person:Philippe Rocca-Serra RNAOntology Ruthenium structure mapping assay OBI:0001039 inline probing RNA structure mapping PMID:10573122 and PMID: 18369975 is a single-nucleotide-resolution ribonucleic acid structure mapping assay which uses intromolecular reactivity to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure Person: Philippe Rocca-Serra RNA ontology inline probing RNA structure mapping OBI:0001040 current amplification function A current amplification function is an amplification function that increases the amplitude of a current. EAGLE-I current amplification function OBI:0001041 stabilization function A stabilization function is a function that holds or isolates an entity such as an instrument or specimen steadfast or at an unfluctuating level or quantity. EAGLE-I isolation function stabilization function OBI:0001042 pump function a transfer unction where the transfer requires work to move the entity, often against a gradient. EAGLE-I pump function OBI:0001043 cell transfer function A cell harvester has a cell transfer function. is a transfer function that displaces cells from one place to another EAGLE-I cell transfer function OBI:0001044 angiograph A device that records the patterns of pulse waves inside blood vessels. PERSON: Erik Segerdell http://medical-dictionary.thefreedictionary.com/angiograph angiograph OBI:0001045 capillary blotter A device that is used to transfer nucleic acids from agarose gels onto a membrane, based on the movement of buffer from a reservoir through the gel and the blotting membrane to a stack of dry blotting paper by capillary force. The molecules are carried to the blotting membrane on which they are adsorbed. PERSON: Erik Segerdell http://www.biometra.de/ capillary blotter OBI:0001046 bioreactor A device or system that supports a biologically active environment. ALAN SAYS NOT AN INSTRUMENT PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Bioreactor bioreactor OBI:0001047 pH meter A device that is used to measure the pH (acidity or alkalinity) of a liquid. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/PH_meter pH meter OBI:0001048 digital camera An image acquisition device that takes video or still photographs, or both, digitally by recording images via an electronic image sensor. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Digital_camera digital camera OBI:0001049 chip spotting device A device for dropping and immobilizing a solution of biomolecules, for example, nucleic acids such as probe DNA, mRNA, and peptide nucleic acid (PNA), and proteins on a DNA microarray surface to manufacture a DNA microarray. PERSON: Erik Segerdell United States Patent 7416705 chip spotting device OBI:0001050 RNA extraction/purification instrument A device that is used to isolate and collect RNA for subsequent molecular analysis. PERSON: Erik Segerdell PERSON: Erik Segerdell RNA extraction/purification instrument OBI:0001051 DNA extract The output of an extraction process in which DNA molecules are purified in order to exclude DNA from organellas. Person: Jie Zheng Group: UPenn group DNA extract OBI:0001052 two-photon laser/detector A light source used in fluorescence imaging that allows the imaging of living tissue up to a depth of 1 mm, based on the concept that two photons of low energy can excite a fluorophore in a quantum event, resulting in the emission of a fluorescence photon, typically at a higher energy than either of the two excitatory photons. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Two-photon_excitation_microscopy two-photon laser/detector OBI:0001053 electrophoresis system A device that moves charged particles through a medium by using an electric field induced by electrodes. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Category:Electrophoresis electrophoresis system OBI:0001054 PET synthesizer A device that is used to produce targeted molecular pharmaceuticals for use in positron emission tomography. PERSON: Erik Segerdell PERSON: Erik Segerdell PET synthesizer OBI:0001055 spinning-disk confocal microscope A confocal microscope that uses a Nipkow disk, a mechanical, geometrically operating image scanning device. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Nipkow_disk spinning-disk confocal microscope OBI:0001056 DNA synthesizer An oligonucleotide synthesizer that is used to custom-build DNA molecules to contain a particular sequence of nucleotides. PERSON: Erik Segerdell http://www.globalspec.com/LearnMore/Labware_Scientific_Instruments/Clinical_Research_Labware/DNA_Synthesizers DNA synthesizer OBI:0001057 high performance liquid chromatography instrument A liquid chromatography instrument that consists of a reservoir of mobile phase, a pump, an injector, a separation column, and a detector. The pump (rather than gravity) provides the higher pressure required to propel the mobile phase and analyte through the densely packed column. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/High_performance_liquid_chromatography high performance liquid chromatography instrument OBI:0001058 microplate reader A measurement device that detects biological, chemical or physical events of samples in microtiter plates. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Plate_reader microplate reader OBI:0001059 ELISA microplate reader A microplate reader that is used for enzyme-linked immunosorbent assays (ELISA). PERSON: Erik Segerdell PERSON: Erik Segerdell ELISA microplate reader OBI:0001060 spot cutter A robotic device that is used to excise spots from gels. PERSON: Erik Segerdell PERSON: Erik Segerdell spot cutter OBI:0001061 microwave synthesis system A device that is used to apply microwave irradiation to chemical reactions. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Microwave_chemistry microwave synthesis system OBI:0001062 densitometer A device that measures the degree of darkness (the optical density) of a photographic or semitransparent material or of a reflecting surface. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Densitometer densitometer OBI:0001063 automatic staining machine A device that is used to automatically stain tissue sections on slides or tissue specimens. PERSON: Erik Segerdell PERSON: Erik Segerdell automatic staining machine OBI:0001064 automatic tissue processor A device for processing histological tissue having a tissue carrier basket suspended from a turntable overlying a plurality of beakers suspended from a carrier plate. The turntable is raised, indexed, and lowered by a suitable driving mechanism to move the tissue basket sequentially through the beakers. Timers can each be programmed to control the movement of the turntable to provide various different cycles for processing the tissue. Some of the beakers are received in individual thermal baths to heat and control the temperature of the substances received in the beakers for treating the tissue. PERSON: Erik Segerdell United States Patent 3762362 automatic tissue processor OBI:0001065 stereo microscope An optical microscope that uses two separate optical paths with two objectives and two eyepieces to provide slightly different viewing angles to the left and right eyes. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Optical_microscope#Stereo_microscope stereo microscope OBI:0001066 top loading balance A balance that consists of a metal plate on which to place an object and a digital readout of the measurement of its mass. PERSON: Erik Segerdell PERSON: Erik Segerdell top loading balance OBI:0001067 perfusion station A device or system in which perfusion units are integrated. PERSON: Erik Segerdell PERSON: Erik Segerdell perfusion station OBI:0001068 SPECT scanner A nuclear medicine tomographic imaging device that uses gamma rays to provide 3D information, typically presented as cross-sectional slices through the specimen but with the ability to be freely reformatted or manipulated as required. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Single_photon_emission_computed_tomography SPECT scanner OBI:0001069 array manufacturer role a manufacturer role which is played by the person or organization that manufactured the array PERSON: Chris Stoeckert, Jie Zheng MO_695 array_manufacturer array manufacturer role OBI:0001070 scintillation counter A device that is used to measure ionizing radiation. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Scintillation_counter scintillation counter OBI:0001071 programmable array microscope A confocal microscope that uses a programmable spatial light modulator for generating an arbitrary pattern of conjugate illumination and detection apertures. PERSON: Erik Segerdell Verveer et al, Journal of Microscopy, vol. 189, pt. 3, pp. 192-8 programmable array microscope OBI:0001072 cryostat A device consisting of a vessel, similar in construction to a vacuum flask, that is used to maintain cold cryogenic temperatures. FIX THIS DEFINITION PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Cryostat cryostat OBI:0001073 microtome knife maker A glass cutting and breaking device that is used to produce glass knives used in ultramicrotomy. PERSON: Erik Segerdell PERSON: Erik Segerdell microtome knife maker OBI:0001074 cryofixation device A device that is used for the fixation or stabilization of biological materials as the first step in specimen preparation for electron microscopy. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Cryofixation cryofixation device OBI:0001075 hybridization oven A device that creates an appropriate environment for nucleic acid hybridization. PERSON: Erik Segerdell PERSON: Erik Segerdell hybridization oven OBI:0001076 incubator shaker An incubating device that provides shaking motion for biomedical applications (e.g., cell cultures). PERSON: Erik Segerdell PERSON: Erik Segerdell incubator shaker OBI:0001077 small-animal image acquisition device A device that is used to image small laboratory animals (e.g., rats and mice) in vivo. PERSON: Erik Segerdell PERSON: Erik Segerdell small-animal image acquisition device OBI:0001078 infrared image acquisition device An image acquisition device that is responsive to an infrared emissive target within a given field of view. PERSON: Erik Segerdell United States Patent 4107530 infrared image acquisition device OBI:0001079 confocal microscope A microscope that is used to increase micrograph contrast and/or reconstruct three-dimensional images by using a spatial pinhole to eliminate out-of-focus light in specimens that are thicker than the focal plane. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Confocal_microscopy confocal microscope OBI:0001080 patch clamp device A device used in electrophysiology that allows the study of single or multiple ion channels in cells. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Patch_clamp patch clamp device OBI:0001081 gel imaging system A device that is used to acquire images of laboratory gels. PERSON: Erik Segerdell PERSON: Erik Segerdell gel imaging system OBI:0001082 protein separation apparatus A device that is used for the separation of proteins. PERSON: Erik Segerdell PERSON: Erik Segerdell protein separation apparatus OBI:0001083 multichannel electronic pipette A multichannel pipette that can be programmed by the user to aspirate a volume of liquid reagent or sample and dispense the aspirated volume or a series of aliquots in successive dispensing operations. PERSON: Erik Segerdell http://www.faqs.org/patents/app/20090196797 multichannel electronic pipette OBI:0001084 vitrification apparatus A device that is used to effect the transition of a substance into a glass. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Glass_transition vitrification apparatus OBI:0001085 radiography instrument An image acquisition device that uses ionizing electromagnetic radiation such as X-rays to view objects. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Medical_radiography radiography instrument OBI:0001086 radiation measurement device A device that consists of a radiosensitive detector and a means of recording the effects of radiation on the detector. PERSON: Erik Segerdell PERSON: Erik Segerdell radiation measurement device OBI:0001087 lyophilizer A device that is used to freeze dry material. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Freeze_drying lyophilizer OBI:0001088 tandem mass spectrometer A mass spectrometer in which ions are subjected to two or more sequential stages of analysis (which may be separated spatially or temporally) according to the quotient mass/charge. PERSON: Erik Segerdell http://goldbook.iupac.org/T06250.html tandem mass spectrometer OBI:0001089 microhardness tester A hardness testing device that is used in light-optical microscopes. PERSON: Erik Segerdell United States Patent 4611487 microhardness tester OBI:0001090 multimode microplate reader A microplate reader that can detect multiple types of absorbance, luminescence or fluorescence. PERSON: Erik Segerdell PERSON: Erik Segerdell multimode microplate reader OBI:0001091 mechanical balance A balance that is used to compare the weights of two bodies, to determine the difference in mass (or weight). PERSON: Erik Segerdell http://www.britannica.com/EBchecked/topic/49765/balance mechanical balance OBI:0001092 computer cluster A group of linked computers, working together closely so that in many respects they form a single computer. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Cluster_(computing) computer cluster OBI:0001093 microtome knife sharpener A device that is used to sharpen knives used in microtomy. PERSON: Erik Segerdell PERSON: Erik Segerdell microtome knife sharpener OBI:0001094 plate shaker A device that provides shaking motion for microplates. PERSON: Erik Segerdell PERSON: Erik Segerdell plate shaker OBI:0001095 coagulation analyzer A device for automatically analyzing blood coagulation in a clinical laboratory. PERSON: Erik Segerdell United States Patent 5439646 coagulation analyzer OBI:0001096 laser capture microdissection microscope A microscope that uses low-energy laser beams and special transfer film to lift single cells from a tissue. PERSON: Erik Segerdell http://www.answers.com/topic/laser-capture-microdissection-microscope-in-medicine laser capture microdissection microscope OBI:0001097 liquid extraction robot A liquid handling device that provides automatic liquid extraction. PERSON: Erik Segerdell PERSON: Erik Segerdell liquid extraction robot OBI:0001098 ultrasound machine A device that is used to visualize subcutaneous body structures including tendons, muscles, joints, vessels and internal organs. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Sonography ultrasound machine OBI:0001099 immunoblot scanner A device that is used for the imaging of immunoblots. PERSON: Erik Segerdell PERSON: Erik Segerdell immunoblot scanner OBI:0001100 microcentrifuge A type of centrifuge that is designed for small tubes (0.2 ml to 2.0 ml), has a compact design, and has a small footprint. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Laboratory_centrifuge microcentrifuge OBI:0001101 electronic repeater pipette A micropipette that can be programmed by the user to aspirate a volume of liquid reagent or sample and dispense a series of aliquots in successive dispensing operations. PERSON: Erik Segerdell http://www.faqs.org/patents/app/20090196797 electronic repeater pipette OBI:0001102 electron paramagnetic resonance spectrometer An spectrophotometer that is used to investigate chemical species that have one or more unpaired electrons, such as organic and inorganic free radicals or inorganic complexes possessing a transition metal ion. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Electron_paramagnetic_resonance electron paramagnetic resonance spectrometer OBI:0001103 rocker A device that provides three-dimensional motion for biomedical applications (e.g., gel trays). PERSON: Erik Segerdell PERSON: Erik Segerdell rocker OBI:0001104 analytical balance A balance with weighing pan(s) inside a transparent enclosure that is used to measure mass to a very high degree of precision and accuracy. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Weighing_scale analytical balance OBI:0001105 scanning force microscope A microscope that forms images of surfaces using a physical probe that scans the specimen. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Scanning_probe_microscopy scanning force microscope OBI:0001106 pulsed-field gel electrophoresis system A gel electrophoresis system that is used to separate very large molecules of DNA. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Pulsed_field_gel_electrophoresis pulsed-field gel electrophoresis system OBI:0001107 tissue embedding station A device that is used to perform paraffin embedding of tissue specimens. PERSON: Erik Segerdell PERSON: Erik Segerdell tissue embedding station OBI:0001108 nucleic acid sequencer An device that is used to determine the order of nucleotides in nucleic acid sequences. PERSON: Erik Segerdell PERSON: Erik Segerdell nucleic acid sequencer OBI:0001109 bead array reader A device that is used to acquire and image bead array data. PERSON: Erik Segerdell PERSON: Erik Segerdell bead array reader OBI:0001110 real-time PCR machine An PCR instrument that enables both detection and quantification of one or more specific sequences in a DNA sample. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Real-time_polymerase_chain_reaction real-time PCR machine OBI:0001111 paraffin oven A device that is used for the warming of paraffin embedding medium. PERSON: Erik Segerdell PERSON: Erik Segerdell paraffin oven OBI:0001112 autoclave A device that is used to sterilize equipment and supplies by subjecting them to high pressure steam at 121 C or more, typically for 15 to 20 minutes depending on the size of the load and the contents. PERSON: Erik Segerdell J. Black, Microbiology, Prentice Hall (1993) pg. 334; http://en.wikipedia.org/wiki/Autoclave autoclave OBI:0001113 microplate washer A device that is used to wash immunoassays in microwell strips and plates with professional accuracy. WHAT IS PROFESSIONAL ACCURACY?? PERSON: Erik Segerdell http://www.articlesnatch.com/Article/Microplate-Readers-And-Washers-For-Laboratories/948037 microplate washer OBI:0001114 nucleic acid extraction/purification instrument A device that is used to isolate and collect nucleic acids (DNA or RNA) for subsequent molecular analysis. PERSON: Erik Segerdell PERSON: Erik Segerdell nucleic acid extraction/purification instrument OBI:0001115 ELISA microplate washer A microplate washer that is used for enzyme-linked immunosorbent assays (ELISA). PERSON: Erik Segerdell PERSON: Erik Segerdell ELISA microplate washer OBI:0001116 vacuum manifold A device that is used for the vacuum-driven processing of multiwell strips or plates, or spin columns. IS THIS AN INSTRUMENT? IS THE DEFINTION CORRECT - TO DISTRIBUTE PRESSURE EVENLY. PERSON: Erik Segerdell PERSON: Erik Segerdell vacuum manifold OBI:0001117 DNA extraction/purification instrument A device that is used to isolate and collect DNA for subsequent molecular analysis. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/DNA_extraction DNA extraction/purification instrument OBI:0001118 multichannel pipette A pipetting system that has a plurality of tip fittings and is used for multi-well plate applications. PERSON: Erik Segerdell PERSON: Erik Segerdell multichannel pipette OBI:0001119 cell harvester A device that is used to harvest cells from microplates and deposit samples on a filter mat. NOT AN INSTRUMENT? PERSON: Erik Segerdell PERSON: Erik Segerdell cell harvester OBI:0001120 portable fluorometer A compact fluorometer that can be carried or moved with ease. PERSON: Erik Segerdell PERSON: Erik Segerdell portable fluorometer OBI:0001121 gel electrophoresis system A device that moves charged particles through a medium by using an electric field induced by electrodes. PERSON: Erik Segerdell electrophoresis system http://en.wikipedia.org/wiki/Category:Electrophoresis gel electrophoresis system OBI:0001122 diffractometer A measurement device for analyzing the structure of a material from the scattering pattern produced when a beam of radiation or particles (e.g. X rays or neutrons) interacts with it. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Diffractometer diffractometer OBI:0001123 microdissection instrument A device that is used for the dissection of tissues under magnification. PERSON: Erik Segerdell http://medical-dictionary.thefreedictionary.com/microdissection microdissection instrument OBI:0001124 micropipette puller A device that is used to fabricate glass micropipettes. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Micropipette micropipette puller OBI:0001125 laser scanning confocal microscope A confocal microscope that obtains high-resolution optical images with depth selectivity, in which a laser beam passes through a light source aperture and then is focused by an objective lens into a small (ideally diffraction limited) focal volume within or on the surface of a specimen. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Confocal_laser_scanning_microscopy laser scanning confocal microscope OBI:0001126 digital microscope A microscope that uses optics and a charge-coupled device (CCD) camera to output a digital image to a monitor. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Digital_microscope digital microscope OBI:0001127 freeze substitution system A device or system for dehydrating and then chemically fixing electron microscopy samples at low temperatures in preparation for various treatments including embedding in resins. PERSON: Erik Segerdell doi:10.1017/S143192760707866X freeze substitution system OBI:0001128 micropipette A microinjection device that is used to measure very small volumes of liquids. PERSON: Erik Segerdell http://www.answers.com/topic/micropipette micropipette OBI:0001129 voltage clamp device A device that is used to measure the ion currents across the membrane of excitable cells, such as neurons, while holding the membrane voltage at a set level. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Voltage_clamp voltage clamp device OBI:0001130 vacuum oven A device that heats materials in a vacuum. PERSON: Erik Segerdell PERSON: Erik Segerdell vacuum oven OBI:0001131 slide warmer A device that is used to heat microscope slides. PERSON: Erik Segerdell PERSON: Erik Segerdell slide warmer OBI:0001132 capillary electrophoresis instrument An electrophoresis system that is used to separate ionic species by their charge and frictional forces and mass. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Capillary_electrophoresis capillary electrophoresis instrument OBI:0001133 denaturing high-performance liquid chromatography instrument A high performance liquid chromatography instrument that employs temperature-dependent separation of DNA containing mismatched base pairs from PCR-amplified DNA fragments for chromatographic mutation analysis. PERSON: Erik Segerdell doi:10.1385/1-59259-850-1:173 denaturing high-performance liquid chromatography instrument OBI:0001134 agarose gel electrophoresis system A gel electrophoresis system that is used to separate DNA or RNA molecules by size, achieved by moving negatively charged nucleic acid molecules through an agarose matrix with an electric field. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Agarose_gel_electrophoresis agarose gel electrophoresis system OBI:0001135 balance A measuring instrument that is used to determine the weight or mass of an object. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Weighing_scale balance OBI:0001136 surface plasmon resonance instrument A tool for measuring adsorption of material onto planar metal (typically gold and silver) surfaces or onto the surface of metal nanoparticles. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Surface_plasmon_resonance surface plasmon resonance instrument OBI:0001137 protein sequencer An device that is used to determine the order of amino acids in protein sequences. PERSON: Erik Segerdell PERSON: Erik Segerdell protein sequencer OBI:0001138 X-ray source A device that is used to generate X-rays. PERSON: Erik Segerdell x-ray generator http://en.wikipedia.org/wiki/X-ray_generator X-ray source OBI:0001139 liquid chromatography instrument A chromatography device that dissolves a mixture in liquid mobile phase to separate the analyte to be measured from other molecules in the mixture and allows it to be isolated PERSON: Matthew Brush PERSON: Matthew Brush liquid chromatography instrument OBI:0001140 spike-in quality control role a reference substance role that is borne by a material entity with a known amount which is mixed into the evaluant of assays for quality control or data normalization purposes PERSON: Chris Stoeckert, Jie Zheng, Bjoern Peter MO_937 spike_quality_control spike-in quality control role OBI:0001141 individual organism identifier a CRID symbol used to distinguish one individual organism from another. PERSON: Chris Stoeckert, Jie Zheng MO_169 Individual individual organism identifier OBI:0001142 dye swap quality control role a reference substance role that is borne by a material entity used in a dye swap design experiment for quality control or data normalization purposes PERSON: Chris Stoeckert, Jie Zheng MO_524 dye_swap_quality_control dye swap quality control role OBI:0001143 labeled nucleic acid extract a labeled specimen that is the output of a labeling process and has grain labeled nucleic acid for detection of the nucleic acid in future experiments. Person: Jie Zheng labeled extract MO_221 labeledExtract labeled extract labeled nucleic acid extract OBI:0001144 binding constant The predicted or measured binding affinity of a peptide to a MHC molecule can be captured in the binding constants "IC50 = 12 nM" or "t 1/2 = 30 minutes". A binding datum about the disposition of two or more material entities to form complexes which comes in the form of a scalar and unit that are utilized in equations that model the binding process 10/6/11 BP: The distinction between binding datum and binding constant is based on the later being part of an equation. That should be captured in the logical definition here, and used to make it to a defined class. PERSON: Bjoern Peters, Randi Vita, Jason Greenbaum binding constant OBI:0001145 3D structure determination of bound complex assay Determination of a 3D structure of an antibody binding a protein by X-Ray crystallography, which identifies the specific binding site of the antibody. A 3D structure determination assay in which a complex of 2 or more material enties is characterized which provides information on their binding configuration. IEDB IEDB 3D structure determination of bound complex assay OBI:0001146 binding assay Determination of KD value for an antibody binding a protein using a BIACORE assay. Using plate bound antigen in an ELISA to determine if a mixture of serum antibodies bind the antigen.nnThe following are NOT binding assays, as the desired output is not binding data: RNA microarray experiments to determine levels of gene expression. ChIP experiments to determine where in DNA a transcription factor binds. Using an IL-2 antibody on an ELISA plate to determine presence of IL-2 after stimulating a T cell culture. An assay with the objective to characterize the disposition of two or more material entities to form a complex. PERSON:Bjoern Peters, Randi Vita, Jason Greenbaum PERSON:Bjoern Peters, Randi Vita, Jason Greenbaum binding assay OBI:0001147 cell culture expansion a processual entity that results in the increase of cell numbers including grow of yeast and bacteria PERSON: Chris Stoeckert, Jie Zheng MO_758 grow BP: add it as subclass of 'cell culturing' JZ: No 'cell culturing' in OBI Has term 'cell co-culturing' and 'maintaining cell culture'. Don't think either of it fit. So leave the term under process. cell culture expansion OBI:0001148 gene knock out a genetic transformation that renders a gene non-functional, e.g. due to a point mutation, or the removal of all, or part of, the gene using recombinant methods. PERSON: Chris Stoeckert, Jie Zheng MO_771 gene_knock_out gene knock out OBI:0001149 gene knock in a genetic transformation that involves the insertion of a protein coding cDNA sequence at a particular locus in an organism's chromosome. Typically, this is done in mice since the technology for this process is more refined, and because mouse embryonic stem cells are easily manipulated. The difference between knock-in technology and transgenic technology is that a knock-in involves a gene inserted into a specific locus, and is a "targeted" insertion. PERSON: Chris Stoeckert, Jie Zheng MO_437 gene_knock_in WEB: http://en.wikipedia.org/wiki/Gene_Knock-in gene knock in OBI:0001150 chromosomal substitution A genetic transformation in which all, or part, of a chromosome from a donor replaces that of the recipient. It does not include chromosome recombination. For single gene insertion, use the term 'gene knock in'. PERSON: Chris Stoeckert, Jie Zheng MO_995 chromosomal_substitution chromosomal substitution OBI:0001151 genetically modified material a material entity, organism or cell, that is the output of a genetic transformation process. PERSON: Jie Zheng GROUP: OBI term is proposed by BP on Oct 25, 2010 dev call genetically modified material OBI:0001152 transfection a genetic transformation which relies on the use of physical, electrical and chemical phenomena to introduce DNA or RNA into a cell PERSON: Chris Stoeckert, Jie Zheng MO_366 transfection transfection OBI:0001153 genetic transformation objective a material transformation objective aims to create genetically modified organism or cell Person: Jie Zheng Person: Jie Zheng suggested to be added by BP and AR during Oct 25, 2010 dev call genetic transformation objective OBI:0001154 induced mutation a genetic transformation that the modification of the genetic material (either coding or non-coding) of an organism is caused by mutagenic compounds or irradiation. PERSON: Chris Stoeckert, Jie Zheng MO_564 induced_mutation induced mutation OBI:0001155 3D structural organization datum The atom coordinates found in a PDB (Protein Data Bank) file, generated by X Ray crystallography or NMR. A measurement datum that describes the structural orientation of a material entity in 3D space. PERSON: Jason Greenbaum, Randi Vita, Bjoern Peters 3D structural organization datum OBI:0001156 age since planting measurement datum An age measurement datum that is the result of the measurement of the age of an organism since planting, the process of placing a plant in media (e.g. soil) to allow it to grow, which excludes sowing. PERSON:Chris Stoeckert, Jie Zheng MO_495 planting Discussed by Jie and Chris, proposed to combine with different kinds of processes as initial time point. Proposed 'age measurement assay' is proceeded by some process. The process can be any kind of process defined in OBI. Think it is more flexible. However, it is hard to model due to lake of temporal predicates on Nov 15, 2010 dev call. Term proposed by Bjoern on Nov 8, 2010 dev call Supported by Alan on Nov 15, 2010 dev call age since planting measurement datum OBI:0001157 age since hatching measurement datum An age measurement datum that is the result of the measurement of the age of an organism since hatching, the process of emergence from an egg. PERSON:Chris Stoeckert, Jie Zheng MO_745 hatching age since hatching measurement datum OBI:0001158 age measurement assay An assay that measures the duration of temporal interval of a process that is part of the life of the bearer, where the initial time point of the measured process is the beginning of some transitional state of the bearer such as birth or when planted. This assay measures time not developmental stage. we recognize that development takes different time periods under different conditions such as media / temperature. For example, age measurement assay of fly age, the output likes 28 days but not mid-life of age at room temperature. PERSON: Alan Ruttenberg OBI group age measurement assay OBI:0001159 age since egg laying measurement datum An age measurement datum that is the result of the measurement of the age of an organism since egg laying, the process of the production of egg(s) by an organism. PERSON:Chris Stoeckert, Jie Zheng MO_767 egg laying age since egg laying measurement datum OBI:0001160 assay validation objective an objective specification to check the accuracy or the quality of the results of an assay by comparison with independent results PERSON: Chris Stoeckert, Jie Zheng GROUP: Penn Group assay validation objective OBI:0001161 age since germination measurement datum An age measurement datum that is the result of the measurement of the age of an organism since germination, the process consisting of physiological and developmental changes by a seed, spore, pollen grain (microspore), or zygote that occur after release from dormancy, and encompassing events prior to and including the first visible indications of growth. Definition of germination comes from GO. However, the term is deprecated from GO now because it is a grouping term without biological significance. PERSON:Chris Stoeckert, Jie Zheng MO_590 germination age since germination measurement datum OBI:0001162 validation by reverse transcription PCR design a study design in which checks the accuracy or the quality of the result of an assay by comparing with reverse transcription PCR results PERSON: Chris Stoeckert, Jie Zheng MO_986 reverse_transcription_PCR_quality_control validation by reverse transcription PCR design OBI:0001163 age since eclosion measurement datum An age measurement datum that is the result of the measurement of the age of an organism since eclosion, the process of emergence of an adult insect from its pupa or cocoon. PERSON:Chris Stoeckert, Jie Zheng MO_876 eclosion age since eclosion measurement datum OBI:0001164 age since sowing measurement datum An age measurement datum that is the result of the measurement of the age of an organism since sowing, the process of placing a seed or spore in some media with the intention to invoke germination. PERSON:Chris Stoeckert, Jie Zheng MO_748 sowing age since sowing measurement datum OBI:0001165 age since coitus measurement datum An age measurement datum that is the result of the measurement of the age of an organism since coitus, the process of copulation that occurs during the process of sexual reproduction. PERSON:Chris Stoeckert, Jie Zheng MO_783 coitus age since coitus measurement datum OBI:0001166 validation by real time PCR design a study design in which the accuracy or the quality of the result of an assay is checked by comparing with real time PCR results PERSON: Chris Stoeckert, Jie Zheng MO_434 real_time_PCR_quality_control validation by real time PCR design OBI:0001167 age measurement datum A time measurement datum that is the result of measurement of age of an organism note that we are currently defining subtypes of age measurement datum that specify when the age is relative to, e.g. planting, as we don't have adequate temporal predicates yet. life of bearer doesn't imply organism this assay measures time not developmental stage. we recognize that development can take different time periods under different conditions such as media / temperature age as a quality is dubious; we plan to revisit stages in development are currently handled with controlled vocabulary, such as 2-somite stage PERSON: Alan Ruttenberg, Chris Stoeckert, Jie Zheng MO_178 Age In MageTab file, we use initialTimePoint (a process) + age (a number expected) + TimeUnit (definied in UO, such as year, hour, day, etc.) Now we use the term label indicating the start time point of measuring the age, (number + TimeUnit) are expected instances of the class discussed on Nov 15, dev call All subtype will be defined by textual definition now. age measurement datum OBI:0001168 age since fertilization measurement datum An age measurement datum that is the result of the measurement of the age of an organism since fertilization, the process of the union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. Definition of fertilization comes from GO. PERSON:Chris Stoeckert, Jie Zheng MO_701 fertilization age since fertilization measurement datum OBI:0001169 age since birth measurement datum An age measurement datum that is the result of the measurement of the age of an organism since birth, the process of emergence and separation of offspring from the mother. PERSON:Chris Stoeckert, Jie Zheng MO_710 birth age since birth measurement datum OBI:0001170 reverse transcription polymerase chain reaction assay an assay that evaluates the concentration of RNA in a sample in which an RNA strand is first reverse transcribed into its DNA complement (complementary DNA, or cDNA) using the enzyme reverse transcriptase, and the resulting cDNA is amplified using traditional or real-time PCR. PERSON: Chris Stoeckert, Jie Zheng GROUP: Penn Group reverse transcription polymerase chain reaction assay OBI:0001171 half life datum (t 1/2) The time it takes for 50% of a class of stochastic processes to occur. Bjoern Peters t 1/2 Bjoern Peters half life datum (t 1/2) OBI:0001172 dose response curve A data item of paired values, one indicating the dose of a material, the other quantitating a measured effect at that dose. The dosing intervals are chosen so that effect values be interpolated by a plotting a curve. Bjoern Peters; Randi Vita dose response curve OBI:0001173 service providing a training course for UCSD employees how to run a DNA sequencer; sequencing a DNA sample provided by a service consumer restricted to non-human samples; giving access to tissue samples in a biobank within OHSU; JAX shipping mice from their colony A planned process in which a service provider performs a task (i.e. a planned process) for a service consumer. Carlo; Matt OBI workshop San Diego 2011 service OBI:0001174 passive immunization Giving VIG (concentrated antibodies from vaccinated donors) to a patient that is infected with smallpox. Transferring epitope specific T cells from one mouse into another. The injection of immune effector material (antibodies, T cells or B cells) into an organism so that the organisms immune system gains its immune effector function to recognize specific antigens. PERSON: Bjoern Peters, Randi Vita, Jason Greenbaum adoptive transfer passive immunization OBI:0001175 selective organism creation objective an objective specification to generate a population or type of organism within species that have some uniform behavioral, morphological, physiological, or genetic characteristics with similarly bred organisms. PERSON: Chris Stoeckert, Jie Zheng WEB: wikipedia http://en.wikipedia.org/wiki/Cultivar http://en.wikipedia.org/wiki/Ecotype http://en.wikipedia.org/wiki/Strain_%28biology%29 selective organism creation objective OBI:0001176 Individual epitope immunization in vivo Injection of a peptide T cell epitope into a mouse An immunization in which an individual epitope is administered into a host organism. 3/16/11 BP: This should have as a logical definition the exclusion that the immunogen cannot be something beyond the epitope itself. I don't know if that is possible to do here. PERSON:Bjoern Peters, Jason Greenbaum, Randi Vita Individual epitope immunization in vivo OBI:0001177 RNA sequencing RNA sequencing is a sequencing process which uses ribonucleic acid as input and results in a the creation of RNA sequence information artifact BP 12/21:Created based on a request from Melanie Bjoern Peters Bjoern Peters RNA sequencing OBI:0001178 efficacy of epitope intervention experiment An experiment that tests if inducing an epitope specific immune response in an organism has an effect, such as the ability to prevent, treat or excarbate diseases in the organism. Bjoern Peters efficacy of in vivo intervention efficacy of epitope intervention experiment OBI:0001179 epitope protection from infectious challenge experiment An epitope protection experiment in which the ability of the epitope to protect the host from an infection is assessed. Bjoern Peters protection from infectious challenge epitope protection from infectious challenge experiment OBI:0001180 half maximal effective concentration (EC50) Determining the potentency of a drug / antibody / toxicant by measuring a graded dose response curve, and determining the concentration of the compound where 50% of its maximal effect is observed. half maximal effective concentration (EC50) is a scalar measurement datum corresponding to the concentration of a compound which induces a response halfway between the baseline and maximum after some specified exposure time. Bjoern Peters; Randi Vita wikipedia half maximal effective concentration (EC50) OBI:0001181 binding datum A data item that states if two or more material entities have the disposition to form a complex, and if so, how strong that disposition is. Bjoern Peters; Randi Vita binding datum OBI:0001182 negative binding datum A binding datum that states that there is no significant disposition of two or more entities to form a complex negative binding datum OBI:0001183 epitope protection from tumor challenge experiment An epitope protection experiment in which the ability of the epitope to protect the host from developing tumors is assessed. Bjoern Peters tumor burden after challenge epitope protection from tumor challenge experiment OBI:0001184 epitope protection experiment an epitope intervention experiment that tests the efficacy of inducing an immune epitope response to prevent disease in a host. Bjoern Peters protection from challenge epitope protection experiment OBI:0001185 selectively maintained organism An organism that is bred to have some uniform behavioral, morphological, physiological, or genetic characteristics with similarly bred organisms Bjoern Peters, Helen Parkinson, Philippe Rocca-Serra, Jie Zheng, Chris Stoeckert cultivar ecotype strain MO_9 StrainOrLine, MO_71 Ecotype, MO_124 Cultivar selectively maintained organism OBI:0001186 epitope protection from infectious challenge experiment based on pathogen burden An epitope protection from infectious challenge experiment in which the readout is a reduction in the presence of pathogens in the host compared to controls. Bjoern Peters pathogen burden after infectious challenge epitope protection from infectious challenge experiment based on pathogen burden OBI:0001187 infectious agent detection assay Culturing a sputum sample on agar medium to detect bacterial growth; Stain slices of liver from a mouse to count presence of infectious centers. An assay in which the presence or amount of an infectious agent in an input material is detected in an evaluant 2/22/2011, BP: This should probably be an analyte assay, but the logical definition of those is currently restricted to 'scattered molecular aggregates', which excludes using infectious agents as analytes. See below (realizes some ('evaluant role' and (role_of some material_entity))) and (realizes some ('analyte role' and (role_of some 'infectious agent'))) and (achieves_planned_objective some 'analyte measurement objective') Bjoern Peters, Randi Vita, Jason Greenbaum infectious agent detection assay OBI:0001188 epitope disease exacerbation experiment an epitope intervention experiment that tests the ability of inducing an epitope immune response to increase the severity of an existing disease in the host. Bjoern Peters exacerbation assay epitope disease exacerbation experiment OBI:0001189 epitope protection experiment based on survival an epitope protection experiment that determines the success of the epitope intervention based on increased survival of the host. Bjoern Peters host survival after challenge epitope protection experiment based on survival OBI:0001190 epitope treatment experiment an epitope intervention experiment that tests the ability of inducing an epitope immune response to treat an existing disease in the host. Bjoern Peters decreased disease symptoms after treatment epitope treatment experiment OBI:0001191 half maximal inhibitory concentration (IC50) Interpolating that at a dose of IC50=12 nM, half of the binding of a comptetitive ligand is inhibited. Half maximal inhibitory concentration (IC50) is a scalar measurement datum that measures the effectiveness of a compound to competitively inhibit a given process, and corresponds to the concentration of the compound at which it reaches half of its maximum inhibitory effect. Bjoern Peters; Randi Vita wikipedia half maximal inhibitory concentration (IC50) OBI:0001192 epitope specific immune intervention An administration in vivo to either actively or passively immunize an organism in order to induce a response against a specific immune epitope Person: Bjoern Peters, Randi Vita, Jason Greenbaum epitope specific immune intervention OBI:0001193 epitope specific cytokine production by T cells A process of cytokine production by T cells resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl epitope specific cytokine production by T cells OBI:0001194 ELISPOT assay measuring epitope specific transforming growth factor-beta production by T cells An assay of epitope specific transforming growth factor-beta production by T cells that uses an ELISPOT assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB TGFb release|ELISPOT ELISPOT assay measuring epitope specific transforming growth factor-beta production by T cells OBI:0001195 operator variation design A study design that assesses the operator performance and relation to data consistency and quality. Person: Chris Stoeckert, Jie Zheng MO_519 operator_variation_design operator variation design OBI:0001196 cytometric bead array assay measuring epitope specific IP-10 production by T cells An assay of epitope specific IP-10 production by T cells that uses a cytometric bead array assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CXCL10/IP-10 release|cytometric bead array cytometric bead array assay measuring epitope specific IP-10 production by T cells OBI:0001197 comparative genome hybridization by array design A study design that detects genomic copy number variations using microarray technology. Person: Chris Stoeckert, Jie Zheng MO_856 comparative_genome_hybridization_design comparative genome hybridization by array design OBI:0001198 biological activity assay measuring epitope specific interleukin-27 production by T cells A T cell epitope specific cytokine production assay that detects interleukin-27 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-27 release|biological activity biological activity assay measuring epitope specific interleukin-27 production by T cells OBI:0001199 in vivo design A study design that is conducted entirely in a living organism, e.g. a compound treatment in a mouse model. Person: Chris Stoeckert, Jie Zheng MO_454 in_vivo_design in vivo design OBI:0001200 genotyping by high throughput sequencing design A study design that classifies an individual or group of individuals on the basis of alleles, haplotypes, SNPs using high througput sequencing techniques. Person: Chris Stoeckert, Jie Zheng MO_560 genotyping_design genotyping by high throughput sequencing design OBI:0001201 epitope specific tolerance induction by T cells A process of tolerance induction by T cells resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl epitope specific tolerance induction by T cells OBI:0001202 innate behavior design A study design in which the innate behavior of the organism is examined, e.g. path finding in bees. Person: Chris Stoeckert, Jie Zheng MO_355 innate_behavior_design innate behavior design OBI:0001203 detection of specific nucleic acids with complementary probes assay measuring epitope specific transforming growth factor-beta production by T cells An assay of epitope specific transforming growth factor-beta production by T cells that uses a detection of specific nucleic acids with complementary probes assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB TGFb release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific transforming growth factor-beta production by T cells OBI:0001204 SNP microarray a DNA microarray used to detect polymorphisms in DNA samples Person: Helen Parkinson EFO_0002703 SNP array SNP microarray OBI:0001205 cell component comparison design A study design that compares samples from different cell components. Person: Chris Stoeckert, Jie Zheng MO_1019 cell_component_comparison_design cell component comparison design OBI:0001206 ELISPOT assay measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells An assay of epitope specific granulocyte macrophage colony stimulating factor production by T cells that uses an ELISPOT assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB GM-CSF release|ELISPOT ELISPOT assay measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells OBI:0001207 epitope specific macrophage inflammatory protein-1 alpha production by T cells A process of macrophage inflammatory protein-1 alpha production by T cells resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl epitope specific macrophage inflammatory protein-1 alpha production by T cells OBI:0001208 epitope specific T cell activation A process of T cell activation resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl epitope specific T cell activation OBI:0001209 biological activity assay measuring epitope specific interleukin-10 production by T cells A T cell epitope specific cytokine production assay that detects interleukin-10 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-10 release|biological activity biological activity assay measuring epitope specific interleukin-10 production by T cells OBI:0001210 cytometric bead array assay measuring epitope specific transforming growth factor-beta production by T cells An assay of epitope specific transforming growth factor-beta production by T cells that uses a cytometric bead array assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB TGFb release|cytometric bead array cytometric bead array assay measuring epitope specific transforming growth factor-beta production by T cells OBI:0001211 ex vivo design A study design where all or part of an organism is removed and studied in vitro, e.g. part of a mouse is removed and cultured in vitro. A cell culture with an established cell line is an in vitro experiment. Person: Chris Stoeckert, Jie Zheng MO_808 ex_vivo_design ex vivo design OBI:0001212 epitope specific type IV hypersensitivity by T cells A process of type IV hypersensitivity by T cells resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl epitope specific type IV hypersensitivity by T cells OBI:0001214 normalization testing design A study design that tests different normalization procedures. Person: Chris Stoeckert, Jie Zheng MO_729 normalization_testing_design normalization testing design OBI:0001215 intracellular material detection assay measuring epitope specific perforin release A T cell epitope specific perforin release assay that uses an intracellular material detection by flow cytometry assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB perforin release|intracellular staining intracellular material detection assay measuring epitope specific perforin release OBI:0001216 cell culture analyte detection bioassay measuring epitope specific interleukin-2 production by T cells An assay of epitope specific interleukin-2 production by T cells that uses a cell culture analyte detection bioassay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-2 release|bioassay cell culture analyte detection bioassay measuring epitope specific interleukin-2 production by T cells OBI:0001217 biological activity assay measuring epitope specific interleukin-22 production by T cells A T cell epitope specific cytokine production assay that detects interleukin-22 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-22 release|biological activity biological activity assay measuring epitope specific interleukin-22 production by T cells OBI:0001218 biological activity assay measuring epitope specific interleukin-8 production by T cells A T cell epitope specific cytokine production assay that detects interleukin-8 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-8 release|biological activity biological activity assay measuring epitope specific interleukin-8 production by T cells OBI:0001219 epitope specific chemokine (C-C motif) ligand 1 production by T cells A process of chemokine (C-C motif) ligand 1 production by T cells resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl epitope specific chemokine (C-C motif) ligand 1 production by T cells OBI:0001220 cell culture analyte detection bioassay measuring epitope specific interleukin-10 production by T cells An assay of epitope specific interleukin-10 production by T cells that uses a cell culture analyte detection bioassay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-10 release|bioassay cell culture analyte detection bioassay measuring epitope specific interleukin-10 production by T cells OBI:0001221 ChIP-chip by SNP array assay An assay where chromatin immunoprecipitation (ChIP) is used in combination with SNP microarray technology Group: ArrayExpress production team EFO_0002764 ChIP-chip by SNP array ChIP-chip by SNP array assay OBI:0001222 ELISA measuring epitope specific RANTES production by T cells An assay of epitope specific RANTES production by T cells that uses an ELISA. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CCL5/RANTES release|ELISA ELISA measuring epitope specific RANTES production by T cells OBI:0001223 cytometric bead array assay measuring epitope specific interleukin-1 beta production by T cells An assay of epitope specific interleukin-1 beta production by T cells that uses a cytometric bead array assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-1b release|cytometric bead array cytometric bead array assay measuring epitope specific interleukin-1 beta production by T cells OBI:0001225 genetic population background information genotype information 'C57BL/6J Hnf1a+/-' in this case, C57BL/6J is the genetic population background information a genetic characteristics information which is a part of genotype information that identifies the population of organisms proposed and discussed on San Diego OBI workshop, March 2011 Group: OBI group Group: OBI group genetic population background information OBI:0001226 environmental history design A study design in which some aspect of the organism's environmental history is studied, such as exposure to teratogen, radiation, climate etc. Person: Chris Stoeckert, Jie Zheng MO_698 environmental_history_design environmental history design OBI:0001227 ELISPOT assay measuring epitope specific interleukin-6 production by T cells An assay of epitope specific interleukin-6 production by T cells that uses an ELISPOT assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-6 release|ELISPOT ELISPOT assay measuring epitope specific interleukin-6 production by T cells OBI:0001228 biological activity assay measuring epitope specific helper T cell enhancement of a B cell mediated immune response A T cell epitope specific helper activity assay that detects the ability of a T cell epitope to enhance an antibody response. IEDB IEDB antibody help|biological activity biological activity assay measuring epitope specific helper T cell enhancement of a B cell mediated immune response OBI:0001229 plasmon resonance assay measuring the dissociation constant [KD] of a T cell epitope:MHC:TCR complex A T cell epitope equilibrium dissociation constant (KD) determination assay that uses a surface plasmon resonance assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB dissociation constant KD|surface plasmon resonance (SPR)|nM plasmon resonance assay measuring the dissociation constant [KD] of a T cell epitope:MHC:TCR complex OBI:0001230 biological activity assay measuring epitope specific interleukin-5 production by T cells A T cell epitope specific cytokine production assay that detects interleukin-5 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-5 release|biological activity biological activity assay measuring epitope specific interleukin-5 production by T cells OBI:0001231 ELISA measuring epitope specific transforming growth factor-beta production by T cells An assay of epitope specific transforming growth factor-beta production by T cells that uses an ELISA. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB TGFb release|ELISA ELISA measuring epitope specific transforming growth factor-beta production by T cells OBI:0001232 biological activity assay measuring epitope specific RANTES production by T cells A T cell epitope specific cytokine production assay that detects RANTES production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CCL5/RANTES release|biological activity biological activity assay measuring epitope specific RANTES production by T cells OBI:0001233 biological activity assay measuring epitope specific granulocyte macrophage colony stimulating factor production by T cells A T cell epitope specific cytokine production assay that detects granulocyte macrophage colony stimulating factor production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB GM-CSF release|biological activity biological activity assay measuring epitope specific granulocyte macrophage colony stimulating factor production by T cells OBI:0001234 epigenetic modification identification objective A molecular feature identification objective that aims to detect epigenetic modifications, such as DNA methylation, histone modifications. Chris Stoeckert, Jie Zheng Person: Chris Stoeckert epigenetic modification identification objective OBI:0001235 transcription profiling by tiling array assay An assay in which the transcriptome of a biological sample is analysed using a tiling path array. Person: James Malone EFO_0002769 transcription profiling by tiling array transcription profiling by tiling array assay OBI:0001236 ELISA measuring epitope specific interleukin-22 production by T cells An assay of epitope specific interleukin-22 production by T cells that uses an ELISA. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-22 release|ELISA ELISA measuring epitope specific interleukin-22 production by T cells OBI:0001237 biological activity assay measuring epitope specific interleukin-21 production by T cells A T cell epitope specific cytokine production assay that detects interleukin-21 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-21 release|biological activity biological activity assay measuring epitope specific interleukin-21 production by T cells OBI:0001238 ELISA measuring epitope specific interleukin-9 production by T cells An assay of epitope specific interleukin-9 production by T cells that uses an ELISA. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-9 release|ELISA ELISA measuring epitope specific interleukin-9 production by T cells OBI:0001239 transcription profiling by high throughput sequencing design A study design in which sequencing technology (e.g. Solexa/454) is used to generate RNA sequence, analyse the transcibed regions of the genome, and/or to quantitate transcript abundance Person: Chris Stoeckert, Jie Zheng Group: ArrayExpress production team transcription profiling by high throughput sequencing design OBI:0001240 intracellular cytokine staining assay measuring epitope specific interleukin-6 production by T cells An assay of epitope specific interleukin-6 production by T cells that uses an intracellular cytokine staining assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-6 release|ICS intracellular cytokine staining assay measuring epitope specific interleukin-6 production by T cells OBI:0001241 cell culture analyte detection bioassay measuring epitope specific interleukin-4 production by T cells An assay of epitope specific interleukin-4 production by T cells that uses a cell culture analyte detection bioassay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-4 release|bioassay cell culture analyte detection bioassay measuring epitope specific interleukin-4 production by T cells OBI:0001242 detection of specific nucleic acids with complementary probes assay measuring epitope specific tumor necrosis factor production by T cells A T cell epitope specific tumor necrosis factor production assay that uses a detection of specific nucleic acids with complementary probes assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB TNFa release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific tumor necrosis factor production by T cells OBI:0001243 cytometric bead array assay measuring epitope specific monocyte chemotactic protein-1 production by T cells An assay of epitope specific monocyte chemotactic protein-1 production by T cells that uses a cytometric bead array assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CCL2/MCP-1 release|cytometric bead array cytometric bead array assay measuring epitope specific monocyte chemotactic protein-1 production by T cells OBI:0001244 ELISA measuring epitope specific interleukin-23 production by T cells An assay of epitope specific interleukin-23 production by T cells that uses an ELISA. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-23 release|ELISA ELISA measuring epitope specific interleukin-23 production by T cells OBI:0001245 detection of specific nucleic acids with complementary probes assay measuring epitope specific perforin release A T cell epitope specific perforin release assay that uses a detection of specific nucleic acids with complementary probes assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB perforin release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific perforin release OBI:0001246 ELISA measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells An assay of epitope specific tumor necrosis factor superfamily cytokine production by T cells that uses an ELISA. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB TNF release|ELISA ELISA measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells OBI:0001247 genotyping by high throughput sequencing assay An assay in which high througput sequencer is used to detect polymorphisms in DNA samples Person: James Malone EFO_0002771: genotyping by high throughput sequencing genotyping by high throughput sequencing assay OBI:0001248 ChIP-chip assay an assay that aims to investigate the interactions between protein and DNA relying on chromatin immunoprecipitation ('ChIP') combined with microarray technology ('chip'). Specially, it allows the identification of protein binding sites on a genome-wide basis. Person: James Malone ChIP-on-chip assay WEB: http://en.wikipedia.org/wiki/ChIP-on-chip Philippe Rocca-Serra ChIP-chip assay OBI:0001249 epitope specific T cell tolerance induction A process of T cell tolerance induction resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl epitope specific T cell tolerance induction OBI:0001250 obsolete intracellular material detection by flow cytometry assay of epitope specific cytotoxic T cell degranulation An intracellular material detection by flow cytometry assay that measures epitope specific cytotoxic T cell degranulation PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) T cell degranulation by intracellular staining obsolete intracellular material detection by flow cytometry assay of epitope specific cytotoxic T cell degranulation true OBI:0001251 biological activity assay measuring epitope specific interleukin-13 production by T cells A T cell epitope specific cytokine production assay that detects interleukin-13 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-13 release|biological activity biological activity assay measuring epitope specific interleukin-13 production by T cells OBI:0001252 array platform variation design A study design in which the array platform is compared, e.g. Agilent versus Affymetrix. Person: Chris Stoeckert, Jie Zheng MO_899 array_platform_variation_design array platform variation design OBI:0001253 biological activity assay measuring interleukin-9 production by T cells A T cell epitope specific cytokine production assay that detects interleukin-9 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-9 release|biological activity biological activity assay measuring interleukin-9 production by T cells OBI:0001254 epitope specific interleukin-3 production by T cells A process of interleukin-3 production by T cells resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl epitope specific interleukin-3 production by T cells OBI:0001255 detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-5 production by T cells An assay of epitope specific interleukin-5 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-5 release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-5 production by T cells OBI:0001256 epitope specific lymphotoxin A production by T cells A process of lymphotoxin A production by T cells resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl epitope specific lymphotoxin A production by T cells OBI:0001257 epitope specific interleukin-1 alpha production by T cells A process of interleukin-1 alpha production by T cells resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl epitope specific interleukin-1 alpha production by T cells OBI:0001258 ChIP-seq design A study design which aims to identify protein and DNA interactions using a combination of chromatin immunoprecipitation and high throughput sequencing. Massively parallel sequence analyses are used in conjunction with whole-genome sequence databases to analyze the interaction pattern of any protein with DNA, or the pattern of any epigenetic chromatin modifications. Person: Chris Stoeckert, Jie Zheng http://en.wikipedia.org/wiki/Chip-Sequencing ChIP-seq design OBI:0001259 translational bias design A study design that characterizes the association of transcripts and translation machinery. Person: Chris Stoeckert, Jie Zheng MO_939 translational_bias_design translational bias design OBI:0001260 ELISA measuring epitope specific interleukin-3 production by T cells An assay of epitope specific interleukin-3 production by T cells that uses an ELISA. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-3 release|ELISA ELISA measuring epitope specific interleukin-3 production by T cells OBI:0001261 ELISA measuring epitope specific interleukin-1 alpha production by T cells An assay of epitope specific interleukin-1 alpha production by T cells that uses an ELISA. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-1a release|ELISA ELISA measuring epitope specific interleukin-1 alpha production by T cells OBI:0001262 epitope specific interleukin-27 production by T cells A process of interleukin-27 production by T cells resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl epitope specific interleukin-27 production by T cells OBI:0001263 biological activity assay measuring epitope specific helper T cell enhancement of a T cell mediated immune response A T cell epitope specific helper activity assay that detects the ability of a T cell epitope to enhance a T cell response. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB T cell help|biological activity biological activity assay measuring epitope specific helper T cell enhancement of a T cell mediated immune response OBI:0001264 biological activity assay measuring epitope specific transforming growth factor-beta production by T cells A T cell epitope specific cytokine production assay that detects transforming growth factor-beta production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB TGFb release|biological activity biological activity assay measuring epitope specific transforming growth factor-beta production by T cells OBI:0001265 FWER adjusted p-value http://ugrad.stat.ubc.ca/R/library/LPE/html/mt.rawp2adjp.html A quantitative confidence value resulting from a multiple testing error correction method which adjusts the p-value used as input to control for Type I error in the context of multiple pairwise tests PERS:Philippe Rocca-Serra adapted from wikipedia (http://en.wikipedia.org/wiki/Familywise_error_rate) FWER adjusted p-value OBI:0001266 DNA methylation profiling by high throughput sequencing assay An assay in which the methylation state of DNA is determined and is compared between samples using sequencing based technology Group: ArrayExpress production team, James Malone, Helen Parkinson EFO_0002761 methylation profiling by high throughput sequencing Philippe Rocca-Serra DNA methylation profiling by high throughput sequencing assay OBI:0001267 epitope specific transforming growth factor-beta production by T cells A process of transforming growth factor-beta production by T cells resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl epitope specific transforming growth factor-beta production by T cells OBI:0001268 detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-12 production by T cells An assay of epitope specific interleukin-12 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-12 release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-12 production by T cells OBI:0001269 biological activity assay measuring epitope specific cytotoxic T cell degranulation A T cell epitope dependent biological activity assay that detects cytotoxic T cell degranulation. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB degranulation|biological activity biological activity assay measuring epitope specific cytotoxic T cell degranulation OBI:0001270 cell culture analyte detection bioassay measuring epitope specific transforming growth factor-beta production by T cells An assay of epitope specific transforming growth factor-beta production by T cells that uses a cell culture analyte detection bioassay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB TGFb release|bioassay cell culture analyte detection bioassay measuring epitope specific transforming growth factor-beta production by T cells OBI:0001271 RNA-seq assay An assay in which sequencing technology (e.g. Solexa/454) is used to generate RNA sequence, analyse the transcibed regions of the genome, and or to quantitate transcript abundance PERSON: James Malone transcription profiling by high throughput sequencing EFO_0002770 transcription profiling by high throughput sequencing JZ: should be inferred as 'DNA sequencing'. Will check in the future. an assay that uses high-throughput sequencing technologies to sequence cDNA in order to get information about a sample's RNA content. RNA-Seq provides researchers with efficient ways to measure transcriptome data experimentally, allowing them to get information such as how different alleles of a gene are expressed, detect post-transcriptional mutations or identify gene fusions. WEB: http://en.wikipedia.org/wiki/RNA-Seq RNA-seq assay OBI:0001272 ELISPOT assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells An assay of epitope specific tumor necrosis factor superfamily cytokine production by T cells that uses an ELISPOT assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB TNF release|ELISPOT ELISPOT assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells OBI:0001273 cell culture analyte detection bioassay measuring epitope specific interleukin-5 production by T cells An assay of epitope specific interleukin-5 production by T cells that uses a cell culture analyte detection bioassay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-5 release|bioassay cell culture analyte detection bioassay measuring epitope specific interleukin-5 production by T cells OBI:0001274 genotyping by array assay An assay in which an array is used to detect polymorphisms in DNA samples Group: ArrayExpress production team EFO_0002767: genotyping by array genotyping by array assay OBI:0001275 epitope specific interleukin-16 production by T cells A process of interleukin-16 production by T cells resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl epitope specific interleukin-16 production by T cells OBI:0001276 biological activity assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells A T cell epitope specific cytokine production assay that detects production of chemokine (C-C motif) ligand 1 by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CCL1/TCA-3 release|biological activity biological activity assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells OBI:0001277 detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-2 production by T cells An assay of epitope specific interleukin-2 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-2 release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-2 production by T cells OBI:0001278 DNA methylation profiling by array design A study design in which the methylation state of DNA is determined and is compared between samples using array technology. Person: Chris Stoeckert, Jie Zheng GROUP: ArrayExpress production team DNA methylation profiling by array design OBI:0001279 detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-22 production by T cells An assay of epitope specific interleukin-22 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-22 release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-22 production by T cells OBI:0001280 biological activity assay measuring epitope specific interleukin-16 production by T cells A T cell epitope specific cytokine production assay that detects interleukin-16 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-16 release|biological activity biological activity assay measuring epitope specific interleukin-16 production by T cells OBI:0001281 ELISA measuring epitope specific IP-10 production by T cells An assay of epitope specific IP-10 production by T cells that uses an ELISA. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CXCL10/IP-10 release|ELISA ELISA measuring epitope specific IP-10 production by T cells OBI:0001282 translation profiling assay An assay in which surface-bound, translationally competent ribosome complexes are used to generate a translation profile for mRNA, which mRNA may be a single molecular species, or a combination of species, including complex mixtures such as those found in the set of mRNAs isolated from a cell or tissue. One or more components of the surface-bound ribosome complex may be labeled at specific positions to permit analysis of multiple or single molecules for determination of ribosomal conformational changes and translation kinetics. Translation profiles are used as the basis for comparison of an mRNA or set of mRNA species. The translation profile can be used to determine such characteristics as kinetics of initiation, kinetic of elongation, identity of the polypeptide product, and the like. Analysis of translation profiles may be used to determine differential gene expression, optimization of mRNA sequences for expression, screening drug candidates for an effect on translation. PERSON: James Malone EFO_0001033 translation profiling translation profiling assay OBI:0001283 ELISA measuring epitope specific interleukin-15 production by T cells An assay of epitope specific interleukin-15 production by T cells that uses an ELISA. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-15 release|ELISA ELISA measuring epitope specific interleukin-15 production by T cells OBI:0001284 cytometric bead array assay measuring epitope specific interleukin-12 production by T cells An assay of epitope specific interleukin-12 production by T cells that uses a cytometric bead array assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-12 release|cytometric bead array cytometric bead array assay measuring epitope specific interleukin-12 production by T cells OBI:0001285 in vitro design A study design that is done in a test tube or a culture dish, e.g. A bacterial invasion assay in an established cell culture. Person: Chris Stoeckert, Jie Zheng MO_347 in_vitro_design in vitro design OBI:0001286 RNAi profiling by array design A study design in which experiment double stranded RNA is synthesized with a sequence complementary to a gene(s) of interest and introduced into a cell or organism, where it is recognized as exogenous genetic material and activates the RNAi pathway resulting in knockdown of the transcripts and providing a means to study downstream changes in gene expression. Person: Chris Stoeckert, Jie Zheng Group: ArrayExpress production team RNAi profiling by array design OBI:0001288 ELISA measuring epitope specific lymphotoxin A production by T cells An assay of epitope specific lymphotoxin A production by T cells that uses an ELISA. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB lymphotoxin A/TNFb release|ELISA ELISA measuring epitope specific lymphotoxin A production by T cells OBI:0001289 cytometric bead array assay measuring epitope specific interleukin-5 production by T cells An assay of epitope specific interleukin-5 production by T cells that uses a cytometric bead array assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-5 release|cytometric bead array cytometric bead array assay measuring epitope specific interleukin-5 production by T cells OBI:0001290 transcription profiling by array design A study design that identifies forms and abundance of transcripts in the genome using microarray technology. Person: Chris Stoeckert, Jie Zheng MO_533 transcript_identification_design transcription profiling by array design OBI:0001291 detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-17 production by T cells An assay of epitope specific interleukin-17 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-17 release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-17 production by T cells OBI:0001292 biological activity assay measuring epitope specific interleukin-15 production by T cells A T cell epitope specific cytokine production assay that detects interleukin-15 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-15 release|biological activity biological activity assay measuring epitope specific interleukin-15 production by T cells OBI:0001293 disease state design A study design in which the pathological condition of a part, organ, or system of an organism is studied. The etiology may be from infection, genetic defect, or environmental stress. Person: Chris Stoeckert, Jie Zheng MO_902 disease_state_design disease state design OBI:0001294 wild type organism genotype information C57BL/6J wild type a genotype information about an organism and includes information that there are no known modifications to the genetic background. Generally it is the genotype information of a representative individual from a class of organisms. proposed and discussed on San Diego OBI workshop, March 2011 Group: OBI group Group: OBI group wild type organism genotype information OBI:0001295 biological activity assay measuring epitope specific interleukin-17 production by T cells A T cell epitope specific cytokine production assay that detects interleukin-17 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-17 release|biological activity biological activity assay measuring epitope specific interleukin-17 production by T cells OBI:0001296 cytometric bead array assay measuring epitope specific interleukin-17 production by T cells An assay of epitope specific interleukin-17 production by T cells that uses a cytometric bead array assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-17 release|cytometric bead array cytometric bead array assay measuring epitope specific interleukin-17 production by T cells OBI:0001297 cytometric bead array assay measuring epitope specific interleukin-10 production by T cells An assay of epitope specific interleukin-10 production by T cells that uses a cytometric bead array assay. IEDB IEDB IL-10 release|cytometric bead array cytometric bead array assay measuring epitope specific interleukin-10 production by T cells OBI:0001298 detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-21 production by T cells An assay of epitope specific interleukin-21 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-21 release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-21 production by T cells OBI:0001299 intracellular cytokine staining assay measuring epitope specific interleukin-5 production by T cells An assay of epitope specific interleukin-5 production by T cells that uses an intracellular cytokine staining assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-5 release|ICS intracellular cytokine staining assay measuring epitope specific interleukin-5 production by T cells OBI:0001300 cytometric bead array assay measuring epitope specific interleukin-2 production by T cells An assay of epitope specific interleukin-2 production by T cells that uses a cytometric bead array assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-2 release|cytometric bead array cytometric bead array assay measuring epitope specific interleukin-2 production by T cells OBI:0001301 cell culture analyte detection bioassay measuring epitope specific interleukin-16 production by T cells An assay of epitope specific interleukin-16 production by T cells that uses a cell culture analyte detection bioassay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-16 release|bioassay cell culture analyte detection bioassay measuring epitope specific interleukin-16 production by T cells OBI:0001302 ELISA measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells An assay of epitope specific macrophage inflammatory protein-1 alpha production by T cells that uses an ELISA. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CCL3/MIP-1a release|ELISA ELISA measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells OBI:0001303 intracellular cytokine staining assay measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells An assay of epitope specific granulocyte macrophage colony stimulating factor production by T cells that uses an intracellular cytokine staining assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB GM-CSF release|ICS intracellular cytokine staining assay measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells OBI:0001304 RNAi profiling by array assay An assay in which double stranded RNA is synthesized with a sequence complementary to a gene(s) of interest and introduced into a cell or organism, where it is recognized as exogenous genetic material and activates the RNAi pathway resulting in knockdown of the transcripts and providing a means to study downstream changes in gene expression. PERSON: James Malone EFO_0001030 RNAi profiling by array RNAi profiling by array assay OBI:0001305 genotype information Genotype information can be: Mus musculus wild type (in this case the genetic population background information is Mus musculus), C57BL/6J Hnf1a+/- (in this case, C57BL/6J is the genetic population background information and Hnf1a+/- is the allele information a genetic characteristics information that is about the genetic material of an organism and minimally includes information about the genetic background and can in addition contain information about specific alleles, genetic modifications, etc. discussed on San Diego OBI workshop, March 2011 Group: OBI group Group: OBI group genotype information OBI:0001306 RNA stability design A study design that examines the stability and/or decay of RNA transcripts. Person: Chris Stoeckert, Jie Zheng MO_553 RNA_stability_design RNA stability design OBI:0001307 tiling microarray a DNA microarray which has short fragments of nucleic acid immobilized on a substrate. These are designed to cover the whole genome of the target species. Tiling arrays are used to determine genome binding in ChIP assays or to identify transcribed regions. Person: Helen Parkinson genome tiling array EFO_0002704: tiling array tiling microarray OBI:0001308 biological activity assay measuring epitope specific IP-10 production by T cells A T cell epitope specific cytokine production assay that detects IP-10 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CXCL10/IP-10 release|biological activity biological activity assay measuring epitope specific IP-10 production by T cells OBI:0001309 intracellular cytokine staining assay measuring epitope specific interleukin-13 production by T cells An assay of epitope specific interleukin-13 production by T cells that uses an intracellular cytokine staining assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-13 release|ICS intracellular cytokine staining assay measuring epitope specific interleukin-13 production by T cells OBI:0001310 species comparison design A study design that assays differences between distinct species. Person: Chris Stoeckert, Jie Zheng MO_675 species_design species comparison design OBI:0001311 X-ray crystallography assay determining the 3D structure of a T cell epitope:MHC:TCR complex A T cell epitope 3D structure determination assay that uses an X-ray crystallography assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB 3D structure|x-ray crystallography|angstroms X-ray crystallography assay determining the 3D structure of a T cell epitope:MHC:TCR complex OBI:0001313 transcription profiling by RT-PCR design A study design which aims to examine the transcriptome of a biological sample by reverse transcription PCR (RT-PCR). Person: Chris Stoeckert, Jie Zheng Group: ArrayExpress production team transcription profiling by RT-PCR design OBI:0001314 epitope specific T cell enhancement of B cell mediated immune response A process of T cell enhancement of B cell mediated immune response resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl epitope specific T cell enhancement of B cell mediated immune response OBI:0001315 ELISA measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells An assay of epitope specific chemokine (C-C motif) ligand 1 production by T cells that uses an ELISA. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CCL1/TCA-3 release|ELISA ELISA measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells OBI:0001316 epitope specific interleukin-21 production by T cells A process of interleukin-21 production by T cells resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl epitope specific interleukin-21 production by T cells OBI:0001317 flow cytometry assay measuring cell-cell binding of a T cell epitope:MHC:TCR complex A T cell epitope qualitative binding assay that uses a cell-cell binding detection by flow cytometry assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB T cell- APC binding|binding assay flow cytometry assay measuring cell-cell binding of a T cell epitope:MHC:TCR complex OBI:0001318 proteomic profiling by array assay An assay that proteins in a sample are detected, quantified or otherwise analysed, e.g. antibody profiling using an array based technology Person: James Malone EFO_0002765 proteomic profiling by array proteomic profiling by array assay OBI:0001319 cell culture analyte detection bioassay measuring epitope specific interferon-gamma production by T cells An assay of epitope specific interferon-gamma production by T cells that uses a cell culture analyte detection bioassay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IFNg release|bioassay cell culture analyte detection bioassay measuring epitope specific interferon-gamma production by T cells OBI:0001322 ELISPOT assay measuring epitope specific granzyme B release by T cells A T cell epitope specific granzyme B release assay that uses an ELISPOT assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB granzyme B release|ELISPOT ELISPOT assay measuring epitope specific granzyme B release by T cells OBI:0001323 microRNA profiling by array design A study design in which a microRNA array is used to analyse the microRNA component of the transcriptome. Person: Chris Stoeckert, Jie Zheng Group: ArrayExpress production team microRNA profiling by array design OBI:0001324 in vivo assay measuring T cell epitope specific tolerance induction An efficacy of T cell epitope intervention experiment that uses a tolerance induction intervention experiment. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB tolerance|in vivo assay in vivo assay measuring T cell epitope specific tolerance induction OBI:0001325 detection of specific nucleic acids with complementary probes assay measuring epitope specific RANTES production by T cells An assay of epitope specific RANTES production by T cells that uses a detection of specific nucleic acids with complementary probes assay. IEDB IEDB CCL5/RANTES release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific RANTES production by T cells OBI:0001326 cytometric bead array assay measuring epitope specific interleukin-4 production by T cells An assay of epitope specific interleukin-4 production by T cells that uses a cytometric bead array assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-4 release|cytometric bead array cytometric bead array assay measuring epitope specific interleukin-4 production by T cells OBI:0001327 biological activity assay measuring epitope specific lymphotoxin A production by T cells A T cell epitope specific cytokine production assay that detects lymphotoxin A production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB lymphotoxin A/TNFb release|biological activity biological activity assay measuring epitope specific lymphotoxin A production by T cells OBI:0001328 organism development design A study design that assays events associated with development. Development applies to organism(s) acquiring a mature state. Person: Chris Stoeckert, Jie Zheng MO_892 development_or_differentiation_design organism development design OBI:0001329 family history design A study design in which the family history such as traits, characteristics, susceptibility to disease is studied. Person: Chris Stoeckert, Jie Zheng MO_544 family_history_design family history design OBI:0001330 ELISA measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells An assay of epitope specific chemokine (C-X-C motif) ligand 9 production by T cells that uses an ELISA. IEDB IEDB CXCL9/MIG release|ELISA ELISA measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells OBI:0001331 transcription profiling identification objective A molecular feature identification objective that aims to characterize the abundance of transcripts Person: Chris Stoeckert, Jie Zheng Group: Penn Group transcription profiling identification objective OBI:0001332 DNA methylation profiling by array assay An assay in which the methylation state of DNA is determined and is compared between samples using array technology Person: James Malone EFO_0002759 methylation profiling by array Philippe Rocca-Serra DNA methylation profiling by array assay OBI:0001333 biological activity assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells A T cell epitope specific cytokine production assay that detects macrophage inflammatory protein-1 alpha production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CCL3/MIP-1a release|biological activity biological activity assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells OBI:0001334 epitope specific granulocyte colony stimulating factor production by T cells A process of granulocyte colony stimulating factor production by T cells resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl epitope specific granulocyte colony stimulating factor production by T cells OBI:0001335 microRNA profiling by array assay An assay in which a microRNA array is used to analyse the microRNA component of the transcriptome. PERSON: James Malone EFO_0000753 microRNA profiling by array microRNA profiling by array assay OBI:0001336 quality control testing design A study design in which some aspects of the experiment is quality controlled for the purposes of quality assurance. Person: Chris Stoeckert, Jie Zheng MO_981 quality_control_testing_design quality control testing design OBI:0001337 clinical history design A study design that the organism's clinical history of diagnosis, treatments, e.g. vaccinations, surgery etc. is studied. Person: Chris Stoeckert, Jie Zheng MO_832 clinical_history_design clinical history design OBI:0001339 detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-4 production by T cells An assay of epitope specific interleukin-4 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-4 release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-4 production by T cells OBI:0001341 cell culture analyte detection bioassay measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells An assay of epitope specific granulocyte macrophage colony stimulating factor production by T cells that uses a cell culture analyte detection bioassay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB GM-CSF release|bioassay cell culture analyte detection bioassay measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells OBI:0001342 intracellular cytokine staining assay measuring epitope specific interleukin-21 production by T cells An assay of epitope specific interleukin-21 production by T cells that uses an intracellular cytokine staining assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-21 release|ICS intracellular cytokine staining assay measuring epitope specific interleukin-21 production by T cells OBI:0001343 detection of specific nucleic acids with complementary probes assay measuring epitope specific monocyte chemotactic protein-1 production by T cells An assay of epitope specific monocyte chemotactic protein-1 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CCL2/MCP-1 release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific monocyte chemotactic protein-1 production by T cells OBI:0001344 ELISA measuring epitope specific monocyte chemotactic protein-1 production by T cells An assay of epitope specific monocyte chemotactic protein-1 production by T cells that uses an ELISA. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CCL2/MCP-1 release|ELISA ELISA measuring epitope specific monocyte chemotactic protein-1 production by T cells OBI:0001345 biological activity assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells A T cell epitope specific cytokine production assay that detects chemokine (C-C motif) ligand 4 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CCL4/MIP-1b release|biological activity biological activity assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells OBI:0001346 ELISA measuring epitope specific interleukin-21 production by T cells An assay of epitope specific interleukin-21 production by T cells that uses an ELISA. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-21 release|ELISA ELISA measuring epitope specific interleukin-21 production by T cells OBI:0001348 in vivo skin test assay measuring T cell epitope specific type IV hypersensitivity An efficacy of T cell epitope intervention experiment that detects epitope specific type IV hypersensitivity. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB type IV hypersensitivity (DTH)|in vivo skin test in vivo skin test assay measuring T cell epitope specific type IV hypersensitivity OBI:0001349 cytometric bead array assay measuring epitope specific interleukin-13 production by T cells An assay of epitope specific interleukin-13 production by T cells that uses a cytometric bead array assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-13 release|cytometric bead array cytometric bead array assay measuring epitope specific interleukin-13 production by T cells OBI:0001350 detection of specific nucleic acids with complementary probes assay measuring epitope specific interferon-gamma production by T cells An assay of epitope specific interferon-gamma production by T cells that uses a detection of specific nucleic acids with complementary probes assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IFNg release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific interferon-gamma production by T cells OBI:0001351 epitope specific tumor necrosis factor superfamily cytokine production by T cells A process of tumor necrosis factor superfamily cytokine production by T cells resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl epitope specific tumor necrosis factor superfamily cytokine production by T cells OBI:0001352 allele information genotype information 'C57BL/6J Hnf1a+/-' in this case, Hnf1a+/- is the allele information a genetic alteration information that about one of two or more alternative forms of a gene or marker sequence and differing from other alleles at one or more mutational sites based on sequence. Polymorphisms are included in this definition. discussed on San Diego OBI workshop, March 2011 Person: Chris Stoeckert, Jie Zheng MO_58 Allele allele information OBI:0001353 cytometric bead array assay measuring epitope specific tumor necrosis factor production by T cells A T cell epitope specific tumor necrosis factor production assay that uses a cytometric bead array assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB TNFa release|cytometric bead array cytometric bead array assay measuring epitope specific tumor necrosis factor production by T cells OBI:0001354 ELISPOT assay measuring epitope specific interleukin-17 production by T cells An assay of epitope specific interleukin-17 production by T cells that uses an ELISPOT assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-17 release|ELISPOT ELISPOT assay measuring epitope specific interleukin-17 production by T cells OBI:0001356 detection of specific nucleic acids with complementary probes assay measuring epitope specific interferon-beta production by T cells An assay of epitope specific interferon-beta production by T cells that uses a detection of specific nucleic acids with complementary probes assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IFNb release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific interferon-beta production by T cells OBI:0001357 detection of specific nucleic acids with complementary probes assay measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells An assay of epitope specific granulocyte macrophage colony stimulating factor production by T cells that uses a detection of specific nucleic acids with complementary probes assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB GM-CSF release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells OBI:0001358 post-transcriptional modification design A study design in which a modification of the transcriptome, proteome (not genome) is made, for example RNAi, antibody targeting. Person: Chris Stoeckert, Jie Zheng MO_392 cellular_modification_design post transcription modification design? or more clear RNAi design / antibody targeting design? need to check the use cases post-transcriptional modification design OBI:0001359 ELISA measuring epitope specific interleukin-8 production by T cells An assay of epitope specific interleukin-8 production by T cells that uses an ELISA. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-8 release|ELISA ELISA measuring epitope specific interleukin-8 production by T cells OBI:0001360 cytometric bead array assay measuring epitope specific interleukin-6 production by T cells An assay of epitope specific interleukin-6 production by T cells that uses a cytometric bead array assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-6 release|cytometric bead array cytometric bead array assay measuring epitope specific interleukin-6 production by T cells OBI:0001361 transcription profiling by RT-PCR assay An assay in which the transcriptome of a biological sample is analysed by reverse transcription PCR (RT-PCR) Person: Anna Farne EFO_0002943: transcription profiling by RT-PCR transcription profiling by RT-PCR assay OBI:0001362 epitope specific chemokine (C-C motif) ligand 4 production by T cells A process of chemokine (C-C motif) ligand 4 production by T cells resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl epitope specific chemokine (C-C motif) ligand 4 production by T cells OBI:0001363 biological activity assay measuring epitope specific interleukin-23 production by T cells A T cell epitope specific cytokine production assay that detects interleukin-23 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-23 release|biological activity biological activity assay measuring epitope specific interleukin-23 production by T cells OBI:0001364 genetic alteration information a genetic characteristics information that is about known changes or the lack thereof from the genetic background, including allele information, duplication, insertion, deletion, etc. proposed and discussed on San Diego OBI workshop, March 2011 Group: OBI group Group: OBI group genetic alteration information OBI:0001365 cellular process design A study design that aims to study the processes that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. Person: Chris Stoeckert, Jie Zheng MO_810 cellular_process_design cellular process design OBI:0001366 epitope specific RANTES production by T cells A process of RANTES production by T cells resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl epitope specific RANTES production by T cells OBI:0001367 detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-10 production by T cells An assay of epitope specific interleukin-10 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-10 release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-10 production by T cells OBI:0001368 cytometric bead array assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells An assay of epitope specific tumor necrosis factor superfamily cytokine production by T cells that uses a cytometric bead array assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB TNF release|cytometric bead array cytometric bead array assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells OBI:0001369 wild type allele information an allele information that is about the allele found most frequently in natural populations, or in standard laboratory stocks for a given organism. discussed on San Diego OBI workshop, March 2011 Person: Chris Stoeckert, Jie Zheng MO_605 genotype wild type allele information OBI:0001370 intracellular cytokine staining assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells An assay of epitope specific chemokine (C-C motif) ligand 4 production by T cells that uses an intracellular cytokine staining assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CCL4/MIP-1b release|ICS intracellular cytokine staining assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells OBI:0001371 epitope specific granzyme B production by T cells A process of granzyme B production by T cells resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl epitope specific granzyme B production by T cells OBI:0001373 epitope specific interleukin-8 production by T cells A process of interleukin-8 production by T cells resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl epitope specific interleukin-8 production by T cells OBI:0001374 injury design A study design in which the response of an organism(s) to injury or damage is studied. Person: Chris Stoeckert, Jie Zheng MO_726 injury_design injury design OBI:0001376 intracellular cytokine staining assay measuring epitope specific interleukin-3 production by T cells An assay of epitope specific interleukin-3 production by T cells that uses an intracellular cytokine staining assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-3 release|ICS intracellular cytokine staining assay measuring epitope specific interleukin-3 production by T cells OBI:0001377 organism status comparison design A study design that compares samples from live and dead organisms. Person: Chris Stoeckert, Jie Zheng MO_841 organism_status_design organism status comparison design OBI:0001378 ELISA measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells An assay of epitope specific chemokine (C-C motif) ligand 4 production by T cells that uses an ELISA. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CCL4/MIP-1b release|ELISA ELISA measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells OBI:0001379 cytometric bead array assay measuring epitope specific interferon-gamma production by T cells An assay of epitope specific interferon-gamma production by T cells that uses a cytometric bead array assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IFNg release|cytometric bead array cytometric bead array assay measuring epitope specific interferon-gamma production by T cells OBI:0001380 biological activity assay measuring epitope specific interleukin-18 production by T cells A T cell epitope specific cytokine production assay that detects interleukin-18 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-18 release|biological activity biological activity assay measuring epitope specific interleukin-18 production by T cells OBI:0001381 epitope specific interleukin-23 production by T cells A process of interleukin-23 production by T cells resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl epitope specific interleukin-23 production by T cells OBI:0001382 detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-27 production by T cells An assay of epitope specific interleukin-27 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-27 release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-27 production by T cells OBI:0001383 detection of specific nucleic acids with complementary probes assay measuring epitope specific IP-10 production by T cells An assay of epitope specific IP-10 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CXCL10/IP-10 release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific IP-10 production by T cells OBI:0001384 cell culture analyte detection bioassay measuring epitope specific interleukin-3 production by T cells An assay of epitope specific interleukin-3 production by T cells that uses a cell culture analyte detection bioassay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-3 release|bioassay cell culture analyte detection bioassay measuring epitope specific interleukin-3 production by T cells OBI:0001385 intracellular cytokine staining assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells An assay of epitope specific tumor necrosis factor superfamily cytokine production by T cells that uses an intracellular cytokine staining assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB TNF release|ICS intracellular cytokine staining assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells OBI:0001386 epitope specific monocyte chemotactic protein-1 production by T cells A process of monocyte chemotactic protein-1 production by T cells resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl epitope specific monocyte chemotactic protein-1 production by T cells OBI:0001387 genotyping by array design A study design that classifies an individual or group of individuals on the basis of alleles, haplotypes, SNPs using microarray technology. Person: Chris Stoeckert, Jie Zheng MO_560 genotyping_design genotyping by array design OBI:0001388 biological activity assay measuring epitope specific interleukin-1 alpha production by T cells A T cell epitope specific cytokine production assay that detects interleukin-1 alpha production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-1a release|biological activity biological activity assay measuring epitope specific interleukin-1 alpha production by T cells OBI:0001389 detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-6 production by T cells An assay of epitope specific interleukin-6 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-6 release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-6 production by T cells OBI:0001390 biological activity assay measuring epitope specific interferon-beta production by T cells A T cell epitope specific cytokine production assay that detects interferon-beta production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IFNb release|biological activity biological activity assay measuring epitope specific interferon-beta production by T cells OBI:0001391 biological activity assay measuring epitope specific interleukin-12 production by T cells A T cell epitope specific cytokine production assay that detects interleukin-12 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-12 release|biological activity biological activity assay measuring epitope specific interleukin-12 production by T cells OBI:0001392 in vivo assay measuring epitope specific T cell killing A T cell epitope specific killing assay that uses an in vivo cell mediated cell killing assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB cytotoxicity|in vivo assay in vivo assay measuring epitope specific T cell killing OBI:0001393 comparative genomic hybridization by array assay An assay in which changes in DNA sequence copy number are analysed using a microarray. For example the analysis of LOH in tumor cells vs a non diseased sample or the comparison of clinical isolated of disease causing bacteria. Person: James Malone array CGH EFO_0000749: comparative genomic hybridization by array Philippe Rocca-Serra comparative genomic hybridization by array assay OBI:0001394 epitope specific cytotoxic T cell degranulation A process of cytotoxic T cell degranulation resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl epitope specific cytotoxic T cell degranulation OBI:0001395 detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-23 production by T cells An assay of epitope specific interleukin-23 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-23 release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-23 production by T cells OBI:0001396 stimulus or stress design A study design in which the response of an organism(s) to the stress or stimulus is studied, e.g. osmotic stress, heat shock, radiation exposure, behavioral treatment etc. Person: Chris Stoeckert, Jie Zheng MO_568 stimulus_or_stress_design stimulus or stress design OBI:0001397 cytometric bead array assay measuring epitope specific granulocyte colony stimulating factor production by T cells An assay of epitope specific granulocyte colony stimulating factor production by T cells that uses a cytometric bead array assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB G-CSF release|cytometric bead array cytometric bead array assay measuring epitope specific granulocyte colony stimulating factor production by T cells OBI:0001398 protein and DNA interaction identification objective A sequence feature identification objective that aims to characterize the interactions between protein and DNA which includes identification of transcription factor binding sites. Person: Chris Stoeckert, Jie Zheng MO_933 binding_site_identification_design protein and DNA interaction identification objective OBI:0001399 epitope specific interleukin-22 production by T cells A process of interleukin-22 production by T cells resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl epitope specific interleukin-22 production by T cells OBI:0001400 biological activity assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells A T cell epitope specific cytokine production assay that detects tumor necrosis factor superfamily cytokine production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB TNF release|biological activity biological activity assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells OBI:0001401 protocol optimization design A study design where different protocols or protocol parameters are compared aims to find an optimized protocol Person: Chris Stoeckert, Jie Zheng MO_934 optimization_design protocol optimization design OBI:0001402 promoter activity detection by reporter gene assay measuring epitope specific interleukin-2 production by T cells An assay of epitope specific interleukin-2 production by T cells that uses a promoter activity detection by reporter gene assay. IEDB IEDB IL-2 release|reporter gene assay promoter activity detection by reporter gene assay measuring epitope specific interleukin-2 production by T cells OBI:0001403 ChIP-chip design A study design which aims to identify protein binding sites in genomic DNA by a combination of chromatin immunoprecipitation and DNA microarray (chip) assays. Person: Chris Stoeckert, Jie Zheng ChIP-on-chip design MO_933 binding_site_identification_design ChIP-chip design OBI:0001404 genetic characteristics information a data item that is about genetic material including polymorphisms, disease alleles, and haplotypes. Person: Chris Stoeckert, Jie Zheng MO_66 IndividualGeneticCharacteristics MO definition: The genotype of the individual organism from which the biomaterial was derived. Individual genetic characteristics include polymorphisms, disease alleles, and haplotypes. examples in ArrayExpress wild_type MutaMouse (CD2F1 mice with lambda-gt10LacZ integration) AlfpCre; SNF5 flox/knockout p53 knock out C57Bl/6 gp130lox/lox MLC2vCRE/+ fer-15; fem-1 df/df pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid) genetic characteristics information OBI:0001405 cytometric bead array assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells An assay of epitope specific macrophage inflammatory protein-1 alpha production by T cells that uses a cytometric bead array assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CCL3/MIP-1a release|cytometric bead array cytometric bead array assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells OBI:0001406 biological activity assay measuring epitope specific interleukin-3 production by T cells A T cell epitope specific cytokine production assay that detects interleukin-3 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-3 release|biological activity biological activity assay measuring epitope specific interleukin-3 production by T cells OBI:0001407 biological activity assay measuring epitope specific T cell activation A T cell epitope dependent biological activity assay that detects T cell activation. IEDB IEDB activation|biological activity biological activity assay measuring epitope specific T cell activation OBI:0001408 imprinting design A study design where differences in genetic imprinting of maternally- and paternally-inherited chromosomes (e.g., due to in vivo differences in chemical modification and/or chromatin structure) are compared. Person: Chris Stoeckert, Jie Zheng MO_914 imprinting_design imprinting design OBI:0001409 cell cycle design A study design that assays events that occur in relation to the cell cycle, which is the period between the formation of a cell, by division of its mother cell and the time when the cell itself divides to form two daughter cells. Person: Chris Stoeckert, Jie Zheng MO_822 cell_cycle_design cell cycle design OBI:0001410 translation profiling design A study design in which surface-bound, translationally competent ribosome complexes are used to generate a translation profile for mRNA, where mRNA may be a single molecular species, or a combination of species, including complex mixtures such as those found in the set of mRNAs isolated from a cell or tissue. One or more components of the surface-bound ribosome complex may be labeled at specific positions to permit analysis of multiple or single molecules for determination of ribosomal conformational changes and translation kinetics. Translation profiles are used as the basis for comparison of an mRNA or set of mRNA species. The translation profile can be used to determine such characteristics as kinetics of initiation, kinetic of elongation, identity of the polypeptide product, and the like. Analysis of translation profiles may be used to determine differential gene expression, optimization of mRNA sequences for expression, screening drug candidates for an effect on translation. Person: Chris Stoeckert, Jie Zheng Group: ArrayExpress production team translation profiling design OBI:0001411 cell type comparison design A study design that compares cells of different type, for example different cell lines. Person: Chris Stoeckert, Jie Zheng MO_764 cell_type_comparison_design cell type comparison design OBI:0001412 cytometric bead array assay measuring epitope specific RANTES production by T cells An assay of epitope specific RANTES production by T cells that uses a cytometric bead array assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CCL5/RANTES release|cytometric bead array cytometric bead array assay measuring epitope specific RANTES production by T cells OBI:0001413 cell culture analyte detection bioassay measuring epitope specific interleukin-6 production by T cells An assay of epitope specific interleukin-6 production by T cells that uses a cell culture analyte detection bioassay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-6 release|bioassay cell culture analyte detection bioassay measuring epitope specific interleukin-6 production by T cells OBI:0001414 biological activity assay measuring epitope specific interferon-gamma production by T cells A T cell epitope specific cytokine production assay that detects interferon-gamma production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IFNg release|biological activity biological activity assay measuring epitope specific interferon-gamma production by T cells OBI:0001415 epitope specific interleukin-9 production by T cells A process of interleukin-9 production by T cells resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl epitope specific interleukin-9 production by T cells OBI:0001416 biological activity assay measuring epitope specific tumor necrosis factor production by T cells An assay of epitope specific tumor necrosis factor superfamily cytokine production by T cells that detects tumor necrosis factor production. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB TNFa release|biological activity biological activity assay measuring epitope specific tumor necrosis factor production by T cells OBI:0001417 ChIP-chip by tiling array design A study design which aims to identify protein binding sites in genomic DNA by a combination of chromatin immunoprecipitation and tiling microarray (chip) assays. Person: Chris Stoeckert, Jie Zheng Group: ArrayExpress production team ChIP-chip by tiling array design OBI:0001418 dose response design A study design that examines the relationship between the size of the administered dose and the extent of the response. Person: Chris Stoeckert, Jie Zheng MO_485 dose_response_design dose response design OBI:0001419 ChIP-chip by tiling array assay An assay where chromatin immunoprecipitation (ChIP) is used in combination with tiling microarray technology Group: ArrayExpress production team EFO_0002762 ChIP-chip by tiling array ChIP-chip by tiling array assay OBI:0001420 epitope specific helper T cell enhancement of T cell mediated immune response A process of helper T cell enhancement of T cell mediated immune response resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl epitope specific helper T cell enhancement of T cell mediated immune response OBI:0001421 epitope specific interferon-beta production by T cells A process of interferon-beta production by T cells resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl epitope specific interferon-beta production by T cells OBI:0001422 organism part comparison design A study design that compares tissues, regions, organs within or between organisms Person: Chris Stoeckert, Jie Zheng MO_953 organism_part_comparison_design organism part comparison design OBI:0001423 intracellular material detection measuring epitope specific granzyme B release by T cells A T cell epitope specific granzyme B release assay that uses an intracellular material detection by flow cytometry assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB granzyme B release|intracellular staining intracellular material detection measuring epitope specific granzyme B release by T cells OBI:0001425 protein binding site identification design A study design that investigates protein binding sites on nucleic acids. Person: Chris Stoeckert, Jie Zheng MO_933 binding_site_identification_design protein binding site identification design OBI:0001426 sex comparison design A study design that assays differences associated with an organism's sex, gender or mating type. Person: Chris Stoeckert, Jie Zheng MO_575 sex_design sex comparison design OBI:0001427 transcription profiling by tiling array design A study design in which gene expression on a genome-wide basis is evaluated, without bias toward coding or noncoding regions, using tiling arrays containing oligonucleotides that are either overlapping or spaced at regular intervals. Person: Chris Stoeckert, Jie Zheng MO_507 tiling_path_design transcription profiling by tiling array design OBI:0001429 cell differentiation design A study design that assays events associated with cell development or differentiation. Person: Chris Stoeckert, Jie Zheng MO_892 development_or_differentiation_design cell differentiation design OBI:0001430 transcription profiling design A study design that identifies forms and abundance of transcripts in the genome. Person: Chris Stoeckert, Jie Zheng MO_533 transcript_identification_design transcription profiling design OBI:0001432 operon identification design A study design that identifies locations and members of operons in a genome. Person: Chris Stoeckert, Jie Zheng MO_772 operon_identification_design operon identification design OBI:0001433 radio immuno assay measuring epitope specific interferon-gamma production by T cells An assay of epitope specific interferon-gamma production by T cells that uses a radio immuno assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IFNg release|radio immuno assay (RIA) radio immuno assay measuring epitope specific interferon-gamma production by T cells OBI:0001435 DNA methylation profiling by high throughput sequencing design A study design in which the methylation state of DNA is determined and is compared between samples using high throughput sequencing technology. Person: Chris Stoeckert, Jie Zheng GROUP: ArrayExpress production team DNA methylation profiling by high throughput sequencing design OBI:0001436 biological activity assay measuring epitope specific granzyme B release by T cells A T cell epitope specific cytotoxic T cell degranulation assay that detects granzyme B release by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB granzyme B release|biological activity biological activity assay measuring epitope specific granzyme B release by T cells OBI:0001437 intracellular cytokine staining assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells An assay of epitope specific chemokine (C-X-C motif) ligand 9 production by T cells that uses an intracellular cytokine staining assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CXCL9/MIG release|ICS intracellular cytokine staining assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells OBI:0001438 ELISA measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells An assay of epitope specific macrophage inflammatory protein-1 gamma production by T cells that uses an ELISA. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CCL9/MIP-1g release|ELISA ELISA measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells OBI:0001439 epitope specific chemokine (C-X-C motif) ligand 9 production by T cells A process of chemokine (C-X-C motif) ligand 9 production by T cells resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl epitope specific chemokine (C-X-C motif) ligand 9 production by T cells OBI:0001440 all pairs design A study design in which all specimens are compared to every other specimen. Person: Chris Stoeckert, Jie Zheng MO_565 all_pairs all pairs design OBI:0001441 proteomic profiling by array design A study design in which proteins in a sample are detected, quantified or otherwise analysed, e.g. antibody profiling using an array based technology Person: Chris Stoeckert, Jie Zheng Group: ArrayExpress production team proteomic profiling by array design OBI:0001442 q-value PMID: 20483222. Comp Biochem Physiol Part D Genomics Proteomics. 2008 Sep;3(3):234-42. Analysis of Sus scrofa liver proteome and identification of proteins differentially expressed between genders, and conventional and genetically enhanced lines. "After controlling the false discovery rate (FDR</=0.1) using the Storey q value only four proteins (EPHX1, CAT, PAH, ST13) were shown to be differentially expressed between genders (Males/Females) and two proteins (SELENBP2, TAGLN) were differentially expressed between two lines (Transgenic/Conventional pigs)" A quantitative confidence value that measures the minimum false discovery rate that is incurred when calling that test significant. To compute q-values, it is necessary to know the p-value produced by a test and possibly set a false discovery rate level. PERS:Philippe Rocca-Serra FDR adjusted p-value Adapted from several sources, including http://.en/wikipedia.org/wiki/False_discovery_rate http://svitsrv25.epfl.ch/R-doc/library/qvalue.html q-value OBI:0001444 genotyping design A study design that classifies an individual or group of individuals on the basis of alleles, haplotypes, SNPs. Person: Chris Stoeckert, Jie Zheng MO_560 genotyping_design genotyping design OBI:0001445 biological activity assay measuring epitope specific interleukin-2 production by T cells A T cell epitope specific cytokine production assay that detects interleukin-2 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-2 release|biological activity biological activity assay measuring epitope specific interleukin-2 production by T cells OBI:0001446 epitope specific interleukin-15 production by T cells A process of interleukin-15 production by T cells resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl epitope specific interleukin-15 production by T cells OBI:0001447 epitope specific macrophage inflammatory protein-1 gamma production by T cells A process of macrophage inflammatory protein-1 gamma production by T cells resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl epitope specific macrophage inflammatory protein-1 gamma production by T cells OBI:0001448 individual genetic characteristics comparison design A study design where genotype, haplotype, or other individual genetic characteristics are compared. Person: Chris Stoeckert, Jie Zheng MO_527 individual_genetic_characteristics_design individual genetic characteristics comparison design OBI:0001449 biological activity assay measuring epitope specific interleukin-1 beta production by T cells A T cell epitope specific cytokine production assay that detects interleukin-1 beta production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-1b release|biological activity biological activity assay measuring epitope specific interleukin-1 beta production by T cells OBI:0001450 biological activity assay measuring epitope specific interleukin-4 production by T cells A T cell epitope specific cytokine production assay that detects interleukin-4 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-4 release|biological activity biological activity assay measuring epitope specific interleukin-4 production by T cells OBI:0001451 biological activity assay measuring epitope specific interleukin-6 production by T cells A T cell epitope specific cytokine production assay that detects interleukin-6 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-6 release|biological activity biological activity assay measuring epitope specific interleukin-6 production by T cells OBI:0001452 cell culture analyte detection bioassay measuring epitope specific tumor necrosis factor production by T cells A T cell epitope specific tumor necrosis factor production assay that uses a cell culture analyte detection bioassay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB TNFa release|bioassay cell culture analyte detection bioassay measuring epitope specific tumor necrosis factor production by T cells OBI:0001453 intracellular cytokine staining assay measuring epitope specific lymphotoxin A production by T cells An assay of epitope specific lymphotoxin A production by T cells that uses an intracellular cytokine staining assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB lymphotoxin A/TNFb release|ICS intracellular cytokine staining assay measuring epitope specific lymphotoxin A production by T cells OBI:0001454 pathogenicity design A study design in which an infective agent such as a bacterium, virus, protozoan, fungus etc. infects a host organism(s) and the infective agent is assayed. Person: Chris Stoeckert, Jie Zheng MO_807 pathogenicity_design pathogenicity design OBI:0001455 ELISPOT assay measuring epitope specific interleukin-5 production by T cells An assay of epitope specific interleukin-5 production by T cells that uses an ELISPOT assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-5 release|ELISPOT ELISPOT assay measuring epitope specific interleukin-5 production by T cells OBI:0001456 biological activity assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells A T cell epitope specific cytokine production assay that detects macrophage inflammatory protein-1 gamma production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CCL9/MIP-1g release|biological activity biological activity assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells OBI:0001457 cytometric bead array assay measuring epitope specific interleukin-8 production by T cells An assay of epitope specific interleukin-8 production by T cells that uses a cytometric bead array assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-8 release|cytometric bead array cytometric bead array assay measuring epitope specific interleukin-8 production by T cells OBI:0001459 biological activity assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells A T cell epitope specific cytokine production assay that detects chemokine (C-X-C motif) ligand 9 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CXCL9/MIG release|biological activity biological activity assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells OBI:0001460 genetic modification design A study design in which an organism(s) is studied that has had genetic material removed, rearranged, mutagenized or added, such as in a knock out. Person: Chris Stoeckert, Jie Zheng MO_447 genetic_modification_design genetic modification design OBI:0001461 ELISA measuring epitope specific granzyme B release by T cells A T cell epitope specific granzyme B release assay that uses an ELISA. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB granzyme B release|ELISA ELISA measuring epitope specific granzyme B release by T cells OBI:0001462 epitope specific IP-10 production by T cells A process of IP-10 production by T cells resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl epitope specific IP-10 production by T cells OBI:0001463 transcription profiling by array assay An assay in which the transcriptome of a biological sample is analysed using array technology. JZ: add alternative term: 'RNA profiling by array assay' requested by ENCODE developer. See tracker: https://sourceforge.net/p/obi/obi-terms/757/ Person: James Malone RNA profiling by array assay EFO_0002768: transcription profiling by array transcription profiling by array assay OBI:0001464 strain comparison design A study design that assays differences between multiple strains, cultivars, serovars, isolates, lines from organisms of a single species. Person: Chris Stoeckert, Jie Zheng MO_462 strain_or_line_design strain comparison design OBI:0001465 biological activity assay measuring epitope specific monocyte chemotactic protein-1 production by T cells A T cell epitope specific cytokine production assay that detects monocyte chemotactic protein-1 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CCL2/MCP-1 release|biological activity biological activity assay measuring epitope specific monocyte chemotactic protein-1 production by T cells OBI:0001466 intracellular cytokine staining assay measuring epitope specific interleukin-12 production by T cells An assay of epitope specific interleukin-12 production by T cells that uses an intracellular cytokine staining assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-12 release|ICS intracellular cytokine staining assay measuring epitope specific interleukin-12 production by T cells OBI:0001467 in vivo assay measuring T cell epitope specific disease exacerbation An efficacy of T cell epitope intervention experiment that uses a disease exacerbation in vivo intervention experiment. IEDB IEDB disease exacerbation|in vivo assay in vivo assay measuring T cell epitope specific disease exacerbation OBI:0001468 cell specimen A specimen primarily composed of cells collected from a multicellular organism or a cell culture PERSON: Chris Stoeckert, Jie Zheng MO_612 cell cell specimen OBI:0001469 monospecific T cell recognition assay measuring MHC ligand processing and presentation A MHC ligand processing and presentation assay in which the presence of a specific ligand in an eluate is detected using the response of T cells that are known to be monospecific for that ligand as a readout. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB ligand presentation|T cell recognition monospecific T cell recognition assay measuring MHC ligand processing and presentation OBI:0001470 epitope specific interleukin-17F production by T cells A process of interleukin-17F production by T cells resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2011-06-27; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl epitope specific interleukin-17F production by T cells OBI:0001471 T cell epitope specific immune intervention Injecting a mouse with peptide SIINFEKL to induce a T cell response against the peptide An epitope specific immune intervention in which the induced response targets a T cell epitope PERSON: Randi Vita, Jason Greenbaum, Bjoern Peters IEDB T cell epitope specific immune intervention OBI:0001472 specimen with known storage state A specimen for which it is known whether it has been subjected to storage of a specified type. PERSON: Chris Stoeckert, Jie Zheng MO_95 BiosourceType specimen with known storage state OBI:0001473 in vivo assay measuring T cell epitope specific protection from tumor challenge A T cell epitope in vivo intervention experiment that uses a protection from challenge in vivo intervention experiment based on tumor burden. IEDB IEDB tumor burden after challenge|in vivo assay in vivo assay measuring T cell epitope specific protection from tumor challenge OBI:0001474 lowess group transformation A lowess transformation where a potentially different normalization curve is generated and used for two or more groups (delineated by some criteria); criteria could include blocks (e.g. print-tip groups) on an array, or the day on which mass spectrometry was performed. Person: Elisabetta Manduchi MO_861 lowess_group_normalization lowess group transformation OBI:0001475 in vivo assay measuring T cell epitope specific protection from infectious challenge based on pathogen burden A T cell epitope in vivo intervention experiment that uses a protection from challenge in vivo intervention experiment based on pathogen burden. IEDB IEDB pathogen burden after challenge|in vivo assay in vivo assay measuring T cell epitope specific protection from infectious challenge based on pathogen burden OBI:0001476 phage display binding assay Using a commercial library of phages that produce random peptide sequences to infect E coli cells, and screening them for binding to a selecting antibody of unknown specificity. By iteratively using phages from selected E coli cells and repeating this process, phages encoding high affinity peptides for the antibody are selected, sequenced, and thereby the specificity of the antibody is elucidated. A binding assay in which a collection of phages expressing a library of different peptides or protein fragnments is used to infect cells, followed by screening for cells that bind a protein of interest, and identifiying the sequence of infecting phages to determine a suitable binding partner. IEDB IEDB phage display binding assay OBI:0001477 lowess transformation A data transformation of normalizing ratio data by using a locally weighted polynomial regression (typically after a log transformation). The regression can be performed on log ratios resulting from the relation of two data sets versus the average log intensity data from the same two data sets or it can be performed on raw or log transformed values from one data set versus values from another. The goal could be to remove intensity-dependent dye-specific effects from the set of pair wise ratios. This method can be applied globally, or limited by one or more specified criteria. Person: Elisabetta Manduchi MO_720 lowess_normalization lowess transformation OBI:0001478 mass spectrometry assay measuring MHC ligand processing and presentation A MHC ligand processing and presentation assay that uses a mass spectrometry assay to identify eluted ligands IEDB IEDB ligand presentation|mass spectrometry mass spectrometry assay measuring MHC ligand processing and presentation OBI:0001479 tissue specimen A specimen that derives from an anatomical part or substance arising from an organism. Examples of tissue specimen include tissue, organ, physiological system, blood, or body location (arm). PERSON: Chris Stoeckert, Jie Zheng MO_954 organism_part tissue specimen OBI:0001480 phage display library panning Screening a libray of M13 phages displaying random peptide sequences for binding to the MHC molecule HLA-A*02:02 resulting in a subset of phages that encode peptides that bind. Phage display library panning is a process in which a diverse collection of phages encoding peptides or proteins are screened and the ones encoding active peptides/proteins are selected in an iterative process similar to natural selection. Jason Greenbaum, Randi Vita, Bjoern Peters IEDB, http://en.wikipedia.org/wiki/Phage_display phage display library panning OBI:0001481 lowess global transformation A lowess transformation where the same normalization curve is used for all members of the data set; e.g. Features on an array, picked spots on a gel, or measured metabolites in a sample. Person: Elisabetta Manduchi MO_692 lowess_global_normalization lowess global transformation OBI:0001482 intracellular cytokine staining assay measuring epitope specific transforming growth factor-beta production by T cells An assay of epitope specifictransforming growth factor-beta production by T cells that uses an intracellular cytokine staining assay. IEDB IEDB TGFb release|ICS intracellular cytokine staining assay measuring epitope specific transforming growth factor-beta production by T cells OBI:0001483 cell collecting A planned process that collects cells from culture. PERSON: Chris Stoeckert, Jie Zheng MO_982 harvest cell collecting OBI:0001484 biological activity assay measuring T cell epitope specific in vivo activity A T cell epitope dependent biological activity determination assay that uses an in vivo intervention experiment. IEDB IEDB in vivo activity|biological activity biological activity assay measuring T cell epitope specific in vivo activity OBI:0001485 purified MHC molecule preparation HLA A*0201 that was purified from cell lysate using an HLA class I specific antibody A mixture containing MHC molecules that was purified to remove non-MHC molecular entities. BP: 06/09/11: This needs to be coordinated with the broader treatment of 'purified materials' in general. Bjoern Peters purified MHC molecule preparation OBI:0001486 disposition to be bound by an MHC protein complex Is the disposition borne by a material entity that is realized in a process of being bound in the antigen binding grove of an MHC protein complex. PERSON: Jason Greenbaum, Randi Vita, Bjoern Peters MHC ligand disposition IEDB disposition to be bound by an MHC protein complex OBI:0001487 B cell epitope specific immune intervention Injecting a mouse with recombinant antibody targeting an anthrax epitope An epitope specific immune intervention in which the induced response targets a B cell epitope PERSON: Randi Vita, Jason Greenbaum, Bjoern Peters IEDB B cell epitope specific immune intervention OBI:0001488 epitope tolerance induction experiment An efficacy of epitope intervention experiment that tests the ability of the intervention to decrease an existing immune response IEDB IEDB tolerance induction epitope tolerance induction experiment OBI:0001489 mass spectrometry assay measuring MHC ligand processing and presentation of MHC ligands eluted from cellular MHC A mass spectrometry of MHC ligands assay that identifies eluted ligands from cell bound MHC. IEDB IEDB ligand presentation|cellular MHC/mass spectrometry mass spectrometry assay measuring MHC ligand processing and presentation of MHC ligands eluted from cellular MHC OBI:0001490 cytometric bead array measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells An assay of epitope specific granulocyte macrophage colony stimulating factor production by T cells that uses a cytometric bead array assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB GM-CSF release|cytometric bead array cytometric bead array measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells OBI:0001491 radioactivity detection binding assay binding assay that uses radioactivity detection as an indicator of binding PERSON:Bjoern Peters, Randi Vita IEDB radioactivity detection binding assay OBI:0001492 in vivo assay measuring T cell epitope specific protection based on survival A T cell epitope in vivo intervention experiment that uses a protection from challenge in vivo intervention experiment based on survival. IEDB IEDB survival from challenge|in vivo assay in vivo assay measuring T cell epitope specific protection based on survival OBI:0001493 cell bound MHC competitive binding assay of a MHC:ligand complex using T cell epitope recognition A cell bound MHC binding assay that uses a T cell epitope recognition assay. IEDB IEDB qualitative binding|cellular MHC/T cell inhibition cell bound MHC competitive binding assay of a MHC:ligand complex using T cell epitope recognition OBI:0001494 linear amplification An example is the use of the T7 promoter for amplification by transcribing many RNA copies. An enzymatic amplification which amplifies nucleic acid sequence by making many copies off the same template. PERSON: Chris Stoeckert, Jie Zheng MO_997 linear_amplification linear amplification OBI:0001495 biological activity assay measuring epitope specific T cell helper activity A T cell epitope dependent biological activity assay that detects the ability of epitope specific helper T cells to enhance either B cell or T cell adaptive immune response function. IEDB IEDB helper response|biological activity biological activity assay measuring epitope specific T cell helper activity OBI:0001496 intracellular cytokine staining assay measuring epitope specific interleukin-22 production by T cells An assay of epitope specific interleukin-22 production by T cells that uses an intracellular cytokine staining assay. IEDB IEDB IL-22 release|ICS intracellular cytokine staining assay measuring epitope specific interleukin-22 production by T cells OBI:0001497 biological activity assay measuring epitope specific perforin release by T cells A T cell epitope specific cytotoxic T cell degranulation assay that detects perforin release by T cells. IEDB IEDB perforin release|biological activity biological activity assay measuring epitope specific perforin release by T cells OBI:0001498 atmosphere A growth environment pertaining to the atmospheric conditions that is used to culture or grow an organism. PERSON: Chris Stoeckert, Jie Zheng MO_219 atmosphere atmosphere OBI:0001499 fluorescence detection binding assay binding assay that uses fluorescence detection as an indicator of binding PERSON:Bjoern Peters, Randi Vita IEDB fluorescence detection binding assay OBI:0001500 coelution assay measuring MHC ligand processing and presentation using T cell recognition of HPLC fractionated eluate compared to synthetic ligand A MHC ligand processing and presentation assay in which an HPL chromatography is run to separate an input mixture of ligands eluted from MHC into fractions. These fractions are tested for recognition by T cells and compared to the recognition of a synthetic ligand that is presumed to be the recognized epitope. Identical HPLC fractionation and T cell recognition patterns confirm that the specific ligand was presented by MHC molecules. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB ligand presentation|coelution coelution assay measuring MHC ligand processing and presentation using T cell recognition of HPLC fractionated eluate compared to synthetic ligand OBI:0001501 fluorescence detection assay Using a laser to stimulate a cell culture that was previously labeled with fluorescent antibodies to detect light emmission at a different wavelength in order to determine the presence of surface markers the antibodies are specific for. An assay in which a material's fluorescence is determined. IEDB IEDB fluorescence detection assay OBI:0001502 epitope specific perforin production by T cells The production of perforin, an immune mediator molecule involved in T cell degranulation, resulting from the recognition of a T cell epitope. Should be linked to a GO process, which will be requested by IEDB team. Along with granzyme B production, should be tied to T cell degranulation PERSON: Bjoern Peters, Randi Vita epitope specific perforin production by T cells OBI:0001503 MHC protein complex binding to ligand The peptide SIINFEKL binding to an empty murine H-2 Kb molecule to form a complex. The process in which a ligand binds to an MHC molecule to form a stable complex 6/13/11 BP: The disposition referenced is the one of the ligand to bind the molecule. This along with binding as a function / process needs to be figured out with GO which is inconsistent at this point. PERSON: Bjoern Peters; Randi Vita IEDB MHC protein complex binding to ligand OBI:0001504 dissection A planned process that separates and isolates tissues for surgical purposes, or for the analysis or study of their structures. PERSON: Chris Stoeckert, Jie Zheng EFO_0003856 dissection MO_374 dissect dissection OBI:0001505 purification A planned process to separate a material entity into different compositions of which one or more have are purified fractions that contain higher concentration of a desired component, while others contain impurities and are not of interest PERSON: Chris Stoeckert, Jie Zheng MO_406 purify purification OBI:0001506 specimen with pre- or post-mortem status A specimen that has been established to be taken from a live (pre-mortem) or dead (post-mortem) organism. organizational term, used in description of specimen that is created from known pre- or post-mortem status PERSON: Chris Stoeckert, Jie Zheng MO_84 OrganismStatus specimen with pre- or post-mortem status OBI:0001507 in vivo assay measuring T cell epitope specific treatment of disease An efficacy of T cell epitope intervention experiment that detects a decrease in disease. IEDB IEDB decreased disease|in vivo assay in vivo assay measuring T cell epitope specific treatment of disease OBI:0001508 sampling time measurement datum A time measurement datum when an observation is made or a sample is taken from a material as measured from some reference point. Person: Chris Stoeckert time point MO_738 timepoint sampling time measurement datum OBI:0001509 Edman degradation assay measuring MHC ligand processing and presentation A MHC ligand processing and presentation assay that uses Edman degradation to identify the eluted ligands PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB ligand presentation|Edman degradation Edman degradation assay measuring MHC ligand processing and presentation OBI:0001510 mass spectrometry assay measuring MHC ligand processing and presentation of MHC ligands eluted from secreted MHC A mass spectrometry of MHC ligands that identifies eluted ligands from secreted MHC. IEDB IEDB ligand presentation|secreted MHC/mass spectrometry mass spectrometry assay measuring MHC ligand processing and presentation of MHC ligands eluted from secreted MHC OBI:0001511 disposition to be a product of antigen processing and presentation The disposition of the peptide AALKNLPLI to be created from the source protein long-chain-fatty-acid--CoA ligase 3 in murine macrophages through cleavage before residue 599 and after residue 607 by the proteasome and subsequent transport into the ER. A disposition of a material entity to be presented by MHC molecules on the cell surface as a result of antigen processing by an antigen presenting cell. IEDB IEDB disposition to be a product of antigen processing and presentation OBI:0001512 cytometric bead array assay measuring epitope specific interleukin-17A production by T cells A T cell epitope specific interleukin-17A production assay that uses a cytometric bead array assay. IEDB IEDB IL-17A release|cytometric bead array cytometric bead array assay measuring epitope specific interleukin-17A production by T cells OBI:0001513 purified MHC competitive binding assay of a MHC:ligand complex using radioactivity detection A purified MHC binding assay that uses radioactivity detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB qualitative binding|purified MHC/competitive/radioactivity purified MHC competitive binding assay of a MHC:ligand complex using radioactivity detection OBI:0001514 minimal inhibitory concentration A scalar measurement datum that indicates the lowest concentration at which a specific compound significantly inhibits a process from occurring compared to in the absence of the compound. Created following request by Albert Goldfain PERSON:Bjoern Peters Bjoern Peters, coordinated with Albert Goldfain minimal inhibitory concentration OBI:0001515 material maintenance service model organism colony maintanance A material processing service in which a service provider makes physical modifications to a specified input material, such that at least one of the specified outputs of this process is a modified version of a specified input material. PERSON: Carlo Torniai PERSON: Matthew Brush PERSON: Matthew Brush Here we need to go back to the defintoin of storage process. It has object specification which is material maintenance. Not necessareley a material maintenance is needed in a storage process. material maintenance service OBI:0001516 cell lysate MHC direct binding assay measuring half maximal effective concentration [EC50] of a MHC:ligand complex using radioactivity detection A cell lysate MHC ligand binding half maximal effective concentration (EC50) determination assay that uses radioactivity detection to measure direct ligand binding. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB half maximal effective concentration (EC50)|lysate MHC/direct/radioactivity|nM cell lysate MHC direct binding assay measuring half maximal effective concentration [EC50] of a MHC:ligand complex using radioactivity detection OBI:0001517 cell bound MHC competitive binding assay measuring half maximal inhibitory concentration [IC50] of a MHC:ligand complex using radioactivity detection A cell bound MHC ligand binding half maximal inhibitory concentration (IC50) determination assay that uses radioactivity detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB half maximal inhibitory concentration (IC50)|cellular MHC/competitive/radioactivity|nM cell bound MHC competitive binding assay measuring half maximal inhibitory concentration [IC50] of a MHC:ligand complex using radioactivity detection OBI:0001518 epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells A process of tumor necrosis factor (ligand) superfamily member 11 production by T cells resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2011-11-10; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: assay_mappings.owl epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells OBI:0001519 cell lysate MHC direct binding assay of a MHC:ligand complex using fluorescence detection A cell lysate MHC binding assay that uses fluorescence detection to detect direct binding. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB qualitative binding|lysate MHC/direct/fluorescence cell lysate MHC direct binding assay of a MHC:ligand complex using fluorescence detection OBI:0001520 cell bound MHC competitive binding assay measuring half maximal inhibitory concentration [IC50] of a MHC:ligand complex using fluorescence detection A cell bound MHC ligand binding half maximal inhibitory concentration (IC50) determination assay that uses fluorescence detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB half maximal inhibitory concentration (IC50)|cellular MHC/competitive/fluorescence|nM cell bound MHC competitive binding assay measuring half maximal inhibitory concentration [IC50] of a MHC:ligand complex using fluorescence detection OBI:0001521 ELISA measuring epitope specific granulocyte colony stimulating factor production by T cells An assay of epitope specific granulocyte colony stimulating factor production by T cells that uses an ELISA. IEDB IEDB G-CSF release|ELISA ELISA measuring epitope specific granulocyte colony stimulating factor production by T cells OBI:0001522 sequence assembly algorithm An algorithm used to assemble individual sequence reads into larger contiguous sequences (contigs). Assembly details include but are not limited to assembler type (overlap-layout-consensus, deBruijn), assembler version, and any relevant quality control information such as per cent known genes/ESTs captured. Person: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Assembly Algorithm NIAID GSCID-BRC sequence assembly algorithm OBI:0001523 cytometric bead array assay measuring epitope specific interleukin-17F production by T cells A T cell epitope specific interleukin-17F production assay that uses a cytometric bead array assay. IEDB IEDB IL-17F release|cytometric bead array cytometric bead array assay measuring epitope specific interleukin-17F production by T cells OBI:0001524 cell bound MHC direct binding assay measuring equilibrium association constant [KA] of a MHC:ligand complex using fluorescence detection A cell bound MHC ligand binding equilibrium association constant (KA) determination assay that uses fluorescence detection to detect direct binding. IEDB IEDB association constant KA|cellular MHC/direct/fluorescence|1/M cell bound MHC direct binding assay measuring equilibrium association constant [KA] of a MHC:ligand complex using fluorescence detection OBI:0001525 PDB file The file found in the pdb with the identifier 3pe4 http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=NO&structureId=3pe4 A 3d structural organization datum capturing the results of X-ray crystallography or NMR experiment that is formatted as specified by the Protein Databank (http://www.wwpdb.org/docs.html). A PDB file can describe the structure of multiple molecules, each of which has a different chain identifier assigned. PERSON: Bjoern Peters, Dorjee Tamang, Jason Greenbaum PDB file OBI:0001526 epitope specific interleukin-17A production by T cells A process of interleukin-17A production by T cells resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2011-11-10; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: assay_mappings.owl epitope specific interleukin-17A production by T cells OBI:0001527 support service An help desk for an instrument or a software. A service in which the service provider assists the consumer in activities directly or indirectly associated with the production and analysis of experimental research data. PERSON: Carlo Torniai PERSON: Matthew Brush PERSON; Carlo Torniai support service OBI:0001528 material service A service performing DNA sequencing, a service preforming cell analysis. A service performing cell line immortalization A service which has a material entity as specified input and/or specified output. PERSON: Carlo Torniai PERSON: Matthew Brush PERSON: Carlo Torniai material service OBI:0001529 data analysis service Statistaical analysis service, data visualization service A service in which a service consumer provides some input data and a service provider transforms, models, or interprets the input data and returns this generated data as output. PERSON: Carlo Torniai PERSON: Matthew Brush PERSON: Matthew Brush data analysis service OBI:0001530 data service Data analysis service such statistical abalysis or storage service such data backup. A service that has some information content entity as input and output. PERSON: Carlo Torniai PERSON: Matthew Brush PERSON: Carlo Torniai Information content entity was used as specified input and output since it was more appropriate then data item or dataset. data service OBI:0001531 purified MHC direct binding assay measuring half life of a MHC:ligand complex using fluorescence detection A purified MHC ligand half life of binding determination assay that uses fluorescence detection to measure direct ligand binding. IEDB IEDB half life|purified MHC/direct/fluorescence|min purified MHC direct binding assay measuring half life of a MHC:ligand complex using fluorescence detection OBI:0001532 cytometric bead array assay measuring epitope specific interleukin-9 production by T cells An assay of epitope specific interleukin-9 production by T cells that uses a cytometric bead array assay. IEDB IEDB IL-9 release|cytometric bead array cytometric bead array assay measuring epitope specific interleukin-9 production by T cells OBI:0001533 data storage service A service offering data backup A storage service in which a service consumer provides data as input which a service provider stores and returns as output in its original form. PERSON: Carlo Torniai PERSON: Matthew Brush PERSON: Matthew Brush data storage service OBI:0001534 purified MHC competitive binding assay measuring binding of a MHC:ligand complex using fluorescence detection A purified MHC binding assay that uses fluorescence detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation. IEDB IEDB qualitative binding|purified MHC/competitive/fluorescence purified MHC competitive binding assay measuring binding of a MHC:ligand complex using fluorescence detection OBI:0001535 epitope specific interleukin-7 production by T cells A process of interleukin-7 production by T cells resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2011-11-10; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: assay_mappings.owl epitope specific interleukin-7 production by T cells OBI:0001536 equilibrium dissociation constant (KD) KD = 32 nM is the equilibrium dissociation rate found for peptide SIINFEKL binding to H-2 Kb A binding constant defined as the ratio of kon over koff (on-rate of binding divided by off-rate) PERSON: Bjoern Peters, Randi Vita IEDB equilibrium dissociation constant (KD) OBI:0001537 purified MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex using fluorescence detection A purified MHC ligand binding equilibrium dissociation constant (KD) determination assay that uses fluorescence detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB dissociation constant KD|purified MHC/competitive/fluorescence|nM purified MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex using fluorescence detection OBI:0001538 training service A service that offers training for a specific instrument or technique. A course to learn how to use a microscope A service in which the service provider offers educational materials or events, such as courses, workshops or graduate programs, to the service consumer. PERSON: Carlo Torniai PERSON: Matthew Brush PERSON: Matthew Brush training service OBI:0001539 cell bound MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex using fluorescence detection A cell bound MHC ligand binding equilibrium dissociation constant (KD) determination assay that uses fluorescence detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation. IEDB IEDB dissociation constant KD|cellular MHC/competitive/fluorescence|nM cell bound MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex using fluorescence detection OBI:0001540 obsolete T cell recognition of eluted MHC ligand assay Using proliferation of a T cell line specific for SIINFEKL in response to material eluted from a cell as evidence that SIINFEKL was presented by MHC on that cell. An assay that identifies an MHC ligand using a T cell response assay as a readout PERSON: Randi Vita, Bjoern Peters IEDB T cell recognition obsolete T cell recognition of eluted MHC ligand assay true OBI:0001541 purified MHC direct binding assay measuring binding on rate [kon] of a MHC:ligand complex using fluorescence detection A purified MHC ligand binding on rate (kon) determination assay that uses fluorescence detection to measure direct ligand binding. IEDB IEDB on rate|purified MHC/direct/fluorescence|nM^-1s^-1 purified MHC direct binding assay measuring binding on rate [kon] of a MHC:ligand complex using fluorescence detection OBI:0001542 detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-13 production by T cells An assay of epitope specific interleukin-13 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. IEDB IEDB IL-13 release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-13 production by T cells OBI:0001543 purified MHC direct binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex approximated by EC50 using fluorescence detection A purified MHC ligand binding equilibrium dissociation constant (KD) determination assay that uses fluorescence detection to measure direct ligand binding and provides EC50 values determined under assay conditions where the EC50 approximates a KD value. IEDB IEDB dissociation constant KD (~EC50)|purified MHC/direct/fluorescence|nM purified MHC direct binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex approximated by EC50 using fluorescence detection OBI:0001544 cell lysate MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex using radioactivity detection A cell lysate MHC ligand binding equilibrium dissociation constant (KD) determination assay that uses radioactivity detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB dissociation constant KD|lysate MHC/competitive/radioactivity|nM cell lysate MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex using radioactivity detection OBI:0001545 intracellular cytokine staining assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells An assay of epitope specific macrophage inflammatory protein-1 alpha production by T cells that uses an intracellular cytokine staining assay. IEDB IEDB CCL3/MIP-1a release|ICS intracellular cytokine staining assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells OBI:0001546 comparative phenotypic assessment Interpreting data from assays that evaluate the qualities or dispositions inhering in an organism or organism part and comparing it to data from other organisms to make a conclusion about a phenotypic difference Philly workshop 2011 Philly workshop 2011 6/1/2012: We will utilize 'comparative qualities' once they are available in BFO2 comparative phenotypic assessment OBI:0001547 material analysis service Services performing DNA sequencing or Cell Analysis A service in which a service consumer provides some input material and a service provider performs some analysis of this material to generate data that is returned to the service consumer. PERSON: Carlo Torniai PERSON: Matthew Brush PERSON: Matthew Brush material analysis service OBI:0001548 equilibrium association constant (KA) KA = 10^-12 M^-1 is the equilibirum association constant maximally found for antibody binding to haptens. A binding constant defined as the ratio of koff over kon (off-rate of binding divided by on-rate) PERSON: Bjoern Peters, Randi Vita IEDB equilibrium association constant (KA) OBI:0001549 cell bound MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex using radioactivity detection A cell bound MHC ligand binding equilibrium dissociation constant (KD) determination assay that uses radioactivity detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB dissociation constant KD|cellular MHC/competitive/radioactivity|nM cell bound MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex using radioactivity detection OBI:0001550 cell bound MHC binding assay measuring binding of a MHC:ligand complex A MHC binding qualitative binding to ligand assay measuring MHC ligand binding using MHC present on cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB qualitative binding|cellular MHC cell bound MHC binding assay measuring binding of a MHC:ligand complex OBI:0001551 access service A service that provides acess to a mass spectrometer. A service in which a service consumer receives the right to use a resource (instrument, database, software, etc) that is owned or managed by a service provider. Ownership of the accessed resource remains with the service provider during and after provision of service. Need to come up wiht a proper logical defintion. One option woudl be to dfine provides_access_to property as shortcut of participants in a process. PERSON: Carlo Torniai PERSON: Matthew Brush PERSON: Matthew Brush access service OBI:0001552 intracellular cytokine staining assay measuring epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells A T cell epitope specific tumor necrosis factor (ligand) superfamily member 11 production assay that uses an intracellular cytokine staining assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB TNFSF11/RANKL release|ICS intracellular cytokine staining assay measuring epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells OBI:0001553 assay measuring a binding constant of a MHC:ligand complex A MHC:ligand binding assay that measures a binding constant. IEDB IEDB binding constant|binding assay assay measuring a binding constant of a MHC:ligand complex OBI:0001554 rate measurement datum The rate of disassociation of a peptide from a complex with an MHC molecule measured by the ratio of bound and unbound peptide per unit of time. A scalar measurement datum that represents the number of events occuring over a time interval PERSON: Bjoern Peters, Randi Vita IEDB rate measurement datum OBI:0001555 purified MHC binding assay measuring binding of a MHC:ligand complex A MHC binding qualitative binding to ligand assay using MHC in a purified MHC molecule preparation. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB qualitative binding|purified MHC purified MHC binding assay measuring binding of a MHC:ligand complex OBI:0001556 cell lysate MHC direct binding assay of a MHC:ligand complex using radioactivity detection A cell lysate MHC binding assay that uses radioactivity detection to detect direct binding. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB qualitative binding|lysate MHC/direct/radioactivity cell lysate MHC direct binding assay of a MHC:ligand complex using radioactivity detection OBI:0001557 material storage service A service that offers liquid nitrogen stroage. A storage service in which a service consumer provides some material as input which a service provider stores and returns as output. PERSON: Carlo Torniai PERSON: Matthew Brush PERSON: Matthew Brush material storage service OBI:0001558 cell bound MHC direct binding assay measuring half life of a MHC:ligand complex using radioactivity detection A cell bound MHC ligand half life of binding determination assay that uses radioactivity detection to measure direct ligand binding. IEDB IEDB half life|cellular MHC/direct/radioactivity|min cell bound MHC direct binding assay measuring half life of a MHC:ligand complex using radioactivity detection OBI:0001559 cell bound MHC direct binding assay measuring half life of a MHC:ligand complex using fluorescence detection A cell bound MHC ligand half life of binding determination assay that uses fluorescence detection to measure direct ligand binding. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB half life|cellular MHC/direct/fluorescence|min cell bound MHC direct binding assay measuring half life of a MHC:ligand complex using fluorescence detection OBI:0001560 obsolete cell lysate MHC binding constant determination assay An assay that measures the affinity of a ligand to a MHC in a cell lysate preparation and that quantifies the affinity with a binding constant. PERSON: Bjoern Peters IEDB obsolete cell lysate MHC binding constant determination assay true OBI:0001561 cell bound MHC direct binding assay measuring half maximal effective concentration [EC50] of a MHC:ligand complex using fluorescence detection A cell bound MHC ligand binding half maximal effective concentration (EC50) determination assay that uses fluorescence detection to measure direct ligand binding. IEDB IEDB half maximal effective concentration (EC50)|cellular MHC/direct/fluorescence|nM cell bound MHC direct binding assay measuring half maximal effective concentration [EC50] of a MHC:ligand complex using fluorescence detection OBI:0001562 intracellular cytokine staining assay measuring epitope specific interleukin-17F production by T cells A T cell epitope specific interleukin-17F production assay that uses an intracellular cytokine staining assay. IEDB IEDB IL-17F release|ICS intracellular cytokine staining assay measuring epitope specific interleukin-17F production by T cells OBI:0001563 material processing service A service for cell line creation. A service providing cel line immortalization. A service in which a service provider makes physical changes to a specified input material entity with the objective of producing a new material entity form input materials, or modifying the input material entity, and returning this as output to the service consumer. PERSON: Carlo Torniai PERSON: Matthew Brush PERSON: Carlo Torniai material processing service OBI:0001564 purified MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex approximated by IC50 using radioactivity detection A purified MHC ligand binding equilibrium dissociation constant (KD) determination assay that uses radioactivity detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation and provides IC50 values determined under assay conditions where the IC50 approximates a KD value. IEDB IEDB dissociation constant KD (~IC50)|purified MHC/competitive/radioactivity|nM purified MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex approximated by IC50 using radioactivity detection OBI:0001565 cell lysate MHC direct binding assay measuring half life of a MHC:ligand complex using radioactivity detection A cell lysate MHC ligand half life of binding determination assay that uses radioactivity detection to measure direct ligand binding. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB half life|lysate MHC/direct/radioactivity|min cell lysate MHC direct binding assay measuring half life of a MHC:ligand complex using radioactivity detection OBI:0001566 50% dissociation of binding temperature (Tm) Preparing a complex of a purified HLA-A*02:01 bound to a specific peptide ligand, varying the temperature while detecting the fraction of bound complexes with a complex conformation specific antibody, and interpolating the temperature at which 50% of complexes are dissociated. A binding datum that specifies the temperature at which half of the binding partners are forming a complex and the other half are unbound. PERSON: Bjoern Peters, Randi Vita melting temperature (Tm) IEDB 50% dissociation of binding temperature (Tm) OBI:0001567 cell lysate MHC direct binding assay measuring binding off rate [koff] of a MHC:ligand complex using radioactivity detection A cell lysate MHC ligand binding off rate measurement (koff) determination assay that uses radioactivity detection to measure direct ligand binding. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB off rate|lysate MHC/direct/radioactivity|1/s cell lysate MHC direct binding assay measuring binding off rate [koff] of a MHC:ligand complex using radioactivity detection OBI:0001568 purified MHC competitive binding assay measuring half maximal inhibitory concentration [IC50] of a MHC:ligand complex using radioactivity detection A purified MHC ligand binding half maximal inhibitory concentration (IC50) determination assay that uses radioactivity detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB half maximal inhibitory concentration (IC50)|purified MHC/competitive/radioactivity|nM purified MHC competitive binding assay measuring half maximal inhibitory concentration [IC50] of a MHC:ligand complex using radioactivity detection OBI:0001569 purified MHC direct binding assay measuring binding off rate [koff] of a MHC:ligand complex using fluorescence detection A purified MHC ligand binding off rate measurement (koff) determination assay that uses fluorescence detection to measure direct ligand binding. IEDB IEDB off rate|purified MHC/direct/fluorescence|1/s purified MHC direct binding assay measuring binding off rate [koff] of a MHC:ligand complex using fluorescence detection OBI:0001570 biological activity assay measuring epitope specific vascular endothelial growth factor production by T cells A T cell epitope specific cytokine production assay that detects vascular endothelial growth factor production by T cells. IEDB IEDB VEGF release|biological activity biological activity assay measuring epitope specific vascular endothelial growth factor production by T cells OBI:0001571 equilibrium dissociation constant (KD) approximated by IC50 A measurement of an IC50 value under specific assay conditions approximates KD, namely the binding reaction is at an equilibrium, there is a single population of sites on the receptor that competitor and ligand are binding to, and the concentration of the receptor must be much less than the KD for the competitor and the ligand. In this case, according to Cheng and Prussoff, KD = IC50 / (1 + Lstot / KDs), in which Lstot is the total concentration of the labeled competitor and KDs is the KD value of that competitor. PERSON: Bjoern Peters, Randi Vita http://dx.doi.org/10.1016/0006-2952(73)90196-2 equilibrium dissociation constant (KD) approximated by IC50 OBI:0001572 obsolete cell bound MHC binding constant determination assay An assay that measures the affinity of a ligand to MHC moleculs bound to the cell surface and that quantifies the affinity with a binding constant. PERSON: Bjoern Peters IEDB obsolete cell bound MHC binding constant determination assay true OBI:0001573 DNA sequence data The part of a FASTA file that contains the letters ACTGGGAA A sequence data item that is about the primary structure of DNA OBI call; Bjoern Peters OBI call; Melanie Courtout 8/29/11 call: This is added after a request from Melanie and Yu. They should review it further. This should be a child of 'sequence data', and as of the current definition will infer there. DNA sequence data OBI:0001574 obsolete cell lysate MHC competitive binding assay using radioactivity detection competitive inhibition of binding assay measuring MHC ligand binding by radioactivity detection using MHC derived from a cell lysate PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) cell lysate MHC competitive binding using radioactivity obsolete cell lysate MHC competitive binding assay using radioactivity detection true OBI:0001575 assigning gene property based on phenotypic assessment Interpreting data from assays that evaluate the qualities or dispositions inhering in an organism or organism part and comparing it to data from other organisms that have a defined genetic difference, and assigning a property to the product of the targeted gene as a result. Philly workshop 2011 Philly workshop 2011 assigning gene property based on phenotypic assessment OBI:0001576 obsolete purified MHC binding constant determination assay An assay that measures the affinity of a ligand to a purified MHC complex preparation and that quantifies the affinity with a binding constant. PERSON: Bjoern Peters IEDB obsolete purified MHC binding constant determination assay true OBI:0001577 cytometric bead array assay measuring epitope specific intracellular cytokine staining (ICS) IL-22 production by T cells An assay of epitope specific interleukin-22 production by T cells that uses a cytometric bead array assay. IEDB IEDB IL-22 release|cytometric bead array cytometric bead array assay measuring epitope specific intracellular cytokine staining (ICS) IL-22 production by T cells OBI:0001578 ELISA measuring epitope specific vascular endothelial growth factor production by T cells An assay of epitope specific vascular endothelial growth factor production by T cells that uses an ELISA. IEDB IEDB VEGF release|ELISA ELISA measuring epitope specific vascular endothelial growth factor production by T cells OBI:0001579 cell lysate MHC binding assay measuring binding of a MHC:ligand complex A MHC binding qualitative binding to ligand assay using MHC in a cell lysate. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB qualitative binding|lysate MHC cell lysate MHC binding assay measuring binding of a MHC:ligand complex OBI:0001580 material transport service A service for chemical disposal A service in which a service provider facilitates the transport of some material entity to a specified destination for the service consumer. PERSON: Carlo Torniai PERSON: Matthew Brush PERSON: Carlo Torniai material transport service OBI:0001581 equilibrium dissociation constant (KD) approximated by EC50 A measurement of an EC50 value under specific assay conditions approximates KD, namely the binding reaction is at an equilibrium, and the concentration of the receptor must be much less than the KD for the ligand. PERSON: Bjoern Peters, Randi Vita Assay Development: Fundamentals and Practices, By Ge Wu, page 74 equilibrium dissociation constant (KD) approximated by EC50 OBI:0001582 obsolete cell bound MHC direct binding assay direct binding assay measuring MHC ligand binding using MHC derived from a cell PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) cell bound MHC direct binding obsolete cell bound MHC direct binding assay true OBI:0001583 half life of binding datum The 45 minute period in which one half of the complexes formed by peptide ligand bound to a HLA-A*0201molecule disassociate. A half life datum of the time it takes for 50% of bound complexes in an ensemble to disassociate in absence of re-association. PERSON: Bjoern Peters, Randi Vita IEDB half life of binding datum OBI:0001584 purified MHC direct binding assay measuring binding of a MHC:ligand complex using phage display A purified MHC binding assay that uses a phage display binding assay to measure direct ligand binding. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB qualitative binding|purified MHC/direct/phage display purified MHC direct binding assay measuring binding of a MHC:ligand complex using phage display OBI:0001585 cytometric bead array assay measuring epitope specific interleukin-7 production by T cells An assay of epitope specific interleukin-7 production by T cells that uses a cytometric bead array assay. IEDB IEDB IL-7 release|cytometric bead array cytometric bead array assay measuring epitope specific interleukin-7 production by T cells OBI:0001586 purified MHC direct binding assay measuring half life of a MHC:ligand complex using radioactivity detection A purified MHC ligand half life of binding determination assay that uses radioactivity detection to measure direct ligand binding. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB half life|purified MHC/direct/radioactivity|min purified MHC direct binding assay measuring half life of a MHC:ligand complex using radioactivity detection OBI:0001587 biological activity assay measuring epitope specific interleukin-7 production by T cells A T cell epitope specific cytokine production assay that detects interleukin-7 production by T cells. IEDB IEDB IL-7 release|biological activity biological activity assay measuring epitope specific interleukin-7 production by T cells OBI:0001588 binding A peptide binding to an MHC molecule to form a complex. The process of material entities forming complexes. 9/28/11 BP: The disposition referenced is the one of the ligand to bind the molecule. This along with binding as a function / process needs to be figured out with GO which is inconsistent at this point. PERSON: Bjoern Peters, Randi Vita IEDB binding OBI:0001589 intracellular cytokine staining assay measuring epitope specific interleukin-17A production by T cells A T cell epitope specific interleukin-17A production assay that uses an intracellular cytokine staining assay. IEDB IEDB IL-17A release|ICS intracellular cytokine staining assay measuring epitope specific interleukin-17A production by T cells OBI:0001590 purified MHC direct binding assay measuring binding of a MHC:ligand complex using fluorescence detection A purified MHC binding assay that uses fluorescence detection to measure direct ligand binding. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB qualitative binding|purified MHC/direct/fluorescence purified MHC direct binding assay measuring binding of a MHC:ligand complex using fluorescence detection OBI:0001591 direct binding assay Detecting the binding of a fluorescently labeled antibody to a peptide bound to the bottom of an ELISA plate, by incubating the antibody in the well, washing the plate, and detecing fluorescence which is a proxy for the presence of the bound antibody. a binding assay that measures the formation or disassociation of a complex of 2 material entities directly without use of a competitve ligand. PERSON:Bjoern Peters, Randi Vita IEDB direct binding assay OBI:0001592 purified MHC direct binding assay measuring half maximal effective concentration [EC50] of a MHC:ligand complex using fluorescence detection A purified MHC ligand binding half maximal effective concentration (EC50) determination assay that uses fluorescence detection to measure direct ligand binding. IEDB IEDB half maximal effective concentration (EC50)|purified MHC/direct/fluorescence|nM purified MHC direct binding assay measuring half maximal effective concentration [EC50] of a MHC:ligand complex using fluorescence detection OBI:0001593 competitive inhibition of binding assay Detecting the inhibition of binding of a fluorescently labeled antibody to its known protein ligand bound to the bottom of an ELISA plate, by incubating the antibody in the presence of a peptide of interest, adding it to the plate, washing the plate, and detecing fluorescence which is a proxy for the presence of the bound antibody. Reduction in binding due to the presence of the peptide indicates that the antibody binds the peptide. A binding assay that detects the inhibition of binding between 2 material entities known to form a complex by the addition of a third material entity of interest. Inhibition of binding between the 2 materials reflects binding by the third material. IEDB IEDB competitive inhibition of binding assay OBI:0001594 cell bound MHC competitive binding assay of a MHC:ligand complex using fluorescence detection A cell bound MHC binding assay that uses fluorescence to detect loss of binding of a known reference ligand due to competition by the ligand under investigation PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB qualitative binding|cellular MHC/competitive/fluorescence cell bound MHC competitive binding assay of a MHC:ligand complex using fluorescence detection OBI:0001595 X-ray crystallography assay determining the 3D structure of a MHC:ligand complex A MHC binding 3D structure determination of MHC molecule:epitope complex assay that uses an X-ray crystallography assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB 3D structure|x-ray crystallography|angstroms X-ray crystallography assay determining the 3D structure of a MHC:ligand complex OBI:0001596 PDB file chain The 'D' chain in the PDB file 2BSE identifies the heavy chain of the antibody in the protein:antibody complex A 3D structural organization datum that is part of a PDB file and has a specific chain identifier that identifies the entire information on a subset of the material entities PERSON: Bjoern Peters, Dorjee Tamang, Jason Greenbaum IEDB PDB file chain OBI:0001597 cell bound MHC competitive binding assay measuring half maximal inhibitory concentration [IC50] of a MHC:ligand complex using T cell epitope recognition A cell bound MHC ligand binding half maximal inhibitory concentration (IC50) determination assay that uses a T cell epitope recognition assay to measure ligand binding. IEDB IEDB half maximal inhibitory concentration (IC50)|cellular MHC/T cell inhibition|nM cell bound MHC competitive binding assay measuring half maximal inhibitory concentration [IC50] of a MHC:ligand complex using T cell epitope recognition OBI:0001598 data maintenance service A database management service, a web hosting service. A maintenance service in which a service provider actively manages or maintains data or a database for the service consumer. Maintenance of the data is performed to maintain its integrity or enhance its quality or utility for the consumer, but new data is not generated as a result of the maintenance. PERSON: Carlo Torniai PERSON: Matthew Brush PERSON: Matthew Brush data maintenance service OBI:0001599 cell bound MHC competitive binding assay of a MHC:ligand complex using radioactivity detection A cell bound MHC binding assay that uses radioactivity detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation. IEDB IEDB qualitative binding|cellular MHC/competitive/radioactivity cell bound MHC competitive binding assay of a MHC:ligand complex using radioactivity detection OBI:0001600 biological activity assay measuring epitope specific granulocyte colony stimulating factor production by T cells A T cell epitope specific cytokine production assay that detects granulocyte colony stimulating factor production by T cells. IEDB IEDB G-CSF release|biological activity biological activity assay measuring epitope specific granulocyte colony stimulating factor production by T cells OBI:0001601 cytometric bead array assay measuring epitope specific intracellular cytokine staining (ICS) IL-21 production by T cells An assay of epitope specific interleukin-21 production by T cells that uses a cytometric bead array assay. IEDB IEDB IL-21 release|cytometric bead array cytometric bead array assay measuring epitope specific intracellular cytokine staining (ICS) IL-21 production by T cells OBI:0001602 cell bound MHC direct binding assay of a MHC:ligand complex using radioactivity detection A cell bound MHC binding assay that uses radioactivity detection to detect direct binding. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB qualitative binding|cellular MHC/direct/radioactivity cell bound MHC direct binding assay of a MHC:ligand complex using radioactivity detection OBI:0001603 binding off rate measurement datum (koff) A rate measurement datum of how quickly bound complexes disassociate PERSON: Bjoern Peters, Randi Vita IEDB binding off rate measurement datum (koff) OBI:0001604 purified MHC direct binding assay measuring 50% dissociation of binding temperature [Tm] of a MHC:ligand complex using fluorescence detection A purified MHC binding assay that uses fluorescence detection to measure the 50% dissociation of binding temperature of direct ligand binding. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB 50% dissociation temperature|purified MHC/direct/fluorescence|°C purified MHC direct binding assay measuring 50% dissociation of binding temperature [Tm] of a MHC:ligand complex using fluorescence detection OBI:0001605 binding on rate measurement datum (kon) A rate measurement datum of how quickly bound complexes form PERSON: Bjoern Peters, Randi Vita IEDB binding on rate measurement datum (kon) OBI:0001606 cell bound MHC direct binding assay of a MHC:ligand complex using fluorescence detection A cell bound MHC binding assay that uses fluorescence detection to detect direct binding. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB qualitative binding|cellular MHC/direct/fluorescence cell bound MHC direct binding assay of a MHC:ligand complex using fluorescence detection OBI:0001607 biological activity assay measuring epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells An assay of epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells that detects tumor necrosis factor production. IEDB IEDB TNFSF11/RANKL release|biological activity biological activity assay measuring epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells OBI:0001608 purified MHC direct binding assay of a MHC:ligand complex using radioactivity detection A purified MHC binding assay that uses radioactivity detection to measure direct ligand binding. IEDB IEDB qualitative binding|purified MHC/direct/radioactivity purified MHC direct binding assay of a MHC:ligand complex using radioactivity detection OBI:0001609 intracellular cytokine staining assay measuring epitope specific interleukin-8 production by T cells An assay of epitope specific interleukin-8 production by T cells that uses an intracellular cytokine staining assay. IEDB IEDB IL-8 release|ICS intracellular cytokine staining assay measuring epitope specific interleukin-8 production by T cells OBI:0001610 cytometric bead array assay measuring epitope specific intracellular cytokine staining (ICS) IL-223 production by T cells An assay of epitope specific interleukin-23 production by T cells that uses a cytometric bead array assay. IEDB IEDB IL-23 release|cytometric bead array cytometric bead array assay measuring epitope specific intracellular cytokine staining (ICS) IL-223 production by T cells OBI:0001611 obsolete purified MHC direct binding assay direct binding assay measuring MHC ligand binding using MHC derived from a purified MHC molecule preparation PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) purified MHC direct binding obsolete purified MHC direct binding assay true OBI:0001612 epitope specific vascular endothelial growth factor production by T cells A process of vascular endothelial growth factor production by T cells resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2011-11-10; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: assay_mappings.owl epitope specific vascular endothelial growth factor production by T cells OBI:0001613 purified MHC competitive binding assay measuring half maximal inhibitory concentration [IC50] of a MHC:ligand complex using fluorescence detection A purified MHC ligand binding half maximal inhibitory concentration (IC50) determination assay that uses fluorescence detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB half maximal inhibitory concentration (IC50)|purified MHC/competitive/fluorescence|nM purified MHC competitive binding assay measuring half maximal inhibitory concentration [IC50] of a MHC:ligand complex using fluorescence detection OBI:0001614 GenBank ID A CRID symbol uniquely indentifies the submitted GeneBank sequence record. Person: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group GenBank Record ID NIAID GSCID-BRC GenBank ID OBI:0001615 investigation description A textual entity that describes an investigation. Person: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group study description project description NIAID GSCID-BRC investigation description OBI:0001616 specimen identifier A CRID symbol denotes a specimen and used to distinguish one specimen from another in an investigation. Person: Chris Stoeckert, Jie Zheng specimen ID NIAID GSCID-BRC metadata working group Specimen ID NIAID GSCID-BRC specimen identifier OBI:0001617 PubMed ID A CRID symbol that is sufficient to look up a citation from the PubMed, a literature database of life sciences and biomedical information. Person: Chris Stoeckert, Jie Zheng PMID PubMed Identifier Website: http://en.wikipedia.org/wiki/Wikipedia:PMID Publication Citation NIAID GSCID-BRC PubMed ID OBI:0001618 average depth of sequence coverage An average value of the depth of sequence coverage based both on external (e.g. Cot-based size estimates) and internal (average coverage in the assembly) measures of genome size. Person: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Depth of Coverage - Average NIAID GSCID-BRC average depth of sequence coverage OBI:0001619 specimen collection time measurement datum A time measurement datum that is the measure of the time when the specimens are collected. Person: Chris Stoeckert, Jie Zheng collection date NIAID GSCID-BRC metadata working group Specimen Collection Date NIAID GSCID-BRC specimen collection time measurement datum OBI:0001620 latitude coordinate measurement datum A measurement datum that is the measure of the latitude coordinate of a site. Person: Chris Stoeckert, Jie Zheng latitude NIAID GSCID-BRC metadata working group Specimen Collection Location - Latitude NIAID GSCID-BRC latitude coordinate measurement datum OBI:0001621 longitude coordinate measurement datum A measurement datum that is the measure of the longitude coordinate of a site. Person: Chris Stoeckert, Jie Zheng longitude NIAID GSCID-BRC metadata working group Specimen Collection Location - Longitude NIAID GSCID-BRC longitude coordinate measurement datum OBI:0001622 investigation title A textual entity that denotes an investigation. Person:Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group study title project title NIAID GSCID-BRC investigation title OBI:0001623 organism identification objective A biological feature identification objective to identify the organism species in a specimen. Person: Chris Stoeckert, Jie Zheng Penn Group organism identification objective OBI:0001624 organism identification assay An assay that identifies the organism species in a specimen. Person: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Organism Detection Method NIAID GSCID-BRC organism identification assay OBI:0001625 sequence annotation algorithm An algorithm used to identify sequence features (e.g. protein coding regions) in the assembled contig sequence. This may also include a description of any manual curation that may have generated or validated the annotation. Person: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Annotation Algorithm NIAID GSCID-BRC sequence annotation algorithm OBI:0001626 Bioinformatics Resource Center An organization that is one of the Internet-based research centers established and funded by NIAID (the National Institute of Allergy and Infectious Diseases). The Bioinformatics Resource Centers (BRCs) were formed in response to the threats posed by emerging and re-emerging pathogens, particularly CDC Category A, B, and C pathogens, and their potential use in bioterrorism. The intention of NIAID in funding these bioinformatics centers is to assist researchers involved in the experimental characterization of such pathogens and the formation of drugs, vaccines, or diagnostic tools to combat them. Person: Chris Stoeckert, Jie Zheng BRC Website: http://en.wikipedia.org/wiki/Bioinformatics_Resource_Centers NIAID GSCID-BRC Bioinformatics Resource Center OBI:0001627 country name A textual entity that denotes a geographic location that is a site or part of a site that is identified as a country in the political geography. Person: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Website: http://en.wikipedia.org/wiki/Country Specimen Collection Location - Country NIAID GSCID-BRC country name OBI:0001628 investigation identifier A CRID symbol used to identify an investigation. Person: Chris Stoeckert, Jie Zhneg NIAID GSCID-BRC metadata working group project ID NIAID GSCID-BRC investigation identifier OBI:0001629 grant identifier A CRID symbol used to identify a grant. Person: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group grant ID NIAID GSCID-BRC grant identifier OBI:0001630 analytical chromatography Detection of the presence of blood group A specific antibodies by passing a serum sample through an affinity column containing blood group A carbohydrate, and quantifying the protein content eluted from the column. An analyte assay that uses a biomaterial's preferential affinity for either the mobile phase or the stationary phase to separate it from other materials and thereby detect its presence in an input material. IEDB IEDB analytical chromatography OBI:0001631 electron microscopy imaging assay Using gold labeled antibodies to stain a mouse brain slice and use electron microscopy to generate an image that shows the location of the antibodies within the tissue structure. An imaging assay in which an electrons are used to probe the density, shape and composition of an input material which are detected in an electron microscope and utilized to produce an image of the material. IEDB IEDB electron microscopy imaging assay OBI:0001632 immuno staining assay Detection of the presence of VCAM molecules on the surface of cells in a histology slide using an enzyme-linked antibody followed by enzyme activation to release a dye. A detection of molecular label assay in which the label is attached to an antibody so that substances are marked based on the antibody's binding specificity. IEDB IEDB immuno staining assay OBI:0001633 purified material A mixture of peptide molecules that has been run through an HPLC column to remove 65 A material entity that is generated by a purification process in which an input material is separated to obtain a fraction with a higher concentration of a desired component GROUP: OBI call OBI conference call purified material OBI:0001634 calorimetric binding assay A solution of a proteins is titrated into a solution containing a specific antibody. The heat released upon their interaction (ΔH) is monitored over time where each peak represents a heat change associated with the injection of a small volume of sample into the reaction cell. As successive amounts of the ligand are titrated into the cell, the quantity of heat absorbed or released is in direct proportion to the amount of binding. As the system reaches saturation, the heat signal diminishes until only heats of dilution are observed. A binding curve is then obtained from a plot of the heats from each injection against the ratio of protein and antibody in the cell . A binding assay in which the heat generated or absorbed during a binding event is measured, which allows determination of binding constants, reaction stoichiometry, enthalpy and entropy. IEDB IEDB calorimetric binding assay OBI:0001635 antibody binding detection by fluorescence quenching The binding affinity of Fab 4-4-20 for the fluorescein molecule was determined using the fluorescence quenching assay, by placing the Fab and the fluorescein together in a well and measuring the fluorescence after each addition of increasing concentrations of the Fab (PMID: 8637844). A binding assay in which affinity is measured by detecting a change in fluorescence (usually quenching) that occurs upon binding of the antibody to the ligand. The fluorescent signal that is affected by binding is either from an exogenous fluorophore attached to the ligand, or is the intrisic fluorescence of aromatic (tryptophan) residues on the binding site of the antibody (no conjugated fluorophore necessary) or, less commonly, on the ligand binding region (epitope). IEDB IEDB antibody binding detection by fluorescence quenching OBI:0001636 grant A plan specification of organization A to give money to organization B so that B conducts investigations. Organization A has funder role and Organization B has research organization role. Discussed on Feb 13, 2012 dev call. Details see the tracker: https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891&atid=886178 Group: OBI OBI AR: Grant isn't a plan specification, it has a part which is a plan specification. See tracker: https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891&atid=886178 grant OBI:0001638 antigen inhibition assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex approximated by IC50 A B cell epitope equilibrium dissociation constant (KD) assay that provides IC50 values determined under assay conditions where the IC50 approximates a KD value using a B cell epitope antigen inhibition of binding assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB dissociation constant KD|antigen inhibition (~ IC50)|nM antigen inhibition assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex approximated by IC50 OBI:0001639 biological activity assay measuring epitope specific Ig-mediated histamine release A B cell epitope specific activation of additional immune response in vitro assay that detects histamine release. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB histamine release|biological activity biological activity assay measuring epitope specific Ig-mediated histamine release OBI:0001640 biological activity assay measuring epitope specific immunoglobulin-mediated antigen activation A B cell epitope dependent biological activity determination assay that detects antigen activation. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB antigen activation|biological activity biological activity assay measuring epitope specific immunoglobulin-mediated antigen activation OBI:0001641 biological activity assay measuring epitope specific complement-dependent cytotoxicity A B cell epitope specific activation of additional immune response in vitro assay that detects complement-dependent cytotoxicity. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB complement-dependent cytotoxicity|biological activity biological activity assay measuring epitope specific complement-dependent cytotoxicity OBI:0001642 biological activity assay measuring epitope specific antibody-dependent cellular cytotoxicity A B cell epitope specific activation of additional immune response in vitro assay that detects antibody-dependent cellular cytotoxicity. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB antibody-dependent cellular cytotoxicity|biological activity biological activity assay measuring epitope specific antibody-dependent cellular cytotoxicity OBI:0001643 biological activity assay measuring epitope specific immunoglobulin-mediated neutralization A B cell epitope dependent biological activity determination assay that detects neutralization of the antigen. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB neutralization |biological activity biological activity assay measuring epitope specific immunoglobulin-mediated neutralization OBI:0001644 biological activity assay measuring epitope specific opsonization A B cell epitope specific activation of additional immune response in vitro assay that detects opsonization. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB opsonization|biological activity biological activity assay measuring epitope specific opsonization OBI:0001645 calorimetry assay measuring binding of a B cell epitope:antibody complex A B cell epitope qualitative binding to antibody assay that uses a calorimetric binding assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB qualitative binding|calorimetry calorimetry assay measuring binding of a B cell epitope:antibody complex OBI:0001646 electron microscopy assay determining the 3D structure of a B cell epitope:antibody complex A B cell epitope 3D structure determination assay that uses an electron microscopy imaging assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB 3D structure|electron microscopy electron microscopy assay determining the 3D structure of a B cell epitope:antibody complex OBI:0001647 NMR assay determining the 3D structure of a B cell epitope:antibody complex A B cell epitope 3D structure determination assay that uses a nuclear magnetic resonance assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB 3D structure|nuclear magnetic resonance (NMR) NMR assay determining the 3D structure of a B cell epitope:antibody complex OBI:0001648 cross blocking assay measuring binding of a B cell epitope:antibody complex A B cell epitope qualitative binding to antibody assay that uses an antibody cross-blocking assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB qualitative binding|cross blocking cross blocking assay measuring binding of a B cell epitope:antibody complex OBI:0001649 RIA measuring binding of a B cell epitope:antibody complex A B cell epitope qualitative binding to antibody assay that uses a radio immuno assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB qualitative binding|radio immuno assay (RIA) RIA measuring binding of a B cell epitope:antibody complex OBI:0001650 immunoblot assay measuring binding of a B cell epitope:antibody complex A B cell epitope qualitative binding to antibody assay that uses an immunoblot assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB qualitative binding|western blot immunoblot assay measuring binding of a B cell epitope:antibody complex OBI:0001651 plasmon resonance assay measuring binding of a B cell epitope:antibody complex A B cell epitope qualitative binding to antibody assay that uses a surface plasmon resonance assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB qualitative binding|surface plasmon resonance (SPR) plasmon resonance assay measuring binding of a B cell epitope:antibody complex OBI:0001652 immuno staining assay measuring binding of a B cell epitope:antibody complex A B cell epitope qualitative binding to antibody assay that uses an immuno staining assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB qualitative binding|immuno staining immuno staining assay measuring binding of a B cell epitope:antibody complex OBI:0001653 immunoprecipitation assay measuring binding of a B cell epitope:antibody complex A B cell epitope qualitative binding to antibody assay that uses an immunoprecipitation assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB qualitative binding|immunoprecipitation immunoprecipitation assay measuring binding of a B cell epitope:antibody complex OBI:0001654 mass spectrometry assay measuring binding of a B cell epitope:antibody complex A B cell epitope qualitative binding to antibody assay that uses a mass spectrometry assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB qualitative binding|mass spectrometry mass spectrometry assay measuring binding of a B cell epitope:antibody complex OBI:0001655 phage display assay measuring binding of a B cell epitope:antibody complex A B cell epitope qualitative binding to antibody assay that uses a phage display binding assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB qualitative binding|phage display phage display assay measuring binding of a B cell epitope:antibody complex OBI:0001656 electron microscopy assay measuring binding of a B cell epitope:antibody complex A B cell epitope qualitative binding to antibody assay that uses an electron microscopy imaging assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB qualitative binding|electron microscopy electron microscopy assay measuring binding of a B cell epitope:antibody complex OBI:0001657 ELISA measuring binding of a B cell epitope:antibody complex A B cell epitope qualitative binding to antibody assay that uses an enzyme-linked immunosorbent assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB qualitative binding|ELISA ELISA measuring binding of a B cell epitope:antibody complex OBI:0001658 ELISPOT assay measuring binding of a B cell epitope:antibody complex A B cell epitope qualitative binding to antibody assay that uses an enzyme-linked immunospot assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB qualitative binding|ELISPOT ELISPOT assay measuring binding of a B cell epitope:antibody complex OBI:0001659 flow cytometry assay measuring binding of a B cell epitope:antibody complex A B cell epitope qualitative binding to antibody assay that uses a flow cytometry assay. IEDB IEDB qualitative binding|flow cytometry flow cytometry assay measuring binding of a B cell epitope:antibody complex OBI:0001660 intracellular material detection assay measuring epitope specific granzyme A release by T cells A T cell epitope specific granzyme A release assay that uses an intracellular material detection by flow cytometry assay. IEDB IEDB granzyme A release|intracellular staining intracellular material detection assay measuring epitope specific granzyme A release by T cells OBI:0001661 chromatography assay measuring binding of a B cell epitope:antibody complex A B cell epitope qualitative binding to antibody assay that uses an analytical chromatography assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB qualitative binding|chromatography chromatography assay measuring binding of a B cell epitope:antibody complex OBI:0001662 NMR assay measuring binding of a B cell epitope:antibody complex A B cell epitope qualitative binding to antibody assay that uses a nuclear magnetic resonance assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB qualitative binding|nuclear magnetic resonance (NMR) NMR assay measuring binding of a B cell epitope:antibody complex OBI:0001663 ELISA measuring epitope specific granulysin release by T cells A T cell epitope specific granulysin release assay that uses an ELISA. IEDB IEDB granulysin release|ELISA ELISA measuring epitope specific granulysin release by T cells OBI:0001664 intracellular material detection assay measuring epitope specific granulysin release by T cells A T cell epitope specific granulysin release assay that uses an intracellular material detection by flow cytometry assay. IEDB IEDB granulysin release|intracellular staining intracellular material detection assay measuring epitope specific granulysin release by T cells OBI:0001665 cell bound MHC direct binding assay measuring the off rate [koff] of a MHC:ligand complex using fluorescence detection A cell bound MHC ligand binding off rate measurement (koff) determination assay that uses fluorescence detection to measure direct ligand binding. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB off rate|cellular MHC/direct/fluorescence|1/s cell bound MHC direct binding assay measuring the off rate [koff] of a MHC:ligand complex using fluorescence detection OBI:0001666 cell bound MHC direct binding assay measuring binding on rate [kon] of a MHC:ligand complex using fluorescence detection A cell bound MHC ligand binding on rate (kon) determination assay that uses fluorescence detection to measure direct ligand binding. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB on rate|cellular MHC/direct/fluorescence|nM^-1s^-1 cell bound MHC direct binding assay measuring binding on rate [kon] of a MHC:ligand complex using fluorescence detection OBI:0001667 purified MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex approximated by IC50 using fluorescence detection A purified MHC ligand binding equilibrium dissociation constant (KD) determination assay that uses fluorescence detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation and provides IC50 values determined under assay conditions where the IC50 approximates a KD value. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB dissociation constant KD (~IC50)|purified MHC/competitive/fluorescence|nM purified MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex approximated by IC50 using fluorescence detection OBI:0001668 split-ubiquitin assay Split-ubiquitin two-hybrid assay to analyze protein-protein interactions at the endosome: application to Saccharomyces cerevisiae Bro1 interacting with ESCRT complexes, the Doa4 ubiquitin hydrolase, and the Rsp5 ubiquitin ligase. Nikko E, André B. Eukaryot Cell. 2007 Aug;6(8):1266-77. Epub 2007 May 18. PMID: 17513562 is a kind of yeast 2 hybrid system which enables membrane soluble proteins to be screened. two integral membrane proteins to be studied are fused to two different ubiquitin moieties: a C-terminal ubiquitin moiety (\"Cub\", residues 35–76) and an N-terminal ubiquitin moiety (\"Nub\", residues 1–34). These fused proteins are called the bait and prey, respectively. In addition to being fused to an integral membrane protein, the Cub moiety is also fused to a transcription factor (TF) that can be cleaved off by ubiquitin specific proteases. Upon bait–prey interaction, Nub and Cub-moieties assemble, reconstituting the split-ubiquitin. The reconstituted split-ubiquitin molecule is recognized by ubiquitin specific proteases, which cleave off the reporter protein, allowing it to induce the transcription of reporter genes. PERSON:Philippe Rocca-Serra; Marcus Chibucos adapted from wikipedia add regulatory region DNA binding;sequence-specific DNA binding;obo:GO:0000975;obo:GO:0043565; split-ubiquitin assay OBI:0001669 far-Western blot Studying protein-protein interactions via blot overlay or Far Western blot. Hall RA. Methods Mol Biol. 2004;261:167-74. Review. PMID: 15064457 is a adaptation on the western blot assay to explore protein-protein interaction. The assay involves separating target proteins on an SDS-PAGE gel, blotting to a membrane, hybridization with a protein probe and visualization using a probe-directed antibody. PERSON:Philippe Rocca-Serra; Marcus Chibucos adapted from ECO, PMID:18079728 far-Western blot OBI:0001670 RNA protection assay Absolute concentrations of mRNA for type I and type VI collagen in the canine meniscus in normal and ACL-deficient knee joints obtained by RNase protection assay. Wildey GM, Billetz AC, Matyas JR, Adams ME, McDevitt CA. J Orthop Res. 2001 Jul;19(4):650-8. PMID: 11518275 RPA is a technique to assess the presence and estimate abundance of transcript species by first creating an homo or heteroduplex by adding a specific, complementary sequence to the sequence of interest and then exposing the mixture of ribonuclease, which will degrade only single stranded molecules. A detection step will reveal if the sample contained a sequence of interest. PERSON:Philippe Rocca-Serra; Marcus Chibucos RPA; RNAse protection assay adapted from wikipedia + PMID:16491611 RNA protection assay OBI:0001671 electrophoretic mobility shift assay Electrophoretic mobility shift assay reveals a novel recognition sequence for Setaria italica NAC protein. Puranik S, Kumar K, Srivastava PS, Prasad M. Plant Signal Behav. 2011 Oct;6(10):1588-90. Epub 2011 Oct 1. PMID: 21918373 is an assay which aims to provide information about Protein-DNA or Protein-RNA interaction and which used gel electrophoresis and relies on the fact the molecular interactions will cause the heterodimer to be retarded on the gel when compared to controls corresponding to protein extract alone and protein extract + neutral nucleic acid. PERSON:Philippe Rocca-Serra; Marcus Chibucos EMSA,gel shift assay, gel mobility shift assay, band shift assay, gel retardation assay PMID:6269071 electrophoretic mobility shift assay OBI:0001672 gene knock-down assay is an assay which transiently disrupts gene transcripts by expressing antisense RNA constructs or delivering RNA interfering molecules in cells. PERSON:Philippe Rocca-Serra; Marcus Chibucos PMID:17430206 gene knock-down assay OBI:0001673 nano-cap analysis of gene expression Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan. PMID:20543846 nano-CAGE is a type of CAGE developed to work from very low amount (nanogram scale) of mRNA samples PERSON:Philippe Rocca-Serra; Marcus Chibucos nano-CAGE PMID: 20543846 nano-cap analysis of gene expression OBI:0001674 cap analysis of gene expression 5' end-centered expression profiling using cap-analysis gene expression and next-generation sequencing. Takahashi H, Lassmann T, Murata M, Carninci P. Nat Protoc. 2012 Feb 23;7(3):542-61. doi: 10.1038/nprot.2012.005. PMID: 22362160 An assay which aims at monitoring RNA transcript abundances in biological samples by extracting 5' ends of capped transcripts, RTPCR and sequence those. Copy numbers of CAGE tags provide a way of quantification and provide a measure of expression of the transcriptome PERSON:Philippe Rocca-Serra; Marcus Chibucos CAGE PMID:14663149 cap analysis of gene expression OBI:0001675 ELISA measuring epitope specific interleukin-17A production by T cells A T cell epitope specific interleukin-17A production assay that uses an ELISA. IEDB IEDB IL-17A release|ELISA ELISA measuring epitope specific interleukin-17A production by T cells OBI:0001676 detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-7 production by T cells An assay of epitope specific interleukin-7 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. IEDB IEDB IL-7 release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-7 production by T cells OBI:0001677 epitope specific granulysin production by T cells A process of granulysin production by T cells resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2011-6-24; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: MMExpressionsTcell.txt epitope specific granulysin production by T cells OBI:0001678 epitope specific granzyme A production by T cells A process of granzyme A production by T cells resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2011-6-24; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: MMExpressionsTcell.txt epitope specific granzyme A production by T cells OBI:0001679 yeast 2-hybrid Strong FANCA/FANCG but weak FANCA/FANCC interaction in the yeast 2-hybrid system. Reuter T, Herterich S, Bernhard O, Hoehn H, Gross HJ. Blood. 2000 Jan 15;95(2):719-20. PMID: 10627486 yeast 2 hybrid screen is an assay meant to discover protein–protein interactions and protein–DNA interactions by testing for physical interactions (such as binding) between two proteins or a single protein and a DNA molecule, respectively. The premise behind the test is the activation of downstream reporter gene(s) by the binding of a transcription factor onto an upstream activating sequence (UAS). For two-hybrid screening, the transcription factor is split into two separate fragments, called the binding domain (BD) and activating domain (AD). The BD is the domain responsible for binding to the UAS and the AD is the domain responsible for the activation of transcription.[1][2] The Y2H is thus a protein-fragment complementation assay. PERSON:Philippe Rocca-Serra; Marcus Chibucos Y2H adapted from wikipedia add regulatory region DNA binding;GO:0043565; yeast 2-hybrid OBI:0001680 Sos-recruitment assay The Sos-recruitment system as a tool to analyze cellular localization of plant proteins: membrane localization of Arabidopsis thaliana PEPINO/PASTICCINO2. Schönhofer-Merl S, Torres-Ruiz RA. Mol Genet Genomics. 2010 May;283(5):439-49. Epub 2010 Mar 19. PMID: 20300944 is a kind of yeast 2 hybrid system where mammalian guanyl nucleotide exchange factor (GEF) Sos is recruited to the Saccharomyces cerevisiae plasma membrane harboring a temperature-sensitive Ras GEF, Cdc25-2, allowing growth at the nonpermissive temperature. Using the Sos recruitment system, interacting proteins for targeted domain can be detected. PERSON:Philippe Rocca-Serra; Marcus Chibucos SRS adapted from the original publication by Aronheim et al, 1997. PMID: 9154808 add regulatory region DNA binding;GO:0043565; Sos-recruitment assay OBI:0001681 yeast one-hybrid Yeast one-hybrid assays for gene-centered human gene regulatory network mapping. Nat Methods. 2011 Oct 30;8(12):1050-2. doi: 10.1038/nmeth.1764. PMID: 22037702 The one-hybrid variation of this technique is designed to investigate protein–DNA interactions and uses a single fusion protein in which the AD is linked directly to the binding domain. PERSON:Philippe Rocca-Serra; Marcus Chibucos Y1H PMID: 22218861 add regulatory region DNA binding;obo:GO:0000975; yeast one-hybrid OBI:0001682 bacterial one-hybrid A systematic characterization of factors that regulate Drosophila segmentation via a bacterial one-hybrid system. Noyes MB, Meng X, Wakabayashi A, Sinha S, Brodsky MH, Wolfe SA. Nucleic Acids Res. 2008 May;36(8):2547-60. Epub 2008 Mar 10. PMID: 18332042 is a method for identifying the sequence-specific target site of a DNA-binding domain. In this system, a given transcription factor (TF) is expressed as a fusion to a subunit of RNA polymerase. In parallel, a library of randomized oligonucleotides representing potential TF target sequences, is cloned into a separate vector containing the selectable genes HIS3 and URA3. If the DNA-binding domain (bait) binds a potential DNA target site (prey) in vivo, it will recruit RNA polymerase to the promoter and activate transcription of the reporter genes in that clone. The two reporter genes, HIS3 and URA3, allow for positive and negative selections, respectively. At the end of the process, positive clones are sequenced and examined with motif-finding tools in order to resolve the favoured DNA target sequence PERSON:Philippe Rocca-Serra; Marcus Chibucos B1H http://en.wikipedia.org/wiki/Bacterial_one-hybrid_system add regulatory region DNA binding;obo:GO:0000975; bacterial one-hybrid OBI:0001683 chromosome organization assay by fluorescence in-situ hybridization Duplication of intrachromosomal insertion segments 4q32→q35 confirmed by comparative genomic hybridization and fluorescent in situ hybridization.PMID:22384449 is an in-situ hybridization assay that uses fluorescence as means of detection chromosomal integrity Changed label from fluorescence in-situ hybridization as per tracker item #788 PERSON:Philippe Rocca-Serra; Marcus Chibucos FISH chromosome organization assay by fluorescence in-situ hybridization OBI:0001684 methylation-specific polymerase chain reaction Methylation status of breast cancer resistance protein detected by methylation-specific polymerase chain reaction analysis is correlated inversely with its expression in drug-resistant lung cancer cells. PMID: 18219662 is an assay which uses initial modification of DNA by sodium bisulfite, converting all unmethylated, but not methylated, cytosines to uracil, and subsequent amplification with primers specific for methylated versus unmethylated DNA. 2015-03-30 OBI dev call: The assay was defined as equvivalent to (assay and (has_specified_input some 'binding complex 3D structure determination assay') and (has_specified_output some ('data item' and ('is about' some 'regulation of DNA methylation')))) and (achieves_planned_objective some 'epigenetic modification identification objective') 'binding complex 3D structure determination assay' is a process and cannot be the input of another process which cause inconsistent. In the call, we decided to remove axiom and will discuss it in the assay harmonization discussion. see tracker: https://sourceforge.net/p/obi/obi-terms/747/ PERSON:Philippe Rocca-Serra; Marcus Chibucos MSP PMID:8790415 methylation-specific polymerase chain reaction OBI:0001685 amplification of intermethylated sites (AIMS) assay Analysis of DNA methylation by amplification of intermethylated sites (AIMS).PMID:18987810 amplification of intermethylated sites (AIMS) is an assay appropriate for genome-wide estimates of DNA methylation and the discovery of specific methylated sequences. AIMS is based on the differential enzymatic digestion of genomic DNA with methylation-sensitive and methylation-insensitive isoschizomers followed by restrained PCR amplification of methylated sequences. PERSON:Philippe Rocca-Serra; Marcus Chibucos AIMS assay,intermethylated site amplification PMID: 18987810 amplification of intermethylated sites (AIMS) assay OBI:0001686 in-situ hybridization Use of in situ hybridization to examine gene expression in the embryonic, neonatal, and adult urogenital system. PMID:22639265 is an assay using artificially induced nucleic hybridization to localize a specific DNA or RNA sequence in a portion or section of tissue PERSON:Philippe Rocca-Serra; Marcus Chibucos ISH PMID:9021518 in-situ hybridization OBI:0001687 contact representative role A role inhering in a person who represents an institution, organization, or service provider and realized when communication is directed at them about the entity they represent. Discussed on May 7, 2012 dev call propose:contact role, type of organization role, and create shortcut relation between 'organization role' and 'organization' ? Whether it works for communicating author in manuscript or not? Tracker: https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891&atid=886178 Person: Chris Stoeckert NIAID GSCID-BRC contact representative role OBI:0001689 cytochalasin-induced inhibition of actin polymerization assay is an assay which uses compound cytochalasin (CHEBI: 23528) to block actin polymerization-dependent cell motility (GO:0070358) and actin filament polymerization (GO:0030041). PERSON:Philippe Rocca-Serra; Marcus Chibucos add ;actin filament polymerization obo:GO:0070358; cytochalasin-induced inhibition of actin polymerization assay OBI:0001690 molecular function identification objective is an objective specification which aims to discover molecular function realized by a molecular entity PERSON:Philippe Rocca-Serra OBI group molecular function identification objective OBI:0001691 cellular structure feature identification objective is an objective specification which aims to discover cellular structure properties PERSON:Philippe Rocca-Serra OBI group cellular structure feature identification objective OBI:0001692 in vivo assay measuring B cell epitope specific protection from fertility An efficacy of B cell epitope intervention experiment that uses a protection from challenge in vivo intervention experiment based on reduction of fertility. PERSON:Randi Vita, James Overton, Bjoern Peters IEDB protection from fertility|in vivo assay in vivo assay measuring B cell epitope specific protection from fertility OBI:0001693 in vivo assay measuring B cell epitope specific tolerance induction An efficacy of B cell epitope intervention experiment that uses a tolerance induction intervention experiment. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB tolerance|in vivo assay in vivo assay measuring B cell epitope specific tolerance induction OBI:0001694 in vivo assay measuring B cell epitope specific induction of hypersensitivity An efficacy of B cell epitope intervention experiment that detects a hypersensitivity response by monitoring skin reactions. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB hypersensitivity|in vivo assay in vivo assay measuring B cell epitope specific induction of hypersensitivity OBI:0001695 biological activity assay measuring epitope specific immune complex formation A B cell epitope specific activation of additional immune response in vitro assay that detects agglutination. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB agglutination|biological activity biological activity assay measuring epitope specific immune complex formation OBI:0001696 in vivo assay measuring B cell epitope specific protection based on survival A B cell epitope in vivo intervention experiment that uses a protection from challenge in vivo intervention experiment based on survival. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB survival from challenge|in vivo assay in vivo assay measuring B cell epitope specific protection based on survival OBI:0001697 in vivo assay measuring B cell epitope specific treatment of disease An efficacy of B cell epitope intervention experiment that detects a decrease in disease. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB decreased disease|in vivo assay in vivo assay measuring B cell epitope specific treatment of disease OBI:0001698 biological activity assay measuring B cell epitope specific in vivo activity A B cell epitope dependent biological activity determination assay that uses an in vivo intervention experiment. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB in vivo activity|biological activity biological activity assay measuring B cell epitope specific in vivo activity OBI:0001699 antibody cross-blocking assay Testing two antibodies that bind the HBV core protein for the ability of one antibody pre-incubated with the protein in solution to inhibit binding to the other antibody which is plate-bound in an ELISA format. A competitive inhibition of binding assay in which two antibodies that are known to bind the same antigen are tested for the ability of one antibody to inhibit binding of the other antibody to the antigen, thereby determining if they have overlapping binding sites. IEDB antibody inhibition of antibody binding IEDB antibody cross-blocking assay OBI:0001700 immunoprecipitation assay Determining if a cell is producing a protein using a protein specific antibody to immunoprecipitate the cell lysate. Determining if the serum of a patient contains antibodies against HBV core protein by immunoprecipitating purified HBV core protein with the patients serum. An analyte assay in which an input material is mixed with antibodies and bound antigen:antibody complexes are separated out using immunoprecipitation. Either the antibody has known specificy, and the antigen mixture is tested for the presence of a specific antigen, or the antigen solution is well defined and the antibody solution is tested for the presence of antigen specific antibodies. IEDB IEDB immunoprecipitation assay OBI:0001701 antigen inhibition assay measuring binding of a B cell epitope:antibody complex A B cell epitope qualitative binding to antibody assay that measures the ability of an antigen to inhibit antibody binding to a known ligand. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB qualitative binding|antigen inhibition antigen inhibition assay measuring binding of a B cell epitope:antibody complex OBI:0001702 immunoglobulin binding to epitope Binding of the LA5 antibody to a discontinuous set of amino acid residues on the surface of the D8 protein of Vaccinia virus a process of an immunoglobulin complex binding to a material entity at the immunoglobulin complementarity determining region (CDR). PERSON: Bjoern Peters, Randi Vita IEDB immunoglobulin binding to epitope OBI:0001703 assay measuring qualitiative binding of a B cell epitope:antibody complex A B cell epitope recognition assay that detects qualitative binding. IEDB IEDB qualitative binding|binding assay assay measuring qualitiative binding of a B cell epitope:antibody complex OBI:0001704 biological activity assay measuring epitope specific activation of additional immune response in vitro A B cell epitope dependent biological activity determination assay that detects secondary in vitro activity. IEDB IEDB secondary in vitro activity|biological activity biological activity assay measuring epitope specific activation of additional immune response in vitro OBI:0001705 biological activity assay measuring epitope specific antigen inhibition of antibody activity A B cell epitope dependent biological activity determination assay that detects inhibition of the antibody's activity by the antigen. IEDB IEDB antibody activity inhibition|biological activity biological activity assay measuring epitope specific antigen inhibition of antibody activity OBI:0001706 assay measuring B cell epitope specific biological activity A B cell epitope recognition assay that detects biological activity. IEDB IEDB biological activity|any method assay measuring B cell epitope specific biological activity OBI:0001707 immunoglobulin mediated histamine release The release of histamine by cells stimulated through their Fc receptors which are loaded with immunoglobulins. 4/26/12, BP: We want to import this from GO, which currently only has IgE mediated histamine release. We have requested the term, but need to use this as a placeholder in the meanwhile. PERSON: Bjoern Peters, Randi Vita IEDB immunoglobulin mediated histamine release OBI:0001708 assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex A B cell epitope binding constant determination assay that measures the dissociation constant KD. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB dissociation constant KD|binding assay|nM assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex OBI:0001709 assay measuring a binding constant of a B cell epitope:antibody complex A B cell epitope recognition assay that quantitavely characterizes the binding of an antibody / BCR with a ligand by determining a binding constant. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB binding constant|binding assay assay measuring a binding constant of a B cell epitope:antibody complex OBI:0001710 in vivo assay measuring B cell epitope specific protection from challenge An efficacy of B cell epitope intervention experiment that uses a protection from challenge in vivo intervention experiment. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB protection from challenge|in vivo assay in vivo assay measuring B cell epitope specific protection from challenge OBI:0001711 in vivo assay measuring B cell epitope specific disease exacerbation An efficacy of B cell epitope intervention experiment that uses a disease exacerbation in vivo intervention experiment. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB disease exacerbation|in vivo assay in vivo assay measuring B cell epitope specific disease exacerbation OBI:0001712 obsolete B cell epitope direct binding assay A direct binding assay using a assay PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) direct binding assay obsolete B cell epitope direct binding assay true OBI:0001713 B cell epitope specific opsonization opsonization resulting from antibody binding to epitope PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2012-05-03; Spreadsheet: BcellAssays.xls; Worksheet: Especific template; Mapping: ebcell_specific_mappings.owl B cell epitope specific opsonization OBI:0001714 B cell epitope specific immunoglobulin-mediated neutralization immunoglobulin-mediated neutralization resulting from antibody binding to epitope PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2012-05-03; Spreadsheet: BcellAssays.xls; Worksheet: Especific template; Mapping: ebcell_specific_mappings.owl B cell epitope specific immunoglobulin-mediated neutralization OBI:0001715 obsolete B cell epitope competitive binding assay A competitive inhibition of binding assay using a assay PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) competitive binding assay obsolete B cell epitope competitive binding assay true OBI:0001716 B cell epitope specific complement-dependent cytotoxicity complement-dependent cytotoxicity resulting from antibody binding to epitope PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2012-05-03; Spreadsheet: BcellAssays.xls; Worksheet: Especific template; Mapping: ebcell_specific_mappings.owl B cell epitope specific complement-dependent cytotoxicity OBI:0001717 B cell epitope specific antibody-dependent cellular cytotoxicity antibody-dependent cellular cytotoxicity resulting from antibody binding to epitope PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2012-05-03; Spreadsheet: BcellAssays.xls; Worksheet: Especific template; Mapping: ebcell_specific_mappings.owl B cell epitope specific antibody-dependent cellular cytotoxicity OBI:0001718 assay measuring the on rate [kon] of a B cell epitope:antibody complex A B cell epitope binding constant determination assay that measures the on rate. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB on rate|binding assay|M^-1s^-1 assay measuring the on rate [kon] of a B cell epitope:antibody complex OBI:0001719 assay measuring the association constant [KA] of a B cell epitope:antibody complex A B cell epitope binding constant determination assay that measures the association constant KA. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB association constant KA|binding assay|1/nM assay measuring the association constant [KA] of a B cell epitope:antibody complex OBI:0001720 B cell epitope specific immune complex formation immune complex formation resulting from antibody binding to epitope PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2012-05-03; Spreadsheet: BcellAssays.xls; Worksheet: Especific template; Mapping: ebcell_specific_mappings.owl B cell epitope specific immune complex formation OBI:0001721 3D structure determining assay of a 3D B cell epitope:antibody complex A B cell epitope recognition assay that characterizes the 3D structure of an antibody / BCR with a ligand. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB 3D structure|any method 3D structure determining assay of a 3D B cell epitope:antibody complex OBI:0001722 B cell epitope specific hypersensitivity hypersensitivity resulting from antibody binding to epitope PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2012-05-03; Spreadsheet: BcellAssays.xls; Worksheet: Especific template; Mapping: ebcell_specific_mappings.owl B cell epitope specific hypersensitivity OBI:0001723 assay measuring the off rate [koff] of a B cell epitope:antibody complex A B cell epitope binding constant determination assay that measures the off rate. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB off rate|binding assay|1/s assay measuring the off rate [koff] of a B cell epitope:antibody complex OBI:0001724 biological activity assay measuring epitope specific hemagglutination inhibition A B cell epitope qualitative binding to antibody assay that uses a viral hemagglutination inhibition assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB hemagglutination inhibition|biological activity biological activity assay measuring epitope specific hemagglutination inhibition OBI:0001725 B cell epitope specific histamine secretion mediated by immunoglobulin histamine secretion mediated by immunoglobulin resulting from antibody binding to epitope PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2012-05-03; Spreadsheet: BcellAssays.xls; Worksheet: Especific template; Mapping: ebcell_specific_mappings.owl B cell epitope specific histamine secretion mediated by immunoglobulin OBI:0001726 quenching assay measuring binding of a B cell epitope:antibody complex A B cell epitope qualitative binding to antibody assay that uses an antibody binding detection by fluorescence quenching. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB qualitative binding|quenching quenching assay measuring binding of a B cell epitope:antibody complex OBI:0001727 RIA measuring the dissociation constant [KD] of a B cell epitope:antibody complex A B cell epitope equilibrium dissociation constant (KD) determination assay that uses a radio immuno assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB dissociation constant KD|radio immuno assay (RIA)|nM RIA measuring the dissociation constant [KD] of a B cell epitope:antibody complex OBI:0001728 ELISA measuring the dissociation constant [KD] of a B cell epitope:antibody complex A B cell epitope equilibrium dissociation constant (KD) determination assay that uses an enzyme-linked immunosorbent assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB dissociation constant KD|ELISA|nM ELISA measuring the dissociation constant [KD] of a B cell epitope:antibody complex OBI:0001729 quenching assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex A B cell epitope equilibrium dissociation constant (KD) determination assay that uses an antibody binding detection by fluorescence quenching assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB dissociation constant KD|quenching|nM quenching assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex OBI:0001730 surface plasmon resonance assay measuring the association constant [KA] of a B cell epitope:antibody complex A B cell epitope equilibrium association constant (KA) determination assay that uses a surface plasmon resonance assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB association constant KA|surface plasmon resonance (SPR)|1/nM surface plasmon resonance assay measuring the association constant [KA] of a B cell epitope:antibody complex OBI:0001731 surface plasmon resonance assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex A B cell epitope equilibrium dissociation constant (KD) determination assay that uses a surface plasmon resonance assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB dissociation constant KD|surface plasmon resonance (SPR)|nM surface plasmon resonance assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex OBI:0001732 quenching assay measuring the association constant [KA] of a B cell epitope:antibody complex A B cell epitope equilibrium association constant (KA) determination assay that uses an antibody binding detection by fluorescence quenching assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB association constant KA|quenching|1/nM quenching assay measuring the association constant [KA] of a B cell epitope:antibody complex OBI:0001733 calorimetry assay measuring the association constant [KA] of a B cell epitope:antibody complex A B cell epitope equilibrium association constant (KA) determination assay that uses a calorimetric binding assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB association constant KA|calorimetry|1/nM calorimetry assay measuring the association constant [KA] of a B cell epitope:antibody complex OBI:0001734 calorimetry assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex A B cell epitope equilibrium dissociation constant (KD) determination assay that uses a calorimetric binding assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB dissociation constant KD|calorimetry|nM calorimetry assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex OBI:0001735 ELISA measuring the association constant [KA] of a B cell epitope:antibody complex A B cell epitope equilibrium association constant (KA) determination assay that uses an enzyme-linked immunosorbent assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB association constant KA|ELISA|1/nM ELISA measuring the association constant [KA] of a B cell epitope:antibody complex OBI:0001736 RIA measuring the association constant [KA] of a B cell epitope:antibody complex A B cell epitope equilibrium association constant (KA) determination assay that uses a radio immuno assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB association constant KA|radio immuno assay (RIA)|1/nM RIA measuring the association constant [KA] of a B cell epitope:antibody complex OBI:0001737 obsolete B cell epitope specific X-ray crystallography assay A X-ray crystallography assay measuring epitope specfic antibody binding event in angstroms PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) X-ray crystallography [Ã…] obsolete B cell epitope specific X-ray crystallography assay true OBI:0001738 X-ray crystallography assay determining the 3D structure of a B cell epitope:antibody complex A B cell epitope 3D structure determination assay that uses an X-ray crystallography assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB 3D structure|x-ray crystallography|angstroms X-ray crystallography assay determining the 3D structure of a B cell epitope:antibody complex OBI:0001739 surface plasmon resonance assay measuring the off rate [koff] of a B cell epitope:antibody complex A B cell epitope binding off rate measurement (koff) determination assay that uses a surface plasmon resonance assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB off rate|surface plasmon resonance (SPR)|1/s surface plasmon resonance assay measuring the off rate [koff] of a B cell epitope:antibody complex OBI:0001740 quenching assay measuring the off rate [koff] of a B cell epitope:antibody complex A B cell epitope binding off rate measurement (koff) determination assay that uses an antibody binding detection by fluorescence quenching assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB off rate|quenching|1/s quenching assay measuring the off rate [koff] of a B cell epitope:antibody complex OBI:0001741 surface plasmon resonance assay measuring the on rate [kon] of a B cell epitope:antibody complex A B cell epitope on rate measurement (kon) determination assay that uses a surface plasmon resonance assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB on rate|surface plasmon resonance (SPR)|M^-1s^-1 surface plasmon resonance assay measuring the on rate [kon] of a B cell epitope:antibody complex OBI:0001742 quenching assay measuring the on rate [kon] of a B cell epitope:antibody complex A B cell epitope on rate measurement (kon) determination assay that uses an antibody binding detection by fluorescence quenching assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB on rate|quenching|M^-1s^-1 quenching assay measuring the on rate [kon] of a B cell epitope:antibody complex OBI:0001743 detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-1 beta production by T cells An assay of epitope specific interleukin-1 beta production by T cells that uses a detection of specific nucleic acids with complementary probes assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-1b release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-1 beta production by T cells OBI:0001744 intracellular cytokine staining assay measuring epitope specific interleukin-1 alpha production by T cells An assay of epitope specific interleukin-1 alpha production by T cells that uses an intracellular cytokine staining assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-1a release|ICS intracellular cytokine staining assay measuring epitope specific interleukin-1 alpha production by T cells OBI:0001745 ELISPOT assay measuring epitope specific interleukin-1 alpha production by T cells An assay of epitope specific interleukin-1 alpha production by T cells that uses an ELISPOT assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-1a release|ELISPOT ELISPOT assay measuring epitope specific interleukin-1 alpha production by T cells OBI:0001746 detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-1 alpha production by T cells An assay of epitope specific interleukin-1 alpha production by T cells that uses a detection of specific nucleic acids with complementary probes assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-1a release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-1 alpha production by T cells OBI:0001747 cytometric bead array assay measuring epitope specific interleukin-1 alpha production by T cells An assay of epitope specific interleukin-1 alpha production by T cells that uses a cytometric bead array assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-1a release|cytometric bead array cytometric bead array assay measuring epitope specific interleukin-1 alpha production by T cells OBI:0001748 ELISPOT assay measuring epitope specific interferon-beta production by T cells An assay of epitope specific interferon-beta production by T cells that uses an ELISPOT assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IFNb release|ELISPOT ELISPOT assay measuring epitope specific interferon-beta production by T cells OBI:0001749 intracellular cytokine staining assay measuring epitope specific interferon-beta production by T cells An assay of epitope specific interferon-beta production by T cells that uses an intracellular cytokine staining assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IFNb release|ICS intracellular cytokine staining assay measuring epitope specific interferon-beta production by T cells OBI:0001750 intracellular cytokine staining assay measuring epitope specific granulocyte colony stimulating factor production by T cells An assay of epitope specific granulocyte colony stimulating factor production by T cells that uses an intracellular cytokine staining assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB G-CSF release|ICS intracellular cytokine staining assay measuring epitope specific granulocyte colony stimulating factor production by T cells OBI:0001751 ELISA measuring epitope specific interferon-beta production by T cells An assay of epitope specific interferon-beta production by T cells that uses an ELISA. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IFNb release|ELISA ELISA measuring epitope specific interferon-beta production by T cells OBI:0001752 detection of specific nucleic acids with complementary probes assay measuring epitope specific granulocyte colony stimulating factor production by T cells An assay of epitope specific granulocyte colony stimulating factor production by T cells that uses a detection of specific nucleic acids with complementary probes assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB G-CSF release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific granulocyte colony stimulating factor production by T cells OBI:0001753 ELISPOT assay measuring epitope specific granulocyte colony stimulating factor production by T cells An assay of epitope specific granulocyte colony stimulating factor production by T cells that uses an ELISPOT assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB G-CSF release|ELISPOT ELISPOT assay measuring epitope specific granulocyte colony stimulating factor production by T cells OBI:0001754 cytometric bead array assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells An assay of epitope specific chemokine (C-X-C motif) ligand 9 production by T cells that uses a cytometric bead array assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CXCL9/MIG release|cytometric bead array cytometric bead array assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells OBI:0001755 selection criterion rats should be aged between 6 and 8 weeks and weight between 180-250grams A directive information entity which defines and states a principle of standard by which selection process may take place. Person: Philippe Rocca-Serra selection rule OBI discussion summarized under the following tracker item : http://sourceforge.net/p/obi/obi-terms/678/ selection criterion OBI:0001756 ELISPOT assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells An assay of epitope specific chemokine (C-X-C motif) ligand 9 production by T cells that uses an ELISPOT assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CXCL9/MIG release|ELISPOT ELISPOT assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells OBI:0001757 detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells An assay of epitope specific chemokine (C-X-C motif) ligand 9 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CXCL9/MIG release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells OBI:0001758 ELISPOT assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells An assay of epitope specific chemokine (C-C motif) ligand 4 production by T cells that uses an ELISPOT assay. IEDB IEDB CCL4/MIP-1b release|ELISPOT ELISPOT assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells OBI:0001759 detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-X-C motif) ligand 12 production by T cells An assay of epitope specific chemokine (C-X-C motif) ligand 12 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CXCL12/SDF-1 release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-X-C motif) ligand 12 production by T cells OBI:0001760 detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-X-C motif) ligand 13 production by T cells An assay of epitope specific chemokine (C-X-C motif) ligand 13 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CXCL13/BLC release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-X-C motif) ligand 13 production by T cells OBI:0001761 detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-X-C motif) ligand 16 production by T cells An assay of epitope specific chemokine (C-X-C motif) ligand 16 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CXCL16 release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-X-C motif) ligand 16 production by T cells OBI:0001762 detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 21 production by T cells An assay of epitope specific chemokine (C-C motif) ligand 21 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CCL21/SLC release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 21 production by T cells OBI:0001763 detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 22 production by T cells An assay of epitope specific chemokine (C-C motif) ligand 22 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CCL22/MDC release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 22 production by T cells OBI:0001764 cytometric bead array assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells An assay of epitope specific chemokine (C-C motif) ligand 4 production by T cells that uses a cytometric bead array assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CCL4/MIP-1b release|cytometric bead array cytometric bead array assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells OBI:0001765 detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells An assay of epitope specific chemokine (C-C motif) ligand 4 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. IEDB IEDB CCL4/MIP-1b release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells OBI:0001766 detection of specific nucleic acids with complementary probes assay measuring epitope specific vascular endothelial growth factor production by T cells An assay of epitope specific vascular endothelial growth factor production by T cells that uses a detection of specific nucleic acids with complementary probes assay. IEDB IEDB VEGF release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific vascular endothelial growth factor production by T cells OBI:0001767 detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 19 production by T cells An assay of epitope specific chemokine (C-C motif) ligand 19 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CCL19/MIP-3b release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 19 production by T cells OBI:0001768 intracellular cytokine staining assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells An assay of epitope specific chemokine (C-C motif) ligand 1 production by T cells that uses an intracellular cytokine staining assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CCL1/TCA-3 release|ICS intracellular cytokine staining assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells OBI:0001769 specimen collector role An Investigation agent role borne by a person or organization which is realized in a specimen collection process. Person: Jie Zheng, Chris Stoeckert Penn Group NIAID GSCID-BRC specimen collector role OBI:0001770 intracellular cytokine staining assay measuring epitope specific vascular endothelial growth factor production by T cells An assay of epitope specific vascular endothelial growth factor production by T cells that uses an intracellular cytokine staining assay. IEDB IEDB VEGF release|ICS intracellular cytokine staining assay measuring epitope specific vascular endothelial growth factor production by T cells OBI:0001771 ELISPOT assay measuring epitope specific vascular endothelial growth factor production by T cells An assay of epitope specific vascular endothelial growth factor production by T cells that uses an ELISPOT assay. IEDB IEDB VEGF release|ELISPOT ELISPOT assay measuring epitope specific vascular endothelial growth factor production by T cells OBI:0001772 biological activity assay measuring epitope specific interleukin-17F production by T cells An assay of epitope specific interleukin-17 production by T cells that detects interleukin-17F production. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-17F release|biological activity biological activity assay measuring epitope specific interleukin-17F production by T cells OBI:0001773 biological activity assay measuring epitope specific interleukin-17A production by T cells An assay of epitope specific interleukin-17 production by T cells that detects interleukin-17A production. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-17A release|biological activity biological activity assay measuring epitope specific interleukin-17A production by T cells OBI:0001774 biological activity assay measuring epitope specific chemokine (C-C motif) ligand 21 production by T cells A T cell epitope specific cytokine production assay that detects chemokine (C-C motif) ligand 21 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CCL21/SLC release|biological activity biological activity assay measuring epitope specific chemokine (C-C motif) ligand 21 production by T cells OBI:0001775 biological activity assay measuring epitope specific chemokine (C-C motif) ligand 19 production by T cells A T cell epitope specific cytokine production assay that detects chemokine (C-C motif) ligand 19 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CCL19/MIP-3b release|biological activity biological activity assay measuring epitope specific chemokine (C-C motif) ligand 19 production by T cells OBI:0001776 biological activity assay measuring epitope specific chemokine (C-X-C motif) ligand 12 production by T cells A T cell epitope specific cytokine production assay that detects chemokine (C-X-C motif) ligand 12 production by T cells. IEDB IEDB CXCL12/SDF-1 release|biological activity biological activity assay measuring epitope specific chemokine (C-X-C motif) ligand 12 production by T cells OBI:0001777 biological activity assay measuring epitope specific chemokine (C-C motif) ligand 22 production by T cells A T cell epitope specific cytokine production assay that detects chemokine (C-C motif) ligand 22 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CCL22/MDC release|biological activity biological activity assay measuring epitope specific chemokine (C-C motif) ligand 22 production by T cells OBI:0001778 biological activity assay measuring epitope specific chemokine (C-X-C motif) ligand 16 production by T cells A T cell epitope specific cytokine production assay that detects chemokine (C-X-C motif) ligand 16 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CXCL16 release|biological activity biological activity assay measuring epitope specific chemokine (C-X-C motif) ligand 16 production by T cells OBI:0001779 biological activity assay measuring epitope specific chemokine (C-X-C motif) ligand 13 production by T cells A T cell epitope specific cytokine production assay that detects chemokine (C-X-C motif) ligand 13 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CXCL13/BLC release|biological activity biological activity assay measuring epitope specific chemokine (C-X-C motif) ligand 13 production by T cells OBI:0001780 ELISPOT assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells An assay of epitope specific macrophage inflammatory protein-1 alpha production by T cells that uses an ELISPOT assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CCL3/MIP-1a release|ELISPOT ELISPOT assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells OBI:0001781 cytometric bead array assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells An assay of epitope specific macrophage inflammatory protein-1 gamma production by T cells that uses a cytometric bead array assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CCL9/MIP-1g release|cytometric bead array cytometric bead array assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells OBI:0001782 detection of specific nucleic acids with complementary probes assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells An assay of epitope specific macrophage inflammatory protein-1 gamma production by T cells that uses a detection of specific nucleic acids with complementary probes assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CCL9/MIP-1g release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells OBI:0001783 intracellular cytokine staining assay measuring epitope specific monocyte chemotactic protein-1 production by T cells An assay of epitope specific monocyte chemotactic protein-1 production by T cells that uses an intracellular cytokine staining assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CCL2/MCP-1 release|ICS intracellular cytokine staining assay measuring epitope specific monocyte chemotactic protein-1 production by T cells OBI:0001784 ELISPOT assay measuring epitope specific monocyte chemotactic protein-1 production by T cells An assay of epitope specific monocyte chemotactic protein-1 production by T cells that uses an ELISPOT assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CCL2/MCP-1 release|ELISPOT ELISPOT assay measuring epitope specific monocyte chemotactic protein-1 production by T cells OBI:0001785 intracellular cytokine staining assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells An assay of epitope specific macrophage inflammatory protein-1 gamma production by T cells that uses an intracellular cytokine staining assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CCL9/MIP-1g release|ICS intracellular cytokine staining assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells OBI:0001786 ELISPOT assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells An assay of epitope specific macrophage inflammatory protein-1 gamma production by T cells that uses an ELISPOT assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CCL9/MIP-1g release|ELISPOT ELISPOT assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells OBI:0001787 cytometric bead array assay measuring epitope specific vascular endothelial growth factor production by T cells An assay of epitope specific vascular endothelial growth factor production by T cells that uses a cytometric bead array assay. IEDB IEDB VEGF release|cytometric bead array cytometric bead array assay measuring epitope specific vascular endothelial growth factor production by T cells OBI:0001788 detection of specific nucleic acids with complementary probes assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells An assay of epitope specific tumor necrosis factor superfamily cytokine production by T cells that uses a detection of specific nucleic acids with complementary probes assay. IEDB IEDB TNF release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells OBI:0001789 intracellular cytokine staining assay measuring epitope specific RANTES production by T cells An assay of epitope specific RANTES production by T cells that uses an intracellular cytokine staining assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CCL5/RANTES release|ICS intracellular cytokine staining assay measuring epitope specific RANTES production by T cells OBI:0001790 ELISPOT assay measuring epitope specific RANTES production by T cells An assay of epitope specific RANTES production by T cells that uses an ELISPOT assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CCL5/RANTES release|ELISPOT ELISPOT assay measuring epitope specific RANTES production by T cells OBI:0001791 ELISPOT assay measuring epitope specific lymphotoxin A production by T cells An assay of epitope specific lymphotoxin A production by T cells that uses an ELISPOT assay. IEDB IEDB lymphotoxin A/TNFb release|ELISPOT ELISPOT assay measuring epitope specific lymphotoxin A production by T cells OBI:0001792 detection of specific nucleic acids with complementary probes assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells An assay of epitope specific macrophage inflammatory protein-1 alpha production by T cells that uses a detection of specific nucleic acids with complementary probes assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CCL3/MIP-1a release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells OBI:0001793 cytometric bead array assay measuring epitope specific lymphotoxin A production by T cells An assay of epitope specific lymphotoxin A production by T cells that uses a cytometric bead array assay. IEDB IEDB lymphotoxin A/TNFb release|cytometric bead array cytometric bead array assay measuring epitope specific lymphotoxin A production by T cells OBI:0001794 detection of specific nucleic acids with complementary probes assay measuring epitope specific lymphotoxin A production by T cells An assay of epitope specific lymphotoxin A production by T cells that uses a detection of specific nucleic acids with complementary probes assay. IEDB IEDB lymphotoxin A/TNFb release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific lymphotoxin A production by T cells OBI:0001795 ELISPOT assay measuring epitope specific IP-10 production by T cells An assay of epitope specific IP-10 production by T cells that uses an ELISPOT assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CXCL10/IP-10 release|ELISPOT ELISPOT assay measuring epitope specific IP-10 production by T cells OBI:0001796 intracellular cytokine staining assay measuring epitope specific IP-10 production by T cells An assay of epitope specific IP-10 production by T cells that uses an intracellular cytokine staining assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CXCL10/IP-10 release|ICS intracellular cytokine staining assay measuring epitope specific IP-10 production by T cells OBI:0001797 ELISPOT assay measuring epitope specific interleukin-9 production by T cells An assay of epitope specific interleukin-9 production by T cells that uses an ELISPOT assay. IEDB IEDB IL-9 release|ELISPOT ELISPOT assay measuring epitope specific interleukin-9 production by T cells OBI:0001798 intracellular cytokine staining assay measuring epitope specific interleukin-9 production by T cells An assay of epitope specific interleukin-9 production by T cells that uses an intracellular cytokine staining assay. IEDB IEDB IL-9 release|ICS intracellular cytokine staining assay measuring epitope specific interleukin-9 production by T cells OBI:0001799 detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-9 production by T cells An assay of epitope specific interleukin-9 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. IEDB IEDB IL-9 release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-9 production by T cells OBI:0001800 ELISPOT assay measuring epitope specific interleukin-8 production by T cells An assay of epitope specific interleukin-8 production by T cells that uses an ELISPOT assay. IEDB IEDB IL-8 release|ELISPOT ELISPOT assay measuring epitope specific interleukin-8 production by T cells OBI:0001801 detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-8 production by T cells An assay of epitope specific interleukin-8 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. IEDB IEDB IL-8 release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-8 production by T cells OBI:0001802 ELISPOT assay measuring epitope specific interleukin-3 production by T cells An assay of epitope specific interleukin-3 production by T cells that uses an ELISPOT assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-3 release|ELISPOT ELISPOT assay measuring epitope specific interleukin-3 production by T cells OBI:0001803 ELISA measuring epitope specific interleukin-7 production by T cells An assay of epitope specific interleukin-7 production by T cells that uses an ELISA. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-7 release|ELISA ELISA measuring epitope specific interleukin-7 production by T cells OBI:0001804 ELISPOT assay measuring epitope specific interleukin-7 production by T cells An assay of epitope specific interleukin-7 production by T cells that uses an ELISPOT assay. IEDB IEDB IL-7 release|ELISPOT ELISPOT assay measuring epitope specific interleukin-7 production by T cells OBI:0001805 intracellular cytokine staining assay measuring epitope specific interleukin-7 production by T cells An assay of epitope specific interleukin-7 production by T cells that uses an intracellular cytokine staining assay. IEDB IEDB IL-7 release|ICS intracellular cytokine staining assay measuring epitope specific interleukin-7 production by T cells OBI:0001806 intracellular cytokine staining assay measuring epitope specific interleukin-27 production by T cells An assay of epitope specific interleukin-27 production by T cells that uses an intracellular cytokine staining assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-27 release|ICS intracellular cytokine staining assay measuring epitope specific interleukin-27 production by T cells OBI:0001807 cytometric bead array assay measuring epitope specific interleukin-3 production by T cells An assay of epitope specific interleukin-3 production by T cells that uses a cytometric bead array assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-3 release|cytometric bead array cytometric bead array assay measuring epitope specific interleukin-3 production by T cells OBI:0001808 detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-3 production by T cells An assay of epitope specific interleukin-3 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-3 release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-3 production by T cells OBI:0001809 biological activity assay measuring epitope specific granzyme A release by T cells A T cell epitope specific cytotoxic T cell degranulation assay that detects granzyme A release by T cells. IEDB IEDB granzyme A release|biological activity biological activity assay measuring epitope specific granzyme A release by T cells OBI:0001810 biological activity assay measuring epitope specific granulysin release by T cells A T cell epitope specific cytotoxic T cell degranulation assay that detects granulysin release by T cells. IEDB IEDB granulysin release|biological activity biological activity assay measuring epitope specific granulysin release by T cells OBI:0001811 cytometric bead array assay measuring epitope specific interleukin-27 production by T cells An assay of epitope specific interleukin-27 production by T cells that uses a cytometric bead array assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-27 release|cytometric bead array cytometric bead array assay measuring epitope specific interleukin-27 production by T cells OBI:0001812 intracellular cytokine staining assay measuring epitope specific interleukin-23 production by T cells An assay of epitope specific interleukin-23 production by T cells that uses an intracellular cytokine staining assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-23 release|ICS intracellular cytokine staining assay measuring epitope specific interleukin-23 production by T cells OBI:0001813 ELISPOT assay measuring epitope specific interleukin-27 production by T cells An assay of epitope specific interleukin-27 production by T cells that uses an ELISPOT assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-27 release|ELISPOT ELISPOT assay measuring epitope specific interleukin-27 production by T cells OBI:0001814 ELISA measuring epitope specific interleukin-27 production by T cells An assay of epitope specific interleukin-27 production by T cells that uses an ELISA. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-27 release|ELISA ELISA measuring epitope specific interleukin-27 production by T cells OBI:0001815 detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-18 production by T cells An assay of epitope specific interleukin-18 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-18 release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-18 production by T cells OBI:0001816 epitope specific chemokine (C-X-C motif) ligand 13 production by T cells A process of chemokine (C-X-C motif) ligand 13 production by T cells resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2012-11-16; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: MMExpressionsTcell.txt epitope specific chemokine (C-X-C motif) ligand 13 production by T cells OBI:0001817 ELISPOT assay measuring epitope specific interleukin-18 production by T cells An assay of epitope specific interleukin-18 production by T cells that uses an ELISPOT assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-18 release|ELISPOT ELISPOT assay measuring epitope specific interleukin-18 production by T cells OBI:0001818 epitope specific chemokine (C-X-C motif) ligand 12 production by T cells A process of chemokine (C-X-C motif) ligand 12 production by T cells resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2012-11-16; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: MMExpressionsTcell.txt epitope specific chemokine (C-X-C motif) ligand 12 production by T cells OBI:0001819 epitope specific chemokine (C-C motif) ligand 22 production by T cells A process of chemokine (C-C motif) ligand 22 production by T cells resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2012-11-16; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: MMExpressionsTcell.txt epitope specific chemokine (C-C motif) ligand 22 production by T cells OBI:0001820 epitope specific chemokine (C-X-C motif) ligand 16 production by T cells A process of chemokine (C-X-C motif) ligand 16 production by T cells resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2012-11-16; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: MMExpressionsTcell.txt epitope specific chemokine (C-X-C motif) ligand 16 production by T cells OBI:0001821 ELISPOT assay measuring epitope specific interleukin-22 production by T cells An assay of epitope specific interleukin-22 production by T cells that uses an ELISPOT assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-22 release|ELISPOT ELISPOT assay measuring epitope specific interleukin-22 production by T cells OBI:0001822 ELISPOT assay measuring epitope specific interleukin-23 production by T cells An assay of epitope specific interleukin-23 production by T cells that uses an ELISPOT assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-23 release|ELISPOT ELISPOT assay measuring epitope specific interleukin-23 production by T cells OBI:0001823 epitope specific chemokine (C-C motif) ligand 21 production by T cells A process of chemokine (C-C motif) ligand 21 production by T cells resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2012-11-16; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: MMExpressionsTcell.txt epitope specific chemokine (C-C motif) ligand 21 production by T cells OBI:0001824 intracellular cytokine staining assay measuring epitope specific interleukin-18 production by T cells An assay of epitope specific interleukin-18 production by T cells that uses an intracellular cytokine staining assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-18 release|ICS intracellular cytokine staining assay measuring epitope specific interleukin-18 production by T cells OBI:0001825 epitope specific chemokine (C-C motif) ligand 19 production by T cells A process of chemokine (C-C motif) ligand 19 production by T cells resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2012-11-16; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: MMExpressionsTcell.txt epitope specific chemokine (C-C motif) ligand 19 production by T cells OBI:0001826 ELISPOT assay measuring epitope specific interleukin-21 production by T cells An assay of epitope specific interleukin-21 production by T cells that uses an ELISPOT assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-21 release|ELISPOT ELISPOT assay measuring epitope specific interleukin-21 production by T cells OBI:0001827 detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells An assay of epitope specific chemokine (C-C motif) ligand 1 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CCL1/TCA-3 release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells OBI:0001828 cytometric bead array assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells An assay of epitope specific chemokine (C-C motif) ligand 1 production by T cells that uses a cytometric bead array assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CCL1/TCA-3 release|cytometric bead array cytometric bead array assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells OBI:0001829 ELISPOT assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells An assay of epitope specific chemokine (C-C motif) ligand 1 production by T cells that uses an ELISPOT assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CCL1/TCA-3 release|ELISPOT ELISPOT assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells OBI:0001830 ELISPOT assay measuring epitope specific interleukin-17F production by T cells A T cell epitope specific interleukin-17F production assay that uses an ELISPOT. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-17F release|ELISPOT ELISPOT assay measuring epitope specific interleukin-17F production by T cells OBI:0001831 ELISA measuring epitope specific interleukin-17F production by T cells A T cell epitope specific interleukin-17F production assay that uses an ELISA. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-17F release|ELISA ELISA measuring epitope specific interleukin-17F production by T cells OBI:0001832 detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-17F production by T cells A T cell epitope specific interleukin-17F production assay that uses a detection of specific nucleic acids with complementary probes assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-17F release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-17F production by T cells OBI:0001833 ELISPOT assay measuring epitope specific interleukin-17A production by T cells A T cell epitope specific interleukin-17A production assay that uses an ELISPOT. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-17A release|ELISPOT ELISPOT assay measuring epitope specific interleukin-17A production by T cells OBI:0001834 drawing a conclusion Concluding that the length of the hypotenuse is equal to the square root of the sum of squares of the other two sides in a right-triangle. Concluding that a gene is upregulated in a tissue sample based on the band intensity in a western blot. Concluding that a patient has a infection based on measurement of an elevated body temperature and reported headache. Concluding that there were problems in an investigation because data from PCR and microarray are conflicting. A planned process in which new information is inferred from existing information. drawing a conclusion OBI:0001835 cytometric bead array assay measuring epitope specific interleukin-18 production by T cells An assay of epitope specific interleukin-18 production by T cells that uses a cytometric bead array assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-18 release|cytometric bead array cytometric bead array assay measuring epitope specific interleukin-18 production by T cells OBI:0001836 detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-16 production by T cells An assay of epitope specific interleukin-16 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-16 release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-16 production by T cells OBI:0001837 ELISA measuring epitope specific interleukin-16 production by T cells An assay of epitope specific interleukin-16 production by T cells that uses an ELISA. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-16 release|ELISA ELISA measuring epitope specific interleukin-16 production by T cells OBI:0001838 ELISPOT assay measuring epitope specific interleukin-16 production by T cells An assay of epitope specific interleukin-16 production by T cells that uses an ELISPOT assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-16 release|ELISPOT ELISPOT assay measuring epitope specific interleukin-16 production by T cells OBI:0001839 intracellular cytokine staining assay measuring epitope specific interleukin-16 production by T cells An assay of epitope specific interleukin-16 production by T cells that uses an intracellular cytokine staining assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-16 release|ICS intracellular cytokine staining assay measuring epitope specific interleukin-16 production by T cells OBI:0001840 detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-17A production by T cells A T cell epitope specific interleukin-17A production assay that uses a detection of specific nucleic acids with complementary probes assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-17A release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-17A production by T cells OBI:0001841 intracellular cytokine staining assay measuring epitope specific interleukin-1 beta production by T cells An assay of epitope specific interleukin-1 beta production by T cells that uses an intracellular cytokine staining assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-1b release|ICS intracellular cytokine staining assay measuring epitope specific interleukin-1 beta production by T cells OBI:0001842 ELISPOT assay measuring epitope specific interleukin-1 beta production by T cells An assay of epitope specific interleukin-1 beta production by T cells that uses an ELISPOT assay. IEDB IEDB IL-1b release|ELISPOT ELISPOT assay measuring epitope specific interleukin-1 beta production by T cells OBI:0001843 detection of specific nucleic acids with complementary probes measuring epitope specific interleukin-15 production by T cells An assay of epitope specific interleukin-15 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-15 release|RNA/DNA detection detection of specific nucleic acids with complementary probes measuring epitope specific interleukin-15 production by T cells OBI:0001844 ELISPOT assay measuring epitope specific interleukin-12 production by T cells An assay of epitope specific interleukin-12 production by T cells that uses an ELISPOT assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-12 release|ELISPOT ELISPOT assay measuring epitope specific interleukin-12 production by T cells OBI:0001845 intracellular cytokine staining assay measuring epitope specific interleukin-15 production by T cells An assay of epitope specific interleukin-15 production by T cells that uses an intracellular cytokine staining assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-15 release|ICS intracellular cytokine staining assay measuring epitope specific interleukin-15 production by T cells OBI:0001846 ELISPOT assay measuring epitope specific interleukin-15 production by T cells An assay of epitope specific interleukin-15 production by T cells that uses an ELISPOT assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-15 release|ELISPOT ELISPOT assay measuring epitope specific interleukin-15 production by T cells OBI:0001848 chromatin interaction analysis by paired-end tag sequencing Zhang, et al. ChIA-PET analysis of transcriptional chromatin interactions. Methods. 2012 Nov;58(3):289-99. [PMID:22926262] An assay that incorporates chromatin immunoprecipitation (ChIP)-based enrichment, chromatin proximity ligation, Paired-End Tags, and high-throughput sequencing to determine de novo long-range chromatin interactions genome-wide. Person: Venkat Malladi, Chris Stoeckert, Jie Zheng ChIA-PET ChIA-PET assay http://en.wikipedia.org/wiki/ChIA-PET ENCODE project chromatin interaction analysis by paired-end tag sequencing OBI:0001849 structural analysis by paired-end tag sequencing Yao, et al. Long Span DNA Paired-End-Tag (DNA-PET) Sequencing Strategy for the Interrogation of Genomic Structural Mutations and Fusion-Point-Guided Reconstruction of Amplicons. PLoS One. 2012;7(9):e46152 [PMID:23029419] An assay that incorporates Paired-End Tags and sequencing technology to determine structural variants. Person: Venkat Malladi, Chris Stoeckert, Jie Zheng DNA-PET DNA-PET assay Yao, et al. Long Span DNA Paired-End-Tag (DNA-PET) Sequencing Strategy for the Interrogation of Genomic Structural Mutations and Fusion-Point-Guided Reconstruction of Amplicons. PLoS One. 2012;7(9):e46152 [PMID:23029419] ENCODE project structural analysis by paired-end tag sequencing OBI:0001850 transcript analysis by paired-end tag sequencing Ruan, et al. Genome wide full-length transcript analysis using 5' and 3' paired-end-tag next generation sequencing (RNA-PET). Methods Mol Biol. 2012;809:535-62. [PMID:22113299] An assay that incorporates Paired-End Tags and sequencing technology to determine transcripts, gene structures, and gene expressions. Person: Venkat Malladi, Chris Stoeckert, Jie Zheng RNA-PET RNA-PET assay Ruan, et al. Genome wide full-length transcript analysis using 5' and 3' paired-end-tag next generation sequencing (RNA-PET). Methods Mol Biol. 2012;809:535-62. [PMID:22113299] ENCODE project transcript analysis by paired-end tag sequencing OBI:0001851 transcription start site identification objective A transcription profiling identification objective that aims to characterize the transcription start sites of genes. Person: Chris Stoeckert, Jie Zheng Penn Group transcription start site identification objective OBI:0001852 paired-end library preparation A library preparation that results in the creation of a library of the 5' and 3' ends of DNA or cDNA fragments using adaptors and endonucleases. The preparation may or may not include cloning process. Person: Venkat Malladi, Jie Zheng Venkat Malladi, Jie Zheng ENCODE project paired-end library preparation OBI:0001853 DNase I hypersensitive sites sequencing assay Sabo, et al. Discovery of functional noncoding elements by digital analysis of chromatin structure. Proc Natl Acad Sci U S A. 2004 Nov 30;101(48):16837-42. [PMID:15550541] An assay to identify the location of regulatory regions, based on the genome-wide sequencing of regions super sensitive to cleavage by DNase I. Person: Venkat Malladi, Chris Stoeckert, Jie Zheng DNase-seq DNase-seq assay http://en.wikipedia.org/wiki/DNase-Seq ENCODE project DNase I hypersensitive sites sequencing assay OBI:0001854 protein and RNA interaction identification objective A sequence feature identification objective that aims to characterize the interactions between protein and RNA. JZ: Term added for ENCODE project requested assays. Definition adapted from 'protein and DNA interaction identification objective'. Person: Jie Zheng Jie Zheng protein and RNA interaction identification objective OBI:0001857 RNP (ribonuclear particle) immunoprecipitation high- throughput sequencing assay Zhao et al. Genome-wide identification of polycomb-associated RNAs by RIP-seq. Molecular Cell (2010) vol. 40 (6) pp. 939-53 [PMID:21172659] An assay that combines immunoprecipitation of an RNA-binding protein and RNA-seq to identify mRNAs associated with selected RNA binding proteins (RBPs). Person: Venkat Malladi, Chris Stoeckert, Jie Zheng RIP-seq RIP-seq assay Zhao et al. Genome-wide identification of polycomb-associated RNAs by RIP-seq. Molecular Cell (2010) vol. 40 (6) pp. 939-53 [PMID:21172659] ENCODE project RNP (ribonuclear particle) immunoprecipitation high- throughput sequencing assay OBI:0001858 cross-linking immunoprecipitation high-throughput sequencing assay Heulga et al. Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins. Cell Rep. 2012 Feb 23;1(2):167-78. [PMID:22574288] An assay that employs UV-crosslinking between RNA and the protein, followed by immunoprecipitation with antibodies for the protein, fragmentation, and high-throughput used for screening for RNA sequences that interact with a particular RNA-binding protein. Person: Venkat Malladi, Chris Stoeckert, Jie Zheng CLIP-seq CLIP-seq assay HITS-CLIP Licatalosi et al. HITS-CLIP yields genome-wide insights into brain alternative RNA processing. Nature. 2008 Nov 27 456: 464-469 [PMID:18978773] ENCODE project cross-linking immunoprecipitation high-throughput sequencing assay OBI:0001859 formaldehyde-assisted isolation of regulatory elements assay Giresi, et al. FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin. Genome Research 17 (6): 877–85. [PMID:17179217] An assay to determine the sequences of those DNA regions in the genome associated with regulatory activity. Person: Venkat Malladi, Chris Stoeckert, Jie Zheng FAIRE-seq FAIRE-seq assay http://en.wikipedia.org/wiki/FAIRE-Seq ENCODE project formaldehyde-assisted isolation of regulatory elements assay OBI:0001861 methylation-sensitive restriction enzyme sequencing assay Maunakea et al. Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature. 2010 Jul 8;466(7303):253-7. [PMID:20613842] An assay that identifies unmethylated CpGs by use of methylation sensitive restriction enzymes to fragment DNA. Person: Venkat Malladi, Chris Stoeckert, Jie Zheng MRE-seq MRE-seq assay Maunakea et al. Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature. 2010 Jul 8;466(7303):253-7. [PMID:20613842] ENCODE project methylation-sensitive restriction enzyme sequencing assay OBI:0001862 reduced representation bisulfite sequencing assay Meissner et al. Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis. Nucleic Acids Res. 2005; 33(18): 5868–5877. [PMCID: PMC1258174] A bisulfite sequencing assay that identifies genomic methylation patterns by using a bisulfite based protocol that enriches CG-rich parts of the genome. Person: Venkat Malladi, Chris Stoeckert, Jie Zheng RRBS RRBS assay reduced representation bisulfite-seq Meissner et al. Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis. Nucleic Acids Res. 2005; 33(18): 5868–5877. [PMCID: PMC1258174] ENCODE project reduced representation bisulfite sequencing assay OBI:0001863 shotgun bisulfite-seq assay Cokus et al. Shotgun bisulfite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature. 2008 Mar 13;452(7184):215-9. [PMID:18278030]. A bisulfite sequencing assay that identifies methylated cytosines across the genome using high throughput sequencing. Person: Venkat Malladi, Chris Stoeckert, Jie Zheng Shotgun bisulfite sequencing WGBS WGSBS whole genome bisulfite sequencing whole-genome shotgun bisulfite sequencing Cokus et al. Shotgun bisulfite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature. 2008 Mar 13;452(7184):215-9. [PMID:18278030] ENCODE project shotgun bisulfite-seq assay OBI:0001864 RNA Annotation and Mapping of Promoters for the Analysis of Gene Expression assay Batut et al. High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression. Genome Research. 2013 Jan;23(1):169-80. [PMID:22936248] An assay that identifies transcription start sites (TSS), the quantification of their expression and the characterization of their transcripts using high throughput sequencing. Person: Venkat Malladi, Chris Stoeckert, Jie Zheng RAMPAGE Batut et al. High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression. Genome Research. 2013 Jan;23(1):169-80. [PMID:22936248] ENCODE project RNA Annotation and Mapping of Promoters for the Analysis of Gene Expression assay OBI:0001865 assay array A device made to be used in an analyte assay for immobilization of substances that bind the analyte at regular spatial positions on a surface. PERSON: Chris Stoeckert, Jie Zheng, Alan Ruttenberg Penn Group assay array OBI:0001866 secondary cultured cell A cultured cell that has been passaged or derives from a cell that has been passaged in culture. The term 'secondary cell culture' is generally used in biological texts/protocols to refer to any culture following an initial passage. We include it here because there are often a number of passages between a primary culture and the establishment of a stable, homogenous cell line. Such cultures are considered to be 'secondary cultures' but not 'cell lines' during this intermediate passaging/selection period between their derivation from a 'primary cell culture' and derivation into a 'cell line', which is a more specific type of secondary culture. Person: Matthew Brush PERSON: Matthew Brush A secondary cultured cell has been passaged in culture or is a descendant of such a cell that is derived through propagation in culture. secondary cultured cell OBI:0001867 establishing cell line a process whereby a new type of cell line is created, either through passaging of a primary cell culture to relative genetic stability and compositional homogeneity, or through some experimental modification of an existing cell line to produce a new line with novel characteristics (e.g. immortalization or some other stable genetic modification, or selection of some defined subset). 2013-4-20 MHB: For cases of initial establilshment of a line from a primary culture, successive passaging and/or selection processes can confer increasing degrees of genetic stability and compositional homogeneity as compared to the input primary culture. Historically, many texts consider the first passage as the clearest point to define the beginning of a line. However, in practice it is more often that case that more than one passage, and possibly additional selective techniques, may be required before a culture is deemed to have sufficient stability and homogeneity to be considered cell line. This is the view taken in OBI. Regardless, what is important is that some intentional, experimental step has been taken to establish a more homogenous and stable culture that can be characterized and progatated over time. Person: Matthew Brush PERSON:Matthew Brush establishing cell line OBI:0001868 genetic material A nucleic acid macromolecule that is part of a cell or virion and is inherited from an immediate ancestor, or incorporated in a manner that it has the disposition to be replicated and inherited by descendants. MHB 3-22-13: Discussions are ongoing about the label of this class, given consideration of a second class that covers nucleic acid parts of cells or virions that participate in gene expression processes as a template for expression or a direct effector of expression of some other genetic element (e.g. an siRNA), but are not necessarily heritable by progeny or inherited from ancestors. So things like transiently transfected plasmids and siRNAs would qualify as instances of this second class, but not of 'genetic material' as defined here. Also, OBI needs to import a class representing virions for an axiom on genetic material (part_of some (cell or virion). genomic material hereditary genetic material OBI developer calls, March 4 2013 and March 11 2013 Naturally occurring or experimentally incorporated nucleic acids that meet these criteria can qualify as genetic/genomic material. Qualifying examples include: (1) inherited chromosomal DNA in germ cells, stem cells, fully differentiated cells, or cell line cells, or the DNA/RNA content of a virion; (2) natural replicons exchanged through horizontal gene transfer mechanisms such as bacterial conjugation, which are capable of replication and inheritance by progeny; (3) a chromosomally integrated gene targeting DNA construct transfected into a cell; or (4) a stable extra-chromosomal replicon delivered into cells, such as a plasmid in bacterial host with ori allowing indefinite propagation. Non-qualifying examples include a transiently transfected plasmid or siRNA oligo (as these are not able to be replicated and inherited by progeny cells). genetic material OBI:0001869 Illumina BeadChip An array that consists of 3-micron silica beads that self assemble in microwells on either of two materials: fiber optic bundles or planar silica slides. PERSON: Chris Stoeckert, Jie Zheng, Alan Ruttenberg, Venkat Malladi http://www.illumina.com/technology/beadarray_technology.ilmn Illumina BeadChip OBI:0001870 Illumina methylation BeadChip A BeadChip made for an analyte assay that generates information about DNA methylation. PERSON: Chris Stoeckert, Jie Zheng, Alan Ruttenberg Penn Group Illumina methylation BeadChip OBI:0001871 LSRFortessa X-20 A flow cytometer analyzer manifactured by Becton ans Dickinson. Can be configured with up to 5 lasers, 488nm, 532 or 561 nm, 640 nm, 405 nm, 355 nm for measuring up to 20 parameters simultaneously. Anna Maria Masci http://www.bdbiosciences.com/instruments/lsrx20/index.jsp?WT.srch=1&gclid=CJjJ8JTR5LoCFXBo7AodZycAbg LSRFortessa X-20 OBI:0001872 sequence assembly process A data transformation that assembles two or more individual sequence reads into contiguous sequences (i.e., contigs). PRS/AGB: changed to restrictions by adding 2 possible specified outputs (N50 and genome coverage) for sequence assembly. Alejandra Gonzalez-Beltran PERSON: Jie Zheng, Chris Stoeckert Philippe Rocca-Serra NIAID GSCID-BRC metadata working group NIAID GSCID-BRC sequence assembly process OBI:0001873 number of errors Gigascience. 2012 Dec 27;1(1):18. doi: 10.1186/2047-217X-1-18. PMID: 23587118. see table2 a data item that is the number of times that a given process failed, as an integer Alejandra Gonzalez-Beltran Philippe Rocca-Serra PRS, AGB number of errors OBI:0001874 random access memory size Gigascience. 2012 Dec 27;1(1):18. doi: 10.1186/2047-217X-1-18. PMID: 23587118. "However, the error correction module in SOAPdenovo was designed for short Illumina reads (35-50 bp), which consumes an excessive amount of computational time and memory on longer reads, for example, over 150 GB memory running for two days using 40-fold 100 bp paired-end Illumina HiSeq 2000 reads" random access memory size is a scalar measurement datum which denotes the amount of physical memory know as random access memory present of a computer or required by a computational process or data transformation Alejandra Gonzalez-Beltran Philippe Rocca-Serra PRS, AGB random access memory size OBI:0001875 cultured immune cell population a cultured cell population comprised of a single type of immune system cell MHB 3-5-13: created as a (temporary) organizational class to organize IEDB immune cultured cell population types. These were all previously labled as 'cell cultures' - and relabeld here as 'cultured cell populations' since a CLO alignment outcome was to use the term 'cell culture' to refer to cultured cells + media. Consult with BP as to whether this organizational class is useful and if so, how to define it. Also check whether the intent was to represent cell populations rather than cell cultures. PERSON:Matthew Brush immune cell culture sample PERSON:Matthew Brush cultured immune cell population OBI:0001876 cell culture A material entity comprised of cultured cells and the media in which they are being propagated or stored. PERSON:Matthew Brush OBI-CLO Alignment Working Group (Spring 2013) A cell culture includes the cells in culture, as well as the media and all additives in which the cells are being grown or in which they are stored. cell culture OBI:0001877 random access memory Random-access memory (RAM) is a form of computer data storage. A random-access device allows stored data to be accessed directly in any random order. In contrast, other data storage media such as hard disks, CDs, DVDs and magnetic tape, as well as early primary memory types such as drum memory, read and write data only in a predetermined order, consecutively, because of mechanical design limitations. Therefore, the time to access a given data location varies significantly depending on its physical location Alejandra Gonzalez-Beltran Philippe Rocca-Serra RAM http://en.wikipedia.org/wiki/RAM last accessed: 2013-12-02 random access memory OBI:0001878 establishing primary cell culture Effects of establishing cell cultures and cell culture conditions on the proliferative life span of human fibroblasts isolated from different tissues and donors of different ages. Exp Cell Res. 2002 Apr 1;274(2):275-87. PMID: 11900488 When harvesting blood from a human, isolating T cells, and then limited dilution cloning of the cells, the establishing_cell_culture step comprises preparing the cells at a certain dilution and plating them in a container with growth medium. an establishing cell culture process whereby cells explanted directly from an organismal source or specimen, and placed in culture for maintenance or propagation as a primary cell culture PERSON: Matthew Brush Cells are originally plated at a certain concentration referred to as seeding density. Upon a first passage this primary culture becomes a secondary cell culture that can be propagated to become a stable and homogneous cell line. This class covers establishment of primary cultures from any native cell - 'in vivo' cells isolated from some multicellular organism, or 'in environment' unicellular organisms isolated from some natural environment. establishing primary cell culture OBI:0001879 reagent A biological or chemical entity that bears a reagent role in virtue of it being intended for application in a scientific technique to participate in (or have molecular parts that participate in) a chemical reaction that facilitates the generation of data about some distinct entity, or the generation of some distinct material specified output. 2013-6-5 MHB: Clarifications regarding the distinction between reagetns and devices were made at the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For examples, see editor note on OBI:device. PERSON:Matthew Brush PERSON:Matthew Brush (copied from ReO) Reagents are distinguished from devices/instruments that also serve as facilitators in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in or have parts that participate in some chemical interaction or reaction during their intended participation in some technique. By contrast, devices do not participate in a chemical reaction/interaction during the technique. Reagents are distinguished from study subjects/evaluants in that study subjects and evaluants are that about which conclusions are drawn and knowledge is sought in an investigation - while reagents, by definition, are not. It should be noted, however, that reagent and study subject/evaluant roles can be borne by instances of the same type of material entity - but a given instance can only realize one of these roles in the execution of a given assay. For example, taq polymerase can bear a reagent role or an evaluant role. In a DNA sequencing assay aimed at generating sequence data about some plasmid, the reagent role of the taq polymerase is realized. In an assay to evaluate the quality of the taq polymerase itself, the evaluant/study subject role of the taq is realized, but not the reagent role since the taq is the subject about which data is generated. In regard to the statement that reagents are 'distinct' from the specified outputs of a technique: note that a reagent may be incorporated into a material output of a technique, as long as the IDENTITY of this output is distinct from that of the bearer of the reagent role. For example, dNTPs input into a PCR are reagents that become part of the material output of this technique, but this output has a new identity (ie that of a 'nucleic acid molecule') that is distinct from the identity of the dNTPs that comprise it. Similarly, a biotin molecule input into a cell labeling technique are reagents that become part of the specified output, but the identity of the output is that of some modified cell specimen which shares identity with the input unmodified cell specimen, and not with the biotin label. Thus, we see that an important criteria of 'reagent-ness' is that it is a facilitator, and not the primary focus of an investigation or material processing technique (ie not the specified subject/evaluant about which knowledge is sought, or the specified output material of the technique). reagent OBI:0001880 organization of specimen provider principal investigator An organization that is the affiliation of the principal investigator providing the specimens for the investigation PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Sample Provider PI's Institution NIAID GSCID-BRC organization of specimen provider principal investigator OBI:0001881 organization of Bioinformatics Resource Center contact person An organization that is the affiliation of the person who is contact representative of a Bioinformatics Resource Center PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Bioinformatics Resource Center Contact's Institution NIAID GSCID-BRC organization of Bioinformatics Resource Center contact person OBI:0001882 target material in specimen specification Some examples of target material are Genome, Purified chromosome, Transcriptome, Phenotype, Proteome. A plan specification which specifies the type of material that will be assayed in an investigation. PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Target Material NIAID GSCID-BRC target material in specimen specification OBI:0001883 Bioinformatics Resource Center contact person A person who is the contact representative of a Bioinformatics Resource Center PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Bioinformatics Resource Center Contact Name NIAID GSCID-BRC Bioinformatics Resource Center contact person OBI:0001884 specimen-based scope of investigation specification Some examples of specimen scope are Monoisolate, Multiisolate, Multi-species, Environment, or Synthetic. A plan specification which specifies the scope of an investigation based on the heterogeneity of organisms or type of material that are the specified input of specimen collection. PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Sample Scope NIAID GSCID-BRC specimen-based scope of investigation specification OBI:0001885 specimen repository organization An organization that provides a service to store and distribute specimens PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Specimen Repository NIAID GSCID-BRC specimen repository organization OBI:0001887 email address of Bioinformatics Resource Center contact person An email address of the person who is contact representative of a Bioinformatics Resource Center PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Bioinformatics Resource Center Contact's email NIAID GSCID-BRC email address of Bioinformatics Resource Center contact person OBI:0001888 sequencing facility contact person A person who is the contact representative at the sequencing facility PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Sequencing Facility Contact Name NIAID GSCID-BRC sequencing facility contact person OBI:0001889 specimen provider principal investigator A person who is a principal investigator and provides the specimen PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Sample Provider Principal Investigator (PI) Name NIAID GSCID-BRC specimen provider principal investigator OBI:0001890 email address of specimen collector An email address of the person collecting the specimen PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Specimen Collector's email NIAID GSCID-BRC email address of specimen collector OBI:0001891 sequencing facility organization An organization that provides sequence determination service PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Sequencing Facility NIAID GSCID-BRC sequencing facility organization OBI:0001892 specification of data to be generated in an investigation Some examples of Project Objectives are Raw sequence reads, Sequence, Analysis, Assembly, Annotation, Variation, Epigenetic markers, expression, maps, phenotype An objective specification which indicates the type of data that will be generated and submitted to a database. PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Project Objectives NIAID GSCID-BRC specification of data to be generated in an investigation OBI:0001893 organization of specimen collector An organization that is the affiliation of the person collecting the specimen PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Specimen Collector's Institution NIAID GSCID-BRC organization of specimen collector OBI:0001894 email address of sequencing facility contact person An email address of the contact representative at the sequencing facility PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Sequencing Facility Contact's email NIAID GSCID-BRC email address of sequencing facility contact person OBI:0001895 specimen collector A person who collects the specimen PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Specimen Collector Name NIAID GSCID-BRC specimen collector OBI:0001896 investigation assay specification Some examples of Project Method are Sequence, Array, Mass Spectrometry A plan specification which indicates the assay type used to obtain data. PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Project Method NIAID GSCID-BRC investigation assay specification OBI:0001897 organization of sequencing facility contact person An organization that is the affiliation of the contact representative at the sequencing facility PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Sequencing Facility Contact's Institution NIAID GSCID-BRC organization of sequencing facility contact person OBI:0001898 comment on investigation A textual entity that is about any of the aspects of an investigation worth noting PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Comments NIAID GSCID-BRC comment on investigation OBI:0001899 target capture specification Some examples of target capture are Whole, CloneEnds, Exome, TargetedLocusLoci, RandomSurvey A plan specification which specifies how the material enrichment procedure will influence the scale, or type of material that will be assayed in the specimen. PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Target Capture NIAID GSCID-BRC target capture specification OBI:0001900 specimen identifier assigned by specimen repository A specimen identifier which is assigned by a specimen repository PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Specimen Repository Sample ID NIAID GSCID-BRC specimen identifier assigned by specimen repository OBI:0001901 specimen identifier assigned by sequencing facility A specimen identifier which is assigned by a sequencing facility PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Sample ID - Sequencing Facility NIAID GSCID-BRC specimen identifier assigned by sequencing facility OBI:0001902 sample preparation for sequencing assay A sample preparation for assay that preparation of nucleic acids for a sequencing assay PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Nucleic Acid Preparation Method NIAID GSCID-BRC sample preparation for sequencing assay OBI:0001903 email address of specimen provider principal investigator An email address of the principal investigator providing the specimens for the investigation PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Sample Provider PI's email NIAID GSCID-BRC email address of specimen provider principal investigator OBI:0001904 sequencing service A service provides sequencing service which is the realization of some sequencing such as RNA and DNA sequencing in which the service provider role is realized. Person: Jie Zheng Adpated from 'DNA sequencing service' NIAID GSCID-BRC sequencing service OBI:0001905 secondary cultured cell population A cultured cell population that is derived through one or more passages in culture. The term 'secondary cell culture' is generally used in biological texts/protocols to refer to any culture of cells following an initial passage. We include it here because there are often a number of passages between a primary culture and the establishment of a stable, homogenous cell line. Such cultures are considered to be 'secondary cultures' but not 'cell lines' during this intermediate passaging/selection period between their derivation from a 'primary cell culture' and derivation into a 'cell line', which is a more specific type of secondary culture. PERSON:Matthew Brush secondary cell culture sample PERSON:Matthew Brush The concept of a 'secondary cultured cell population' covers cell lines as well as cultured cell populations more immediately derived from a primary culture which have yet to achieve adequate genetic stability and compositional homogeneity to be considered a cell line. The extent of the collection of cells in a 'secondary cultured cell population' is restricted only in that all cell members must share a propagation history (ie be derived through a common lineage of passages from an initial culture). Secondary cultured cell populations can be under active culture, stored in a quiescent state for future use, or applied experimentally. secondary cultured cell population OBI:0001906 cancer cell line An immortal cell line derived from a transformed cell that was part of a malignant tumor. cancer cell line OBI:0001907 immortalizing cell line transformation a genetic transformation of a cell line cell with transgenic constructs intended to confer the capability for indefinite propagation in culture immortalizing cell line transformation OBI:0001908 testable hypothesis that fucoidan has a small statistically significant effect on AT3 level but no useful clinical effect as in-vivo anticoagulant, a paraphrase of part of the last paragraph of the discussion section of the paper 'Pilot clinical study to evaluate the anticoagulant activity of fucoidan', by Lowenthal et. al.PMID:19696660 An information content entity that expresses an assertion that is intended to be tested. In the Philly 2013 workshop, we recognized the limitations of "hypothesis textual entity", and we introduced this as more general. The need for the 'textual entity' term going forward is up for future debate. Group:2013 Philly Workshop group hypothesis Group:2013 Philly Workshop group testable hypothesis OBI:0001909 conclusion based on data The conclusion that a gene is upregulated in a tissue sample based on the band intensity in a western blot. The conclusion that a patient has a infection based on measurement of an elevated body temperature and reported headache. The conclusion that there were problems in an investigation because data from PCR and microarray are conflicting. The following are NOT conclusions based on data: data themselves; results from pure mathematics, e.g. "13 is prime". An information content entity that is inferred from data. In the Philly 2013 workshop, we recognized the limitations of "conclusion textual entity", and we introduced this as more general. The need for the 'textual entity' term going forward is up for future debate. Group:2013 Philly Workshop group Group:2013 Philly Workshop group conclusion based on data OBI:0001910 primary cell culture A cell culture comprised of primary cultured cells and the media in which they are being actively propaged or quiescently stored. PERSON:Matthew Brush OBI-CLO Alignment Working Group (Spring 2013) primary cell culture OBI:0001911 cell line culture A cell culture comprised of cell line cells and the media in which they are being actively propagated or quiescently stored. PERSON:Matthew Brush OBI-CLO Alignment Working Group (Spring 2013) A cell line culture includes the cells in culture, as well as the media and all additives/reagents in which the cells are being grown or in which they are stored. cell line culture OBI:0001912 cell freezing medium A processed material that serves as a liquid vehicle for freezing cells for long term quiescent stroage, which contains chemicls needed to sustain cell viability across freeze-thaw cycles. PERSON: Matthew Brush cell freezing medium OBI:0001913 computation run time Gigascience. 2012 Dec 27;1(1):18. doi: 10.1186/2047-217X-1-18. PMID: 23587118. See Table 4 computation run time is a time measurement datum which corresponds the time expressed in second, minute, hour necessary for a computer program to complete a process execution, for example genome assembly. It is an important metrics as it indicates the resource occupancy and computer program efficiency. Alejandra Gonzalez-Beltran Philippe Rocca-Serra computation run time datum PRS,AGB computation run time OBI:0001914 multiplex ligation-mediated amplification A polymerase chain reaction that amplifies multiple targets with a single primer pair mediated by hybridization of a primer with its target sequence using ligation. Chris Stoeckert, Jie Zheng LMA MLPA Multiplex ligation-dependent probe amplification web: http://en.wikipedia.org/wiki/Multiplex_Ligation-dependent_Probe_Amplification Pubmed: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1867615/ multiplex ligation-mediated amplification OBI:0001915 DNA replication timing by array assay Hiranti et al. Global reorganization of replication domains during embryonic stem cell differentiation. PLoS Biol. 2008 October 7;6(10):e245 [PMID:18842067] An assay in which timing of DNA replication is quantified as a function of genome position using array technology. Venkat Malladi, Chris Stoeckert, Jie Zheng Repli-chip Repli-chip assay Hiranti et al. Global reorganization of replication domains during embryonic stem cell differentiation. PLoS Biol. 2008 October 7;6(10):e245 [PMID:18842067] ENCODE project DNA replication timing by array assay OBI:0001916 DNA replication identification objective A molecular feature identification objective that aims to examine charateristics of DNA replication, such as replication time. Chris Stoeckert, Jie Zheng Group: Penn Group DNA replication identification objective OBI:0001917 chromosome conformation identification objective A molecular feature identification objective that aims to determine spatial organization of chromatin. Chris Stoeckert, Jie Zheng Group: Penn Group chromosome conformation identification objective OBI:0001918 RNA-binding protein immunoprecipitation array profiling assay Jain et al. RIP-Chip analysis: RNA-Binding Protein Immunoprecipitation-Microarray (Chip) Profiling. Methods Mol Biol. 2011;703:247-63. [PMID:21125495] An assay that combines immunoprecipitation of an RNA-binding protein and array technology to identify mRNAs associated with selected RNA binding proteins (RBPs). Person: Venkat Malladi, Chris Stoeckert, Jie Zheng RIP-chip RIP-chip assay Jain et al. RIP-Chip analysis: RNA-Binding Protein Immunoprecipitation-Microarray (Chip) Profiling. Methods Mol Biol. 2011;703:247-63. [PMID:21125495] ENCODE project RNA-binding protein immunoprecipitation array profiling assay OBI:0001919 Carbon-copy chromosome conformation capture assay van Berkum et al. Determining spatial chromatin organization of large genomic regions using 5C technology. Methods Mol Biol (2009) vol. 567 pp. 189-213 [PMID:19588094] An assay that is used to analyze the organization of chromosomes at the genome-wide scale. Venkat Malladi, Chris Stoeckert, Jie Zheng 5C 5C assay "Dostie et al. Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements. Genome Res. 2006 October; 16(10):1299-309.[PMID:16954542]" ENCODE project Carbon-copy chromosome conformation capture assay OBI:0001920 DNA replication timing by sequencing assay Hansen et al. Sequencing newly replicated DNA reveals widespread plasticity in human replication timing. Proc Natl Acad Sci U S A. 2010 January 5; 107(1): 139–144. [PMID:19966280] An assay in which timing of DNA replication is quantified as a function of genome position based on genome-wide sequencing. Venkat Malladi, Chris Stoeckert, Jie Zheng Repli-seq Repli-seq assay Hansen et al. Sequencing newly replicated DNA reveals widespread plasticity in human replication timing. Proc Natl Acad Sci U S A. 2010 January 5; 107(1): 139–144. [PMID:19966280] ENCODE project DNA replication timing by sequencing assay OBI:0001921 RNA-binding protein immunoprecipitation tiling array profiling Jain et al. RIP-Chip analysis: RNA-Binding Protein Immunoprecipitation-Microarray (Chip) Profiling. Methods Mol Biol. 2011;703:247-63. [PMID:21125495] A RNA-binding protein immunoprecipitation array profiling assay that combines immunoprecipitation of an RNA-binding protein and RNA tiling array to identify mRNAs associated with selected RNA binding proteins (RBPs). Person: Venkat Malladi, Chris Stoeckert, Jie Zheng Jain et al. RIP-Chip analysis: RNA-Binding Protein Immunoprecipitation-Microarray (Chip) Profiling. Methods Mol Biol. 2011;703:247-63. [PMID:21125495] ENCODE project RNA-binding protein immunoprecipitation tiling array profiling OBI:0001922 microRNA profiling by high throughput sequencing assay Juhlia et al. MicroRNA expression profiling reveals miRNA families regulating specific biological pathways in mouse frontal cortex and hippocampus. PLoS One. 2011;6(6). [PMID: 21731767] A RNA-seq assay in which high throughput sequencing technology is used to analyse the microRNA component of the transcriptome. Person: Venkat Malladi, Chris Stoeckert, Jie Zheng miRNA-seq microRNA-seq microRNA-seq assay http://www.ebi.ac.uk/efo/EFO_0002896 ENCODE project microRNA profiling by high throughput sequencing assay OBI:0001923 protein sequencing by tandem mass spectrometry assay Taylor et al.Implementation and uses of automated de novo peptide sequencing by tandem mass spectrometry. Anal Chem. 2001 Jun;73(11):2594-604. [PMID:11403305] A sequencing assay in which amino acid sequences of proteins is determined using multiple rounds of mass spectrometry and molecule fragmentation. Person: Venkat Malladi, Chris Stoeckert, Jie Zheng Hunt et al. Protein sequencing by tandem mass spectrometry. Proc Natl Acad Sci U S A. 1986;83(17): 6233–6237. [PMID:3462691] ENCODE project protein sequencing by tandem mass spectrometry assay OBI:0001924 micrococcal nuclease digestion followed by high throughput sequencing assay Cui et al.Genome-wide approaches to determining nucleosome occupancy in metazoans using MNase-Seq. Methods Mol Biol. 2012;833:413-9. [PMID:22183607] An assay to identify nucleosome positioning by genome wide sequencing of regions senstative to digestion by micrococal nuclease Person: Venkat Malladi, Chris Stoeckert, Jie Zheng MNase-seq MNase-seq assay Johnson et al. Flexibility and constraint in the nucleosome core landscape of Caenorhabditis elegans chromatin. Genome Res. 2006 Dec;16(12):1505-16. [PMID:17038564] JZ: should be inferred as 'DNA sequencing'. Will check in the future. ENCODE project micrococcal nuclease digestion followed by high throughput sequencing assay OBI:0001925 chromatin immunoprecipitation with exonuclease sequencing assay Rhee et al. Comprehensive Genome-wide Protein-DNA Interactions Detected at Single-Nucleotide Resolution. Cell. 2011 Dec;147(6):1408-19. [PMID:22153082] A ChIP-seq assay to identify protein binding sites using an exonuclease to provide greater binding resolution of immunoprecipitation assay by genome wide sequencing. Person: Venkat Malladi, Chris Stoeckert, Jie Zheng ChIP-exo assay Rhee et al. Comprehensive Genome-wide Protein-DNA Interactions Detected at Single-Nucleotide Resolution. Cell. 2011 Dec;147(6):1408-19. [PMID:22153082] ENCODE project chromatin immunoprecipitation with exonuclease sequencing assay OBI:0001926 microRNA profiling assay A transcription profiling assay in which aims to quantify the microRNA species within a biological sample. Person: Venkat Malladi, Chris Stoeckert, Jie Zheng miRNA expression assay microRNA expression assay Kolbert et al. Multi-Platform Analysis of MicroRNA Expression Measurements in RNA from Fresh Frozen and FFPE Tissues. PLoS One. 2013;8(1):e52517 [PMID: 23382819] ENCODE project microRNA profiling assay OBI:0001928 selection PMID: 24023800. In this study, a set of eleven genes (VATP16, 60 S, UQCC, SMD3, EF1α, UBQ, SAND, GAPDH, ACT, PsaB, PTB2) was evaluated to identify reference genes during the first hours of interaction (6, 12, 18 and 24 hpi) between two V. vinifera genotypes and P. viticola. Two analyses were used for the selection of reference genes: direct comparison of susceptible, Trincadeira, and resistant, Regent, V. vinifera cultivars at 0 h, 6, 12, 18 and 24 hours post inoculation with P. viticola (genotype effect); and comparison of each genotype with mock inoculated samples during inoculation time-course (biotic stress effect). Three statistical methods were used, GeNorm, NormFinder, and BestKeeper, allowing to identify UBQ, EF1α and GAPDH as the most stable genes for the genotype effect. A planned process which results in the creation of group of entity from a larger group by the application of predefined criteria. this term refers to a planned process and therefore is distinct from the notion of 'natural selection', a process covering the operation of natural causes by which those individuals of a species that are best adapted to the environment tend to be preserved and to transmit their characters, while those less adapted die out, so that in the course of generations the degree of adaptation to the environment tends progressively to increase. (as defined by Oxford English Dictionary) Person: Philippe Rocca-Serra selection process OBI selection OBI:0001929 mass value specification A value specification that specifies the mass of some thing. PERSON:Bjoern Peters mass value specification OBI:0001930 categorical value specification A value specification that is specifies one category out of a fixed number of nominal categories PERSON:Bjoern Peters categorical value specification 1 1 OBI:0001931 scalar value specification A value specification that consists of two parts: a numeral and a unit label PERSON:Bjoern Peters scalar value specification OBI:0001932 comparing prediction to measurement A planned process in which predicted values for some thing are compared to measured values for that thing. comparing prediction to measurement OBI:0001933 value specification The value of 'positive' in a classification scheme of "positive or negative"; the value of '20g' on the quantitative scale of mass. An information content entity that specifies a value within a classification scheme or on a quantitative scale. This term is currently a descendant of 'information content entity', which requires that it 'is about' something. A value specification of '20g' for a measurement data item of the mass of a particular mouse 'is about' the mass of that mouse. However there are cases where a value specification is not clearly about any particular. In the future we may change 'value specification' to remove the 'is about' requirement. PERSON:Bjoern Peters value specification OBI:0001934 predicted value an information content entity that has been generated by a prediction process in which an estimate of a value of an entity is made which can be measured but without performing such a measurement. The value specification is intended to be close to the value a measurement process would produce modulo a prediction error. PERSON:Bjoern Peters predicted value OBI:0001935 predicted mass value A predicted value where the prediction specifies the mass of some thing. PERSON:Bjoern Peters predicted mass value OBI:0001936 molecular-labeled material a material entity that is the specified output of an addition of molecular label process that aims to label some molecular target to allow for its detection in a detection of molecular label assay PERSON:Matthew Brush OBI developer call, 3-12-12 molecular-labeled material OBI:0001939 genome coverage Gigascience. 2012 Dec 27;1(1):18. doi: 10.1186/2047-217X-1-18. PMID: 23587118. "The genome coverage increased from 81.16% to 93.91%" A data item that is the total number of bases in reads, divided by genome size, assumed to be the reference size (for instance of 3.10 Gb for human and 2.73 Gb for mouse) and refers to the percentage of the genome that is contained in the assembly based on size estimates; these are usually based on cytological techniques. Genome coverage of 90–95% is generally considered to be good, as most genomes contain a considerable fraction of repetitive regions that are difficult to sequence. So it is not a cause for concern if the genome coverage of an assembly is a bit less than 100%. Alejandra Gonzalez-Beltran Philippe Rocca-Serra A beginner's guide to eukaryotic genome annotation. Yandell M, Ence D. Nat Rev Genet. 2012 Apr 18;13(5):329-42. doi: 10.1038/nrg3174. PMID: 22510764 genome coverage OBI:0001940 N50 Gigascience. 2012 Dec 27;1(1):18. doi: 10.1186/2047-217X-1-18. PMID: 23587118. "Here, the contig and scaffold N50 of the YH genome were ~20.9 kbp and ~22 Mbp" the weighted median item size or N50 is a weighted median of the lengths of items, equal to the length of the longest item i such that the sum of the lengths of items greater than or equal in length to i is greater than or equal to half the length of all of the items. With regard to assemblies the items are typically contigs or scaffolds. It therefore denotes the ability of the software to create contigs and provides information about the resulting sequence assembly Alejandra Gonzalez-Beltran Philippe Rocca-Serra weighted median item size adapted from: "http://genome.cshlp.org/content/21/12/2224.full?sid=74019122-f944-4ccc-bffe-d16fdd0e7d6c" (from table 7) and from "http://www.nature.com/nrg/journal/v14/n3/full/nrg3367.html" N50 OBI:0001941 contig N50 Gigascience. 2012 Dec 27;1(1):18. doi: 10.1186/2047-217X-1-18. PMID: 23587118. "Here, the contig and scaffold N50 of the YH genome were ~20.9 kbp and ~22 Mbp" N50 statistic computed for the contigs produced by the assembly process. A contig N50 is calculated by first ordering every contig by length from longest to shortest. Next, starting from the longest contig, the lengths of each contig are summed, until this running sum equals one-half of the total length of all contigs in the assembly. The contig N50 of the assembly is the length of the shortest contig in this list. Alejandra Gonzalez-Beltran Philippe Rocca-Serra adapted from: nature:http://www.nature.com/nrg/journal/v13/n5/box/nrg3174_BX1.html contig N50 OBI:0001942 grant agency An organization that provides funding support for projects such as investigations. PERSON: Jie Zheng, Chris Stoeckert funding organization NIAID GSCID-BRC metadata working group NIAID GSCID-BRC grant agency 'funding organization' http://vivoweb.org/ontology/core#FundingOrganization OBI:0001943 software pipeline A plan specification that specifies a chain encoded in software of processing elements (processes, threads, coroutines, etc.), arranged so that the output of each element is the input of the next. Usually some amount of buffering is provided between consecutive elements. PERSON: Jie Zheng, Chris Stoeckert WEB: http://en.wikipedia.org/wiki/Pipeline_%28software%29 NIAID GSCID-BRC software pipeline OBI:0001944 sequence annotation A planned process that identifies and reports sequence features (e.g. protein coding regions) in sequence data. PERSON: Jie Zheng, Chris Stoeckert NIAID GSCID-BRC metadata working group NIAID GSCID-BRC sequence annotation OBI:0001945 scaffold N50 Gigascience. 2012 Dec 27;1(1):18. doi: 10.1186/2047-217X-1-18. PMID: 23587118. "Here, the contig and scaffold N50 of the YH genome were ~20.9 kbp and ~22 Mbp" N50 statistic computed for the scaffold produced by the assembly process. The method for computing the value is similar to that of contig N50 but uses scaffold information instead of contig information Alejandra Gonzalez-Beltran Philippe Rocca-Serra adapted from: nature:http://www.nature.com/nrg/journal/v13/n5/box/nrg3174_BX1.html scaffold N50 OBI:0001946 forward PCR primer SP6 promoter, forward primer (SP6 TTTAGGTGACACTATAG) A short oligonucleotide complementary to target DNA (5'->3' on plus strand) that acts as the leader for DNA extension in a PCR reaction. The polymerase starts replication at the 3'-end of the primer, and copies the opposite strand. A primer is characterized by its 'melting temperature' (Tm) and pairs of primers should have similar Tm. Philippe Rocca-Serra 5' primer forward primer sense primer adapted from http://www.ncbi.nlm.nih.gov/projects/genome/probe/doc/Glossary.shtml#p forward PCR primer OBI:0001947 sequence annotation provider A person or organization reporting the feature annotation results from the analysis of a macromolecular sequence. PERSON: Jie Zheng, Chris Stoeckert NIAID GSCID-BRC metadata working group annotation provider NIAID GSCID-BRC sequence annotation provider OBI:0001948 sequence assembly name A textual entity that is used to denote a sequence assembly. PERSON: Jie Zheng, Chris Stoeckert NIAID GSCID-BRC metadata working group assembly name NIAID GSCID-BRC sequence assembly name OBI:0001949 sequence annotation reporting role A reporting party role that is realized by a person or organization who reports the feature annotation results from the analysis of a macromolecular sequence. PERSON: Jie Zheng, Chris Stoeckert NIAID GSCID-BRC metadata working group NIAID GSCID-BRC sequence annotation reporting role OBI:0001951 reverse PCR primer 5' end of luciferase, reverse primer (LucNrev CCTTATGCAGTTGCTCTCC) A short oligonucleotide complementary to target DNA (5'->3' on minus strand) that acts as the leader for DNA extension in a PCR reaction. The polymerase starts replication at the 3'-end of the primer, and copies the opposite strand. A primer is characterized by its 'melting temperature' (Tm) and pairs of primers should have similar Tm. Philippe Rocca-Serra 3' primer antisense primer reverse primer adapted from "http://www.ncbi.nlm.nih.gov/projects/genome/probe/doc/Glossary.shtml#p" reverse PCR primer OBI:0001952 flash freezing A freezing process by which material entities are quickly frozen by subjecting them to cryogenic temperatures, or in direct contact with Liquid nitrogen at -320.8F or -196°C. Person: Mathias Brochhausen, Jie Zheng WEB: http://en.wikipedia.org/wiki/Flash_freezing flash freezing OBI:0001953 freezing A planned process in which a material entity has it's temperature lowered to below the freezing point in order to bring it to a state in which it can be maintained at this lower temperature in order to preserve some of its qualities. Person: Mathias Brochhausen, Jie Zheng Mathias Brochhausen freezing OBI:0001954 ChIP assay PMID: 6379641 Gilmour & Lis. Proc Natl Acad Sci U S A. 1984 Jul;81(14):4275-9. and can be found linked from here: An assay in which protein-DNA complexes are extracted from short regions of chromatin and are reversibly cross linked, immunoprecipitated with antibodies or tags, purified, and amplified with the aim of analysis gene- and promoter-specific known targets Philippe Rocca-Serra chromatin immunoprecipitation assay adapted from CHS protocols, wikipedia, life tech, ChIP-seq term definition as per user (pployd) request and proposal by Alan Ruttenberg http://sourceforge.net/p/obi/obi-terms/707/ ChIP assay OBI:0001955 competitive binding reference ligand role The role of a radiolabeled peptide that is known to bind to the MHC molecule HLA-A*02:01 with high affinity when it is used in a competitive binding assay in which another peptide of interest is tested for its ability to outcompete binding of the labeled peptide in a dose dependent fashion. A positive reference substance role that inheres in a material entity that is known to bind to a target entity, and that is realized in a competitive binding assay that has as specified input the target entity, an evaluant and the positive reference substance, where the binding of the evaluant to the target is measured based on the evaluant's ability to compete with the positive reference substance for binding to the target. Bjoern Peters, Randi Vita, James A. Overton Bjoern Peters competitive binding reference ligand role OBI:0001956 assay using chromatin immunoprecipitation http://www.lifetechnologies.com/uk/en/home/life-science/epigenetics-noncoding-rna-research/chromatin-remodeling/chromatin-immunoprecipitation-chip.html an assay which uses immunoprecipitation and which produces data about protein-DNA interaction or DNA epigenetic modification as per user (pployd) request and proposal by Alan Ruttenberg http://sourceforge.net/p/obi/obi-terms/707/ PERSON: Philippe Rocca-Serra assay using chromatin immunoprecipitation OBI:0001957 hardware testing design A study design that aims to compare different types of hardware for performance, reproducibility, accuracy and precision. Person: Jie Zheng MO_734 hardware_variation_design hardware testing design OBI:0001958 systematic review study design Red blood cell transfusion in patients with traumatic brain injury: a systematic review protocol. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4090399/ The effect of moderate gestational alcohol consumption during pregnancy on speech and language outcomes in children: a systematic review. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3892059/ A study design for identifying in the literature prior studies of a pre-determined phenomenon or set of related phenomena according to certain criteria, extracting findings from these studies, and summarizing these findings and/or attempting to draw new conclusions from them which were not justified by any of the individual, prior studies. Many systematic reviews also assess the quality of the studies so reviewed. PERSON: Bill Hogan systematic review study design OBI:0001959 sequencing library multiplexing http://www.illumina.com/technology/multiplexing_sequencing_assay.ilmn a planned process which consists in running a set of samples as a pool in one single instrument run of data acquisition process while retaining the ability to associate individual results to each of the individual input samples thanks to the use of a multiplex identifier, introduced during the ligation step of the individual library preparation and specific to a given sample. PERSON:Philippe Rocca-Serra OBI sequencing library multiplexing OBI:0001960 taxonomic diversity assessment by targeted gene survey http://www.ncbi.nlm.nih.gov/pubmed/20679230 http://www.ncbi.nlm.nih.gov/pubmed/25367129 is an assay which aims to provide information about taxonomic information and community diversity by mean of sequencing specific genomic regions used as marker of identity or diversity. PERSON:Philippe Rocca-Serra targeted gene survey DNA barcoding OBI environmental gene survey targeted gene survey taxonomic diversity assessment by targeted gene survey OBI:0001961 PCR program https://www.neb.com/protocols/1/01/01/taq-dna-polymerase-with-standard-taq-buffer-m0273 a PCR program is a plan specification which is executed during a polymerase chain reaction (PCR) by a thermocycler instrument that will iterate through the changes in temperature and duration of each of the annealing, denaturation, elongation steps for as many times as specified by the program. PERSON:Philippe Rocca-Serra OBI PCR program OBI:0001962 target gene specification http://www.ncbi.nlm.nih.gov/pubmed/25367129 "performing a profiling of microbial phylogenetic composition using sequencing of 16S rRNA gene (used as target gene) is a directive information specifying a coding genomic region which is the focus of a planned process such as an assay, for instance in a environmental gene survey PERSON:Philippe Rocca-Serra PRS for OBI target gene target gene specification OBI:0001963 target subfragment specification http://www.ncbi.nlm.nih.gov/pubmed/23335919 "performing a profiling of microbial phylogenetic composition using massively-parallel pyrotag sequencing targeting the V9 hypervariable region (used as target subfragment) of the 18S ribosomal RNA (rRNA) gene (used as target gene) is a directive information specifying a genomic region, possibly located in a coding genomic region, which is the focus of a planned process such as an assay, for instance in a environmental gene survey PERSON:Philippe Rocca-Serra PRS for OBI target subfragment target subfragment specification OBI:0001964 decision-theoretic analysis objective An objective specification which what includes a description of two or more alternative actions to take in a particular situation and a metric that enables comparisons of the two actions. The objective specified is achieved in a planned process which includes a data transformation, the output of which is an identification of the 'best' choice according to the metric. The best action to take is typically defined as the one that maximizes expected utility. PERSON: Bill Hogan decision analysis objective PERSON: Bill Hogan decision-theoretic analysis objective OBI:0001965 decision analysis study design a study design that has a decision analysis objective specification as part PERSON: Bill Hogan PERSON: Bill Hogan decision analysis study design OBI:0001966 sequence library deconvolution is a data transformation which uses sequence alignment and 'multiplex identifier sequence' information to pull together all reads belonging to a given single sample following the sequencing of a multiplexed library which combining several samples in one sequencing event PERSON: Philippe Rocca-Serra PRS for OBI sequence library deconvolution OBI:0001967 multiplexing sequence identifier We designed primers specifically to amplify protease and reverse transcriptase from Brazilian HIV subtypes and developed a multiplexing scheme using multiplex identifier tags to minimize cost while providing more robust data than traditional genotyping techniques. in http://www.ncbi.nlm.nih.gov/pubmed/22574170 A multiplexing sequence identifier is a nucleic acid sequence which is used in a ligation step of library preparation process to allow pooling of samples while maintaining ability to identify individual source material and creation of a multiplexed library PERSON:Philippe Rocca-Serra OBI multiplexing sequence identifier OBI:0001968 operational taxonomic unit matrix http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1610290/ Operational Taxonomic Unit matrix is a data item, organized as a table, where organismal taxonomic units, computed by sequence analysis and genetic distance calculation, are counted in a set of biological or environmental samples. The table is used to appraise biodiversity of a population or community of living organism. PERSON:Philippe Rocca-Serra PRS for OBI operational taxonomic unit matrix OBI:0001969 biodiversity assessment objective biodiversity assessment objective is an objective of a planned process aimed at producing data item whose interpretation should provide insight about variety of biological species found in a biological sample at macroscopic or microscopic level PERSON:Philippe Rocca-Serra PRS for OBI biodiversity assessment objective OBI:0001970 multiplexed sequencing library http://www.ncbi.nlm.nih.gov/pubmed/24997861 Nat Methods. 2014 Aug;11(8):834-40. doi: 10.1038/nmeth.3022. Epub 2014 Jul 6. Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. a multiplexed library is a material entity which is the output of a library preparation process that uses a ligation step to attach a unique multiplexing sequence identifier to a specific sample, then mixes several such tagged samples prior to the library amplification process proper. A multiplexed library allows the sequencing of several samples in one sequencing run. PERSON:Philippe Rocca-Serra DNA-barcoded sequencing library PRS for OBI multiplexed sequencing library OBI:0001971 Ion 316 Chip v2 An ion semiconductor chip manufactured by Life Technologies which detects polymerase-driven base incorporation to translate into digital form. The 316 chip is compatible with the Ion Torrent PGM and has a run time of: 3.0 hours for 200 bp reads with an output of 30-50 Mb, 4.9 hours for 400 bp reads with an output of 60 Mb-1 Gb. Issue Tracker #774 https://sourceforge.net/p/obi/obi-terms/774/ PERSON: Sagar Jain Ion 316 Chip Ion PGM 316 Chip Ion PGM 316 Chip v2 http://www.lifetechnologies.com/us/en/home/life-science/sequencing/next-generation-sequencing/ion-torrent-next-generation-sequencing-workflow/ion-torrent-next-generation-sequencing-run-sequence/ion-pgm-ion-proton-system-chips.html Ion 316 Chip v2 OBI:0001972 Ion 318 Chip v2 An ion semiconductor chip manufactured by Life Technologies which detects polymerase-driven base incorporation to translate into digital form. The 318 chip is compatible with the Ion Torrent PGM and has a run time of: 4.4 hours for 200 bp reads with an output of 60 Mb-1 Gb, 7.3 hours for 400 bp reads with an output of 1.2 Gb-2 Gb. Issue Tracker #775 https://sourceforge.net/p/obi/obi-terms/775/ PERSON: Sagar Jain Ion 318 Chip Ion PGM 318 Chip Ion PGM 318 Chip v2 http://www.lifetechnologies.com/us/en/home/life-science/sequencing/next-generation-sequencing/ion-torrent-next-generation-sequencing-workflow/ion-torrent-next-generation-sequencing-run-sequence/ion-pgm-ion-proton-system-chips.html Ion 318 Chip v2 OBI:0001973 ion semiconductor chip An ion detector that is organized as an electronic circuit whose components, such as transistors and resistors, are etched or deposited on a single slice of semiconductor material to produce a chip. The specific chip detects ion charge induced when an ion passes by or hits a surface. Issue Tracker: #776 https://sourceforge.net/p/obi/obi-terms/776/ PERSON: Sagar Jain ion chip ion integrated circuit ion semiconductor http://www.thefreedictionary.com/Semiconductor+chip ion semiconductor chip OBI:0001974 Ion 314 Chip v2 An ion semiconductor chip manufactured by Life Technologies which detects polymerase-driven base incorporation to translate into digital form. The 314 chip is compatible with the Ion Torrent PGM and has a run time of: 2.3 hours for 200 bp reads with an output of 30-50 Mb, 3.7 hours for 400 bp reads with an output of 60-100 Mb. Issue Tracker #766 https://sourceforge.net/p/obi/obi-terms/766/ PERSON: Sagar Jain Ion 314 Chip Ion PGM 314 Chip Ion PGM 314 Chip v2 http://www.lifetechnologies.com/us/en/home/life-science/sequencing/next-generation-sequencing/ion-torrent-next-generation-sequencing-workflow/ion-torrent-next-generation-sequencing-run-sequence/ion-pgm-ion-proton-system-chips.html Ion 314 Chip v2 OBI:0001976 hydrogen/deuterium exchange assay Performing deuterium exchange on a protein by itself and in the presence of a binding partner, degrading the protein into peptide segments and identifying where deuterium exchange occurred by detecting the peptides in Mass Spectrometry. Peptides that have a modified deuteration pattern when the protein was bound to a partner are expected to be part of the binding interface. An assay that uses a chemical reaction whereby a covalently bonded hydrogen atom is replaced by a deuterium atom, or vice versa in order to gather information about the solvent accessibility of parts of a molecule and thus its tertiary structure. IEDB IEDB hydrogen/deuterium exchange assay OBI:0001977 cytometry assay An intracellular material detection by flow cytometry assay measuring peforin inside a culture of T cells. An assay that measures properties of cells. IEDB IEDB cytometry assay OBI:0001978 immunoblot assay An analyte assay that detects specific molecules in an input material by separating it using gel electrophoresis, transfering the separated molecules to a membrane, and staining them with  antibodies specific to the analyte molecules. IEDB IEDB immunoblot assay OBI:0001979 fluorescence quenching binding assay A binding assay in which the proximity of two entities is monitored by measuring a fluorescent signal of one of the entities that gets reduced if the two entities are cliose to each other. IEDB IEDB fluorescence quenching binding assay OBI:0001980 in vivo intervention experiment Comparing the level of allergy symptoms in humans before and post allergy immunotherapy. Testing if injection of a chemical compound into mice will lead to decreased survival. An assay in which the effect of a targeted process (the intervention) on an organism is tested. The intervention in an experiment should be modeled accordingly to the intevention carried out in a human cllinical trial, which is currently modeled as 'study intervention'. This touches the boundaries of study vs. assay. IEDB IEDB in vivo intervention experiment OBI:0001981 disease exacerbation in vivo intervention experiment Injecting a set of mice with a peptide and measuring symtoms to determine if their disease course was more severe than the disease course of a set of mice that were not injected with the same peptide. An in vivo intervention experiment that tests the ability of the intervention to increase the severity of a disease in the host. Should have data about disease severity as readout; could just use disease for now IEDB IEDB disease exacerbation in vivo intervention experiment OBI:0001982 protection from challenge in vivo intervention experiment Injecting a set of mice with a peptide and measuring symtoms to determine if their disease course was less severe than the disease course of a set of mice that were not injected with the same peptide. An in vivo intervention experiment that tests the ability of the intervention to prevent occurrence of a disease in a host. should have challenge as intervention IEDB IEDB protection from challenge in vivo intervention experiment OBI:0001983 tolerance induction intervention experiment Injecting a set of mice with a Der p 2 peptide and measuring the IL-2 response of T cells from those mice when exposed to the Der p 2 protein in vitro to determine if those T cells made less IL-2 than cells taken from mice which were not injected with the same Der p 2 peptide. An in vivo intervention experiment that tests the ability of the intervention to decrease an immune response. should have tolerance induction as intervention IEDB IEDB tolerance induction intervention experiment OBI:0001984 treatment intervention experiment Testing if administering oral histamine-blockers will reduce the number of emergency room visits in severely asthmatic individuals. An in vivo intervention experiment in which the ability of the intervention to reduce or cure the effects of a disease are tested. should have treatment as intervention IEDB IEDB treatment intervention experiment OBI:0001985 microarray assay Measuring if sera from an influenza A virus immunizedmouse binds to Hemagglutinin protein that is immobilized on a microarray. An analyte assay where binding of the analyte to immobilized matrix is measured. IEDB IEDB microarray assay OBI:0001986 immunohistochemistry Staining a brain tissue sample from an Alzheimer's disease patient with antibodies to amyloid beta to identify amyloid plaques. An immunostaining assay to detect and potentially localize antigens within the cells of a tissue section. IEDB IEDB immunohistochemistry OBI:0001987 assay measuring the association constant [KA] of a MHC:ligand complex A MHC binding constant determination assay measuring equilibrium association constant (KA). IEDB IEDB association constant KA|binding assay|1/M assay measuring the association constant [KA] of a MHC:ligand complex OBI:0001988 assay measuring the dissociation constant [KD] of a MHC:ligand complex A MHC binding constant determination assay measuring equilibrium dissociation constant (KD). IEDB IEDB dissociation constant KD|binding assay|nM assay measuring the dissociation constant [KD] of a MHC:ligand complex OBI:0001989 purified MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex using radioactivity detection A purified MHC ligand binding equilibrium dissociation constant (KD) determination assay that uses radioactivity detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation. IEDB IEDB dissociation constant KD|purified MHC/direct/radioactivity|nM purified MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex using radioactivity detection OBI:0001990 assay measuring the half life of a MHC:ligand complex A MHC binding constant determination assay measuring half life of binding. IEDB IEDB half life|binding assay|min assay measuring the half life of a MHC:ligand complex OBI:0001991 assay measuring the half maximal effective concentration [EC50] of a MHC:ligand complex A MHC binding constant determination assay measuring half maximal effective concentration (EC50). IEDB IEDB half maximal effective concentration (EC50)|binding assay|nM assay measuring the half maximal effective concentration [EC50] of a MHC:ligand complex OBI:0001992 assay measuring the half maximal inhibitory concentration [IC50] of a MHC:ligand complex A MHC binding constant determination assay measuring half maximal inhibitory concentration (IC50). IEDB IEDB half maximal inhibitory concentration (IC50)|binding assay|nM assay measuring the half maximal inhibitory concentration [IC50] of a MHC:ligand complex OBI:0001993 assay measuring the off rate measurement [koff] of a MHC:ligand complex A MHC binding constant determination assay measuring binding off rate measurement data item (koff). IEDB IEDB off rate|binding assay|1/s assay measuring the off rate measurement [koff] of a MHC:ligand complex OBI:0001994 assay measuring the MHC ligand binding on rate [kon] of a MHC:ligand complex A MHC binding constant determination assay measuring binding on rate (kon). IEDB IEDB on rate|binding assay|nM^-1s^-1 assay measuring the MHC ligand binding on rate [kon] of a MHC:ligand complex OBI:0001995 chromatography assay measuring the association constant [KA] of a B cell epitope:antibody complex A B cell epitope equilibrium association constant (KA) determination assay that uses an analytical chromatography assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB association constant KA|chromatography|1/nM chromatography assay measuring the association constant [KA] of a B cell epitope:antibody complex OBI:0001996 chromatography assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex A B cell epitope equilibrium dissociation constant (KD) determination assay that uses an analytical chromatography assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB dissociation constant KD|chromatography|nM chromatography assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex OBI:0001997 hydrogen/deuterium exchange assay measuring binding of a B cell epitope:antibody complex A B cell epitope qualitative binding to antibody assay that uses a hydrogen/deuterium exchange assay. IEDB IEDB qualitative binding|hydrogen/deuterium exchange hydrogen/deuterium exchange assay measuring binding of a B cell epitope:antibody complex OBI:0001998 immunohistochemistry assay measuring binding of a B cell epitope:antibody complex A B cell epitope qualitative binding to antibody assay that uses an immunohistochemistry assay. IEDB IEDB qualitative binding|immunohistochemistry immunohistochemistry assay measuring binding of a B cell epitope:antibody complex OBI:0001999 3D structure determining assay of a T cell epitope:MHC:TCR complex A T cell epitope recognition assay that uses a 3D structure determination of bound complex assay. IEDB IEDB 3D structure|any method 3D structure determining assay of a T cell epitope:MHC:TCR complex OBI:0002000 Genome Analyzer IIx Gravina, Michael T., Jenny H. Lin, and Stuart S. Levine. "Lane-by-lane sequencing using Illumina's Genome Analyzer II." BioTechniques 54.5 (2013): 265-269. PMID: 23662897 An Illumina Genome Analyzer II which is manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. The Genome Analyzer IIx is the most widely adopted next-generation sequencing platform and proven and published across the broadest range of research applications. PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg Illumina GA IIx Illumina Genome Analyzer IIx ENCODE group ENCODE project Genome Analyzer IIx OBI:0002001 Illumina HiSeq 2000 Wang J, Qi J, Zhao H, He S, Zhang Y, Wei S, Zhao F. Metagenomic sequencing reveals microbiota and its functional potential associated with periodontal disease. Sci Rep. 2013 May;3:1843. PMID:23673380 A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and a throughput of up to 55 Gb per day. Built upon sequencing by synthesis technology, the machine is optimized for generation of data for multiple samples in a single run. PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng HiSeq 2000 http://res.illumina.com/documents/products/datasheets/datasheet_hiseq_systems.pdf ENCODE project Illumina HiSeq 2000 OBI:0002002 Illumina HiSeq 2500 Spaethling, Jennifer M., and James H. Eberwine. "Single-cell transcriptomics for drug target discovery." Current opinion in pharmacology (2013). pmid:23725882 A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and a throughput of up to 160 Gb per day. Built upon sequencing by synthesis technology, the machine is optimized for generation of data for batching multiple samples or rapid results on a few samples. PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg HiSeq 2500 http://res.illumina.com/documents/products/datasheets/datasheet_hiseq2500.pdf ENCODE project Illumina HiSeq 2500 OBI:0002003 MiSeq Rutvisuttinunt W, Chinnawirotpisan P, Simasathien S, Shrestha SK, Yoon IK, Klungthong C, Fernandez S. Simultaneous and complete genome sequencing of influenza A and B with high coverage by Illumina MiSeq Platform. J Virol Methods. 2013 Nov;193(2):394-404. [PMID:23856301] A DNA sequencer which is manufactured by the Illumina corporation. Built upon sequencing by synthesis technology, the machine provides an end-to-end solution (cluster generation, amplification, sequencing, and data analysis) in a single machine. PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng Illumina MiSeq http://res.illumina.com/documents/products/datasheets/datasheet_miseq.pdf ENCODE project MiSeq OBI:0002004 Methylation 450K BeadChip Naumov, Vladimir A., et al. "Genome-scale analysis of DNA methylation in colorectal cancer using Infinium HumanMethylation450 BeadChips." Epigenetics 8.9 (2013): 0-1. PMID: 23867710 A methylation BeadChip which is manufactured by the Illumina corporation. Built upon BeadChip tehcnology, the array interrogates ~ 485,000 methylation sites per sample at single-nucleotide resolution. PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg Illumina Infinium Human Methylation 450K BeadChip http://www.illumina.com/products/methylation_450_beadchip_kits.ilmn ENCODE project Methylation 450K BeadChip OBI:0002005 Methylation 27K BeadChip Polidoro, Silvia, et al. "Effects of bisphosphonate treatment on DNA methylation in osteonecrosis of the jaw." Mutation Research/Genetic Toxicology and Environmental Mutagenesis 757.2 (2013): 104-113. PMID: 23892139 A methylation BeadChip which is manufactured by the Illumina corporation. Built upon BeadChip tehcnology, the array interrogates ~ 27,000 CpG sites per sample at single-nucleotide resolution. PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg Illumina Infinium Human Methylation 27K BeadChip http://res.illumina.com/documents/products/datasheets/datasheet_dna_methylation_analysis.pdf ENCODE project Methylation 27K BeadChip OBI:0002006 1M-Duo Infinium HD BeadChip Edwards, Todd L., et al. "Genome-Wide Association Study Confirms SNPs in SNCA and the MAPT Region as Common Risk Factors for Parkinson Disease." Annals of human genetics 74.2 (2010): 97-109. PMID: 20070850 A BeadChip which is manufactured by the Illumina corporation. Built upon BeadChip tehcnology, the array integrates ~ 1 million markers per sample for genotyping, and copy number variation (CNV) and Cytogenetic analysis. PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg Illumina Human 1M-Duo Infinium HD BeadChip http://www.illumina.com/technology/infinium_hd_assay.ilmn ENCODE project 1M-Duo Infinium HD BeadChip OBI:0002007 SOLiD 3 Plus System Vissers, Lisenka ELM, et al. "A de novo paradigm for mental retardation." Nature genetics 42.12 (2010): 1109-1112. PMID:21076407 A DNA sequencer which is manufacted by the Applied Biosystems corporation. Built upon SOLiD sequencing technology, the machine generates greater than 1 billion mappable reads per run. PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg Applied Biosystems SOLiD 3 Plus System http://www3.appliedbiosystems.com/cms/groups/mcb_marketing/documents/generaldocuments/cms_072050.pdf ENCODE project SOLiD 3 Plus System OBI:0002008 Mouse 385K Whole Genome CGH Tiling Array Miller, Becky Akiko. Detection and biological assessment of genome structural variation in Plasmodium falciparum. Diss. University of Notre Dame, 2012. http://etd.nd.edu/ETD-db/theses/available/etd-04182012-114744/ A tiling array which is manufactured by the Nimblegen corporation. Built to analyze DNA sequence copy number by comparative genomic hybridization for mouse DNA against 385,000 features. PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg Nimblegen Mouse 385K Whole Genome CGH Tiling Array http://www.nimblegen.com/downloads/support/05434483001_NG_CGHLOH_UGuide_v9p1.pdf ENCODE project Mouse 385K Whole Genome CGH Tiling Array OBI:0002009 Mouse 3x720K Whole Genome CGH Tiling Array Wartman, Lukas D., et al. "Sequencing a mouse acute promyelocytic leukemia genome reveals genetic events relevant for disease progression." The Journal of clinical investigation 121.4 (2011): 1445. PMID:21436584 A tiling array which is manufactured by the Nimblegen corporation. Built to analyze DNA sequence copy number by comparative genomic hybridization for mouse DNA against 3x720,000 features. PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg Nimblegen Mouse 3x720K Whole Genome CGH Tiling Array http://www.nimblegen.com/downloads/support/05434483001_NG_CGHLOH_UGuide_v9p1.pdf ENCODE project Mouse 3x720K Whole Genome CGH Tiling Array OBI:0002010 Human 3x720K Whole Genome CGH Tiling Array Deletion in Xp22.11: PTCHD1 is a candidate gene for X-linked intellectual disability with or without autism PMID:21091464 A tiling array which is manufactured by the Nimblegen corporation. Built to analyze DNA sequence copy number by comparative genomic hybridization for human DNA against 3x720,000 features. PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg Nimblegen Human 3x720K Whole Genome CGH Tiling Array http://www.nimblegen.com/downloads/support/05434483001_NG_CGHLOH_UGuide_v9p1.pdf ENCODE project Human 3x720K Whole Genome CGH Tiling Array OBI:0002011 Human 2.1M Whole-Genome CGH Tiling Array v2.0 Filges, Isabel, et al. "Reduced expression by SETBP1 haploinsufficiency causes developmental and expressive language delay indicating a phenotype distinct from Schinzel–Giedion syndrome." Journal of medical genetics 48.2 (2011): 117-122. PMID:21037274 A tiling array which is manufactured by the Nimblegen corporation. Built to analyze DNA sequence copy number by comparative genomic hybridization for human DNA against 2.1 million features. PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg Nimblegen Human 2.1M Whole-Genome CGH Tiling Array v2.0 http://www.nimblegen.com/downloads/support/05434483001_NG_CGHLOH_UGuide_v9p1.pdf ENCODE project Human 2.1M Whole-Genome CGH Tiling Array v2.0 OBI:0002012 PacBio RS II Spaethling, Jennifer M., and James H. Eberwine. "Single-cell transcriptomics for drug target discovery." Current opinion in pharmacology (2013). pmid:23725882 A DNA sequencer which is manufactured by the Pacific Biosciences corporation. Built upon single molecule real-time sequencing technology, the machine is optimized for generation with long reads and high consensus accuracy. PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg Pacific Biosciences RS II http://www.pacificbiosciences.com/products/ ENCODE project PacBio RS II OBI:0002013 nCounter Human V2 miRNA Expression array Kolbert, Christopher P., et al. "Multi-platform analysis of microRNA expression measurements in RNA from fresh frozen and FFPE tissues." PloS one 8.1 (2013): e52517. PMID:23382819 An array which is manufacutred by NanoString Technologies. Built upon color-coded molecular barcodes technology, the array profiles miRNA with increased specificity and sensitivty than microarrays. PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg http://www.nanostring.com/media/pdf/PDS_nCounter_Human_v2_miRNA_Assay.pdf ENCODE project nCounter Human V2 miRNA Expression array OBI:0002014 DNA methylation profiling by ChIP-chip assay A ChIP-chip assay that identifies sites of DNA methylation. Person: Chris Stoeckert, Jie Zheng DNA methylation ChIP-chip Penn group Beta Cell Biology Consoritum DNA methylation profiling by ChIP-chip assay OBI:0002015 transcription profiling by MPSS assay An assay in which the transcriptome of a biological sample is analysed using Massive Parallel Signature Sequencing (MPSS). Person: Chris Stoeckert, Jie Zheng expression MPSS http://en.wikipedia.org/wiki/Massively_parallel_signature_sequencing Beta Cell Biology Consoritum transcription profiling by MPSS assay OBI:0002016 histone modification identification by ChIP-chip assay A ChIP-chip assay to identify regions containing specific histones and their modifications. Person: Chris Stoeckert, Jie Zheng histone modification ChIP-chip Penn group Beta Cell Biology Consoritum histone modification identification by ChIP-chip assay OBI:0002017 histone modification identification by ChIP-Seq assay A ChIP-seq assay to identify regions containing specific histones and their modifications. Person: Chris Stoeckert, Jie Zheng histone modification ChIP-Seq Penn group Beta Cell Biology Consoritum histone modification identification by ChIP-Seq assay OBI:0002018 transcription factor binding site identification by ChIP-chip assay A ChIP-chip assay to identify binding sites for transcription factors. Person: Chris Stoeckert, Jie Zheng TF Binding ChIP-chip Penn group Beta Cell Biology Consoritum transcription factor binding site identification by ChIP-chip assay OBI:0002019 transcription factor binding site identification by ChIP-Seq assay A ChIP-seq assay to identify binding sites for transcription factors. Person: Chris Stoeckert, Jie Zheng TF Binding ChIP-Seq Penn group Beta Cell Biology Consoritum transcription factor binding site identification by ChIP-Seq assay OBI:0002020 epigenetic modification assay An assay that identifies epigenetic modification including histone modifications, open chromatin, and DNA methylation. Person: Chris Stoeckert, Jie Zheng Penn group Beta Cell Biology Consoritum epigenetic modification assay OBI:0002021 NextSeq 500 A DNA sequencer which is a desktop sequencer ideal for smaller-scale studies manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. Person: Venkat Malladi, Chris Stoeckert, Jie Zheng Illumina NextSeq 500 http://systems.illumina.com/systems/nextseq-sequencer.html ENCODE project NextSeq 500 OBI:0002022 Illumina HiSeq 1000 A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell and a throughput of up to 35 Gb per day. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. Person: Venkat Malladi, Chris Stoeckert, Jie Zheng HiSeq 1000 http://res.illumina.com/documents/products/datasheets/datasheet_hiseq_systems.pdf ENCODE project Illumina HiSeq 1000 OBI:0002023 Human Genome U133 Plus 2.0 tiling array A tiling array which is a comprehensive whole human genome expression array manufactured by the Affymetrix corporation. Built to analyze DNA sequence copy number by comparative genomic hybridization for human DNA against 47,000 transcripts and variants. Person: Venkat Malladi, Chris Stoeckert, Jie Zheng Affymetrix HT Human Genome U133 Plus 2 Array Plate Set HG-U133 Plus 2 HG-U133 Plus 2 array http://www.affymetrix.com/estore/esearch/search.jsp?pd=131455&N=4294967292 ENCODE project Human Genome U133 Plus 2.0 tiling array OBI:0002024 SOLiD 4 System An AB SOLid System which is manufacted by the Applied Biosystems corporation. Built upon SOLiD sequencing technology, the machine generates greater than 1 billion mappable reads per run. Person: Venkat Malladi, Chris Stoeckert, Jie Zheng Applied Biosystems SOLiD 4 System SOLiD 4 http://www.appliedbiosystems.com/absite/us/en/home/applications-technologies/solid-next-generation-sequencing/next-generation-systems/solid-4-system.html?CID=FL-091411_solid4 ENCODE project SOLiD 4 System OBI:0002025 Human Exon 1.0 ST tilling array A tiling microarray which is manufactured by the Affymetrix corporation. Built to analyze 3' DNA sequence copy number by comparative genomic hybridization for human DNA against 28,000 genes. It can be used for gene expression and alternative splicing assay Person: Venkat Malladi, Chris Stoeckert, Jie Zheng Affymetrix Human Exon 1.0 St Array Human Exon 1.0 Human Exon 1.0 ST Array http://www.affymetrix.com/catalog/131453/AFFY/Human+Gene+ST+Arrays#1_1 ENCODE project Human Exon 1.0 ST tilling array OBI:0002026 Human Genome U133 tiling array A tiling array which is manufactured by the Affymetrix corporation. Built to analyze DNA sequence copy number by comparative genomic hybridization for human DNA against 39,000 transcripts and variants. Person: Venkat Malladi, Chris Stoeckert, Jie Zheng Affymetrix HT Human Genome U133 Array Plate Set HG-U133 HG-U133 array http://www.affymetrix.com/estore/esearch/search.jsp?pd=131441&N=4294967292 ENCODE project Human Genome U133 tiling array OBI:0002027 Genome Analyzer IIe An Illumina Genome Analyzer II which is manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. The Genome Analyzer IIe makes industry-leading next-generation sequencing technology accessible to more laboratories. Person: Venkat Malladi, Chris Stoeckert, Jie Zheng Illumina GA IIe Illumina Genome Analyzer IIe http://res.illumina.com/documents/products/datasheets/datasheet_genome_analyzer_iie.pdf ENCODE project Genome Analyzer IIe OBI:0002028 SAGE ditag library preparation A library preparation in which tags identifiying transcripts are created, ligated to form ditags, amplified, concatemerized and ligated into a vector to create a library. Related tracker:https://sourceforge.net/p/obi/obi-terms/720/ Person:Chris Stoeckert PMID:15905473 SAGE ditag library preparation OBI:0002029 serial analysis of gene expression PMID:15905473 A transcription profiling assay which aims to quantify RNA through creating short signature tags of the messages and ligating them into a larger molecule that is than sequenced. Details see tracker: https://sourceforge.net/p/obi/obi-terms/720/ Person:Janos Demeter, Chris Stoeckert, Jie Zheng SAGE PMID:7570003 Saccharomyces Genome Database (SGD) serial analysis of gene expression OBI:0002030 genotyping by tiling array PMID:19521816 A genotyping by array assay that aims to detect variation in (mostly) genomic DNA of an organism, strain, etc relative to some reference sequence employing tiling array technology. Details see tracker: https://sourceforge.net/p/obi/obi-terms/720/ Person:Janos Demeter, Chris Stoeckert, Jie Zheng DNA sequence variation detection by tiling array PMID:19521816 Saccharomyces Genome Database (SGD) genotyping by tiling array OBI:0002031 genotyping by SNP array PMID:20080586 A genotyping by array assay that aims to detect variation in (mostly) genomic DNA of an organism, strain, etc relative to some reference sequence employing snp array technology. Details see tracker: https://sourceforge.net/p/obi/obi-terms/720/ Person:Janos Demeter, Chris Stoeckert, Jie Zheng DNA sequence variation detection by snp array PMID:20393561 Saccharomyces Genome Database (SGD) genotyping by SNP array OBI:0002032 parallel analysis of RNA structure pmid:20811459 A single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing based on deep sequencing fragments of RNAs that were treated with structure-specific enzymes, thus providing simultaneous in vitro profiling of the secondary structure of thousands of RNA species at single nucleotide resolution. Details see tracker: https://sourceforge.net/p/obi/obi-terms/725/ Janos Demeter, Chris Stoeckert PARS pmid:20811459 Saccharomyces Genome Database (SGD) parallel analysis of RNA structure OBI:0002033 translation-associated transcript leader sequencing pmid:23580730 An RNA-seq assay that combines TL-seq with polysome fractionation Details see tracker: https://sourceforge.net/p/obi/obi-terms/725/ Janos Demeter, Chris Stoeckert TATL-seq pmid:23580730 Saccharomyces Genome Database (SGD) translation-associated transcript leader sequencing OBI:0002034 transcript leader sequencing pmid:23580730 An RNA-seq assay combining enzymatic capture of m(7)G-capped mRNA 5' ends with high-throughput sequencing. Details see tracker: https://sourceforge.net/p/obi/obi-terms/725/ Janos Demeter, Chris Stoeckert TL-seq pmid:23580730 Saccharomyces Genome Database (SGD) transcript leader sequencing OBI:0002035 peptide mass fingerprinting A mass spectrometry assay in which an unknown protein of interest is cleaved into smaller peptides, whose absolute masses can be accurately measured with a mass spectrometer. These masses are then compared to values in a database containing known protein sequences. Details see tracker: https://sourceforge.net/p/obi/obi-terms/725/ Janos Demeter, Chris Stoeckert PMF protein fingerprinting ERO:0001668 (http://en.wikipedia.org/wiki/Peptide_mass_fingerprinting) Saccharomyces Genome Database (SGD) peptide mass fingerprinting OBI:0002036 array based nucleic acid structure mapping assay pmid:23580730 An assay which aims to provide information about the in vivo organization/structure of nucleic acids using chemical or enzymatic probes using a microarray. Details see tracker: https://sourceforge.net/p/obi/obi-terms/725/ Janos Demeter, Chris Stoeckert OBI:0000870 Saccharomyces Genome Database (SGD) array based nucleic acid structure mapping assay OBI:0002037 micrococcal nuclease digestion followed by tiling array assay pmid:17873876 An array based nucleic acid structure mapping assay to identify nucleosome positions, genome wide, by detection of regions protected by nucleosomes from digestion by micrococal nuclease using tiling arrays. Details see tracker: https://sourceforge.net/p/obi/obi-terms/725/ Janos Demeter, Chris Stoeckert Saccharomyces Genome Database (SGD) micrococcal nuclease digestion followed by tiling array assay OBI:0002038 ribosomal profiling by sequencing assay Aspden et al., (August 2014). "Extensive translation of small open reading frames revealed by poly-ribo-seq." eLIFE 2014;3:e03528 A RNA-seq assay to sequence only mRNA protected by the ribosome during translation. Person: Venkat Malladi, Chris Stoeckert, Jie Zheng Ribo-seq Ribo-seq assay ribosomal profiling Ingolia, Nicholas T. (28 January 2014). "Ribosome profiling: new views of translation, from single codons to genome scale". Nature Reviews Genetics 15 (3): 205-213. doi:10.1038/nrg3645. PMID 24468696. ENCODE project ribosomal profiling by sequencing assay OBI:0002039 assay for transposase-accessible chromatin using sequencing Kasinathan et al., (February 2014). "High-resolution mapping of transcription factor binding sites on natitve chromatin." Nat Methods 11(2):203-9. doi: 10.1038/nmeth.2766. An assay to capture the location of open chromatin, DNA-binding proteins, individual nucleosomes and chromatin compaction at nucleotide resolution by Tn5 transposase insertion. Person: Venkat Malladi, Chris Stoeckert, Jie Zheng ATAC-seq ATAC-seq assay Buenrostro JD, Giresi PG, Zaba LC, Chang HY, and Greenleaf WJ. (2013) "Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position." Nature Methods ENCODE project assay for transposase-accessible chromatin using sequencing OBI:0002040 chromatin isolation by RNA purification sequencing assay Csorba et al., (November 2014). "Antisense COOLAIR mediates the coordinated switching of chromatin states at FLC during vernalization." Proc Natl Acad Sci 111(45):16160-5. doi: 10.1073/pnas.1419030111. A detection of specific nucleic acids with complementary probes to discover regions of the genome which are bound by a specific RNA (or a by a ribonucleoprotein containing the RNA of interest) using high-throughput sequencing. Person: Venkat Malladi, Chris Stoeckert, Jie Zheng ChIRP-seq ChIRP-seq assay Chromatin Isolation by RNA purification Chu et al. (31 August 2011). "Genomic Maps of Long Noncoding RNA Occupancy Reveal Principles of RNA-Chromatin Interactions". Molecular Cell. ENCODE project chromatin isolation by RNA purification sequencing assay OBI:0002041 self-transcribing active regulatory region sequencing assay Bohla et al., (September 2014). "A functional insulator screen identifies NURF and dREAM components to be required for enhancer-blocking." PLoS One 9(9):e107765. doi: 10.1371/journal.pone.0107765. A RNA-seq assay to identify the sequences that act as transcriptional enhancers in a direct, quantitative, and genome-wide manner from sheared genomic DNA. Person: Venkat Malladi, Chris Stoeckert, Jie Zheng STARR-seq STARR-seq assay self-transcribing active regulatory region sequencing Arnold et al. (January 2013). "Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq". Science 339 (6123): 1074-7. ENCODE project self-transcribing active regulatory region sequencing assay OBI:0002042 carbon-copy chromosome conformation capture assay followed by sequencing assay Fudenberg et al., (November 2014). "High order chromatin architecture shapes the landscape of chromosomal alterations in cancer." Nat Biotechol 29(12):1109-13. doi: 10.1038/nbt.2049. A carbon-copy chromosome conformation capture assay to analyze the organization of chromosomes in an unbiased, genome-wide manner using high throughput sequening following carbon-copy chromosome conformation capture. Person: Venkat Malladi, Chris Stoeckert, Jie Zheng Carbon-copy chromosome conformation capture assay followed by sequencing HiC HiC assay Lieberman-Aiden E, et al. (2009). Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326: 289-293. ENCODE project carbon-copy chromosome conformation capture assay followed by sequencing assay OBI:0002043 individual-nucleotide resolution cross-linking and immunoprecipitation sequencing assay König et al., (18 January 2012). "Protein-RNA interactions: new genomic technologies and perspectives". Nature Reviews Genetics 13 (2): 77-83. doi:10.1038/nrg3141 A cross-linking immunoprecipitation high-throughput sequencing assay to identify protein-RNA interactions by using UV light to covalently bind proteins and RNA molecules, allowing for a very stringent purification of the linked protein-RNA complexes. Person: Venkat Malladi, Chris Stoeckert, Jie Zheng iCLIP iCLIP assay individual-nucleotide resolution cross-linking and immunoprecipitation Huppertz et al., (February 2014). "iCLIP: protein-RNA interactions at nucleotide resolution.". Methods (San Diego, Calif.) 65 (3): 274-87. doi:10.1016/j.ymeth.2013.10.011 ENCODE project individual-nucleotide resolution cross-linking and immunoprecipitation sequencing assay OBI:0002044 RNA Bind-n-Seq assay A RNA-seq assay that comprehensively characterizes sequence and structural specificity of RNA binding proteins (RBPs) Person: Venkat Malladi, Chris Stoeckert, Jie Zheng RBNS RNA Bind-n-Seq RNBS assay Lambert et al., (June 2014). "RNA Bind-n-Seq: quantitative assessment of the sequence and structural binding specificity of RNA binding proteins." Mol Cell. 2014 Jun 5;54(5):887-900. doi: 10.1016/j.molcel.2014.04.016 ENCODE project RNA Bind-n-Seq assay OBI:0002045 poly(A)-site sequencing assay Wu et al., (July 2014). "Genome-wide determination of poly(A) sites in Medicago truncatula: evolutionary conservation of alternative poly(A) site choice. BMC Genomics. 2014 Jul 21;15:615. doi: 10.1186/1471-2164-15-615. A RNA-seq assay for quantitatively profiling RNA polyadenylation at the transcriptome level. Person: Venkat Malladi, Chris Stoeckert, Jie Zheng PAS-seq PAS-seq assay Poly(A)-site sequencing Shepard et al., (April 2011). "Complex and dynamic landscape of RNA polyadenylation revealed by PAS-Seq." RNA. 2011 Apr;17(4):761-72. doi: 10.1261/rna.2581711 ENCODE project poly(A)-site sequencing assay OBI:0002046 surface plasmon resonance sensor chip ProteOn GLC Sensor Chip #176-5011 a device that is used as a binding surface for ligand during a surface plasmon resonance assay, consisting of a glass plate to which a metal film is attached Anna Maria Masci SPR sensor chip biosensor chip sensor chip OBI surface plasmon resonance sensor chip OBI:0002047 enzyme-linked antibody Goat anti-Mouse IgG-HRP (horse radish peroxidase) is an antibody linked to the enzyme horseradish peroxidase (HRP) that catalyzes the conversion of chromogenic substrates into colored products producing light when acting on chemiluminescent substrates (ECL). A processed material that is comprised of an antibody that is covalently linked to an enzyme through bioconjugation. The enzyme can be used as a detection method when the enzyme's reaction produces a detectable signal, for example a color change when the substrate is added. Bjoern Peters, Randi Vita, James A. Overton OBI enzyme-linked antibody OBI:0002048 Illumina HiSeq 3000 A DNA sequencer manufactured by Illumina corporation, with a single flow cell and a throughput of more than 200 Gb per day. PERSON: Sagar Jain, Richard Scheuermann HiSeq 3000 http://www.illumina.com/systems/hiseq-3000-4000.html Illumina HiSeq 3000 OBI:0002049 Illumina HiSeq 4000 A DNA sequencer manufactured by Illumina corporation, with two flow cell and a throughput of more than 400 Gb per day. PERSON: Sagar Jain, Richard Scheuermann HiSeq 4000 http://www.illumina.com/systems/hiseq-3000-4000.html Illumina HiSeq 4000 OBI:0002050 3D structure determining assay of a MHC:ligand complex A MHC:ligand binding assay that uses a 3D structure determination of bound complex assay. IEDB IEDB 3D structure|any method 3D structure determining assay of a MHC:ligand complex OBI:0002051 in vivo assay measuring B cell epitope specific protection from infectious challenge based on pathogen burden A B cell epitope in vivo intervention experiment that uses a protection from challenge in vivo intervention experiment based on pathogen burden. IEDB IEDB pathogen burden after challenge|in vivo assay in vivo assay measuring B cell epitope specific protection from infectious challenge based on pathogen burden OBI:0002052 in vivo assay measuring B cell epitope specific protection from tumor challenge A B cell epitope in vivo intervention experiment that uses a protection from challenge in vivo intervention experiment based on tumor burden. IEDB IEDB tumor burden after challenge|in vivo assay in vivo assay measuring B cell epitope specific protection from tumor challenge OBI:0002053 microarray assay measuring binding of a B cell epitope:antibody complex A B cell epitope qualitative binding to antibody assay that uses a microarray. IEDB IEDB qualitative binding|microarray microarray assay measuring binding of a B cell epitope:antibody complex OBI:0002054 NMR assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex A B cell epitope equilibrium dissociation constant (KD) determination assay that uses a nuclear magnetic resonance assay. IEDB IEDB dissociation constant KD|nuclear magnetic resonance (NMR)|nM NMR assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex OBI:0002055 assay measuring T cell epitope specific biological activity A T cell epitope recognition assay that detects biological activity. IEDB IEDB biological activity|any method assay measuring T cell epitope specific biological activity OBI:0002056 biological activity assay measuring epitope specific chemokine (C-C motif) ligand 17 production by T cells A T cell epitope specific cytokine production assay that detects production of chemokine (C-C motif) ligand 17 production by T cells. IEDB IEDB CCL17/TARC release|biological activity biological activity assay measuring epitope specific chemokine (C-C motif) ligand 17 production by T cells OBI:0002057 biological activity assay measuring epitope specific macrophage migration inhibitory factor (MIF) production by T cells A T cell epitope specific cytokine production assay that detects macrophage migration inhibitory factor (MIF) production by T cells. IEDB IEDB MIF release|biological activity biological activity assay measuring epitope specific macrophage migration inhibitory factor (MIF) production by T cells OBI:0002058 biological activity assay measuring epitope specific oncostatin M production by T cells A T cell epitope specific cytokine production assay that detects oncostatin M production by T cells. IEDB IEDB oncostatin M release|biological activity biological activity assay measuring epitope specific oncostatin M production by T cells OBI:0002059 assay measuring a binding constant of a T cell epitope:MHC:TCR complex A T cell epitope recognition assay that quantitavely characterizes the binding of a TCR with a ligand by determining a binding constant. IEDB IEDB binding constant|binding assay assay measuring a binding constant of a T cell epitope:MHC:TCR complex OBI:0002060 detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 17 production by T cells An assay of epitope specific chemokine (C-C motif) ligand 17 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. IEDB IEDB CCL17/TARC release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 17 production by T cells OBI:0002061 cytometric bead array assay measuring epitope specific chemokine (C-C motif) ligand 22 production by T cells An assay of epitope specific chemokine (C-C motif) ligand 22 production by T cells that uses a cytometric bead array assay. IEDB IEDB CCL22/MDC release|cytometric bead array cytometric bead array assay measuring epitope specific chemokine (C-C motif) ligand 22 production by T cells OBI:0002062 in vitro assay measuring epitope specific T cell killing A T cell epitope specific killing assay that uses an in vitro cell killing assay. IEDB IEDB cytotoxicity|in vitro assay in vitro assay measuring epitope specific T cell killing OBI:0002063 cytometric bead array assay measuring epitope specific granzyme A release by T cells A T cell epitope specific granzyme A release assay that uses a cytometric bead array assay. IEDB IEDB granzyme A release|cytometric bead array cytometric bead array assay measuring epitope specific granzyme A release by T cells OBI:0002064 detection of specific nucleic acids with complementary probes assay measuring epitope specific granzyme A release by T cells A T cell epitope specific granzyme A release assay that uses a detection of specific nucleic acids with complementary probes assay. IEDB IEDB granzyme A release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific granzyme A release by T cells OBI:0002065 cytometric bead array assay measuring epitope specific granzyme B release by T cells A T cell epitope specific granzyme B release assay that uses a cytometric bead array assay. IEDB IEDB granzyme B release|cytometric bead array cytometric bead array assay measuring epitope specific granzyme B release by T cells OBI:0002066 detection of specific nucleic acids with complementary probes assay measuring epitope specific granzyme B release by T cells A T cell epitope specific granzyme B release assay that uses a detection of specific nucleic acids with complementary probes assay. IEDB IEDB granzyme B release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific granzyme B release by T cells OBI:0002067 cytometric bead array assay measuring epitope specific macrophage migration inhibitory factor (MIF) production by T cells An assay of epitope specific macrophage migration inhibitory factor (MIF) production by T cells that uses a cytometric bead array assay. IEDB IEDB MIF release|cytometric bead array cytometric bead array assay measuring epitope specific macrophage migration inhibitory factor (MIF) production by T cells OBI:0002068 cytometric bead array assay measuring epitope specific oncostatin M production by T cells An assay of epitope specific oncostatin M production by T cells that uses a cytometric bead array assay. IEDB IEDB oncostatin M release|cytometric bead array cytometric bead array assay measuring epitope specific oncostatin M production by T cells OBI:0002069 ELISPOT assay measuring epitope specific perforin release by T cells A T cell epitope specific perforin release assay that uses an ELISPOT assay. IEDB IEDB perforin release|ELISPOT ELISPOT assay measuring epitope specific perforin release by T cells OBI:0002070 in vivo assay measuring epitope specific proliferation of T cells A T cell epitope specific proliferation assay that is performed in vivo. IEDB IEDB proliferation|in vivo assay in vivo assay measuring epitope specific proliferation of T cells OBI:0002071 in vitro assay measuring epitope specific proliferation of T cells A T cell epitope specific proliferation assay that is performed on cells in vitro. IEDB IEDB proliferation|in vitro assay in vitro assay measuring epitope specific proliferation of T cells OBI:0002072 assay measuring qualitiative binding of a MHC:ligand complex A MHC:ligand binding assay that detects qualitative binding. IEDB IEDB qualitative binding|binding assay assay measuring qualitiative binding of a MHC:ligand complex OBI:0002073 in vivo assay measuring T cell epitope specific protection from challenge An efficacy of T cell epitope intervention experiment that uses a protection from challenge in vivo intervention experiment. IEDB IEDB protection from challenge|in vivo assay in vivo assay measuring T cell epitope specific protection from challenge OBI:0002074 in vitro assay measuring T cell epitope specific suppression T cell epitope dependent biological activity assay that detects suppression of an in vitro response. PERSON:Randi Vita, James Overton, Bjoern Peters IEDB suppression|in vitro assay in vitro assay measuring T cell epitope specific suppression OBI:0002075 MHC ligand assay An immune epitope assay that detects either the processing and presentation of a ligand by an antigen presenting cell or the binding of a ligand to an MHC molecule. IEDB IEDB ligand presentation/binding|binding assay MHC ligand assay 2 OBI:0002076 collection of specimens Blood cells collected from multiple donors over the course of a study. A material entity that has two or more specimens as its parts. Details see tracker: https://sourceforge.net/p/obi/obi-terms/778/ Person: Chris Stoeckert, Jie Zheng OBIB, OBI Biobank collection of specimens OBI:0002077 specimens derived from shared ancestor Aliquoting one specimen to multiple tubes and the collection of the aliquoted specimens are a specimen family. Slicing a tissue specimen into multiple sections for microscopy. A collection of specimens derived from one common specimen via one or more material processing process(es). Details see tracker: https://sourceforge.net/p/obi/obi-terms/778/ Chris Stoeckert, Jie Zheng specimen family Helena Ellis, Anna Maria Masci, OBIB, OBI Biobank specimens derived from shared ancestor OBI:0002078 specimen set collection process Collection of both blood and urine specimens in one clinical visit; Taking out liver and brain specimens during an autopsy. A specimen collection process that generates multiple specimens from one source (e.g. one organism) during a time period which for the purpose of the study can be considered to be taken at the same sampling time. Chris Stoeckert, Jie Zheng OBIB, OBI specimen set collection process OBI:0002079 specimens collected in one encounter Both blood and urine specimens collected in one clinical visit; liver and brain specimens taken during an autopsy. A collection of specimens that is collected from one source (e.g. one organism) during a time period which for the purpose of the study can be considered to be taken at the same sampling time. Details see tracker: https://sourceforge.net/p/obi/obi-terms/778/ Person: Chris Stoeckert, Jie Zheng specimen set OBIB, OBI Biobank specimens collected in one encounter OBI:0002080 human specimen set A specimen set that is collected from one person during a time period which for the purpose of the study can be considered to be taken at the same sampling time. Details see tracker: https://sourceforge.net/p/obi/obi-terms/778/ Person: Chris Stoeckert, Jie Zheng Helena Ellis, Anna Maria Masci, OBIB, OBI Biobank human specimen set OBI:0002081 specimens collected longitudinally A collection of specimens that was derived from the same source material entity at different time points in order to observe changes in that entity. Details see tracker: https://sourceforge.net/p/obi/obi-terms/778/ Person: Chris Stoeckert Bjoern Peters, OBI specimens collected longitudinally OBI:0002082 reporter gene assay An assay in which expression of a reporter gene is detected that was inserted under the control of a regulatory sequence of interest. tracker item: 781 Chris Stoeckert, Paul D. Thomas reporter gene detection assay Paul D. Thomas, Yang Chai; FaceBase reporter gene assay OBI:0002083 enhancer activity detection by reporter gene assay PMID 19268701: "we experimentally concatenated up to four enhancers from different genes and used a transgenic mouse assay to compare the in vivo activity of these compound elements with that of the single modules" A reporter gene assay in which expression of a reporter gene is detected that was inserted under the control of an enhancer of interest. Tracker item: 781 Paul D. Thomas, Yang Chai enhancer reporter gene assay FaceBase, PMID 24614317 enhancer activity detection by reporter gene assay OBI:0002084 transcription cofactor activity region identification by ChIP-Seq assay PMID 19212405: "we present the results of chromatin immunoprecipitation with the enhancer-associated protein p300 followed by massively parallel sequencing, and map several thousand in vivo binding sites of p300 in mouse embryonic forebrain, midbrain and limb tissue" A ChIP-seq assay to identify regions of chromatin bound to a chromatin modifying protein, e.g. a histone acetyltransferase. Tracker item: 782 Paul D. Thomas, Yang Chai chromatin modifier binding site identification by ChIP-Seq assay FaceBase, PMID 19212405 transcription cofactor activity region identification by ChIP-Seq assay OBI:0002085 transcript expression location detection by hybridization chain reaction PMID 25977364: "Multiplexed imaging of mRNA expression using fluorescent hybridization chain reaction (HCR) quantitatively confirmed the expression profiles of lead cells" An in-situ hybridization in which the location (e.g. anatomical/tissue) of a transcript is detected by a multiplexed fluorescent in situ hybridization, based on orthogonal amplification with hybridization chain reactions (HCR). RNA probes complementary to mRNA targets trigger chain reactions in which fluorophore-labeled RNA hairpins self-assemble into tethered fluorescent amplification polymers. See tracker #783 Paul D. Thomas, Yang Chai transcript expression location detection by fluorescent HCR. PMID 21037591 transcript expression location detection by hybridization chain reaction OBI:0005246 injection function The function of a device realized when administering a substance in vivo, applied particularly to the forcible insertion of a liquid or gas by means of a syringe, pump, etc. PERSON: Alan Ruttenberg PERSON: Melanie Courtot adapted from WEB: http://www.dictionary.net/injection injection function OBI:0100010 Epstein Barr virus transformed B cell PMID: 8777380. Expression of thyroid peroxidase in EBV-transformed B cell lines using adenovirus.Thyroid. 1996 Feb;6(1):23-8. A material entity which results from viral transformation process using EBV as transformation agent when applied to B-cell entity PERSON: Susanna Sansone GROUP: OBI Biomaterial Branch Epstein Barr virus transformed B cell OBI:0100014 chimera An organism which contains cells or tissues with a different genotype PERSON: Helen Parkinson GROUP: OBI chimera OBI:0100015 obsolete_anatomical entity Tissue, organ, system, sperm, blood or body location (arm). An anatomical entity is a material entity that is part of a multicellular organism, and which is large enough so that it forms an identifiable structure in the organism. Specifically, it excludes granular parts of the organism, such as atoms, molecules, cells, which can be removed from the organism without affecting it. It is defined as the union of 'multi-tissue structure', 'body substance' and 'portion of tissue' 10/20/09: This class and all subclasses are currently problematic. They should all be imported from other OBO foundry ontologies. (FMA / CARO / UBERON). Currently two problems exist: There is no cross species anatomy that covers all the entities we need. Secondly: there is not good boundary between anatomical entities and smaller parts in FMA. Currently we will use anatomical entities as if they are valid across species. 13-02-2009: Biomaterial branch: change of label and definition following discussions at the OBI winter meeting 2009. It was felt that 'macroscopic part of multicellular organism' introduce an impractical delineation. IMPORTANT NOTE: OBI 'anatomical entity' would essentially correspond to FMA 'material anatomical entity' rather than FMA 'physical anatomical entity'. OBI does not include 'immaterial anatomical entity' as it would clash with the parent class 'material entity' DOCUMENTATION NOTE: OBI anatomical entity granularity level excludes cell and biological molecules. Biom call - January 2009 - Issues: parasites are not macroscopic part or organism. fetus is_a macroscopic part (but this is up for discussion) equivalent classes 'portion of tissue' or 'multi-tissue structure' or 'portion of organism substance' Superclasses material_entity part_of some organism not super happy about liquids (blood, sperm), as they seem to be 'granular' somewhat, and not form a structure. Bjoern Peters Philippe Rocca-Serra Tina Boussard MO obsolete_anatomical entity true OBI:0100016 blood plasma specimen PMID: 18217225.Sex Transm Dis. 2008 Jan;35(1):55-60. Review.Human immunodeficiency virus viral load in blood plasma and semen: review and implications of empirical findings. a material entity which corresponds to the liquid component of blood, in which the blood cells are suspended. 03/21/2010: BP, blood plasma is defined as the output of certain separation processes, so this is in the domain of OBI, not FMA. PERSON: Maura Gasparetto PERSON: Melanie Courtot PERSON: Philippe Rocca-Serra plasma WEB: http://en.wikipedia.org/wiki/Blood_plasma blood plasma specimen OBI:0100017 blood serum specimen PMID: 18229666.Adv Med Sci. 2007;52 Suppl 1:204-6.Antioxidant activity of blood serum and saliva in patients with periodontal disease treated due to epilepsy. A material entity which derives from blood and corresponds to blood plasma without fibrinogen or the other clotting factors. PERSON: Maura Gasparetto PERSON: Melanie Courtot PERSON: Philippe Rocca-Serra WEB: http://en.wikipedia.org/wiki/Blood_plasma blood serum specimen OBI:0100026 organism animal fungus plant virus A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. 10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms') 13-02-2009: OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. This issue is outside the scope of OBI. GROUP: OBI Biomaterial Branch WEB: http://en.wikipedia.org/wiki/Organism organism OBI:0100035 obsolete_immortal cell a single Hela cell a cell derived from a multicellular organism that has the potential to replicate indefinitely PERSON: Bjoern Peters GROUP: OBI Biomaterial Branch obsolete_immortal cell true OBI:0100039 obsolete_fragment derived from protein the peptide with sequence SIINFEKL, which is eluted from a cell expressing hen egg lysozyme A material entity which is derived from a protein BP:03/21/2010:obsoleted as the class is no longer necessary, and we would otherwise need all kinds of 'fragment derived from' classes. Instead, use composite terms with the relationship 'derived from' some protein OR derived from some part_of protein. PRS:22022008. result from protocol_application where input=protein and output=polypeptide or peptide (to capture: derives_from protein) original term: protein fragment split into synthetic polypeptide and fragment derived from protein THE DEFINITION OF THIS SUGGESTS WE COVER THIS ALREADY IN PEPTIDE/POLYPETIDE. DO WE NEED THIS AND CAN WE DEAL WITH IT IN SOME OTHER WAY? JAMES PERSON: Bjoern Peters GROUP: IEDB obsolete_fragment derived from protein true OBI:0100046 phosphate buffered saline solution PMID: 16279733.Dent Mater J. 2005 Sep;24(3):414-21.PBS buffer solutions with different pH values can change porosity of DNA-chitosan complexes. Phosphate buffered saline (abbreviated PBS) is a buffer solution commonly used in biochemistry. It is a salty solution containing sodium chloride, sodium phosphate and in some preparations potassium chloride and potassium phosphate. The buffer helps to maintain a constant pH. The concentration usually matches the human body (isotonic). PERSON: Melanie Courtot PERSON: Philippe Rocca-Serra PERSON: Tina Boussard PBS buffer WEB: http://en.wikipedia.org/wiki/Phosphate_buffered_saline phosphate buffered saline solution OBI:0100051 specimen Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen. A material entity that has the specimen role. Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. PERSON: James Malone PERSON: Philippe Rocca-Serra GROUP: OBI Biomaterial Branch specimen OBI:0100055 obsolete_cell line cell A material entity that represents generations of a primary culture. had superclass axiom: is_specified_output_of some 'establishing cell culture' PERSON: Susanna Sansone GROUP: OBI Biomaterial Branch obsolete_cell line cell true OBI:0100056 obsolete_immortal cell line culture A cell line that is expected to be capable of indefinite propagation in an vitro culture. 2013-08-09 MHB: Replaced with cell line class from CLO, follwoing outcome of Spring 2013 CLO alignment work. Subclass axioms were: 'has grain' some 'immortal cell line cell' and 'has grain' only 'immortalcell line cell' MHB 3-5-13: This OBI class was formerly called 'immortalized cell line culture', but label changed and definition updated following CLO alignment work in spring of 2013. PERSON:Matthew Brush immortal cell line sample permanent cell line PERSON:Matthew Brush http://purl.obolibrary.org/obo/CLO_0009828 obsolete_immortal cell line culture true OBI:0100058 xenograft Human xenotransplantation (e.g. from pig to human) offers a potential treatment for end-stage organ failure, a significant health problem in parts of the industrialized world A material entity which results from the transplantation of living cells, tissues or organs from on organism of one species to an organism of another species. PERSON: Melanie Courtot PERSON: Philippe Rocca-Serra xenotransplant WEB: http://en.wikipedia.org/wiki/Xenograft xenograft OBI:0100060 cultured cell population A cultured cell population applied in an experiment: "293 cells expressing TrkA were serum-starved for 18 hours and then neurotrophins were added for 10 min before cell harvest." (Lee, Ramee, et al. "Regulation of cell survival by secreted proneurotrophins." Science 294.5548 (2001): 1945-1948). A cultured cell population maintained in vitro: "Rat cortical neurons from 15 day embryos are grown in dissociated cell culture and maintained in vitro for 8–12 weeks" (Dichter, Marc A. "Rat cortical neurons in cell culture: culture methods, cell morphology, electrophysiology, and synapse formation." Brain Research 149.2 (1978): 279-293). A processed material comprised of a collection of cultured cells that has been continuously maintained together in culture and shares a common propagation history. 2013-6-5 MHB: This OBI class was formerly called 'cell culture', but label changed and definition updated following CLO alignment efforts in spring 2013, during which the intent of this class was clarified to refer to portions of a culture or line rather than a complete cell culture or line. PERSON:Matthew Brush cell culture sample PERSON:Matthew Brush The extent of a 'cultured cell population' is restricted only in that all cell members must share a propagation history (ie be derived through a common lineage of passages from an initial culture). In being defined in this way, this class can be used to refer to the populations that researchers actually use in the practice of science - ie are the inputs to culturing, experimentation, and sharing. The cells in such populations will be a relatively uniform population as they have experienced similar selective pressures due to their continuous co-propagation. And this population will also have a single passage number, again owing to their common passaging history. Cultured cell populations represent only a collection of cells (ie do not include media, culture dishes, etc), and include populations of cultured unicellular organisms or cultured multicellular organism cells. They can exist under active culture, stored in a quiescent state for future use, or applied experimentally. cultured cell population OBI:0100061 primary cultured cell population Spleen cells put directly into culture; Cold storage of biopsies from wild endangered native Chilean species in field conditions and subsequent isolation of primary culture cell lines. In Vitro Cell Dev Biol Anim. 2008 Jul 2. PMID: 18594934 cells that have been isolated from some organismal source, expanded in culture, but not undergone a complete passaging (ie are still in culture, or have been lifted from culture and frozen in aliquots for future use) A cultured cell population comprised of cells expanded directly from living tissue prior to being passaged. 2013-6-5 MHB: This OBI class was formerly called 'primary cell culture', but label changed and definition updated following CLO alignment work. Previous definition: 'a primary cell culture is a cell culture where the cells derive from a fresh tissue source.' PERSON:Matthew Brush primary cell culture primary cell culture sample PERSON:Matthew Brush primary cultured cell population 0 consider if we really want to be so strict here . . . ie maybe we we say that they have not been output from an 'establishing cell line' process, but in some cases a passage or two may be allowed for a primary culture. the establishing of a line requires some procedss that attains a degree of homogeneity in the culture. OBI:0100062 obsolete_cell line A split of HeLa cells in active culture, or stored in frozen aliquots. Populations of HEK 293 cells used in experiments such as those documented in "Changes in ultrastructure and endogenous ionic channels activity during culture of HEK 293 cell line". Eur J Pharmacol. 2007 Jul 12;567(1-2):10-8. PMID: 17482592. He, Tong-Chuan, et al. \"Identification of c-MYC as a target of the APC pathway.\" Science 281.5382 (1998): 1509-1512. - \"To evaluate the transcriptional effects of APC, we studied a human colorectal cancer cell line (HT29-APC) containing a zinc-inducible APC gene and a control cell line (HT29–β-Gal) containing an analogous inducible lacZ gene\". Note that common usage in the literature is often of the form \"a human colorectal cancer cell line\", as seen above. But such references to studies in \"a line\" refer to the fact that discrete populations of cells that are input into culturing or experiments, not an entire lineage of cells. It is these discrete populations that we refer to as 'cell lines'. A secondary cultured cell population that represents a genetically stable and homogenous population of cultured cells that shares a common propagation history (ie has been successively passaged together in culture). 2013-08-09 MHB: Replaced with cell line class from CLO, follwoing outcome of Spring 2013 CLO alignment work. Subclass axioms were: 'has grain' some 'cell line cell' and 'has grain' only 'cell line cell' 2013-6-5 MHB: There is considerable ambiguity and inconsistent usage surrounding the term 'cell line' across biomedical communities. For exmaple, it can refer to the maximal collection of all cells in a cultured lineage (e.g. the colelction of all HeLa cells that exist), or to discrete portions of this maximal collection that are stored, exchanged, and applied experimentally (e.g. the dish of HeLa cells I am using in my experiment). A working group of representatives from OBI, CLO, and CL was assembled in spring of 2013 to harmonize modeling and terminology surrounding experimentally cultured cells across Open Biomedical Ontologies, following OBO Foundry principles of orthogonality and re-use. A consensus was reached to apply the term 'cell line' to refer not to a maximal collection of cells of a given type, but to discrete populations of cultured cells that share a common propagation history which has conferred a certain a genetic stability and compositional homogeneity to the population. This meaning reflects its most common usage in domain discourse, and will best support data annotation requirements. This view means that a 'HeLa cell line' would be a subset of all HeLa cells in the world - specifically any subset that has been derived through a shared continuous lineage wherein the cells have always been passaged together and thereby evolved together through the selective pressures imposed by this specific history. Accordingly, 'HeLa cell line' would not be used to refer to collections such as all HeLa cells in a given lab, or all HeLa cells in the ATCC repository, as all cells in these collections do not necessarily share a common culture history. Rather, it could be used to refer to the collection of cells I am culturing at a given moment, or that I apply in an experiment (as such collections typically meet the criteria of having a shared propagation history). This approach seems to accomplish several desirable goals: 1) It allows us to define the term 'cell line' for the community in a precise way that also reflects how the term is most commonly used in the literature and scientific discourse. (2) It gives a definition that provides clear criteria to help specify what are and what are not instances of 'cell lines' in the real world (3) The criteria it provides demarcate populations that represent what researchers actually use in the practice of science - ie are the inputs to culturing, experimentation, and sharing. The cells in such populations will be a relatively uniform population as they have experienced similar selective pressures due to their continuous co-propagation. And this population will also have a single passage number, again owing to their common passaging history. (4) The definition seems to be true to the meaning of the word 'line' - which is suggests a specific lineage of derivation. PERSON:Matthew Brush cell line sample OBI-CLO Alignment Working Group (Spring 2013) http://purl.obolibrary.org/obo/CLO_0000031 1. The term 'line' is used when a culture has undergone an intentional experimental process to establish a more uniform and stable population of cells (see 'establishing cell line'). This will require one or more passages, but may involve additional selection processes. Through such passaging and/or selection processes, the resulting 'line' attains some level of genetic stability and compositional homogeneity which is typically absent in primary cultures. Because of their relative homogeneity, 'lines' are capable of being characterized and stably propagated over a period of time. A *new* cell line can be "established" not only through the passaging/selection of a primary culture, but also through experimental modifications of existing lines (e.g. immortalization, stable genetic modifications, drug selection for a resistant subset, etc.). As defined here, 'cell line' can refer to a population of cells in active culture, applied experimentally, or stored in a quescent state for future use. 2. The definitional criteria provided here for the 'cell line' class demarcates populations that represent what researchers actually use in the practice of science - e.g. as inputs to culturing, experimentation, and sharing. The definition is such that cell lines will exhibit important attributes. For example, they will have a relatively homogenous cell type composition as they have experienced similar selective pressures due to their continuous co-propagation. In addition, these populations can also be characterized by a passage number, again owing to their common passaging history.? 3. Definitinal criteria are intended to be sufficiently clear to specify what are and what are not instances of 'cell lines' in the real world. A 'HeLa cell line' would be a subset of all HeLa cells in the world - specifically any subset that has been derived through a shared continuous lineage wherein the cells have always been passaged together and thereby evolved together through the selective pressures imposed by this common history. Accordingly, 'HeLa cell line' would not be used to refer to the collection of all HeLa cells in a given lab, or all HeLa cells in the ATCC repository, as cells in these collections will likely not all share a common culture history. Rather, 'HeLa cell line' could refer to the collection of cells I am culturing at a given moment, or that I apply in an experiment (as such collections typically meet the criteria of having a shared propagation history). As noted above, it is such collections that are typically referred to in scientific discourse and publications. 4. Notably, the term 'line' has been alternately used by other terminologies and communities to refer to cultures that have been immortalized - ie has attained the capacity for indefinite propagation in vitro. In this ontology, we refer to such cell lines as 'immortal cell lines', and use the term 'cell line' to indicate any culture that has been passaged. obsolete_cell line true OBI:0100063 cultured clonal cell population cell cut Stem cell functions assessed in clonal culture. Soc Gen Physiol Ser. 1988;43:39-45. Review. PMID: 3077557 A cultured cell population comprised of cells which can all be traced back to a single ancestor cell, and which therefore can be treated as identical. PERSON: Susanna Sansone PERSON:Matthew Brush clonal cell culture sample GROUP: OBI Biomaterial Branch cultured clonal cell population OBI:0100064 screening library PMID: 15615535.J Med Chem. 2004 Dec 30;47(27):6864-74.A screening library for peptide activated G-protein coupled receptors. 1. The test set. [cdna_library, phage display library] a screening library is a collection of materials engineered to identify qualities of a subset of its members during a screening process? PRS: 22-02-2008: while working on definition of cDNA library and looking at current example of usage, a screening library should be a defined class -> any material library which has input_role in a screening protocol application change biomaterial to material in definition PERSON: Bjoern Peters GROUP: IEDB 7/13/09: Need to clarify if this meets reagent role definition screening library OBI:0100065 synthetic peptide the synthesized peptide SIINFEKL which also occurs in hen-egg lysozyme a synthetic peptide is an material entity which is artificially engineered and results from the synthesis of a chain of amino acids which may also be found in natural protein and be identical in sequence to a protein fragment changed from synthetic polypeptide to peptide, to get rid of the restriction of having more than 10 amino acids (required by Chebi). Bjoern Peters IEDB PRS:22-02-2008: a chebi entity which has output role in a synthesis protocol application original term: protein fragment split into synthetic polypeptide and fragment derived from protein DS: Is this synthetic an oxymoron to the biomaterial? synthetic peptide OBI:0100066 organ section A liver slice used in a perfusion experiment. Thyroidectomy during laryngectomy for advanced laryngeal carcinoma--whole organ section study with long-term functional evaluation. Clin Otolaryngol Allied Sci. 1995 Apr;20(2):145-9. PMID: 7634521 A processed material which derives from an organ and results from a process of dissection or histological sample preparation a portion(formerly an organ section is portion of an organ removed from the context of the organ) PERSON: Helen Parkinson PERSON: Philippe Rocca-Serra GROUP: CEBS GROUP: OBI Biomaterial Branch organ section OBI:0100067 bronchial alveolar lavage solution containing lung derived T cells, eosinophils, and TNFa. Group of biomaterials present in the bronchial aveolar space of an organism which are collected through lavage including the reagents used to for the lavage process, organisms, cells, and cellular secretions present in the bronchial aveolar space. PERSON: Bjoern Peters BAL GROUP: IEDB bronchial alveolar lavage OBI:0100069 obsolete_polymer A macromolecule is a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. MC, 20100316: Replaced by Chebi polymer and usage polymerization also fixed. James Malone Philippe Rocca-Serra TERM: CHEBI:33839 obsolete_polymer true OBI:0100086 glucose in solution Glucose present in blood A scattered aggregate of glucose molecules in a liquid PERSON: Jie Zheng glucose molecules glucose in solution OBI:0200000 data transformation The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value. A planned process that produces output data from input data. Elisabetta Manduchi Helen Parkinson James Malone Melanie Courtot Philippe Rocca-Serra Richard Scheuermann Ryan Brinkman Tina Hernandez-Boussard data analysis data processing Branch editors data transformation OBI:0200002 logistic-log curve fitting Typically used in an enzyme-linked immunosorbent assay (ELISA) to model the relationship between optical density (OD) and dilution. In this case a and d correspond to the theoretical OD of the assay at zero and infinite concentrations, respectively; c is the dilution associated with the point of symmetry of the sigmoid and is located at the midpoint of the assay found at the inflection point of the curve; b is a curvature parameter and is related to the slope of the curve. A logistic-log curve fitting is a curve fitting where a curve of the form y=d+((a-d)/(1+(x/c)^b)) is obtained, where a, b, c, and d are determined so to optimize its fit to the input data points (x_1, y_1), (x_2, y_2), ..., (x_n, y_n). Elisabetta Manduchi James Malone Melanie Courtot Ryan Brinkman ARTICLE: Plikaytis B.D. et al. (1991), J. Clin. Microbiol. 29(7): 1439-1448 logistic-log curve fitting OBI:0200003 logit-log curve fitting Typically used in an enzyme-linked immunosorbent assay (ELISA) to model the relationship between optical density (OD) and dilution. In this case OD_0 (also referred to OD_min) and OD_infty (also referred to OD_max) correspond to the theoretical OD of the assay at zero and infinite concentrations, respectively. A logit-log curve fitting is a curve fitting where first the limits y_0 an y_infty of y when x->0 and x->infinity, respectively, are estimated from the input data points (x_1, y_1), (x_2,y_2), ..., (x_n, y_n). Then a curve with equation log((y-y_0)/(y_infty-y))=a+b log(x) is obtained, where a and b are determined to optimize its fit to the input data points. The above definition refers to the 'fully specified' logit-log model. The reduced form of this, when it is assumed that y_0=0, is named 'partially specified' logit-log model. Elisabetta Manduchi James Malone Melanie Courtot Ryan Brinkman ARTICLE: Plikaytis B.D. et al. (1991), J. Clin. Microbiol. 29(7): 1439-1448 logit-log curve fitting OBI:0200004 log-log curve fitting Typically used in an enzyme-linked immunosorbent assay (ELISA) to model the relationship between optical density (OD) and dilution. A log-log curve fitting is a curve fitting where first a logarithmic transformation is applied both to the x and the y coordinates of the input data points (x_1, y_1), (x_2, y_2), ..., (x_n, y_n), and then coefficients a and b are determined to optimize the fit of log(y)=a+b*log(x) to these input data points. Elisabetta Manduchi James Malone Melanie Courtot Ryan Brinkman ARTICLE: Plikaytis B.D. et al. (1991), J. Clin. Microbiol. 29(7): 1439-1446 log-log curve fitting OBI:0200005 feature extraction objective A feature extraction objective is a data transformation objective where the aim of the data transformation is to generate quantified values from a scanned image. Elisabetta Manduchi James Malone TERM: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#feature_extraction feature extraction objective OBI:0200006 biexponential transformation This type of transformation is typically used in flow cytometry. A biexponential transformation is a data transformation that, for each (one dimensional) real number input x, outputs an approximation (found, e.g. with the Newton's method) to a solution y of the equation B(y)-x=0, where B denotes a b transformation. Elisabetta Manduchi Joseph Spliden Ryan Brinkman WEB: http://flowcyt.sourceforge.net/gating/latest.pdf biexponential transformation OBI:0200007 box-cox transformation A box-cox transformation is a data transformation according to the methods of Box and Cox as described in the article Box, G. E. P. and Cox, D.R. (1964) An analysis of transformations. Journal of Royal Statistical Society, Series B, vol. 26, pp. 211-246. Ryan Brinkman ARTICLE: Box, G. E. P. and Cox, D.R. (1964), "An analysis of transformations", Journal of Royal Statistical Society, Series B, vol. 26, pp. 211-246. box-cox transformation OBI:0200008 hyperlog transformation This type of transformation is typically used in flow cytometry A hyperlog transformation ia a data transformation that, for each (one dimensional) real number input x, outputs an approximation (found, e.g. with the Newton's method) to a solution y of the equation EH(y)-x=0, where EH denotes an eh transformation. Elisabetta Manduchi Joseph Spliden Ryan Brinkman ARTICLE: Bagwell C.B. (2006), "Hyperlog - a flexible log-like transform for negative, zero, and positive valued data", Cytometry A 64, 34-42." http://flowcyt.sourceforge.net/gating/latest.pdf hyperlog transformation OBI:0200010 loess scale group transformation one-channel Loess scale group normalization applied to data from two one-channel expression microarray assays. A loess scale group transformation one-channel is a loess scale group transformation consisting in the application of a scale adjustment following a loess group transformation one-channel, to render the M group variances similar. Elisabetta Manduchi OTHER: Editor's adjustment based on MGED Ontology term loess scale group transformation one-channel OBI:0200011 logical transformation This type of transformation is typically used in flow cytometry. A logical transformation is a data transformation that, for each (one dimensional) real number input x, outputs an approximation (found, e.g. with the Newton's method) to a solution y of the equation S(y)-x=0, where S denotes an s transformation. Elisabetta Manduchi Joseph Spliden Ryan Brinkman WEB: http://flowcyt.sourceforge.net/gating/latest.pdf logical transformation OBI:0200012 loess scale group transformation two-channel Loess scale group normalization applied to data from a two-channel expression microarray assay. A loess scale group transformation two-channel is a loess scale group transformation consisting in the application of a scale adjustment following a loess group transformation two-channel, to render the M group variances similar. Elisabetta Manduchi OTHER: Adjusted from MGED Ontology loess scale group transformation two-channel OBI:0200013 loess global transformation one-channel Loess global normalization applied to data from two one-channel expression microarray assays, where the curve is obtained using all reporters. The goal is to remove intensity-dependent biases. A loess global transformation one-channel is a loess global transformation in the special case where the input is the result of an MA transformation applied to intensities from two related one-channel assays. Elisabetta Manduchi OTHER: Editor's generalization based on MGED Ontology term loess global transformation one-channel OBI:0200014 split-scale transformation This type of transformation is typically used in flow cytometry A split-scale transformation is a data transformation which is an application of a function f described as follows to a (one dimensional) real number input. f(x)=a*x+b if x=for x>t; where log denotes a logarithmic transformation and a, b, c, d, r, t are real constants, with a, c, d, r, t positive, chosen so that f is continuous with a continuous derivative at the transition point t. Elisabetta Manduchi Joseph Spliden Ryan Brinkman WEB: http://flowcyt.sourceforge.net/gating/latest.pdf split-scale transformation OBI:0200015 loess global transformation two-channel Loess global normalization applied to data from a two-channel expression microarray assay, where the curve is obtained using all reporters. The goal is to remove intensity-dependent biases. A loess global transformation two-channel is a loess global transformation in the special case where the input the result of an MA transformation applied to intensities from the two channels of a two-channel assay. Elisabetta Manduchi OTHER: Editor's generalization based on MGED Ontology term loess global transformation two-channel OBI:0200016 sine transformation sine(0)=0, sine(pi/2)=1, sine(pi)=0, sine(3*pi/2)=-1, sine(pi/6)=1/2, sine(x+2*k*pi)=sine(x) where k is any integer, etc. A sine transformation is a data transformation which consists in applying the sine function to a (one dimensional) real number input. The sine function is one of the basic trigonometric functions and a definition is provided, e.g., at http://mathworld.wolfram.com/Sine.html. Elisabetta Manduchi WEB: http://mathworld.wolfram.com/Sine.html sine transformation OBI:0200017 cosine transformation cosine(0)=1, cosine(pi/2)=0, cosine(pi)=-1, cosine(3*pi/2)=0, cosine(pi/3)=1/2, cosine(x+2*k*pi)=cosine(x) where k is any integer, etc. A cosine transformation is a data transformation which consists in applying the cosine function to a (one dimensional) real number input. The cosine function is one of the basic trigonometric functions and a definition is provided, e.g., at http://mathworld.wolfram.com/Cosine.html. Elisabetta Manduchi Philippe Rocca-Serra WEB: http://mathworld.wolfram.com/Cosine.html cosine transformation OBI:0200018 loess group transformation one-channel A loess group transformation one-channel is a loess group transformation in the special case where the input is the result of an MA transformation applied to intensities from two related one-channel assays. A loess group transformation one-channel is a loess group transformation in the special case where the input is the result of an MA transformation applied to intensities from two related one-channel assays. Elisabetta Manduchi OTHER: Editor's generalization based on MGED Ontology term loess group transformation one-channel OBI:0200019 loess group transformation two-channel A loess group transformation two-channel is a loess group transformation in the special case where the input is the result of an MA transformation applied to intensities from the two channels of a two-channel assay. A loess group transformation two-channel is a loess group transformation in the special case where the input is the result of an MA transformation applied to intensities from the two channels of a two-channel assay. Elisabetta Manduchi OTHER: Editor's generalization based on MGED Ontology term loess group transformation two-channel OBI:0200020 homogeneous polynomial transformation a*x, with a non-zero, is a homogeneous polynomial of degree 1 in 1 variable, a*x^2, with a non-zero, is a homogeneous polynomial of degree 2 in 1 variable; a_1*x_1+...+a_n*x_n, with at least one of the a_i's non-zero, is a homogeneous polynomial of degree one in n variables; a*x_n^3+b*x_1*x_2*x_3, with at least one of a and b non-zero, is a homogeneous polynomial of degree 3 in n variables. A homogeneous polynomial transformation is a polynomial transformation where all the term of the polynomial have the same degree. Elisabetta Manduchi WEB: http://mathworld.wolfram.com/HomogeneousPolynomial.html homogeneous polynomial transformation OBI:0200021 linlog transformation This can be used for microarray normalization, e.g. to normalize the data from a two-channel expression microarray assay, as described in PMID 16646782. A linlog transformation is a data transformation, described in PMID 16646782, whose input is a matrix [y_ik] and whose output is a matrix obtained by applying formula (9) of this paper, where values below an appropriately determined threshold (dependent on the row i) are transformed via a polynomial of degree 1, and values above this threshold are transformed via a logarithm. Elisabetta Manduchi Philippe Rocca-Serra PMID: 16646782 linlog transformation OBI:0200022 variance stabilizing transformation This can be used for expression microarray assay normalization and it is referred to as "variance stabilizing normalization", according to the procedure described e.g. in PMID 12169536. A variance stabilizing transformation is a data transformation, described in PMID 12169536, whose input is a matrix [y_ik] and whose output is a matrix obtained by applying formula (6) in this paper. One of the goals is to obtain an output matrix whose rows have equal variances. The method relies on various assumptions described in the paper. Elisabetta Manduchi James Malone Melanie Courtot variance stabilising transformation PMID: 12169536 variance stabilizing transformation OBI:0200023 loess global transformation A loess global transformation is a loess transformation where only one loess fitting is performed, utilizing one subset of (or possibly all of) the data points in the input so that there is only one resulting loess curve y=f(x) which is used for the transformation. Elisabetta Manduchi James Malone Melanie Courtot Philippe Rocca-Serra OTHER: Editor's generalization based on MGED Ontology term loess global transformation OBI:0200024 loess group transformation A loess group transformation is a loess transformation where the input is partitioned into groups and for each group a loess fitting is performed, utilizing a subset of (or possibly all of) the data points in that group. Thus, a collection of loess curves y=f_i(x) is generated, one per group. Each (x, y) in the input is transformed into (x, y-f_i(x)), where f_i(x) is the curve corresponding to the group to which that data point belongs. Elisabetta Manduchi James Malone Melanie Courtot Philippe Rocca-Serra OTHER: Editor's generalization based on MGED Ontology term loess group transformation OBI:0200025 loess scale group transformation A loess scale group transformation is a data transformation consisting in the application of a scale adjustment following a loess group transformation, to render the group variances for the second variable (y) similar. Has objective scaling. Elisabetta Manduchi James Malone Melanie Courtot OTHER: Editor's generalization based on MGED Ontology term loess scale group transformation OBI:0200026 total intensity transformation single This can be used as a simple normalization method for expression microarray assays. For example, each intensity from a one-channel microarray assay is multiplied by a constant so that the output mean intensity over the microarray equals a desired target T (the multiplicative constant in this case is the T/(mean intensity)). A total intensity transformation single is a data transformation that takes as input an n-dimensional (real) vector and multiplies each component of this vector by a coefficient, where the coefficient is obtained by taking the sum of the input components or of a subset of these, multiplied by a constant of choice. Elisabetta Manduchi Helen Parkinson James Malone Melanie Courtot Philippe Rocca-Serra OTHER: Adjusted from MGED Ontology Note that if the word "sum" is replaced by the word "mean" in the definition, the resulting definition is equivalent. total intensity transformation single OBI:0200027 total intensity transformation paired This can be used as a simple normalization method for the two channels from a two-channel expression microarray assay or from two related one-channel expression microarray assays. A total intensity transformation paired is a data transformation that takes as input two n-dimensional (real) vectors and multiplies each component of the first vector by a coefficient, where the coefficient is obtained by taking the ratio of the sum of the second input components or of a subset of these by the sum of the first input components or of a subset of these (the same subset is used for the two vectors). Elisabetta Manduchi Philippe Rocca-Serra OTHER: Adjusted from MGED Ontology Note that if the word "sum" is replaced by the word "mean" in the definition, the resulting definition is equivalent. total intensity transformation paired OBI:0200028 quantile transformation This can be used for expression microarray assay normalization and it is referred to as "quantile normalization", according to the procedure described e.g. in PMID 12538238. A quantile transformation is a data transformation that takes as input a collection of data sets, where each can be thought as an n-dimensional (real) vector, and which transforms each data set so that the resulting output data sets have equal quantiles. Elisabetta Manduchi PERSON: Elisabetta Manduchi quantile transformation OBI:0200029 mean centering This can be used as a normalization method in expression microarray assays. For example, given a two-channel microarray assay, the log ratios of the two channels (M values) can be mean-centered. A mean centering is a data transformation that takes as input an n-dimensional (real) vector, performs a mean calculation on its components, and subtracts the resulting mean from each component of the input. Elisabetta Manduchi Philippe Rocca-Serra mean centring PERSON: Elisabetta Manduchi mean centering OBI:0200030 median centering This can be used as a normalization method in expression microarray assays. For example, given a two-channel microarray assay, the log ratios of the two channels (M values) can be median-centered. A median centering is a data transformation that takes as input an n-dimensional (real) vector, performs a median calculation on its components, and subtracts the resulting median from each component of the input. Elisabetta Manduchi Philippe Rocca-Serra median centring PERSON: Elisabetta Manduchi median centering OBI:0200031 differential expression analysis objective Analyses implemented by the SAM (http://www-stat.stanford.edu/~tibs/SAM), PaGE (www.cbil.upenn.edu/PaGE) or GSEA (www.broad.mit.edu/gsea/) algorithms and software A differential expression analysis objective is a data transformation objective whose input consists of expression levels of entities (such as transcripts or proteins), or of sets of such expression levels, under two or more conditions and whose output reflects which of these are likely to have different expression across such conditions. Elisabetta Manduchi PERSON: Elisabetta Manduchi differential expression analysis objective OBI:0200032 K-fold cross validation method K-fold cross-validation randomly partitions the original sample into K subsamples. Of the K subsamples, a single subsample is retained as the validation data for testing the model, and the remaining K - 1 subsamples are used as training data. The cross-validation process is then repeated K times (the folds), with each of the K subsamples used exactly once as the validation data. The K results from the folds then can be averaged (or otherwise combined) to produce a single estimation. The advantage of this method over repeated random sub-sampling is that all observations are used for both training and validation, and each observation is used for validation exactly once. 10-fold cross-validation is commonly used Person:Helen Parkinson Tina Boussard K-fold cross validation method OBI:0200033 leave one out cross validation method The authors conducted leave-one-out cross validation to estimate the strength and accuracy of the differentially expressed filtered genes. http://bioinformatics.oxfordjournals.org/cgi/content/abstract/19/3/368 is a data transformation : leave-one-out cross-validation (LOOCV) involves using a single observation from the original sample as the validation data, and the remaining observations as the training data. This is repeated such that each observation in the sample is used once as the validation data 2009-11-10. Tracker: https://sourceforge.net/tracker/?func=detail&aid=2893049&group_id=177891&atid=886178 Person:Helen Parkinson leave one out cross validation method OBI:0200034 jackknifing method simple weighting procedure is suggested for combining information over alleles and loci, and sample variances may be estimated by a jackknife procedure Jacknifing is a re-sampling data transformation process used to estimate the precision of sampling statistics and is a resampling method Helen Parkinson jackknifing http://en.wikipedia.org/wiki/Resampling_%28statistics%29 jackknifing method OBI:0200035 boostrapping Although widely accepted that high throughput biological data are typically highly noisy, the effects that this uncertainty has upon the conclusions we draw from these data are often overlooked. However, in order to assign any degree of confidence to our conclusions, we must quantify these effects. Bootstrap resampling is one method by which this may be achieved. Bootstrapping is a statistical method for estimating the sampling distribution of a statistic by sampling with replacement from the original data, most often with the purpose of deriving robust estimates of standard errors and confidence intervals of a population parameter like a mean, median, proportion, odds ratio, correlation coefficient or regression coefficient Helen Parkinson Bootstrapping is a data transformation process which estimates the precision of sampling statistics by drawing randomly with replacement from a set of data points boostrapping OBI:0200036 Benjamini and Hochberg false discovery rate correction method Statistical significance of the 8 most represented biological processes (GO level 4) among E7 6 month upregulated genes following analysis with DAVID software; Benjamini-Hochberg FDR (false discovery rate) A data transformation process in which the Benjamini and Hochberg method sequential p-value procedure is applied with the aim of correcting false discovery rate 2011-03-31: [PRS]. specified input and output of dt which were missing Helen Parkinson Philippe Rocca-Serra Helen Parkinson Benjamini and Hochberg false discovery rate correction method OBI:0200037 pareto scaling A pareto scaling is a data transformation that divides all measurements of a variable by the square root of the standard deviation of that variable. Elisabetta Manduchi Philippe Rocca-Serra PMID:16762068 pareto scaling OBI:0200040 modular decomposition Molecular decomposition is the partition of a network into distinct subgraphs for the purpose of identifying functional clusters. The network data is run through any of several existing algorithms designed to partition a network into distinct subgraphs for the purpose of isolating groups of functionally linked biological elements such as proteins. Tina Hernandez-Boussard editor modular decomposition OBI:0200041 k-means clustering A k-means clustering is a data transformation which achieves a class discovery or partitioning objective, which takes as input a collection of objects (represented as points in multidimensional space) and which partitions them into a specified number k of clusters. The algorithm attempts to find the centers of natural clusters in the data. The most common form of the algorithm starts by partitioning the input points into k initial sets, either at random or using some heuristic data. It then calculates the mean point, or centroid, of each set. It constructs a new partition by associating each point with the closest centroid. Then the centroids are recalculated for the new clusters, and the algorithm repeated by alternate applications of these two steps until convergence, which is obtained when the points no longer switch clusters (or alternatively centroids are no longer changed). Elisabetta Manduchi James Malone Philippe Rocca-Serra WEB: http://en.wikipedia.org/wiki/K-means k-means clustering OBI:0200042 hierarchical clustering A hierarchical clustering is a data transformation which achieves a class discovery objective, which takes as input data item and builds a hierarchy of clusters. The traditional representation of this hierarchy is a tree (visualized by a dendrogram), with the individual input objects at one end (leaves) and a single cluster containing every object at the other (root). James Malone WEB: http://en.wikipedia.org/wiki/Data_clustering#Hierarchical_clustering hierarchical clustering OBI:0200043 average linkage hierarchical clustering An average linkage hierarchical clustering is an agglomerative hierarchical clustering which generates successive clusters based on a distance measure, where the distance between two clusters is calculated as the average distance between objects from the first cluster and objects from the second cluster. Elisabetta Manduchi PERSON: Elisabetta Manduchi average linkage hierarchical clustering OBI:0200044 complete linkage hierarchical clustering an agglomerative hierarchical clustering which generates successive clusters based on a distance measure, where the distance between two clusters is calculated as the maximum distance between objects from the first cluster and objects from the second cluster. Elisabetta Manduchi PERSON: Elisabetta Manduchi complete linkage hierarchical clustering OBI:0200045 single linkage hierarchical clustering A single linkage hierarchical clustering is an agglomerative hierarchical clustering which generates successive clusters based on a distance measure, where the distance between two clusters is calculated as the minimum distance between objects from the first cluster and objects from the second cluster. Elisabetta Manduchi PERSON: Elisabetta Manduchi single linkage hierarchical clustering OBI:0200049 Benjamini and Yekutieli false discovery rate correction method The expression set was compared univariately between the stroke patients and controls, gene list was generated using False Discovery Rate correction (Benjamini and Yekutieli) A data transformation in which the Benjamini and Yekutieli method is applied with the aim of correcting false discovery rate 2011-03-31: [PRS]. specified input and output of dt which were missing Helen Parkinson Philippe Rocca-Serra Helen Parkinson Benjamini and Yekutieli false discovery rate correction method OBI:0200050 dimensionality reduction A dimensionality reduction is data partitioning which transforms each input m-dimensional vector (x_1, x_2, ..., x_m) into an output n-dimensional vector (y_1, y_2, ..., y_n), where n is smaller than m. Elisabetta Manduchi James Malone Melanie Courtot Philippe Rocca-Serra data projection PERSON: Elisabetta Manduchi PERSON: James Malone PERSON: Melanie Courtot dimensionality reduction OBI:0200051 principal components analysis dimensionality reduction A principal components analysis dimensionality reduction is a dimensionality reduction achieved by applying principal components analysis and by keeping low-order principal components and excluding higher-order ones. Elisabetta Manduchi James Malone Melanie Courtot Philippe Rocca-Serra pca data reduction PERSON: Elisabetta Manduchi PERSON: James Malone PERSON: Melanie Courtot principal components analysis dimensionality reduction OBI:0200052 probabilistic algorithm A probabilistic algorithm is one which involves an element of probability or randomness in the transformation of the data. James Malone PERSON: James Malone probabilistic algorithm OBI:0200053 expectation maximization EM is a probabilistic algorithm used to estimate the maximum likelihood of parameters from existing data where the model involves unobserved latent variables. The input to this method is the data model for which the estimation is performed over and the output is an approximated probability function. James Malone PERSON: James Malone expectation maximization OBI:0200054 global modularity calculation A network graph quality calculation in which an input data set of subgraph modules and their in-degree and out-degree qualities is used to calculate the average modularity of subgraphs within the network. Richard Scheuermann PERSON: Richard Scheuermann global modularity calculation OBI:0200055 dye swap merge A dye swap merge is a replicate analysis which takes as input data from paired two-channel microarray assays where the sample labeled with one dye in the first assay is labeled with the other dye in the second assay and vice versa. The output for each reporter is obtained by combining its (raw or possibly pre-processed) M values in the two assays, where the M value in an assay is defined as the difference of the log intensities in the two channels. This can be used as a normalization step, when appropriate assumptions are met. Elisabetta Manduchi James Malone PERSON: Elisabetta Manduchi PERSON: James Malone dye swap merge OBI:0200056 moving average The moving average is often used to handle data from tiling arrays. A moving average is a data transformation in which center calculations, usually mean calculations, are performed on values within a sliding window across the input data set. Elisabetta Manduchi Helen Parkinson Philippe Rocca-Serra PERSON: Elisabetta Manduchi PERSON: Helen Parkinson moving average OBI:0200057 replicate analysis Replicate analysis can be used in microarray analysis to identify and potentially exclude low quality data. A replicate analysis is a data transformation in which data from replicates are combined, e.g. through descriptive statistics calculations, and the results might be utilized for a variety of purposes, like assessing reproducibility, identifying outliers, normalizing, etc. Elisabetta Manduchi Helen Parkinson PERSON: Helen Parkinson PERSON:Elisabetta Manduchi replicate analysis OBI:0200058 b cell epitope prediction A B cell epitope prediction takes as input an antigen sequence, and through an analysis of this sequence, produces as output a prediction of the likelihood the biomaterial is a B Cell Epitope. Helen Parkinson PERSON: Helen Parkinson b cell epitope prediction OBI:0200059 mhc binding prediction An MHC binding prediction takes an input of a biomaterial sequence and through an analysis of this sequence, produces as output a prediction of the likelihood that the biomaterial will bind to an MHC molecule. Helen Parkinson PERSON: Helen Parkinson mhc binding prediction OBI:0200060 t cell epitope prediction A T cell epitope prediction takes as input an antigen sequence, and through an analysis of this sequence, produces as output a prediction of the likelihood the biomaterial is a T cell epitope. Helen Parkinson PERSON: Helen Parkinson t cell epitope prediction OBI:0200061 data imputation Imputation is a means of filling in missing data values from a predictive distribution of the missing values. The predictive distribution can be created either based on a formal statistical model (i,e, a multivariate normal distribution) or an algorithm. Monnie McGee ARTICLE: Little, RJA and Rubin, DB (2002). Statistical Analysis with Missing Data, Second Edition. John Wiley: Hoboken New Jersey, pp. 59-60. data imputation OBI:0200062 continuum mass spectrum A continuum mass spectrum is a data transformation that contains the full profile of the detected signals for a given ion. PERSON: James Malone PERSON: Tina Hernandez-Boussard PERSON: Tina Boussard continuum mass spectrum OBI:0200063 characteristic path length calculation Quantifying subgraph navigability based on shortest-path length averaged over all pairs of subgraph vertices PERSON: Tina Hernandez-Boussard PERSON: Tina Hernandez-Boussard characteristic path length calculation OBI:0200064 centroid mass spectrum A centroid mass spectrum is a data transformation in which many points are used to delineate a mass spectral peak, is converted into mass-centroided data by a data compression algorithm. The centroided mass peak is located at the weighted center of mass of the profile peak. The normalized area of the peak provides the mass intensity data. Person:Tina Hernandez-Boussard centroid mass spectrum calculation centroiding centroid mass spectrum centroid mass spectrum OBI:0200066 Holm-Bonferroni family-wise error rate correction method t-tests were used with the type I error adjusted for multiple comparisons, Holm's correction (HOLM 1979), and false discovery rate, http://www.genetics.org/cgi/content/full/172/2/1179 a data transformation that performs more than one hypothesis test simultaneously, a closed-test procedure, that controls the familywise error rate for all the k hypotheses at level α in the strong sense. Objective: multiple testing correction 2011-03-14: [PRS]. Class Label has been changed to address the conflict with the definition Also added restriction to specify the output to be a FWER adjusted p-value The 'editor preferred term' should be removed Person:Helen Parkinson Philippe Rocca-Serra WEB: http://en.wikipedia.org/wiki/Holm%E2%80%93Bonferroni_method Holm-Bonferroni family-wise error rate correction method OBI:0200070 edge weighting Edge weighting is the substitution or transformation of edge length using numerical data. Data input include a symmetric adjacency matrix for a network and a second data set, for example a list of interactor pairs and a confidence score associated with the experimental detection of each pair's interaction. Each element in the adjacency matrix is transformed or replaced with the corresponding number in the second data set. Output data are a modified adjacency matrix reflecting the transformed state of the network. Tina Hernandez-Boussard editor was classified under algorithm class which is not acceptable super-class TO BE DEALT WITH STILL BY RICHARD. JAMES edge weighting OBI:0200071 loess transformation A loess transformation is a data transformation that takes as input a collection of real number pairs (x, y) and, after performing (one or more) loess fittings, utilizes the resulting curves to transform each (x, y) in the input into (x, y-f(x)) where f(x) is one of the fitted curves. Elisabetta Manduchi James Malone Melanie Courtot Philippe Rocca-Serra OTHER: Editor's generalization based on MGED Ontology term loess transformation OBI:0200072 curve fitting data transformation A curve fitting is a data transformation that has objective curve fitting and that consists of finding a curve which matches a series of data points and possibly other constraints. Elisabetta Manduchi James Malone Melanie Courtot WEB: http://en.wikipedia.org/wiki/Curve_fitting curve fitting data transformation OBI:0200073 family wise error rate correction method A family wise error rate correction method is a multiple testing procedure that controls the probability of at least one false positive. 2011-03-31: [PRS]. creating a defined class by specifying the necessary output of dt allows correct classification of FWER dt Monnie McGee Philippe Rocca-Serra FWER correction Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 19 family wise error rate correction method OBI:0200074 submatrix extraction When presented with the data from an expression microarray experiment in the form of a matrix, whose rows correspond to genes and whose columns correspond to samples, if one filters some of the genes and/or some of the samples out, the resulting data set corresponds to a submatrix of the original set. A submatrix extraction is a projection whose input is a matrix and whose output is a matrix obtained by selecting certain rows and columns from the input. (Note that, if one represents the input matrix as a vector obtained by concatenating its rows, then extracting a submatrix is equivalent to projecting this vector into that composed by the entries belonging to the rows and columns of interest from the input matrix.) Note that this can be considered as a special case of projection if one represents the input matrix as a vector obtained by concatenating its rows. Then extracting a submatrix is equivalent to projecting this vector into the entries belonging to the rows and columns of interest from the input matrix. Elisabetta Manduchi James Malone Melanie Courtot WEB: http://en.wikipedia.org/wiki/Submatrix submatrix extraction OBI:0200075 row submatrix extraction When presented with the data from an expression microarray experiment in the form of a matrix, whose rows correspond to genes and whose columns correspond to samples, if one filters some of the genes out, the resulting data set corresponds to a row submatrix of the original set. A row submatrix extraction is a submatrix extraction where all the columns of the input matrix are retained and selection only occurs on the rows. Elisabetta Manduchi James Malone Melanie Courtot PERSON: Elisabetta Manduchi PERSON: James Malone PERSON: Melanie Courtot row submatrix extraction OBI:0200076 column submatrix extraction When presented with the data from an expression microarray experiment in the form of a matrix, whose rows correspond to genes and whose columns correspond to samples, if one filters some of the samples out, the resulting data set corresponds to a column submatrix of the original set. A column submatrix extraction is a submatrix extraction where all the rows of the input matrix are retained and selection only occurs on the columns. Elisabetta Manduchi James Malone Melanie Courtot PERSON: Elisabetta Manduchi PERSON: James Malone PERSON: Melanie Courtot column submatrix extraction OBI:0200077 gating Gating is a property-based vector selection with the objective of partitioning a data vector set into vector subsets based on dimension values of individual vectors (events), in which vectors represent individual physical particles (often cells) of a sample and dimension values represent light intensity qualities as measured by flow cytometry. James Malone Josef Spidlen Melanie Courtot Richard Scheuermann Ryan Brinkman PERSON: James Malone PERSON: Josef Spidlen PERSON: Richard Scheuermann PERSON: Ryan Brinkman PERSON:Melanie Courtot gating OBI:0200078 descriptive statistical calculation objective A descriptive statistical calculation objective is a data transformation objective which concerns any calculation intended to describe a feature of a data set, for example, its center or its variability. Elisabetta Manduchi James Malone Melanie Courtot Monnie McGee PERSON: Elisabetta Manduchi PERSON: James Malone PERSON: Melanie Courtot PERSON: Monnie McGee descriptive statistical calculation objective OBI:0200079 mean calculation A mean calculation is a descriptive statistics calculation in which the mean is calculated by taking the sum of all of the observations in a data set divided by the total number of observations. It gives a measure of the 'center of gravity' for the data set. It is also known as the first moment. James Malone Monnie McGee Philippe Rocca-Serra PERSON: James Malone PERSON: Monnie McGee From Monnie's file comments - need to add moment_calculation and center_calculation roles but they don't exist yet - (editor note added by James Jan 2008) mean calculation OBI:0200080 network analysis A data transformation that takes as input data that describes biological networks in terms of the node (a.k.a. vertex) and edge graph elements and their characteristics and generates as output properties of the constituent nodes and edges, the sub-graphs, and the entire network. Richard Scheuermann network topology analysis PERSON: Richard Scheuermann network analysis OBI:0200081 sequence analysis objective A sequence analysis objective is a data transformation objective which aims to analyse some ordered biological data for sequential patterns. James Malone PERSON: James Malone sequence analysis objective OBI:0200082 longitudinal data analysis Longitudinal analysis is a data transformation used to perform repeated observations of the same items over long periods of time. PERSON: James Malone PERSON: Tina Boussard correlation analysis longitudinal data analysis longitudinal data analysis OBI:0200083 survival analysis objective Kaplan meier data transformation A data transformation objective which has the data transformation aims to model time to event data (where events are e.g. death and or disease recurrence); the purpose of survival analysis is to model the underlying distribution of event times and to assess the dependence of the event time on other explanatory variables PERSON: James Malone PERSON: Tina Boussard survival analysis http://en.wikipedia.org/wiki/Survival_analysis survival analysis objective OBI:0200085 mass spectrometry analysis A data transformation which has the objective of spectrum analysis. mass spectrometry analysis OBI:0200086 spread calculation data transformation A spread calculation is a data transformation that has objective spread calculation. James Malone EDITOR spread calculation data transformation OBI:0200088 Kaplan Meier a nonparametric (actuarial) data transformation technique for estimating time-related events. It is a univariate analysis that estimates the probability of the proportion of subjects in remission at a particular time, starting from the initiation of active date (time zero), and takes into account those lost to follow-up or not yet in remission at end of study (censored) PERSON: James Malone PERSON: Tina Boussard http://en.wikipedia.org/wiki/Kaplan%E2%80%93Meier_estimator Kaplan Meier OBI:0200089 multiple testing correction method A multiple testing correction method is a hypothesis test performed simultaneously on M > 1 hypotheses. Multiple testing procedures produce a set of rejected hypotheses that is an estimate for the set of false null hypotheses while controlling for a suitably define Type I error rate Monnie McGee multiple testing procedure PAPER: Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 9-10. multiple testing correction method OBI:0200091 inter-rater reliability objective A study was conducted to determine the inter-rater reliability of common clinical examination procedures proposed to identify patients with lumbar segmental instability. Examples include joint-probability of agreement, Cohen's kappa and the related Fleiss' kappa, inter-rater correlation, concordance correlation coefficient and intra-class correlation. a data transformation objective of determining the concordance or agreement between human judges. Person:Alan Ruttenberg Person:Helen Parkinson inter-rater agreement http://en.wikipedia.org/wiki/Inter-rater_reliability inter-rater reliability objective OBI:0200092 Westfall and Young family wise error rate correction Is a data transformation process in which the Westfall and Young method is applied with the aim of controlling for multiple testing 2011-03-31: [PRS]. specified input and output of dt which were missing PRS: 2011-03-31: set specified input and specified output to the data transformation Helen Parkinson Westfall and Young FWER correction Westfall and Young family wise error rate correction OBI:0200093 polynomial transformation a*x+b, with a non-zero, is a polynomial of degree one in one variable; a*x^2+b*x+c, with a nonzero, is a polynomial of degree 2 in 1 variable; a*x*y+b*y+c, with a non-zero, is a polynomial of degree 2 in 2 variables (x and y); a_1*x_1+...+a_n*x_n+b, with at least one of the a_i's non-zero, is a polynomial of degree one in n variables A polynomial transformation is a data transformation that is obtained through a polynomial, where a polynomial is a mathematical expression involving a sum of powers in one or more variables multiplied by coefficients (e.g. see http://mathworld.wolfram.com/Polynomial.html). The number of variables and the degree are properties of a polynomial. The degree of a polynomial is the highest power of its terms, where the terms of a polynomial are the individual summands with the coefficients omitted. Elisabetta Manduchi WEB: http://mathworld.wolfram.com/Polynomial.html polynomial transformation OBI:0200094 logarithmic transformation A logarithmic transformation is a data transformation consisting in the application of the logarithm function with a given base a (where a>0 and a is not equal to 1) to a (one dimensional) positive real number input. The logarithm function with base a can be defined as the inverse of the exponential function with the same base. See e.g. http://en.wikipedia.org/wiki/Logarithm. Elisabetta Manduchi WEB: http://en.wikipedia.org/wiki/Logarithm logarithmic transformation OBI:0200095 exponential transformation An exponential transformation is a data transformation consisting in the application of the exponential function with a given base a (where a>0 and a is typically not equal to 1) to a (one dimensional) real number input. For alternative definitions and properties of this function see, e.g., http://en.wikipedia.org/wiki/Exponential_function and http://en.wikipedia.org/wiki/Characterizations_of_the_exponential_function. Elisabetta Manduchi WEB: http://en.wikipedia.org/wiki/Characterizations_of_the_exponential_function WEB: http://en.wikipedia.org/wiki/Exponential_function exponential transformation OBI:0200097 non-negative matrix factorization Non-negative matrix factorization is used in text mining where document-term matrix is constructed with the weights of various terms (typically weighted word frequency information) from a set of documents. This matrix is factored into a term-feature and a feature-document matrix. Non negative matrix factorization is a data transformation in which factorises a matrix and which forces that all elements must be equal to or greater than zero. http://en.wikipedia.org/wiki/Non-negative_matrix_factorization non-negative matrix factorization OBI:0200098 soft independent modeling of class analogy analysis Soft independent modeling by class analogy (SIMCA) is a descriptive statistics method for supervised classification of data. The method requires a training data set consisting of samples (or objects) with a set of attributes and their class membership. The term soft refers to the fact the classifier can identify samples as belonging to multiple classes and not necessarily producing a classification of samples into non-overlapping classes. Tina Hernandez-Boussard SIMCA WEB: http://en.wikipedia.org/wiki/Soft_independent_modelling_of_class_analogies soft independent modeling of class analogy analysis OBI:0200099 discriminant function analysis Discriminant function analysis is a form of discriminant analysis used to determine which variables discriminate between two or more naturally occurring groups. Analysis is used to determine which variable(s) are the best predictors of a particular outcome. Tina Hernandez-Boussard WEB: http://www.statsoft.com/textbook/stdiscan.html discriminant function analysis OBI:0200100 canonical variate analysis canonical variate analysis is a form of discriminant analysis that takes several continuous predictor variables and uses the entire set to predict several criterion variables, each of which is also continuous. CVA simultaneously calculates a linear composite of all x variables and a linear composite of all y variables. Unlike other multivariate techniques, these weighted composites are derived in pairs. Each linear combination is called a canonical variate and takes the general linear form. Tina Hernandez-Boussard CVA WEB: http://en.wikipedia.org/wiki/Canonical_analysis canonical variate analysis OBI:0200101 linear discriminant functional analysis Linear discriminant functional analysis (LDFA) is a multivariate technique used in special applications where there are several intact groups (random assignment may be impossible) and they have been measured on several independent measures. Thus, you will want to describe how these groups differ on the basis of these measures. In this case, classification and prediction is the main objective. Tina Hernandez-Boussard PERSON: Tina Hernandez-Boussard linear discriminant functional analysis OBI:0200102 regression analysis method Regression analysis is a descriptive statistics technique that examines the relation of a dependent variable (response variable) to specified independent variables (explanatory variables). Regression analysis can be used as a descriptive method of data analysis (such as curve fitting) without relying on any assumptions about underlying processes generating the data. Tina Hernandez-Boussard BOOK: Richard A. Berk, Regression Analysis: A Constructive Critique, Sage Publications (2004) 978-0761929048 regression analysis method OBI:0200103 multiple linear regression analysis multiple linear regression is a regression method that models the relationship between a dependent variable Y, independent variables Xi, i = 1, ..., p, and a random term epsilon. The model can be written as Y = \beta_0 + \beta_1 X_1 + \beta_2 X_2 + \cdots +\beta_p X_p + \varepsilon where \beta_0 = 0 is the intercept ("constant" term), the \beta_i s are the respective parameters of independent variables, and p is the number of parameters to be estimated in the linear regression. Tina Hernandez-Boussard WEB:http://en.wikipedia.org/wiki/Linear_regression multiple linear regression analysis OBI:0200104 principal component regression The Principal Component Regression method is a regression analysis method that combines the Principal Component Analysis (PCA)spectral decomposition with an Inverse Least Squares (ILS) regression method to create a quantitative model for complex samples. Unlike quantitation methods based directly on Beer's Law which attempt to calculate the absorbtivity coefficients for the constituents of interest from a direct regression of the constituent concentrations onto the spectroscopic responses, the PCR method regresses the concentrations on the PCA scores. Tina Hernandez-Boussard WEB: : http://www.thermo.com/com/cda/resources/resources_detail/1,2166,13414,00.html principal component regression OBI:0200105 partial least square regression analysis Partial least squares regression is an extension of the multiple linear regression model (see, e.g., Multiple Regression or General Stepwise Regression). In its simplest form, a linear model specifies the (linear) relationship between a dependent (response) variable Y, and a set of predictor variables, the X's, so that Y = b0 + b1X1 + b2X2 + ... + bpXp In this equation b0 is the regression coefficient for the intercept and the bi values are the regression coefficients (for variables 1 through p) computed from the data. Tina Hernandez-Boussard PLS-RA ARTICLE: de Jong, S. (1993). SIMPLS: An alternative approach to partial least squares regression. Chemometrics and Intelligent Laboratory Systems, 18: 251-263. partial least square regression analysis OBI:0200106 discriminant analysis Discriminant function analysis is used to determine which variables discriminate between two or more naturally occurring groups. Analysis is used to determine which variable(s) are the best predictors of a particular outcome. Tina Hernandez-Boussard WEB: http://www.statsoft.com/textbook/stdiscan.html discriminant analysis OBI:0200107 partial least square discriminant analysis PLS Discriminant Analysis (PLS-DA) is a discriminant analysis performed in order to sharpen the separation between groups of observations, by hopefully rotating PCA (Principal Components Analysis) components such that a maximum separation among classes is obtained, and to understand which variables carry the class separating information. James Malone PLS-DA WEB: http://www.camo.com/rt/Resources/pls-da.html partial least square discriminant analysis OBI:0200108 eh transformation This type of transformation is typically used in flow cytometry. An eh transformation is a data transformation obtained by applying the function EH described in what follows to a (one dimensional) real number input. EH(x)=exp(x*d/r)+b*(d/r)*x-1, if x>=0, and EH(x)=-exp(-x*d/r)+b*(d/r)*x+1, otherwise. Here exp denotes an exponential transformation and b, d, r are positive real constants with the objective of normalization. Elisabetta Manduchi Joseph Spliden Ryan Brinkman WEB: http://flowcyt.sourceforge.net/gating/latest.pdf eh transformation OBI:0200109 b transformation This type of transformation is typically used in flow cytometry. A b transformation is a data transformation obtained by applying the function B described in what follows to a (one dimensional) real number input. B(x)= a*exp(b*x)-c*exp(-d*x)+f, where exp denotes an exponential transformation and a, b, c, d, f are real constants with a, b, c, d positive with the objective of normalization. Elisabetta Manduchi Joseph Spliden Ryan Brinkman WEB: http://flowcyt.sourceforge.net/gating/latest.pdf b transformation OBI:0200110 s transformation This type of transformation is typically used in flow cytometry. An s transformation is a data transformation obtained by applying the function S described in what follows to a (one dimensional) real number input. S(x)=T*exp(w-m)*(exp(x-w)-(p^2)*exp((w-x)/p)+p^2-1) if x>=w, S(x)=-S(w-x) otherwise; where exp denotes an exponential_transformations, 'p^' denotes the exponential transformation with base p; T, w, m, p are real constants with T, m, and p positive and w non-negative, and where w and p are related by w=2p*ln(p)(p+1) with the objective of normalization. Elisabetta Manduchi Joseph Spliden Ryan Brinkman WEB: http://flowcyt.sourceforge.net/gating/latest.pdf s transformation OBI:0200111 data visualization Generation of a heatmap from a microarray dataset An planned process that creates images, diagrams or animations from the input data. Elisabetta Manduchi James Malone Melanie Courtot Tina Boussard data encoding as image visualization PERSON: Elisabetta Manduchi PERSON: James Malone PERSON: Melanie Courtot PERSON: Tina Boussard Possible future hierarchy might include this: information_encoding >data_encoding >>image_encoding data visualization OBI:0200113 similarity calculation A similarity calculation is a data transformation that attaches to each pair of objects in the input a number that is meant to reflect how 'close' or 'similar' those objects are. Elisabetta Manduchi PERSON: Elisabetta Manduchi similarity calculation OBI:0200114 euclidean distance calculation An euclidean distance calculation is a similarity calculation that attaches to each pair of real number vectors of the same dimension n the square root of the sum of the square differences between corresponding components. The smaller this number, the more similar the two vectors are considered. Elisabetta Manduchi PERSON: Elisabetta Manduchi euclidean distance calculation OBI:0200115 pearson correlation coefficient calculation A pearson correlation coefficient calculation is a similarity calculation which attaches to each pair of random variables X and Y the ratio of their covariance by the product of their standard deviations. Given a series of n measurements of X and Y written as x_i and y_i where i = 1, 2, ..., n, then their Pearson correlation coefficient refers to the "sample correlation coefficient" and is written as the sum over i of the ratios (x_i-xbar)*(y_i-ybar)/((n-1)*s_x*s_y) where xbar and ybar are the sample means of X and Y , s_x and s_y are the sample standard deviations of X and Y. The closer the pearson correlation coefficient is to 1, the more similar the inputs are considered. Elisabetta Manduchi PERSON: Elisabetta Manduchi WEB: http://en.wikipedia.org/wiki/Correlation pearson correlation coefficient calculation OBI:0200116 loess fitting A loess fitting is a curve fitting obtained by localized regression. The latter refers to fitting a polynomial (straight line, quadratic, cubic, etc) to data values within a window covering a fraction of the total number of observations. As the window slides along the axis, a new polynomial is fit to the observations falling within the window. This continues until all points are fit with a local polynomial. The results are then smoothed together to form a curve. The smoothness of loess fits is controlled by a smoothing parameter (often denoted as alpha, usually between 1/4 and 1) and the degree of the polynomial that is fitted by the method (usually denoted by lambda). Monnie McGee Philippe Rocca-Serra ARTICLE: Mathematical details of loess fits are given in Cleveland, William (1993) Visualizing Data. Hobart Press, Summit, New Jersey, pp. 94-101. loess fitting OBI:0200117 mode calculation A mode calculation is a descriptive statistics calculation in which the mode is calculated which is the most common value in a data set. It is most often used as a measure of center for discrete data. James Malone Monnie McGee PERSON: James Malone PERSON: Monnie McGee From Monnie's file comments - need to add center_calculation role but it doesn't exist yet - (editor note added by James Jan 2008) mode calculation OBI:0200118 quantile calculation A quantile calculation is a descriptive statistics calculation in which the kth quantile is the data value for which an approximate k fraction of the data is less than or equal to that value. See http://www.stat.wvu.edu/SRS/Modules/Quantiles/quantiles.html for details. Monnie McGee WEB: http://www.stat.wvu.edu/SRS/Modules/Quantiles/quantiles.html quantile calculation OBI:0200119 median calculation A median calculation is a descriptive statistics calculation in which the midpoint of the data set (the 0.5 quantile) is calculated. First, the observations are sorted in increasing order. For an odd number of observations, the median is the middle value of the sorted data. For an even number of observations, the median is the average of the two middle values. James Malone Monnie McGee PERSON: James Malone PERSON: Monnie McGee From Monnie's file comments - need to add center_calculation role but it doesn't exist yet - (editor note added by James Jan 2008) median calculation OBI:0200120 variance calculation A variance calculation is a descriptive statistics calculation in which the variance is defined as the average squared distance of each observation in the data set to the mean of the data set. It is also known as the second central moment. Monnie McGee PERSON: Monnie McGee From Monnie's file comments - need to add spread_calculation and moment_calculation roles but they don't exist yet - (editor note added by James Jan 2008) variance calculation OBI:0200121 standard deviation calculation A standard deviation calculation is a descriptive statistics calculation defined as the square root of the variance. Also thought of as the average distance of each value to the mean. Monnie McGee PERSON: Monnie McGee From Monnie's file comments - need to add spread calculation role but they doesn't exist yet - (editor note added by James Jan 2008) standard deviation calculation OBI:0200122 interquartile-range calculation The interquartile range is a descriptive statistics calculation defined as the difference between the 0.75 quantile and the 0.25 quantile for a set of data. Monnie McGee PERSON: Monnie McGee From Monnie's file comments - need to add spread calculation role but they doesn't exist yet - (editor note added by James Jan 2008) interquartile-range calculation OBI:0200123 skewness calculation A skewness calculation is a descriptive statistics calculation defined as a parameter that describes how much a distribution (or a data set) varies from a bell-shaped curve. See http://www.riskglossary.com/link/skewness.htm for details. It is also known as the third central moment Monnie McGee WEB: http://www.riskglossary.com/link/skewness.htm From Monnie's file comments - need to add moment calculation role but they doesn't exist yet - (editor note added by James Jan 2008) skewness calculation OBI:0200124 kurtosis calculation A kurtosis calculation is a descriptive statistics calculation defined as a parameter that measures how large or small the tails of a distribution are relative to the mean. For details, see http://davidmlane.com/hyperstat/A53638.html Monnie McGee WEB: http://davidmlane.com/hyperstat/A53638.html From Monnie's file comments - need to add moment calculation role but they doesn't exist yet - (editor note added by James Jan 2008) kurtosis calculation OBI:0200125 data combination A data transformation in which individual input data elements and values are merged together into a output set of data elements and values. Richard Scheuermann data pooling editor data combination OBI:0200126 network graph construction A network analysis in which an input data set describing objects and relationships between objects is transformed into an output representation of these objects as nodes and the relationships as edges of a network graph. Richard Scheuermann PERSON: Richard Scheuermann network graph construction OBI:0200127 weighted network graph construction A network graph construction in which an input data set describing objects and quantitative relationships between objects is transformed into and output representation of these objects as nodes and the quantitative relationships as weighted edges of a network graph. Richard Scheuermann PERSON: Richard Scheuermann weighted network graph construction OBI:0200128 directed network graph construction A network graph construction in which an input data set describing objects and directional relationships between objects is transformed into and output representation of these objects as nodes and the directional relationships as directed edges of a network graph. Richard Scheuermann PERSON: Richard Scheuermann directed network graph construction OBI:0200129 node quality calculation A network analysis in which an input data set describing node objects and edge relationships between node objects is used to determine the output quality of one of the node objects in the network. Richard Scheuermann PERSON: Richard Scheuermann node quality calculation OBI:0200130 node degree calculation A node quality calculation in which an input data set describing object nodes and relationship edges between object nodes is used to enumerate the number of unique relationships of an individual object node. Richard Scheuermann PERSON: Richard Scheuermann node degree calculation OBI:0200131 quantitative node degree calculation A node quality calculation in which an input data set describing object nodes and quantitative relationship edges between object nodes is used to sum all of the quantitative relationships of an individual object node. Richard Scheuermann PERSON: Richard Scheuermann quantitative node degree calculation OBI:0200132 node in-degree calculation A node quality calculation in which an input data set describing object nodes and directional relationship edges between object nodes is used to enumerate the number of unique relationships pointing into an individual object node. Richard Scheuermann PERSON: Richard Scheuermann node in-degree calculation OBI:0200133 node out-degree calculation A node quality calculation in which an input data set describing object nodes and directional relationship edges between object nodes is used to enumerate the number of unique relationships pointing out of an individual object node. Richard Scheuermann PERSON: Richard Scheuermann node out-degree calculation OBI:0200134 node shortest path identification A node quality calculation in which a path describing the shortest path needed to transverse through connected nodes and edges to arrive at a specific target node in the network. Richard Scheuermann PERSON: Richard Scheuermann node shortest path identification OBI:0200135 edge quality calculation A network analysis in which an input data set describing node objects and edge relationships between node objects is used to determine the output quality of one of the edge relationships in the network. Richard Scheuermann PERSON: Richard Scheuermann edge quality calculation OBI:0200136 edge betweenness calculation An edge quality calculation in which the input is a data sets of shortest paths between all pairs of node in the network and the output is the sum of all shortest paths that traverse the specific edge. Richard Scheuermann PERSON: Richard Scheuermann edge betweenness calculation OBI:0200137 network subgraph quality calculation A network analysis in which an input data set describing node objects and edge relationships between node objects is used to determine the output quality of a subgraph partition of the network. Richard Scheuermann PERSON: Richard Scheuermann network subgraph quality calculation OBI:0200138 subgraph degree calculation A network subgraph quality calculation in which an input data set describing subgraphs and relationship edges between subgraphs and other network objects is used to enumerate the number of unique relationships of an individual subgraph. Richard Scheuermann PERSON: Richard Scheuermann subgraph degree calculation OBI:0200139 quantitative subgraph degree calculation A network subgraph quality calculation in which an input data set describing subgraphs and quantitative relationship edges between subgraphs and other network objects is used to sum the quantitative relationships of an individual subgraph. Richard Scheuermann PERSON: Richard Scheuermann quantitative subgraph degree calculation OBI:0200140 mathematical feature feature is a (parent_class) that describes a characteristic, trait or quality of a data transformation This class is temporary and will be placed outside of data transformation ultimately (if it still remains at all after review) James Malone PERSON: James Malone mathematical feature OBI:0200141 log base The log base is a feature of a logarithmic function which is defined in http://en.wikipedia.org/wiki/Logarithm. Its value can be any positive real number different from 1. Elisabetta Manduchi logarithm base logarithmic base WEB: http://en.wikipedia.org/wiki/Logarithm log base OBI:0200143 subgraph in-degree calculation A network subgraph quality calculation in which an input data set describing subgraphs and directional relationship edges between subgraphs and other network objects is used to enumerate the number of unique relationships pointing into an individual subgraph. Richard Scheuermann PERSON: Richard Scheuermann subgraph in-degree calculation OBI:0200144 subgraph out-degree calculation A network subgraph quality calculation in which an input data set describing subgraphs and relationship edges between subgraphs and other network objects is used to enumerate the number of unique relationships pointing out of an individual subgraph. Richard Scheuermann PERSON: Richard Scheuermann subgraph out-degree calculation OBI:0200145 intra subgraph connectivity calculation A network subgraph quality calculation in which an input data set describing internal nodes, edges and node degrees is used to determine the average node degree within the subgraph. Richard Scheuermann PERSON: Richard Scheuermann intra subgraph connectivity calculation OBI:0200146 subgraph modularity calculation A network subgraph quality calculation in which an input data set of subgraph in-degree and out-degree qualities is used to calculate the ratio of indegree to outdegree as a measure of modularity. Richard Scheuermann PERSON: Richard Scheuermann subgraph modularity calculation OBI:0200147 network graph quality calculation A network analysis in which an input data set describing node objects and edge relationships between node objects is used to determine the output quality of the network as a whole. Richard Scheuermann PERSON: Richard Scheuermann network graph quality calculation OBI:0200149 unit-variance scaling A unit-variance scaling is a data transformation that divides all measurements of a variable by the standard deviation of that variable. Elisabetta Manduchi Philippe Rocca-Serra autoscaling PMID:16762068 unit-variance scaling OBI:0200150 MA transformation MA transformations are typically used in microarray data analyses. In this context, the g_i and r_i represent the reporter intensities in the two channels of a 2-channel assay or the reporter intensities in two related one-channel assays. Typically the base used for the logarithm is 2. An MA transformation is a data transformation which takes as input a collection of data points (g_1, r_1), (g_2, r_2), ..., (g_n, r_n) with the r_i and g_i positive real numbers, and whose output is the collection of data points (A_1, M_1), (A_2, M_2), ..., (A_n, M_n) where, for each i, A_i=(log(g_i)+log(r_i))/2 and M_i=log(r_i)-log(g_i). Here log denotes a logarithmic transformation. Elisabetta Manduchi Philippe Rocca-Serra PERSON: Elisabetta Manduchi MA transformation OBI:0200151 exponential base The exponential base is a feature of an exponential function which is defined in http://en.wikipedia.org/wiki/Exponential_function. Its value can be any positive real number (typically different from 1). Elisabetta Manduchi WEB: http://en.wikipedia.org/wiki/Exponential_function exponential base OBI:0200152 polynomial degree The polynomial degree is a feature of a polynomial function defined as the highest power of the polynomial's terms, where the terms of a polynomial are the individual summands with the coefficients omitted. Elisabetta Manduchi PERSON: Elisabetta Manduchi polynomial degree OBI:0200153 number of variables The number of variables is a feature of any function (including polynomial functions) with domain contained in an n-dimensional vector space and is defined as n, the dimension of such space. Elisabetta Manduchi PERSON: Elisabetta Manduchi number of variables OBI:0200154 agglomerative hierarchical clustering An agglomerative hierarchical clustering is a hierarchical clustering which starts with separate clusters and then successively combines these clusters until there is only one cluster remaining. Elisabetta Manduchi James Malone bottom-up hierarchical clustering PERSON: Elisabetta Manduchi agglomerative hierarchical clustering OBI:0200155 divisive hierarchical clustering A divisive hierarchical clustering is a hierarchical clustering which starts with a single cluster and then successively splits resulting clusters until only clusters of individual objects remain. Elisabetta Manduchi James Malone top-down hierarchical clustering PERSON: Elisabetta Manduchi divisive hierarchical clustering OBI:0200156 data partitioning Data partitioning is a data transformation with the objective of partitioning or separating input data into output subsets. James Malone PERSON: Melanie Courtot PERSON: Richard Scheuermann PERSON: Ryan Brinkman data partitioning OBI:0200157 data vector reduction objective Data vector reduction is a data transformation objective in which k m-dimensional input vectors are reduced to j m-dimensional output vectors, where j is smaller than k. James Malone Richard H. Scheuermann PERSON: Richard H. Scheuermann data vector reduction objective OBI:0200160 generalized family wise error rate correction method A generalized FWER correction method is a multiple testing procedure that controls the probability of at least k+1 false positives, where k is a user-supplied integer. Monnie McGee gFWER correction Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 19 generalized family wise error rate correction method OBI:0200161 quantile number of false positives correction method A quantile number of false positives correction method is a MTP that controls for the pth quantile of the distribution of the number of false positives out of the total number of tests performed' Monnie McGee QNFP Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 19 quantile number of false positives correction method OBI:0200162 tail probability for the proportion of false positives correction method A TPPFP correction method is a MTP that controls the probability that the proportion of false positives among all rejected hypotheses is no greater than a constant q, where q is between 0 and 1. Monnie McGee TPPFP correction method Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 20 tail probability for the proportion of false positives correction method OBI:0200163 false discovery rate correction method The false discovery rate is a data transformation used in multiple hypothesis testing to correct for multiple comparisons. It controls the expected proportion of incorrectly rejected null hypotheses (type I errors) in a list of rejected hypotheses. It is a less conservative comparison procedure with greater power than familywise error rate (FWER) control, at a cost of increasing the likelihood of obtaining type I errors. . 2011-03-31: [PRS]. creating a defined class by specifying the necessary output of dt allows correct classification of FDR dt Monnie McGee Philippe Rocca-Serra FDR correction method Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 21 and http://www.wikidoc.org/index.php/False_discovery_rate false discovery rate correction method OBI:0200164 proportion of expected false positives correction method A proportion of expected false positives correction method is a multiple testing procedure that controls the ratio of the expected value of the numbers of false positives to the expected value of the numbers of rejected hypotheses. Monnie McGee PEFP correction method Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 21 proportion of expected false positives correction method OBI:0200165 quantile proportion of false positives correction method A quantile proportion of false positives correction method is a multiple testing procedure that controls the pth quantile of the distribution of the proportion of false positives among the rejected hypothesis (false discovery rate). Monnie McGee QPFP correction method Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 21 quantile proportion of false positives correction method OBI:0200166 data transformation objective normalize objective An objective specification to transformation input data into output data Modified definition in 2013 Philly OBI workshop James Malone PERSON: James Malone data transformation objective OBI:0200167 data normalization objective Quantile transformation which has normalization objective can be used for expression microarray assay normalization and it is referred to as "quantile normalization", according to the procedure described e.g. in PMID 12538238. A normalization objective is a data transformation objective where the aim is to remove systematic sources of variation to put the data on equal footing in order to create a common base for comparisons. Elisabetta Manduchi Helen Parkinson James Malone PERSON: Elisabetta Manduchi PERSON: Helen Parkinson PERSON: James Malone data normalization objective OBI:0200168 correction objective Type I error correction A correction objective is a data transformation objective where the aim is to correct for error, noise or other impairments to the input of the data transformation or derived from the data transformation itself James Malone PERSON: James Malone PERSON: Melanie Courtot correction objective OBI:0200169 normalization data transformation A normalization data transformation is a data transformation that has objective normalization. James Malone PERSON: James Malone normalization data transformation OBI:0200170 averaging data transformation An averaging data transformation is a data transformation that has objective averaging. James Malone PERSON: James Malone averaging data transformation OBI:0200171 partitioning data transformation A partitioning data transformation is a data transformation that has objective partitioning. James Malone PERSON: James Malone partitioning data transformation OBI:0200172 partitioning objective A k-means clustering which has partitioning objective is a data transformation in which the input data is partitioned into k output sets. A partitioning objective is a data transformation objective where the aim is to generate a collection of disjoint non-empty subsets whose union equals a non-empty input set. Elisabetta Manduchi James Malone PERSON: Elisabetta Manduchi partitioning objective OBI:0200173 background correction objective A background correction objective is a data transformation objective where the aim is to remove irrelevant contributions from the measured signal, e.g. those due to instrument noise or sample preparation. Elisabetta Manduchi James Malone PERSON: Elisabetta Manduchi background correction objective OBI:0200174 curve fitting objective A curve fitting objective is a data transformation objective in which the aim is to find a curve which matches a series of data points and possibly other constraints. Elisabetta Manduchi James Malone PERSON: Elisabetta Manduchi curve fitting objective OBI:0200175 class discovery data transformation A class discovery data transformation (sometimes called unsupervised classification) is a data transformation that has objective class discovery. James Malone clustering data transformation unsupervised classification data transformation PERSON: James Malone class discovery data transformation OBI:0200176 Fisher's exact test Fisher's exact test is a data transformation used to determine if there are nonrandom associations between two Fisher's exact test is a statistical significance test used in the analysis of contingency tables where sample sizes are small where the significance of the deviation from a null hypothesis can be calculated exactly, rather than relying on an approximation that becomes exact in the limit as the sample size grows to infinity, as with many statistical tests. James Malone WEB:http://mathworld.wolfram.com/FishersExactTest.html Fisher's exact test OBI:0200177 center calculation objective A mean calculation which has center calculation objective is a data transformation in which the center of the input data is discovered through the calculation of a mean average. A center calculation objective is a data transformation objective where the aim is to calculate the center of an input data set. James Malone PERSON: James Malone center calculation objective OBI:0200178 class discovery objective A class discovery objective (sometimes called unsupervised classification) is a data transformation objective where the aim is to organize input data (typically vectors of attributes) into classes, where the number of classes and their specifications are not known a priori. Depending on usage, the class assignment can be definite or probabilistic. James Malone clustering objective discriminant analysis objective unsupervised classification objective PERSON: Elisabetta Manduchi PERSON: James Malone class discovery objective OBI:0200179 class prediction objective A class prediction objective (sometimes called supervised classification) is a data transformation objective where the aim is to create a predictor from training data through a machine learning technique. The training data consist of pairs of objects (typically vectors of attributes) and class labels for these objects. The resulting predictor can be used to attach class labels to any valid novel input object. Depending on usage, the prediction can be definite or probabilistic. A classification is learned from the training data and can then be tested on test data. James Malone classification objective supervised classification objective PERSON: Elisabetta Manduchi PERSON: James Malone class prediction objective OBI:0200180 spread calculation objective Spread calculation can be achieved by use of a standard deviation, which measures distance from the mean is a data transformation objective whereby the aim is to the calculate the spread of a dataset, spread is a descriptive statistic which describes the variability of values in a data set Awaiting English definition from Monnie McGee James Malone Person:Helen Parkinson spread calculation objective OBI:0200181 center calculation data transformation A center calculation data transformation is a data transformation that has objective of center calculation. James Malone PERSON: James Malone center calculation data transformation OBI:0200182 data vector reduction data transformation A data vector reduction is a data transformation that has objective data vector reduction and that consists of reducing the input vectors k to a smaller number of output vectors j, where j<k. James Malone PERSON: James Malone data vector reduction data transformation OBI:0200183 scaling objective Scaling gene expression data for cross platform analysis http://www.springerprotocols.com/Abstract/doi/10.1007/978-1-59745-454-4_13 is a data transformation objective where all, or some of a data set is adjusted by some data transformation according to some scale, for example a user defined minimum or maximum Awaiting English definition from Monnie McGee James Malone Person:Helen Parkinson scaling objective OBI:0200184 descriptive statistical calculation data transformation A descriptive statistical calculation data transformation is a data transformation that has objective descriptive statistical calculation and which concerns any calculation intended to describe a feature of a data set, for example, its center or its variability. James Malone PERSON: James Malone descriptive statistical calculation data transformation OBI:0200185 scaling data transformation A scaling data transformation is a data transformation that has objective scaling. James Malone PERSON: James Malone scaling data transformation OBI:0200186 error correction objective Application of a multiple testing correction method An error correction objective is a data transformation objective where the aim is to remove (correct for) erroneous contributions arising from the input data, or the transformation itself. James Malone, Helen Parkinson PERSON: James Malone error correction objective OBI:0200187 sequence analysis data transformation A sequence analysis data transformation is a data transformation that has objective sequence analysis and has the aim of analysing ordered biological data for sequential patterns. James Malone EDITOR sequence analysis data transformation OBI:0200188 cross validation objective A cross validation objective is a data transformation objective in which the aim is to partition a sample of data into subsets such that the analysis is initially performed on a single subset, while the other subset(s) are retained for subsequent use in confirming and validating the initial analysis. James Malone rotation estimation objective WEB: http://en.wikipedia.org/wiki/Cross_validation cross validation objective OBI:0200189 merging objective merging of columns from two different data sets A merging objective is a data transformation objective in which the data transformation has the aim of performing a union of two or more sets. James Malone combining objective PERSON: Data Transformation Branch merging objective OBI:0200190 clustered data visualization A data visualization which has input of a clustered data set and produces an output of a report graph which is capable of rendering data of this type. James Malone clustered data visualization OBI:0200191 gene list visualization Adata visualization which has input of a gene list and produces an output of a report graph which is capable of rendering data of this type. James Malone gene list visualization OBI:0200192 classified data visualization A data visualization which has input of a classified data set and produces an output of a report graph which is capable of rendering data of this type. James Malone classified data visualization OBI:0200193 background corrected data visualization A data visualization which has input of a background corrected data set and produces an output of a report graph which is capable of rendering data of this type. James Malone Monnie McGee background corrected data visualization OBI:0200194 survival analysis data transformation A data transformation which has the objective of performing survival analysis. James Malone PERSON: James Malone survival analysis data transformation OBI:0200195 proportional hazards model estimation Proportional hazards model is a data transformation model to estimate the effects of different covariates influencing the times-to-failure of a system. PERSON: James Malone PERSON: Tina Boussard Cox model Cox proportional hazards model WEB: http://en.wikipedia.org/wiki/Cox_proportional_hazards_model proportional hazards model estimation OBI:0200196 correlation study objective A data transformation objective in which correlation is obtained (often measured as a correlation coefficient, ρ) which indicates the strength and direction of a relationship between two random variables. PERSON: Tina Boussard correlation study objective OBI:0200197 spectrum analysis objective Calculation of characteristic path length in mass spectrometry is a data transformation objective where the aim is to analyse some aspect of spectral data by some data transformation process. PERSON: Tina Boussard Person:Helen Parkinson spectrum analysis objective OBI:0200198 tandem mass spectrometry A precursor ion is selected in the first stage, allowed to fragment and then all resultant masses are scanned in the second mass analyzer and detected in the detector that is positioned after the second mass analyzer. This experiment is commonly performed to identify transitions used for quantification by tandem MS. Tandem mass spectrometry is a data transformation that uses two or more analyzers separated by a region in which ions can be induced to fragment by transfer of energy (frequently by collision with other molecules). PERSON: James Malone PERSON: Tina Boussard PERSON: Tina Boussard tandem mass spectrometry OBI:0200199 gas chromatography mass spectrometry Gas chromatography mass spectrometry is a data transformation combining mass spectrometry and gas chromatography for the qualitative as well as quantitative determinations of compounds. PERSON: James Malone PERSON: Tina Boussard PERSON: Tina Boussard gas chromatography mass spectrometry OBI:0200200 chi square test The chi-square test is a data transformation with the objective of statistical hypothesis testing, in which the sampling distribution of the test statistic is a chi-square distribution when the null hypothesis is true, or any in which this is asymptotically true, meaning that the sampling distribution (if the null hypothesis is true) can be made to approximate a chi-square distribution as closely as desired by making the sample size large enough. PERSON: James Malone PERSON: Tina Boussard chi square test OBI:0200201 ANOVA ANOVA or analysis of variance is a data transformation in which a statistical test of whether the means of several groups are all equal. James Malone ANOVA OBI:0300310 sequential design PMID: 17710740.Pharm Stat. 2007 Aug 20.Sequential design approaches for bioequivalence studies with crossover designs. Any design in which the decision as to whether to enroll the next patient, pair of patients, or block of patients is determined by whether the cumulative treatment difference for all previous patients is within specified limits. Enrollment is continued if the difference does not exceed the limits. It is terminated if it does Philippe Rocca-Serra MUSC Provenance: OCI sequential design OBI:0300311 observation design PMID: 12387964.Lancet. 2002 Oct 12;360(9340):1144-9.Deficiency of antibacterial peptides in patients with morbus Kostmann: an observation study. observation design is a study design in which subjects are monitored in the absence of any active intervention by experimentalists. Philippe Rocca-Serra OBI branch derived observation design OBI:0302714 obsolete_collection (of entities of organismal origin) PMID: 18037794. Magn Reson Med Sci. 2007;6(3):139-46. Imaging of a large collection of human embryo using a super-parallel MR microscope.[the Orsay Museum has a nice collection of Impressionnist paintings] a collection is a bfo:aggregate object, that is a set of material object of the same kind 03/17/2010: obsoleted (on call), and replaced by 'material entity' and/or specimen. No need for the 'collection' part of this class any more after merging bfo:aggregate object into material entity, and by dealing with 'specimen' rather than with entities of organismal origin. 2009-11-04, MC: Entity of organismal origin has been deprecated a while ago. We still have collection (of entities of organismal origin). I am not sure we could replace with collection of material entity without altering the meaning (i.e. deprecating the class). In addition, if we do deprecate that class, should we just assert the children under material entity? added during 22-02-2008 biomaterial call to distinguish library and population PERSON: Susanna Sansone set, group, ensemble PERSON: Philippe Rocca-Serra PRS: How can we distinguish with 'collection' as the process of collecting entities, (eg. data collection, urine collection) obsolete_collection (of entities of organismal origin) true OBI:0302716 pool of specimens A pool of specimens is a mixture of a population of samples which have been gathered from one or more sample populations, obtained by the physical process of mixing individual specimens, e.g. mixing the DNA collected from the individual fish. check with advisors as to how to represent multiple instances of any class? a set of specimens which have been gathered from one or more sample_populations, obtained by the physical process of mixing individual specimens, e.g. mixing the DNA collected from the individual fish PERSON: Jennifer Fostel GROUP: CEBS pool of specimens OBI:0302729 chemical solution PMID: 18289311.Anesth Analg. 2008 Apr;106(4):1078-86.Less impairment of hemostasis and reduced blood loss in pigs after resuscitation from hemorrhagic shock using the small-volume concept with hypertonic saline/hydroxyethyl starch as compared to administration of 4% gelatin or 6% hydroxyethyl starch solution. A material entity that is made up of at least 2 scattered molecular aggregates, one playing the role of solvent and the other one playing the role of solute. PERSON: Bjoern Peters PERSON: Philippe Rocca-Serra liquid chemical solution GROUP: OBI Biomaterial Branch chemical solution OBI:0302731 buffer role A buffer of carbonic acid (H2CO3) and bicarbonate (HCO3-) is present in blood plasma, to maintain a pH between 7.35 and 7.45. http://en.wikipedia.org/wiki/Buffer_solution a role which inheres in some molecular entity realized during the process of buffering Person:Helen Parkinson Person:Philippe Rocca-Serra buffer OBI buffer role OBI:0302732 solvent role PMID: 18373502.Transfusion. 2008 Mar 25. Solvent/detergent treatment of platelet concentrates enhances the release of growth factors. solvent role is a role which inheres in a molecular entity capable of ensuring the dissolution of another chemical entity and realized by the process of solvation Philippe Rocca-Serra adpated from wikipedia (http://en.wikipedia.org/wiki/Solvatation) solvent role OBI:0302733 solute role PMID: 18380397.Pharmazie. 2008 Feb;63(2):113-21.Deviations of drug solubility in water-cosolvent mixtures from the Jouyban-Acree model--effect of solute structure. solute role is a role played by a chemical entity which is dissolved by another chemical entity (the solvent) when creating a solution Philippe Rocca-Serra adapted from wikipedia (http://en.wikipedia.org/wiki/Solute) solute role OBI:0302736 comet assay PMID: 18326531.Mutagenesis. 2008 Mar 6.Recommendations for design of the rat comet assay. a comet assay is an assay which utilizes gel electrophoresis on cell exposed to a challenge with the objective to assess DNA damage (DNA breakage) by determining the size and shape of DNA migration in cell placed in an electric field in specific conditions. Philippe Rocca-Serra SCGE assay single cell gel electrophoresis assay PMID:7686265 .Mutat Res. 1993 Jul;288(1):47-63.The single cell gel electrophoresis assay (comet assay): a European review. comet assay OBI:0302737 PCR-SSCP assay PMID: 17334176.Hum Exp Toxicol. 2007 Jan;26(1):9-18.Is there a role for PCR-SSCP among the methods for missense mutation detection of TP53 gene? a PCR-SSCP assay is an assay that identifies DNA sequence variation (mutation, deletion, insertions) using gel electrophoresis technique and denaturating conditions on target DNA sequences amplified using polymerase chain reaction procedure. PERSON: Philippe Rocca-Serra polymerase chain reaction-single strand conformation polymorphism assay PMID: 18219595.Mol Biotechnol. 2008 Feb;38(2):155-63.PCR-SSCP: a method for the molecular analysis of genetic diseases. PCR-SSCP assay OBI:0302743 obsolete_liver PMID: 2104732. Caudate lobe of the liver: anatomy, embryology, and pathology. AJR Am J Roentgenol. 1990 Jan;154(1):87-93. liver is an anatomical entity which constituent are mainly hepatocytes, which has a function of detoxification, hematopoietic center, glucose and fat metabolism management. liver is only found in animals , all Vertebrates and some families of invertebrates PERSON: Philippe Rocca-Serra GROUP: OBI Biomaterial Branch PRS: Test. added for evaluation and validation of possible imports from CARO (or other anatomical resources) obsolete_liver true OBI:0302745 obsolete_adipose tissue PMID: 18435934.Fatty acid composition of adipose tissue and blood in humans and its use as a biomarker of dietary intake.Prog Lipid Res. 2008 Apr 4. adipose tissue is a tissue which main constituents are adipocytes. adipose tissue can be classified base on its location (site) but also based on adipocyte subtypes (brown or white) which reflect functional differences and is only found in animals, Vertebrates or invertebrates. PERSON: Philippe Rocca-Serra GROUP: OBI Biomaterial derived PRS: this class has been added during major biomaterial.owl cleanup for evaluation and testing of imports from CARO obsolete_adipose tissue true OBI:0302835 denatured polymer Is a polymer which has lost secondary or tertiary structure PERSON: Alan Ruttenberg http://en.wikipedia.org/wiki/Denaturation_%28biochemistry%29 denatured polymer OBI:0302837 decapitated organism Ovarian development induced in decapitated female Culex pipiens pallens mosquitoes by infusion of physiological quantities of 20-hydroxyecdysone together with amino acids. J Insect Physiol. 1998 May;44(5-6):525-528. PMID: 12770172 decapitated organism is an organism which has had it's head removed Philippe Rocca-Serra OBI Biomaterial decapitated organism OBI:0302838 validated information PMID: 20084519: "..Three of four interactions were validated via functional magnetic resonance imaging (fMRI) in an independent sample of healthy controls;..." an information content entity which results from a validation process aimed at confirming a claim, a finding or a predicted information entity about a material entity or a process by experimental means. Person:Philippe Rocca-Serra OBI validated information OBI:0302840 curated information PMID: 17344875: A curated compendium of phosphorylation motifs.Nat Biotechnol. 2007 Mar;25(3):285-6. A information content entity that has undergone a digital curation performed by a curator for accuracy checks and compliance with curation requirements. Information which has been assessed for accuracy by domain experts. 2009-11-10 Bjoern Peters. Need to check if this was intended. overlap with 'edited information', and has the same logical restrictions. 2010-01-31 Philippe Rocca-Serra: restriction now changed to be the output of a digital curation process + reflected in example of usage and reference Person:Bjoern Peters Person:Philippe Rocca-Serra OBI curated information OBI:0302846 randomized group participant role A person enrolled in a randomized clinical trial bears a randomized group participant role a role that borne by an organism and realized by some group randomization process Person:Helen Parkinson Philippe Rocca-Serra randomized group participant role OBI:0302847 methylated polymer Binding and penetration of methylated DNA into primary and transformed human cells. Ann N Y Acad Sci. 2008 Aug;1137:36-40. PMID: 18837922 A methylated polymer which has artificially acquired one or more methyl groups Philippe Rocca-Serra OBI Biomaterial methylated polymer OBI:0302859 genetically modified organism A protocol for removal of antibiotic resistance cassettes from human embryonic stem cells genetically modified by homologous recombination or transgenesis. Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 an organism that is the output of a genetic transformation process PERSON: Philippe Rocca-Serra OBI Biomaterial genetically modified organism OBI:0302867 predicted data item A data item that was generated on the basis of a calculation or logical reasoning BP 12/21: Edited the incomplete definition from Philippe. It is still unclear to me if this should be a data item at all, or an information content entity. This will be important, because if we exclude predictions from data items, we will run into issues that we willl have to duplicate things like 'weight datum' etc. all of which can be predicted. Philippe Rocca-Serra; Bjoern Peters predicted data item OBI:0302868 mean-centered data a data item which has been processed by a mean centering data transformation where each output value is produced by subtracting the mean from the inout value Person:Helen Parkinson Person:Philippe Rocca-Serra mean-centered data OBI:0302874 edited document The OBI manuscript is (much) edited imformation A document which is the output of a document editing process Person:Bjoern Peters Philippe Rocca-Serra edited document OBI:0302876 dissolved material entity Salt molecules that have been mixed into water A material entity that has been going through a process of being put into solution Person:Bjoern Peters Philippe Rocca-Serra dissolved material entity OBI:0302884 extraction nucleic acid extraction using phenol chloroform A material separation in which a desired component of an input material is separated from the remainder Current the output of material processing defined as the molecular entity, main component in the output material entity, rather than the material entity that have grain molecular entity. 'nucleic acid extract' is the output of 'nucleic acid extraction' and has grain 'nucleic acid'. However, the output of 'nucleic acid extraction' is 'nucleic acid' rather than 'nucleic acid extract'. We are aware of this issue and will work it out in the future. Person:Bjoern Peters Philippe Rocca-Serra extraction OBI:0302885 filtration PMID: 18524968.Filtration of CSF improves isolation of Mycobacteria.J Clin Microbiol. 2008 Jun 4. filtration is a process which separates components suspended in a fluid based on granularity properties relying on a filter device Philippe Rocca-Serra OBI-Branch: adapted from wikipedia and wordnet filtration OBI:0302886 centrifugation PMID: 18428461.Purification of oligodendrocytes and their progenitors using immunomagnetic separation and Percoll gradient centrifugation. Curr Protoc Neurosci. 2001 May;Chapter 3:Unit 3.12. centrifugation is a process separating molecules by size or density using centrifugal forces generated by a spinning rotor. G-forces of several hundred thousand times gravity are generated in ultracentrifugation Philippe Rocca-Serra adapted from http://www.fao.org/DOCREP/003/X3910E/X3910E06.htm centrifugation OBI:0302887 staining PMID: 18540298. Role of modified bleach method in staining of acid-fast bacilli in lymph node aspirates. Acta Cytol. 2008 May-Jun;52(3):325-8. Staining is a process which results in the addition a class-specific (DNA, proteins, lipids, carbohydrates) dye to a substrate to qualify or quantify the presence of a specific compound. Philippe Rocca-Serra adapted from Wikipedia: http://en.wikipedia.org/wiki/Staining staining OBI:0302888 washing PMID: 6874122. Dialysis leucopenia--no correction after prolonged washing of the membrane. Int J Artif Organs. 1983 May;6(3):113-4. washing is a process by which a material entity acting as contaminant (e.g. excess staining reagent) is removed by application of one or more cycles of solution in flow. Philippe Rocca-Serra OBI-Branch washing OBI:0302889 irradiation PMID: 18563778.Histological and modeling study of skin thermal injury to 2.0 mum laser irradiation.Lasers Surg Med. 2008 Jun 18;40(5):358-370. irradiation is a process by which a material entity is exposed to radiative energy, which could be ionizing radiation (such as gamma rays or X-rays) or not such as UV light or microwaves Philippe Rocca-Serra adapted from wikipedia (http://en.wikipedia.org/wiki/Irradiation) irradiation OBI:0302890 polymerization PMID: 18517209. The electronic role of DNA-functionalized carbon nanotubes: efficacy for in situ polymerization of conducting polymer nanocomposites. J Am Chem Soc. 2008 Jun 25;130(25):7921-8. Epub 2008 Jun 3. polymerization is process by which molecular entity of small mass are aggregated in motifs over the course of a chemical reaction catalyzed by enzymes or other molecular entities acting as catalyst. polymerization results in molecular entity of high molecular weight PRS:22102008: need to import catalyst from CHEBI 35223 Philippe Rocca-Serra OBI-Branch polymerization OBI:0302891 trypsination The use of mild trypsinization conditions in the detachment of endothelial cells to promote subsequent endothelialization on synthetic surfaces. Biomaterials. 2007 Sep;28(27):3928-35. PMID: 17570483 trypsination is a protease cleavage which uses enzyme trypsin to act on proteins present in an input material entity Philippe Rocca-Serra OBI PA trypsination OBI:0302892 enzymatic ligation PMID: 17853876. Enzymatic ligation assisted by nucleases: simultaneous ligation and digestion promote the ordered assembly of DNA. Nat Protoc. 2007;2(9):2198-202. An enzymatic ligation is a planned process in which molecules are joined by covalent bonds through the action of an material entity with a ligase activity Philippe Rocca-Serra OBI-Branch enzymatic ligation OBI:0302893 storage PMID: 18550121.Total Prostate Specific Antigen Stability Confirmed After Long-Term Storage of Serum at -80C. J Urol. 2008 Jun 10. A maintenance process by which material entities that are not actively metabolizing are placed in well identified location and possibly under controlled environment in ad-hoc devices/structures in order to preserve and protect them from decay/alteration and maintain availability Philippe Rocca-Serra OBI-Branch storage OBI:0302894 cell lysis PMID: 18484276.Cell lysis with dimethyl sulphoxide produces stable homogeneous solutions in the dichlorofluorescein oxidative stress assay. Free Radic Res. 2008 May;42(5):435-41. cell lysis is a process by which cell membrane integrity of live cells is compromised and leads to cell death. Cell lysis may be achieved by means of viral action or osmotic shock. BP, JG, RV: There is also a need for the unplanned cell lysis, which is probably not in the scope of OBI, but should be linked to from this process. Philippe Rocca-Serra adapted from wikipedia [http://en.wikipedia.org/wiki/Lysis] cell lysis OBI:0302895 electrocution PMID: 9587208. Electrocution of horses and cattle. Vet Rec. 1998 Apr 4;142(14):376. electrocution is process by which electric current is applied to a material with quality alive and result the termination of life process. Philippe Rocca-Serra OBI branch electrocution OBI:0302896 cervical dislocation PMID: 18246869. Loss of cortical function in mice after decapitation, cervical dislocation, potassium chloride injection, and CO2 inhalation. Comp Med. 2007 Dec;57(6):570-3 cervical dislocation is a process by which a Vertebrate organism has its life terminated by rupturing spinal cord between cervical vertebrae induced by excessive mechanical torsion PRS:21102008: Input must be restricted to Vertebrates (requires import from NCBI tax) Philippe Rocca-Serra OBI branch cervical dislocation OBI:0302897 asphyxiation PMID: 18246869. Loss of cortical function in mice after decapitation, cervical dislocation, potassium chloride injection, and CO2 inhalation. Comp Med. 2007 Dec;57(6):570- asphyxiation is a process by which oxygen supplies are restricted (by mechanical, e.g obstructing airways or chemical means, e.g. increasing CO2 partial pressure) resulting in termination of life in oxygen reliant organisms. Philippe Rocca-Serra OBI branch asphyxiation OBI:0302898 intentional overdosing In vivo measurement of tumor blood oxygenation by near-infrared spectroscopy: immediate effects of pentobarbital overdose or carmustine treatment. J Neurooncol. 1994;22(3):209-20. PMID: 7760097 intentional overdosing is a process by which an excess dose of a chemical compound is given with the intent of causing death Philippe Rocca-Serra lethal injection OBI Biomaterial intentional overdosing OBI:0302899 decapitation PMID: 18246869. Loss of cortical function in mice after decapitation, cervical dislocation, potassium chloride injection, and CO2 inhalation. Comp Med. 2007 Dec;57(6):570- decapitation is a process by which the head of a living organism is physically removed from the body, usually resulting in rapid death (in the case of Rhodnius prolixus, it might take a bit longer..) Philippe Rocca-Serra OBI-Branch decapitation OBI:0302900 group randomization PMID: 18349405. Randomization reveals unexpected acute leukemias in Southwest Oncology Group prostate cancer trial. J Clin Oncol. 2008 Mar 20;26(9):1532-6. A group assignment which relies on chance to assign materials to a group of materials in order to avoid bias in experimental set up. Philippe Rocca-Serra adapted from wikipedia [http://en.wikipedia.org/wiki/Randomization] group randomization OBI:0302901 obsolete_activation PMID: 18566411.Activation of the JAK/STAT-1 Signaling Pathway by IFN-{gamma} Can Down-Regulate Functional Expression of the MHC Class I-Related Neonatal Fc Receptor for IgG.J Immunol. 2008 Jul 1;181(1):449-63. a process by which a material entity status is modified and conferred a capability of reacting (this sounds like a circular definition , hugh!) Alan Ruttenberg 2010/11/22: After OBI call, this is too broad a term, and in any case would be in the scope of GO See tracker: https://sourceforge.net/tracker/index.php?func=detail&aid=3302925&group_id=177891&atid=886178 Philippe Rocca-Serra OBI-Branch obsolete_activation true OBI:0302902 immobilization PMID: 18562258. The immobilization of proteins on biodegradable fibers via biotin-streptavidin bridges.Acta Biomater. 2008 May 23. immbolization is a process by which material entity become (possibly covalently but not necessarily) attached to the surface of another material entity used a substratum. Philippe Rocca-Serra OBI-Branch immobilization OBI:0302903 nucleic acid hybridization PMID: 18555787.Quantitative analysis of DNA hybridization in a flowthrough microarray for molecular testing. Anal Biochem. 2008 May 27. a planned process by which totally or partially complementary, single-stranded nucleic acids are combined into a single molecule called heteroduplex or homoduplex to an extent depending on the amount of complementarity. Philippe Rocca-Serra adapted from wikipedia [http://en.wikipedia.org/wiki/Nucleic_acid_hybridization] hybridization assay nucleic acid hybridization OBI:0302905 elution PMID: 18549238.Theory and Application of the Two-Mode Gradient Elution in Liquid Chromatography Involving Simultaneous Changes in Temperature and Mobile-Phase Composition.Anal Chem. 2008 Jun 13. the process of extracting one material from another by washing with a solvent to remove adsorbed material from an adsorbent (as in washing of loaded ion-exchange resins to remove captured ions) Philippe Rocca-Serra wordnet.princeton.edu/perl/webwn elution OBI:0302906 DNA Subtraction PMID: 10718422. Identification of genes overexpressed in head and neck squamous cell carcinoma using a combination of complementary DNA subtraction and microarray analysis. Laryngoscope. 2000 Mar;110(3 Pt 1):374-81 a material separation process by which repetitive genomic DNA is removed during the construction of cDNA library. Philippe Rocca-Serra OBI-Branch DNA Subtraction OBI:0302908 document editing Wax DB, Beilin Y, Hossain S, Lin HM, Reich DL. Manual editing of automatically recorded data in an anesthesia information management system. Anesthesiology. 2008 Nov;109(5):811-5. PMID: 18946292 is a planned process with specified input original document and specified output edited document Philippe Rocca-Serra and OBI consortium adapted from wikipedia document editing OBI:0302910 prediction Prediction of TF target sites based on atomistic models of protein-DNA complexes. BMC Bioinformatics. 2008 Oct 16;9(1):436. PMID: 18922190 a process by which an event or an entity is described before it actually happens or is being discovered and identified. Philippe Rocca-Serra OBI prediction OBI:0302911 validation PMID: 18557814 . Chemical and genetic validation of dihydrofolate reductase-thymidylate synthase as a drug target in African trypanosomes. Mol Microbiol. 2008 Jun 16. a planned process with objective to check that the accuracy or the quality of a claim or prediction satisfies some criteria and which is assessed by comparing with independent results Philippe Rocca-Serra adapted from wordnet (wkipedia) validation OBI:0302912 electroporation PMID: 18551712. Microfluidic electroporation for selective release of intracellular molecules at the single-cell level. Electrophoresis. 2008 Jun 13. a process in which a significant increase in the electrical conductivity and permeability of the cell plasma membrane caused by an externally applied electrical field. It is usually used in molecular biology as a way of introducing some substance into a cell, such as loading it with a molecular probe, a drug that can change the cell's function, or a piece of coding DNA Philippe Rocca-Serra electropermeabilization WEB:http://en.wikipedia.org/wiki/Electroporation electroporation OBI:0302914 digital curation PMID: 16901087. Supporting the curation of biological databases with reusable text mining.Genome Inform. 2005;16(2):32-44. Digital curation is the process of establishing and developing long term repositories of digital assets for current and future reference by researchers, scientists, and historians, and scholars generally. Philippe Rocca-Serra wikipedia digital curation OBI:0400005 A10-Analyzer A A10 is a flow_cytometer_analyser manufactured by Apogee. It uses an arc lamp as a light source, with choices of 75W Xe, 75W Xe/Hg or 100W Hg arc lamps. It has filters and collectors for up to three fluorescent parameters and two scatter parameters. It uses analog electronics. The A10 can be used for measuring the properties of individual cells. John Quinn http://www.apogeeflow.com/flow_cytometry_products.htm A10-Analyzer OBI:0400006 A40-MiniFCM A A40-MiniFCM is a flow_cytometer_analyser that allows for the choice of one of four lasers (375nm, 405nm,488nm, 532nm, 635nm), and PMTs and filters for collecting up to four parameters. It uses digital electronics. A military version of this cytometer is available as well. The A40-MiniFCM is geared towards the most demanding applications such as archaea, bacteria and large virus. John Quinn http://www.apogeeflow.com/flow_cytometry_products.htm A40-MiniFCM OBI:0400007 analog-to-digital converter The analog to digital converter transformed the analog output from the photomultiplier tube to a digital signal for collection. An analog-to-digital_converter is an instrument that converts an infinite resolution analog signal to a finite resolution digital signal. John Quinn Melanie Courtot A-D A2D http://en.wiktionary.org/wiki/Analog-to-Digital_Converter analog-to-digital converter OBI:0400008 flow cytometer analyzer FACS Calibur, Luminex 100 An analyser is a flow_cytometer that is used to measure properties of particles (whole cells, nuclei, chromosomes, diatoms, plankton, bacteria, viruses) by moving these particles through a detection chamber. An analyser is used to collect data for analysis. John Quinn http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm flow cytometer analyzer OBI:0400009 arc lamp The Jablochkoff Candle Arc lamp is a light source that produces light by an electric arc (or voltaic arc). The lamp consists of two electrodes typically made of tungsten which are separated by a gas. The type of lamp is often named by the gas contained in the bulb; including neon, argon, xenon, krypton, sodium, metal halide, and mercury. The electric arc in an arc lamp consists of gas which is initially ionized by a voltage and is therefore electrically conductive. To start an arc lamp, usually a very high voltage is needed to ignite or strike the arc. This requires an electrical circuit sometimes called an igniter, which is part of a larger circuit called the ballast. The ballast supplies a suitable voltage and current to the lamp as its electrical characteristics change with temperature and time. Older cytometers may use arc lamps to irradiate particles at the interrogation point. John Quinn http://en.wikipedia.org/wiki/Arc_lamp arc lamp OBI:0400010 argon ion laser argon ion laser in a cytometer An argon-ion laser is an ion laser that uses argon ions as the lasing medium. These lasers are used primarily to emit light at wave lengths of 458 nm, 488 nm or 514.5 nm, though it is possible to use them to emit several wavelengths of blue and green light. Argon-ion lasers can emit light at many different wave lenghts, and excite a number of different flourochromes. Daniel Schober John Quinn http://en.wikipedia.org/wiki/Laser#Gas_lasers argon ion laser OBI:0400011 avalanche photodiode C30644E - InGaAs Avalanche Photodiode An avalanche photodiode is typically used to collect photons emitted by forward scatter because it is far less sensitive, and less likely o be burned out, than a PMT. A photodiode with high quantum efficiency and a mechanism for producing gains as high as a few thousand. John Quinn Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 avalanche photodiode OBI:0400012 Bactiflow A Bactiflow is a flow_cytometer_analyser manufactured by Chemunex SA. It is a cell counter for bacteria and other micro organisms. Bacteria are stained with a fluorochrome and the number of particles that fluoresce are counted. The system uses digital electronics, a single laser and a single detector. An ALS version is available as well - Automatic Labeling System. The Bactiflow is specialized cytometer used exclusively for counting microbes. John Quinn http://www.chemunex.com/products/chemframe.htm Bactiflow OBI:0400013 band pass filter 530/30 BP filter, 585/42 BP filter A band pass filter is an optical filter that passes wavelengths of light within a certain range and rejects (attenuates) frequencies outside that range. The passed wavelengths are indicated in the specifications of the filter and its name. A 480/20 band-pass filter pass light with at wavelengths of 460 to 500 nm and attenuates all others. Person:John Quinn http://en.wikipedia.org/wiki/Band_pass_filter band pass filter OBI:0400014 BioSorter1000 BioSorter 1000 at TSRI Flow Cytometry Core Facility A BioSorter1000 is a flow_cytometer_sorter manufactured by Union Biometrica. It includes analog electronics, 488/514 nm multi-line Argon-ion laser for fluorescence and a light stabilized 670 nm forward scatter laser for extinction and time-of-flight. It has filters and PMTs for 3 fluorescent parameters and photodiodes for scatter, time of flight, and extinction. The flow cell is quartz cuvette. The BioSorterTM 1000 is an instrument for analyzing and sorting objects from 200-600 microns in diameter. John Quinn http://www.unionbio.com/products/BioSorter.html BioSorter1000 OBI:0400015 BioSorter2000 BioSorter 2000 at TSRI Flow Cytometry Core Facility A BioSorter2000 is a sorter manufactured by Union Biometrica. It includes analog electronics, 488/514 nm multi-line Argon-ion laser for fluorescence and a light stabilized 670 nm forward scatter laser for extinction and time-of-flight. It has filters and PMTs for 3 fluorescent parameters and photodiodes for scatter, time of flight, and extinction. The flow cell is quartz cuvette. The BioSorterTM 2000 is an instrument for analyzing and sorting objects from 500 microns to 1.5 millimeters in diameter. John Quinn http://www.unionbio.com/products/BioSorter.html BioSorter2000 OBI:0400016 BioSorter250 BioSorter 250 at TSRI Flow Cytometry Core Facility A BioSorter250 is a flow_cytometer_sorter manufactured by Union Biometrica. It includes analog electronics, 488/514 nm multi-line Argon-ion laser for fluorescence and a light stabilized 670 nm forward scatter laser for extinction and time-of-flight. It has filters and PMTs for 3 fluorescent parameters and photodiodes for scatter, time of flight, and extinction. The flow cell is quartz cuvette. The BioSorterTM 250 is an instrument for analyzing and sorting objects from 40-200 microns in diameter. John Quinn http://www.unionbio.com/products/BioSorter.html BioSorter250 OBI:0400017 BioSorter500 BioSorter 500 at TSRI Flow Cytometry Core Facility A BioSorter500 is a flow_cytometer_sorter manufactured by Union Biometrica. It includes analog electronics, 488/514 nm multi-line Argon-ion laser for fluorescence and a light stabilized 670 nm forward scatter laser for extinction and time-of-flight. It has filters and PMTs for 3 fluorescent parameters and photodiodes for scatter, time of flight, and extinction. The flow cell is quartz cuvette. The BioSorterTM 500 is an instrument for analyzing and sorting objects from 100-250 microns in diameter and less than 2mm in length. John Quinn http://www.unionbio.com/products/BioSorter.html BioSorter500 OBI:0400018 Cell Lab Quanta SC A Cell Lab Quanta SC is a flow_cytometer_analyser manufactured by Becman Coulter. It features a mercury arc lamp optimized at 366, 405, and 435 nm, and a 488 nm laser diode. It has filters and PMTs to collect up to 3 fluorescent parameters, and a photodiode for side scatter detection. This cytometer uses Couter-Volume for cell size measurements. The Cell Lab Quanta SC can be used for measuring the properties of individual cells. John Quinn http://www.beckmancoulter.com/cell-lab Cell Lab Quanta SC OBI:0400019 charge plate LSR2 charge plate Part of the fluidics subsystem. Charge plates are used or sorters. They create an charged electric field when particles deemed to be desired for further analysis are shaken form the piexo electric crystal. The charged particles are drawn toward the charged plate, and the altered drop location causes the particles to fall into a collection tube. Charge plates enable sorting. John Quinn Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 charge plate OBI:0400020 cell sorter collection tube LSR2 collection tube Part of the fluidics subsystem. The collection tube is a vessel for capturing cells of interest that have been identified by a sorter. The collection tube is the end location of sorted cells. John Quinn Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 cell sorter collection tube OBI:0400022 Cyan A Cyan is a flow_cytometer_analyser manufactured by Dako Cytomation. It features include digital electronics, three lasers: 488 nm, 635 nm, and 405 nm, and filters and collectors for nine fluorescent parameters and two scatter parameters. The Cyan can be used for measuring the properties of individual cells. John Quinn http://www.dakousa.com/prod_productrelatedinformation?url=gprod_cyan_index.htm Cyan OBI:0400023 CYFlow ML A CyFlow_ML is a flow_cytometer_analyser manufactured by Partec. It is a digital machine which uses 4 light sources: triple laser configurations including new powerful 200mW@488nm blue solid state laser + 100W UV lamp for highest resolution DNA analysis, and can collect 16 optical parameters: FSC1, FSC2, SSC, FL1-FL13. Ultracompact high end desktop multilaser Flow Cytometer for all applications in cell analysis and absolute counting. John Quinn http://www.partec.de/products/cyflow-ml.html CYFlow ML OBI:0400024 CyFlow SL a flow_cytometer_analyser manufactured by Partec. Its specs are: ultracompact and fully equipped mobile/portable instrument, dimensions [cm]: L 43 x H 16 x D 37, highest stability/robustness and highest precision, 5 optical parameters: FSC, SSC, FL-1, FL-2, FL-3, 20mW@488nm blue solid state laser , other laser light sources optional (UV, violet, green, red), WindowsTM XP FloMax (software for real time data acquisition, data display, and data evaluation), parallel 16 bit digital pulse processing Compact mobile Flow Cytometer for any kind of cell analysis and absolute volumetric counting. The CyFlow_SL allows to analyze forward and side scatter signals in combination with up to 3 fluorescence channels. John Quinn http://www.partec.de/products/cyflow.html CyFlow SL OBI:0400025 CyFlow SL3 A CyFlow_Sl3 is a flow_cytometer_analyser manufactured by Partec. Its specs are: ultracompact and fully equipped mobile/portable instrument, dimensions [cm]: L 43 x H 16 x D 37 , highest stability/robustness and highest precision, 5 optical parameters: FSC, SSC, FL-1, FL-2, FL-3, 20mW@488nm blue solid state laser, other laser light sources optional (UV, violet, green, red), WindowsTM XP FloMax (software for real time data acquisition, data display, and data evaluation), parallel 16 bit digital pulse processing. The CyFlow SL3 is a compact and dedicated portable Flow Cytometer for accurate and affordable cell analysis and true volumetric absolute counting in HIV Monitoring and AIDS patient follow-up by precise and direct CD4 and CD4% measurement. John Quinn http://www.partec.de/products/cyflowsl3.html CyFlow SL3 OBI:0400026 CyFlow Space CyFlow Space at TSRI Flow Cytometry Core Facility A CyFlow_Space is a flow_cytometer_sorter manufactured by Partec. Its specs are: 8optical parameters, 6 colours:FSC, SSC, FL1-FL6 , 3laser light sources: 200mW@488nm blue solid state laser 25mW@635nm red diode laser 50mW@405nm violet or 8mW@375nm ultraviolet diode laser _ultracompact desktop high end instrument. Parallel 16bit digital pulse processing. The CyFlow Space is a 6-Colour FCM System and Cell Sorter for Clinical Routine and Research. John Quinn http://www.partec.de/products/cyflowspace.html CyFlow Space OBI:0400027 CytoBuoy flow cytometer analyzer CytoBuoy can be used to conduct extended and/or high frequency time series of phytoplankton distribution and abundance on fixed locations A flow cytometer analyser which is manufactured by Cyto Buoy Inc. They are the buoy mounted version of the CytoSense, equipped with wireless transmission of control and data files. They are a single laser, multi parameter instrument. Various types of micro-laser are offered; available measuring parameters are forward light scatter, side scatter, and fluorescence (max. 9 colour bands). The current series have 5 parameters. John Quinn, Melanie Courtot http://www.cytobuoy.com/ CytoBuoy flow cytometer analyzer OBI:0400028 CytoSence A CytoSense is a flow_cytometer_analyser manufactured by Cyto Buoy Inc. They are a single laser, multi parameter instrument. Various types of micro-laser are offered; available measuring parameters are forward light scatter, side scatter, and fluorescence (max. 9 colour bands). The current series have 5 parameters. The CytoSense is the basic instrument, which can be used for normal laboratory applications, as well as for autonomous monitoring with internal data logging or direct data transmission. The special instrument design and its splashproof housing allow operation on moving platforms and outdoor sites. John Quinn http://www.cytobuoy.com/ CytoSence OBI:0400029 CytoSub A CytoSub is a flow_cytometer_analyser manufactured by Cyto Buoy Inc. They are a single laser, multi parameter instrument. Various types of micro-laser are offered; available measuring parameters are forward light scatter, side scatter, and fluorescence (max. 9 colour bands). The current series have 5 parameters. The CytoSub is the submersible version equipped with a high pressure sample inlet loop and a high pressure housing to allow underwater operation down to 200 m, lowered on a cable or mounted on a flooded underwater vehicle. John Quinn http://www.cytobuoy.com/ CytoSub OBI:0400030 dichroic filter Cy3 Dichroic Filter A dichroic filter is an optical filter which is used to selectively pass light of a small range of colors while reflecting other colors. A dichroic filter passes the specified range of light whereas a dichroic mirror reflects the specified range of light. John Quinn http://en.wikipedia.org/wiki/Dichroic_filter dichroic filter OBI:0400031 dichroic mirror ViewLux Alexa 594 dichroic mirror A dichroic mirror is an optical filter which is used to selectively reflect light of a small range of colors while passing other colors. A dichroic filter passes the specified range of light whereas a dichroic mirror reflects the specified range of light. John Quinn http://en.wikipedia.org/wiki/Dichroic_mirror dichroic mirror OBI:0400032 differential pressure gauge LSR2 differential pressure gauge Part of the fluidics subsystem. The differential pressure gauge monitors the difference between sample and sheath fluid pressures in systems where pressure is used to force the sample fluid to flow in the center of the sheath fluid. A differential pressure gauge can be used by the operator to make sure that the sample fluid is at a greater pressure than the sheath fluid, which maintains a core of sample fluid. John Quinn Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 differential pressure gauge OBI:0400033 diode laser FAX-RS3-H0 diode laser manufactured by Diode Laser Concepts, Inc. A diode laser is a laser in which the active medium is a p-n junction semiconductor laser diode, similar to that found in a light-emitting diode. Laser diodes emit at wavelengths from 375 nm to 1800 nm, and wavelengths of over 3 micrometer have been demonstrated. A diode laser can by used to irradiate cells in a flow cytometer. Daniel Schober John Quinn diode laser OBI:0400034 dye laser Rhodamine 101 dye laser used to irradiate cells in a flow cytometer. A dye laser is a laser in which the lasing medium is a fluorescent dye, usually dissolved in an organic solvent such as ethanol or ethylene glycol. The particular dye used determines the wavelengths the laser can emit. The laser medium is places between two parallel mirrors for light emission amplification. Daniel Schober John Quinn Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 dye laser OBI:0400036 FACS Calibur "FACS Calibur at TFL, BCCRC, Vancouver" The FACS Calibur is one of the most popular cytometers in use for research. John Quinn "http://www.bdbiosciences.com/immunocytometry_systems/products/display_product.php?keyID=45, 2007-05-11" FACS Calibur OBI:0400037 FACS Canto A FACS_Canto is a flow_cytometer_analyser manufactured by Becton Dickinson. It features digital electronics, a solid state 488 nm, and a HeNe 633 nm lasers, and filters and PMTs for collecting up to 6 fluorescent parameters. The FACS_Canto is an analyser usually used in clinical applications. John Quinn http://www.bdbiosciences.com/pdfs/brochures/23-8742-00.pdf FACS Canto OBI:0400038 FACS Canto2 A FACS_Canto2 is a flow_cytometer_analyser manufactured by BD. It features digital electronics, two solid state lasers at 488 and 633 nm with the option for a third 405 nm laser, and filters and collectors for measuring up to 8 fluorescent paramters with either the 2 or 3 laser option. The FACS_Canto2 is an analyser usually used in clinical applications. John Quinn http://www.bdbiosciences.com/cgi-bin/literature/view?part_num=23-8786-01 FACS Canto2 OBI:0400039 FACS Scan A FACS_Scan is a flow_cytometer_analyser manufactured by Becton Dickinson. IT features analog electronics, one 488 nm solid state laser, and the filters and PMTs to collect up to three fluorescent parameters The FACS_Scan is usually used for research applications. John Quinn http://www.brc.ubc.ca/brc/facs.html FACS Scan OBI:0400040 FACSAria FACSAria at TSRI Flow Cytometry Core Facility A FASCSAria is a flow_cytometer_sorter manufactured by Becton Dickinson. It features digital electronics, a solid state 488 nm blue laser, a solid state 407 nm violet laser, and a HeNe (633 nm) ion laser. The Aria has the filters and PMTs to collect side scatter and 9 fluorescent parameters. The Aria has a photodiode detector for forward scatter collector. The flow cell is Quartz cuvette. The FACSAria is a sorter used to collect and analyse cells using up to 11 parameters. John Quinn http://www.bdbiosciences.com/external_files/is/doc/mkt_lit/brochures/SJ-0003-00Aria.pdf FACSAria OBI:0400041 FACSvantage FACSvantage at TSRI Flow Cytometry Core Facility The FACSvantage is a flow_cytometer_sorter manufactured by Becton Dickinson. It has analog electronics, three lasers (several options are available), and the filters and PMTs to collect 6 fluorescent parameters and side scatter, and a photodiode to collect forward scatter. The FACSvantage can be used to analyse, sort and collect cells. John Quinn http://www.bdbiosciences.com/features/products/display_product.php?keyID=42 FACSvantage OBI:0400042 FC 500 A FC_500 is a flow_cytometer_analyser manufactured by Beckman Coulter. It features digital electronics, 488 nm and 635 nm lasers, filters and PMTs for 5 fluorescent parameters, a diode for collecting side scatter and a solid state detector for forward scatter. The FC 500 is an analyser usually used for either research or clinical applications. John Quinn http://www.beckmancoulter.com/products/instrument/flowcytometry/fc500series.asp FC 500 OBI:0400043 flow cell Biofilm Flow Cell Aparatus in the fluidic subsystem where the sheath and sample meet. Can be one of several types; jet-in-air, quartz cuvette, or a hybrid of the two. The sample flows through the center of a fluid column of sheath fluid in the flow cell. Person:John Quinn flow_cell http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm flow cell OBI:0400044 flow cytometer FACS Calibur A flow_cytometer is an instrument for counting, examining and sorting microscopic particles in suspension. It allows simultaneous multiparametric analysis of the physical and/or chemical characteristics of single cells flowing through an optical and/or electronic detection apparatus. A flow cytometer is an instrument that can be used to quantitatively measure the properties of individual cells in a flowing medium. John Quinn http://en.wikipedia.org/wiki/Flow_cytometer flow cytometer OBI:0400045 fluid pressure regulator LSR2 fluid pressure regulator Part of the fluidic subsystem. The fluid pressure regulator maintains constant pressure within the sheath and or sample lines by filling the lines with enough gas to push the fluid at the desired rate. The gas is usually air, and less frequently nitrogen. In the sheath line, the gas is pushed into the sheath tank. In the sample line the gas is pushed into the collection tube. Fluid pressure regulators maintain great enough pressure to push sample fluid out of the tube and sheath fluid out of the sheath tank. Person: John Quinn Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 fluid pressure regulator OBI:0400047 gas laser helium-neon gas laser used to erradiate cells in a flow cytometer. A gas laser is a laser in which the lasing medium is a gas. The laser medium is places between two parallel mirrors for light emission amplification. The gas is excited to emit light via an external light source or an electric current discharging through the gas. Daniel Schober John Quinn http://en.wikipedia.org/wiki/Gas_laser gas laser OBI:0400048 Guava EasyCyte Mini A Guava_EasyCyte_Mini is a flow_cytometer_analyser that includes a single 488 nm laser, and filters and PMTs to collect up to 3 fluorescent parameters. It includes a photodiode forward scatter collector and an optional photodiode for side scatter collection.Guava cytometers use aspiration instead of fluid systems to transport cells within the machine. The mini accepts tubes only for inputting cells or beads. The Guava_EasyCyte_Mini cytometer is a small portable cytometer particularly useful for field measurement. John Quinn http://www.guavatechnologies.com/main/products/easyCyteMini.cfm Guava EasyCyte Mini OBI:0400049 Guava EasyCyte Plus A Guava_EasyCyte_Plus System is a flow_cytometer_analyser that includes a single 488 nm laser, and filters and PMTs to collect up to 4 fluorescent parameters. It includes a photodiode forward scatter collector and an optional photodiode for side scatter collection.Guava cytometers use aspiration instead of fluid systems to transport cells within the machine. The EasyCyte plus accepts 96 well plates as well as tubes. The Guava_EasyCyte_Plus cytometer is a small portable cytometer particularly useful for field measurement. John Quinn http://www.guavatechnologies.com/main/products/easycyte-new.cfm Guava EasyCyte Plus OBI:0400050 Guava Personal Cell Analysis A Guava_Personal_Cell_Analysis System is a flow_cytometer_analyser that includes a single 532 nm laser, and filters and PMTs to collect up to 2 fluorescent parameters. It includes a photodiode forward scatter collector. Guava cytometers use aspiration instead of fluid systems to transport cells within the machine. The PCA96 uses only tubes to introduce specimen. The Guava PCA cytometer is a small portable cytometer particularly useful for field measurement. John Quinn Guava_PCA http://www.guavatechnologies.com/main/products/PCA-new.cfm Guava Personal Cell Analysis OBI:0400051 Guava Personal Cell Analysis-96 The Guava_Personal_Cell_Analysis-96 Systems is a flow_cytometer_analyser that includes a single 532 nm laser, and filters and PMTs to collect up to 2 fluorescent parameters. It includes a photodiode forward scatter collector. Guava cytometers use aspiration instead of fluid systems to transport cells within the machine. The PCA96 uses either tubes or 96 well plates to introduce specimen. The Guava PCA -96 cytometer is a small portable cytometer particularly useful for field measurement. John Quinn Guava_PCA-96 http://www.guavatechnologies.com/main/products/PCA-96new.cfm Guava Personal Cell Analysis-96 OBI:0400052 helium cadmium ion laser KIMMON HeCd 325nm laser A helium-cadmium laser is a metal vapor laser that emits wavelengths of 442, 325 and 354 nms. This laser is a metal vapor laser. A helium-cadmium laser can by used to irradiate cells in a flow cytometer. John Quinn http://en.wikipedia.org/wiki/Laser#Gas_lasers helium cadmium ion laser OBI:0400053 helium neon ion laser A helium neon laser can by used to irradiate cells in a flow cytometer. A helium-neon laser (HeNe) is an ion laser that uses helium and neon gas-ions as lasing medium. HeNe lasers emit at 543 nm and 633 nm most commonly and can also be used at 543, 594, and 611 nm. Daniel Schober John Quinn http://en.wikipedia.org/wiki/Laser#Gas_lasers helium neon ion laser OBI:0400054 Amnis ImageStream The ImageStream is a multispectral_imaging_flow_cytometer manufactured by Amnis. Its has digital electronics, a single standard 488 nm solid state laser. In addition an optional 658 nm and your choice of either a 405 nm or 375 nm solid state laser can be added. Information is collected using cameras. The ImageStream system CCD camera produces six images of each cell, including darkfield, brightfield, and up to four fluorescent colors. Each image is used to calculate over 40 features, so a six-image assay results in ~250 morphometric and photometric features per cell. The ImageStream is a flow cytometer that takes pictures of the cells in flow. It has both components, an Image cytometer and a flow cytometer. It has both components, an Image cytometer and a flow cytometer. John Quinn Melanie Courtot http://www.amnis.com/ Amnis ImageStream OBI:0400055 inFlux Analyzer The inFlux Analyzer is a flow_cytometer_analyser manufactured by Cytopeia. It is a digital machine, with these laser options: Coherent 70, 90, 300 series water cooled lasers, solid state UV 355nm, Violet 408nm, Violet-Blue 479nm, Blue-488nm, Green-531nm, Red-635nm, Red-647nm. Filters and PMTs are used for all parameters (including forward light scatter), and up to 12 PMTs can be included. The Influx analyser can be used to measure the properties of individual cells. John Quinn http://www.cytopeia.com/analyzer.htm inFlux Analyzer OBI:0400056 Influx Cell Sorter Influx Cell Sorter at TSRI Flow Cytometry Core Facility A Influx Cell Sorter is a flow_cytometer_sorter manufactured by Cytopeia. It is a digital machine, with these laser options: Coherent 70, 90, 300 series water cooled lasers, solid state UV 355nm, Violet 408nm, Violet-Blue 479nm, Blue-488nm, Green-531nm, Red-635nm, Red-647nm. The sorting is multi-way, index, and proportional sorting. Filters and PMTs are used for all parameters (including forward light scatter), and up to 12 PMTs can be included. The Influx cell sorter can be used to measure, sort, and collect ndividual cells. John Quinn http://www.cytopeia.com/sorter.htm Influx Cell Sorter OBI:0400059 interrogation_point Interrogation point in BD FACS Calibur Point within the fluidic subsystem at which the laser intersects the stream, illuminating the cells where they emit their fluorescence and scatter the light. The laser irradiates the cell at the interrogation point. John Quinn http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm, 2007-05-11 interrogation_point OBI:0400060 ion laser 2 Watt Lexel 88 Argon Ion laser An ion laser is a gas laser which uses an ionized gas as its lasing medium. Daniel Schober John Quinn http://en.wikipedia.org/wiki/Ion_laser ion laser OBI:0400061 jet_in_air_flow_chamber Jet-in-air flow chamber in DakoCytomation MoFlo high-speed cell sorter A flow cell in which the cells are pinched off as droplets and allowed to drop through the air. The laser intersects with the cell in mid-air. A jet in air flow chamber allows the laser to intersect with the cells without any intermittent media other than air. John Quinn http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm jet_in_air_flow_chamber OBI:0400062 krypton ion laser Lexel 95L krypton laser A krypton-ion laser is an ion laser that uses krypton as the lasing medium. These lasers can emit at 468, 476, 482, 520, 531, 568, 647 (the most powerful line), and 676 nm all at once. They have much lower gain than argon lasers however. Daniel Schober John Quinn krypton ion laser OBI:0400063 LactoScope C4 LactoScope C4 Automatic Economical A LactoScope_C4 is a spectrophotometer with which the composition of milk and milk products is analysed via infrared technology. The LactoScope determines the amount of the constituents fat, protein, lactose and the total solids content with extreme accuracy. Josef Spidlen Melanie Courtot http://www.aicompanies.com/DeltaCD/lacto_ftir_auto.htm LactoScope C4 OBI:0400064 laser A laser is the most common way to irradiate a cell in a flow cytometer. A laser (acronym for light amplification by the stimulated emission of radiation) is a light source that emits photons of the same characteristics in a coherent beam. A laser uses a solid, liquid or gaseous lasing medium, that contains molecules, of which some atoms have electrons that emit photons of the same frequency when falling back to their normal orbital after excitation (pumping) by external means A laser is the most common way to irradiate a cell in a flow cytometer. Daniel Schober light amplification by the stimulated emission of radiation John Quinn http://en.wikipedia.org/wiki/Laser laser OBI:0400065 light source A light source is an optical subsystem that provides light for use in a distant area using a delivery system (e.g., fiber optics). Light sources may include one of a variety of lamps (e.g., xenon, halogen, mercury). Most light sources are operated from line power, but some may be powered from batteries. They are mostly used in endoscopic, microscopic, and other examination and/or in surgical procedures. The light source is part of the optical subsystem. In a flow cytometer the light source directs high intensity light at particles at the interrogation point. The light source in a flow cytometer is usually a laser. Elizabeth M. Goralczyk John Quinn Olga Tchuvatkina Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 light source OBI:0400066 logarithmic voltage amplifier HLVA-100 logarithmic voltage amplifier developed by FEMTO Messtechnik, GmbH A logarithmic voltage amplifier is an analog electronic circuit that puts out a voltage or current proportional to the voltage or current at its input, with logarithmic proportionality. In an analog system, the logarithmic voltage amplifier is used to present parameters with a high dynamic range on a more useful scale. John Quinn Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 logarithmic voltage amplifier OBI:0400067 long pass filter 750 LP filter A long pass filter is an optical filter that passes high wavelengths of light but attenuates (or reduces) wavelengths lower than the cutoff frequency. A long pass filter with a cutoff of 500 nm would pass all wavelengths greater than 500 nm. John Quinn http://en.wikipedia.org/wiki/high-pass_filter long pass filter OBI:0400068 LSR2 LSR2 at TSRI Flow Cytometry Core Facility A LSR2 is a sorter manufactured by Becton Dickinson. It features digital electronics, a solid state 488 nm blue laser and optionally can also have any combination of solid state UV (355 nm) and violet (405 nm) lasers and the a HeNe (633 nm) ion laser. The LSR2 has the filters and PMTs to work with 13 fluorescent parameters. The LSR II is one of the most common sorters in use. John Quinn http://www.bdbiosciences.com/external_files/is/doc/mkt_lit/brochures/live/web_enabled/SJ-0142-00LSR2.pdf LSR2 OBI:0400069 Luminex 100 The Luminex 100 is a flow_cytometer_analyser manufactured by Luminex. It is a single laser system (575 nm) with avalanche photodiodes in red and infrared and a single PMT for fluorescence. The flow chamber is a square quartz cuvette. John Quinn http://www.luminexcorp.com/products/luminex_100IS.html Luminex 100 OBI:0400070 Luminex 200 A Luminex_200 is a flow_cytometer_analyser manufactured by Luminex. The optical specifications are: Reporter laser: 532 nm, nominal output 10 - 15 mW, maximum 500 mW, frequency-doubled diode; mode of operation, continuous wave (CW). Classification laser: 635 nm, 9.1 __ 6%, maximum output 25 mW, diode; mode of operation, continuous wave (CW) Reporter detector: Photomultiplier tube, detection bandwidth of 565 - 585 nm Classification detector and doublet discriminator: Avalanche photo diodes with temperature compensation John Quinn http://www.luminexcorp.com/support/faqs.html Luminex 200 OBI:0400071 MACS Quant A MACS Quant is a flow_cytometer_analyser manufactured by Miltenyi. It uses digital electronics, and has three lasers of wavelengths 405 nm, 488 nm, and 635 nm. It has filters and detectors to collect 7 fluorescent parameters and 2 scatter parameters. The MACS Quant is an analyser usually used in research applications. John Quinn http://www.miltenyi.com MACS Quant OBI:0400073 metal vapor laser Gold vapor laser, Helium-cadmium metal-vapor laser A metal vapor laser is a gas laser in which the lasing medium is metal vapor. A metal vapor laser can by used to irradiate cells in a flow cytometer. John Quinn Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 metal vapor laser OBI:0400074 mixed argon-krypton gas laser argon-krypton laser in a cytometer A mixed argon krypton gas laser is an ion laser in which the lasing medium is a mixture of argon and krypton. A mixed argon-krypton laser can by used to irradiate cells in a flow cytometer. John Quinn http://www.eio.com/repairfaq/sam/laserarg.htm mixed argon-krypton gas laser OBI:0400075 MoFlo MoFlo at TSRI Flow Cytometry Core Facility A MoFlo is a flow_cytometer_sorter manufactured by Dako Cytomation. It features digital electronics, the option to include several lasers (solid state 488 nm, 635 nm, and a 351 nm diode laser), and has the filtering and collection capacity for up to 10 flouresecent parameters. The MoFlo is an instrument that can be used to both analyze quantitatively and collect cells in a flowing medium. John Quinn http://www.dakousa.com/index/prod_search/prod_groups.htm?productareaid=16 MoFlo OBI:0400076 multi-well plate 96 well plate, 48 multiwell plate A particle deliver vessel. A multi-well plate is a vessel that can deliver multiple samples to a flow cytometer in a specified order. It must be used with a plate loader. FG this is synonymous with microtiter plate John Quinn http://www.nuncbrand.com/page.aspx?ID=301 multi-well plate OBI:0400077 neodymium-YAG laser Neodymium-YAG Laser in DURIP99 System A Neodymium-YAG (yttrium aluminum garnet) laser is a solid state laser in which the lasing medium is a solid rod of crystalline material pumped by a flash lamp or a diode laser. Typical output wavelengths are 355, 532, and 1064 nm. A neodymium-YAG laser can by used to irradiate cells in a flow cytometer. Daniel Schober John Quinn neodymium-YAG laser OBI:0400078 obscuration bar obscuration bar in a flow cytometer An obscuration bar is a an optical subsystem which is a strip of metal or other material that serves to block out direct light from the illuminating beam. The obscuration bar prevents the bright light scattered in the forward directions from burning out the collection device. Daniel Schober Flow Cytometry: First Principles, by Alice Longobardi Givan, ISBN-10: 0471382248, ISBN-13: 978-0471382249 John Quinn obscuration bar OBI:0400079 optical filter 720 LP filter, 580/30 BP filter An optical filter is an optical subsystem that selectively transmits light having certain properties (often, a particular range of wavelengths, that is, range of colours of light), while blocking the remainder. They are commonly used in photography, in many optical instruments, and to colour stage lighting Optical filters can be arranged to segregate and collect light by wave length. John Quinn http://en.wikipedia.org/wiki/Optical_filter optical filter OBI:0400080 optical subsystem optical subsystem of a cytometer a device or part of a device that deals with the behavior and properties of light and the interaction of light with matter. Commonly optical subsystems consist of an excitation optics and collection optics. The excitation optics of a flow cytometer optical subsystem consist of the laser and lenses that are used to shape and focus the laser beam. The collections optics consist of a collection lens to collect light emitted from the particle laser beam interaction and a system of optical mirrors and filters to route specified wavelengths of the collected light to designated optical detectors. The optical subsystem in a flow cytometer consists of the equipment used to irradiate particles, and collect the light either emitted or scattered by those particles. DS: Is 'subsystem' necessary or is 'optical_system' enough. Not sure its graph position since an optical subsystem is not necessarily an instrument, but more likely part of one. Person: Daniel Schober John Quinn optical subsystem OBI:0400081 particle delivery vessel FC 500 particle delivery vessel Part of the fluidics subsystem. A particle delivery vessel is used to introduce either a single sample or multiple samples to a flow cytometer. The most common particle delivery vessel is a sample tube. John Quinn Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 FG: this should be delted - particle delivery is a role that an object can play particle delivery vessel OBI:0400082 photodetector A photomultiplier tube, a photo diode A photodetector is a device used to detect and measure the intensity of radiant energy through photoelectric action. In a cytometer, photodetectors measure either the number of photons of laser light scattered on impact with a cell (for example), or the flourescence emitted by excitation of a fluorescent dye. John Quinn http://einstein.stanford.edu/content/glossary/glossary.html photodetector OBI:0400083 photodiode Avalanche photodiode A photodiode is a semiconductor photodetector used to detect light and generate an electrical current. Typically used in forward scatter (FSC) detection. The photodiode collects the forward light scatter in a cytometer. John Quinn http://cyto.mednet.ucla.edu/Protocols/flow.htm photodiode OBI:0400084 photomultiplier tube R9647 by manufactured by Hamamatsu A photomultiplier is a device that is normally in the form of a tube, that uses a photocathode to convert photons into photoelectrons which are then amplified. PMTs are typically used to detect SSC and fluorescent parameters. Cytometers have a PMT for each color they can collect. John Quinn http://cyto.mednet.ucla.edu/Protocols/flow.htm photomultiplier tube OBI:0400085 piezo electric crystal quartz piezoelectric crystal, topaz piezoelectric crystal, piezoelectric crystal in a sonar Apparatus in the fluidic subsystem of sorters that vibrates to break up the stream coming out of the flow chamber into droplets for sorting. The peizo electric crystal vibrates in a manner that breaks off droplets at regular intervals. Not all droplets contain a cell. John Quinn http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm think this is natural thing, not a device HP/JF piezo electric crystal OBI:0400086 plate loader FC 500 plate loader Part of the fluidics system. A plate loader positions the wells of a multi-well plate under the aspiration tube is a preset order. A plate loader is used for high throughput applications. measurement function is not corret as discussed on April 26 dev call. Will add new function such as positioning function. Add to tracker will discuss in the future. John Quinn http://www.beckmancoulter.com/literature/Bioresearch/P-10202A.pdf plate loader OBI:0400087 preamplifier Built in preamplifier in a Hamamatsu H9656 PMT A preamplifier is part of the electronics subsystem. It converts the current output from its associated detector to a voltage. The preamplifier is the first stage in analog electronics signal processing. John Quinn Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 preamplifier OBI:0400088 quartz cuvette flow chamber CVF-Q-10 flow chamber, CV-Q-10 flow chamber A flow cell in which the laser irradiates the cell as it passes through a quartz cuvette. A quartz cuvette flow chamber can be used to allow the laser to irradiate cells. John Quinn http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm quartz cuvette flow chamber OBI:0400089 Reflection Reflection at TSRI Flow Cytometry Core Facility A Reflection is a sorter manufactured by iCyte. It uses digital signal processing, and can be configured with lasers of the users choice from among these excitation wavelengths: 355, 405,488, 532, 635nm. It accommodates up to 48 traditional PMTs. Options include an acousto-optical tunable filter (AOTF) and 16 channel spectrometer (370 to 730 nm). The various detection components can be uniquely configured across multiple Highly Automated Parallel Sorting (HAPS) modules. The Reflection can be used to analyse, sort, and collect cells. John Quinn http://www.i-cyt.com/reflection.htm Reflection OBI:0400091 cytometer sample tube sample tube in a cytometer A particle delivery vessel. The cytometer sample tube is a vessel in which the sample is introduced to the cytometer. Frequently the tube is placed on the cytometer in such a manner that a seal is formed between the tube and cytometer, and gas is used to create enough pressure to push the sample out of the tube and into the cytometer. John Quinn Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 cytometer sample tube OBI:0400094 sheath tank LSR2 sheath tank Part of the fluidics system. The sheath tank is the vessel that holds the sheath fluid at a constant pressure, allowing for it to be pushed into the flow chamber at a constant rate. The sheath tank holds the pressurized sheath fluid. John Quinn Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 sheath tank OBI:0400095 short pass filter 620 SP filter A short pass filter is an optical filter that passes low wavelengths of light but attenuates (or reduces) wavelengths higher than the cutoff frequency. A short pass filter with a cutoff of 500 nm would pass all wavelengths less than 500 nm. John Quinn http://en.wikipedia.org/wiki/Low-pass_filter short pass filter OBI:0400096 solid state laser Solid State Heat Capacity Laser developed at DOE's Lawrence Livermore National Laboratory for the USA Army's Space and Missile Defense Command A solid-state laser is a laser that uses a lasing medium that is a solid, rather than a liquid such as dye lasers or a gas such as gas lasers. Semiconductor-based diode lasers are also in the solid state, but are generally considered separately from solid-state lasers. The first laser developed was an optical pumped ruby crystal solid state laser. Daniel Schober http://en.wikipedia.org/wiki/Solid-state_laser solid state laser OBI:0400097 Somacount A Somacount is a flow_cytometer_analyser manufactured by Bently Instruments. It is a specialized tool for counting somatic cells in milk by specifically staining them with Ethidium Bromide and counting the cells that fluoresce. It has one laser, and the filters and a PMT for the single parameter. There are three sizes available, the 150, 300, and 500 with the number indicating the maximum number of cells that can be analysed per hour. The Somacount is an example of a very specific use cytometer; it exclusively counts somatic cells in milk. John Quinn http://www.bentleyinstruments.com/somacount.html#Anchor-Bentley-49575 Somacount OBI:0400098 SomaScope SomaScope Mark II Automatic Economical The SomaScope is an instrument to quantify somatic cells in milk. Josef Spidlen "http://www.aicompanies.com/DeltaCD/soma_auto_adv.htm, 2007-05-10" SomaScope OBI:0400099 flow cytometer sorter BioSorter2000, LSR2 A flow_cytometer_sorter is a flow_cytometer that analyzes and separates or sorts particles passing through (based on properties measured during analysis) to collect cells of interest. John Quinn Melanie Courtot http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm flow cytometer sorter OBI:0400100 syringe pump NE-1000 Single Syringe Pump Part of the fluidics system. A syringe pump can be used to inject the sample fluid and cells into the sheath fluid in the flow chamber. Syringe pumps are useful for creating stable flow rates. Person:John Quinn http://www.answers.com/topic/syringe, 2007-05-11 syringe pump OBI:0400101 voltage amplifier Linear amplifier, log amplifier, microwave amplifier A voltage amplifier is a device that amplifies the voltage signal. Frank Gibson John Quinn http://en.wiktionary.org/wiki/amplifier voltage amplifier OBI:0400102 waste tank LSR2 waste tank Part of the fluidics systems. In analyzers the sheath and sample fluid, once analyzed is dumped into a waste tank. The waste tank is where the fluids passing through the cytometer end up after the analysis is finished. Person:John Quinn Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 waste tank OBI:0400103 DNA sequencer ABI 377 DNA Sequencer, ABI 310 DNA Sequencer A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences. Trish Whetzel MO DNA sequencer OBI:0400104 array scanner GenePix 4200A, GenePix4000B An processed material which acquires images of fluorescence (induced with lasers) from labeled molecules on the surface of the microarray chip Trish Whetzel GROUP: MGED Ontology array scanner OBI:0400105 arrayer BioRobotics Microgrid II TAS, Affymetrix GMS 417 a device which deposits biological material onto a substrate in a defined pattern. Trish Whetzel MO_697 arrayer arrayer OBI:0400106 centrifuge A device with a rapidly rotating container that applies centrifugal force to its contents Melanie Courtot Person: Jennifer Fostel Trish Whetzel http://en.wikipedia.org/wiki/Centrifuge centrifuge OBI:0400107 computer Apple PowerBook, Dell OptiPlex A computer is an instrument which manipulates (stores, retrieves, and processes) data according to a list of instructions. Melanie Courtot Trish Whetzel http://en.wikipedia.org/wiki/Computer computer OBI:0400108 heating block An instrument used to heat and/or maintain material at a set temperature. A heating block is an instrument or part of an instrument which raises or maintains the temperature of a sample to a defined constant temperature during certain parts of an assay Daniel Schober MO heating block OBI:0400109 homogenizer mortar, blender A homogenizer is an instrument for the homogenization of various types of material, such as tissue, plant, food, soil, and many others. Melanie Courtot Trish Whetzel http://en.wikipedia.org/wiki/Homogenizer homogenizer OBI:0400110 hybridization chamber Glass Array Hybridization Cassette A device which is used to maintain constant contact of a liquid on an array. This can be either a glass vial or slide. Trish Whetzel MO_563 hybridization_chamber hybridization chamber OBI:0400111 hybridization station Labnet Problot12 A device which is used to maintain the temperature of one or more hybridization_chamber(s) at a defined, constant temperature. Trish Whetzel MO_497 hybridization station hybridization station OBI:0400112 liquid handler Beckman BioMek 2000 a device that is used for automated liquid transfer and handling. liquid_handling_instrument MO_868 liquid_handler DS: Is this class justified? Its a unnamed class. If so, put a fluidic_system and the fluidic_subsystem as subclasses. TW: This is required by MO. FG & DS: Capture as function. All: Needs to be reviewed, according to query use case. If we keep it its kept as unnamed owl class. The liquid handling class remains but as an undefined class with are unlikely to have children. It is expected that the reasoner would classifiy appropriate classes under this class that meet the have the liquid_handling function relation. DS: Is this class justified? Its a unnamed class. If so, put a fluidic_system and the fluidic_subsystem as subclasses. TW: This is required by MO. FG: Or as function. liquid handler OBI:0400113 oligonucleotide synthesizer Automated Multiplex Oligonucleotide Synthesizer An instrument used to chemically synthesize oligonucleotides. Trish Whetzel MO oligonucleotide synthesizer OBI:0400114 sonicator Sonicator 3000 A device that converts a variable electrical current to mechanical vibration of a metallic probe. The device is used for the lysis of cells, the mixing of compounds or solutions, to framgent molecules of DNA, or to create emulsions. Trish Whetzel MO sonicator OBI:0400115 spectrophotometer Helios Gamma Spectrophotometer A spectrophotometer is an instrument that measures the intensity of light as a function of the color, or more specifically, the wavelength of light, transmitted by a substance. Melanie Courtot Trish Whetzel MO spectrophotometer OBI:0400116 thermal cycler Piko(tm) 96-well Thermal Cycler An instrument that is capable of repeatedly altering and maintaining specific temperatures for defined periods of time. Melanie Courtot Trish Whetzel DNA_amplifier PCR_machine Polymerase_Chain_Reaction_ machine thermocycler MO thermal cycler OBI:0400117 vacuum dryer Model 777 Microarray Oven An instrument which removes liquid by the application of negative pressure, i.e. vacuum. Trish Whetzel MO vacuum dryer OBI:0400118 vortexer VWR Genie 2 A vortexer is an instrument that mixes small vials of liquid by creating a rotation of the liquid around its own center. It consists of an electric motor with the drive shaft oriented vertically and attached to a cupped rubber piece mounted slightly off-center. As the motor runs the rubber piece oscillates rapidly in a circular motion. When a test tube or other appropriate container is pressed into the rubber cup (or touched to its edge) the motion is transmitted to the liquid inside and a vortex is created. Melanie Courtot Trish Whetzel vortex_mixer http://en.wikipedia.org/wiki/Vortex_mixer vortexer OBI:0400119 microarray wash station ArrayIt(r) Microarray Wash Station a device that is used to wash Affymetrix-type arrays. Trish Whetzel MO_626 wash_station microarray wash station OBI:0400120 temperature control bath VWR Signature Deep-Chamber Heated Water Bath. A water bath is used for temperatures up to 100 degrees C. An oil bath is employed for temperatures over 100 degrees C. A temperature_control_bath is a device that has the function to regulate the temperature of a material, the function to contain fluid and the function to vary and maintain the temperature of the contained fluid. Heat exchange (energy transfer) between the material and the heating element is facilitated via the contained fluid. A temperature_control_bath is composed of a container, a heating element and/or a cooling element and a means to adjust the needed temperature. In most cases also a timer and a means to stir the fluid is provided as well. Alan Ruttenburg Daniel Schober Frank Gibson OBI Instrument branch DS: This was heated_bath. It was renamed to reflect the possability that the same bath can be used for cooling. We can now define the temperature variables and based on that infer if it is a cooling device or a heating device (also quite relative to surrounding temperature). temperature control bath OBI:0400121 molecular crosslinker Stratalinker a device that is able to chemically join two or more molecules. AL: if we intend that other ontologies can be used in conjunction with OBI, we shouldn't have such a general term used specifically for chemically joining two or more molecules. I'm sure there are other "crosslinkers" that are on a much different scale in engineering etc. I have moved the original label to be an alternative term, and have renamed the main label accordingly. Trish Whetzel molecular crosslinker MO ?? cannot be found in MO molecular crosslinker OBI:0400135 image cytometer The most common current application of image cytometry is for DNA analysis, followed by quantitation of immunohistochemical staining. An image_cytometer is an instrument for image-based study or measurement of cells. Melanie Courtot http://web.mit.edu/solab/Research/ImageCytometry.html image cytometer OBI:0400137 cytometer A cytometer is an instrument for counting and measuring cells. Melanie Courtot http://medical.merriam-webster.com/medical/cytometer cytometer OBI:0400140 gel tank CHEF gel box, slab gel box, capillary electrophoresis a device which holds a gel and running buffers to allow electrophoresis to be performed. A gel tank has the function to contain and to control the contained environment and transfer energy from an energy supply through the running buffers to the gel matrix and the material with charged molecules in an electric field across a porous matrix or medium with the objective to separate the charged molecules. Person:Frank Gibson Person:Kevin Clancy electrophoresis box electrophoresis unit sep:00095 gel tank OBI:0400142 power supply A AC/DC transformer that generates the reqired power for an electrophoresis apparatus A power supply is an device or part of a device that permits the required application of a defined electrical charge to an instrument. The power supply may permit the defined application of a given amount of current for a defined length of time. Daniel Schober Frank Gibson PSU electrical power supply power pack power supply unit PERSON: Daniel Schober sep:00093 was power_pack, maps to SEP electrical_power_supply power supply OBI:0400143 fluorometer laser/detector in capillary electrophoresis apparatus, NanoDrop ND-3300 A fluorometer is an instrument for the detection and measurement of parameters of fluoresence, which in turn are used to identify the presence and amount of specific molecules in the sample. Allyson Lister Kevin Lister OBI fluorometer OBI:0400146 multispectral imaging flow cytometer A multispectral_imaging_flow_cytometer is an instrument which combines quantitative image analysis and flow cytometry in a single platform. It measures the amount, location and movement of molecules on, in, or between cells, and the location and co-localization of multiple markers on or in cells. It can also quantitate morphologically distinct cell subpopulations. Melanie Courtot MIFC http://www.amnis.com/ multispectral imaging flow cytometer OBI:0400147 microarray An affymetrix U133 array is a microarray. Microarrays include 1 and 2-color arrays, custom and commercial arrays (e.g, Affymetrix, Agilent, Nimblegen, Illumina, etc.) for expression profiling, DNA variant detection, protein binding, and other genomic and functional genomic assays. A processed material that is made to be used in an analyte assay. It consists of a physical immobilisation matrix in which substances that bind the analyte are placed in regular spatial position. Daniel Schober PERSON: Chris Stoeckert microarray OBI:0400148 DNA microarray Moran G, Stokes C, Thewes S, Hube B, Coleman DC, Sullivan D (2004). "Comparative genomics using Candida albicans DNA microarrays reveals absence and divergence of virulence-associated genes in Candida dubliniensis". Microbiology 150: 3363-3382. doi:10.1099/mic.0.27221-0. PMID 15470115 A DNA-microarray is a microarray that is used as a physical 2D immobilisation matrix for DNA sequences. DNA microarray-bound DNA fragments are used as targets for a hybridising probed sample. PERSON: Daniel Schober PERSON: Frank Gibson DNA Chip DNA-array Web:<http://en.wikipedia.org/wiki/DNA_microarray>@2008/03/03 DNA microarray OBI:0400149 protein microarray The most common protein microarray is the antibody microarray, where antibodies are spotted onto the protein chip and are used as capture molecules to detect proteins from cell lysate solutions. A protein-microarray is a microarray, ususlly a piece of glass, on which different molecules of protein have been affixed at separate locations in an ordered manner. These are used to identify protein-protein or protein-small molecule interactions. Daniel Schober PERSON: Daniel Schober protein microarray OBI:0400153 droplet sorter A droplet sorter is part_of a flow cytometer sorter that converts the carrier fluid stream into individual droplets, and these droplets are directed into separate locations for recovery (enriching the original sample for particles of interest based on qualities determined by gating) or disposal. OBI Instrument branch OBI Instrument branch droplet sorter OBI:0400155 water bath A water bath was used to allow for cell incubation at 38 degree centigrade for 8 hours. A water bath is a temperature control bath in which a water acts as contact medium enabling temperature transfer from the heating element or cooling element to the sample. The temperature can be controlled in the 0 to 100 degree centigrade range (under normal pressure). Daniel Schober PERSON: Daniel Schober water bath OBI:0400157 oil bath An oil bath was used to allow for fast reaction of two chemical compounds during a 2 hour period. An oil bath is a temperature control bath in which oil acts as contact medium for the temperature transfer (from heating or cooling elements to the sample). Daniel Schober PERSON: Daniel Schober oil bath OBI:0400158 digital-to-analog converter A digital-to-analog_converter is used to convert a computergenerated discrete signal into a continuous analog one, e.g. a sound. A digital-to-analog_converter is an instrument that converts a finite resolution digital signal into an infinite resolution analog signal. Daniel Schober PERSON: Daniel Schober digital-to-analog converter OBI:0400168 microtome PMID: 9974145.Serial sectioning of thick tissue with a novel vibrating blade microtome. Brain Res Brain Res Protoc. 1999 Jan;3(3):302-7. A microtome is a mechanical instrument used to cut biological specimens into very thin segments for further treatment (e.g. ISH) and ultimately microscopic or histologic examination. Most microtomes provide cooling facilities (cryo-microtome) and use a steel blade to cut a slice of defined thickness. Some are automatic, and some are driven by hand. PERSON: Phillippe Rocca-Serra PERSON: Daniel Schober microtome OBI:0400169 microscope PMID:18466942. A light and transmission electron microscope study of hepatic portal tracts in the rhesus monkey (Macacus rhesus). Tissue Cell. 2008 May 6 A microscope is an instrument which magnifies the view on objects (too small to be viewed by the naked eye) under increased resolution. A microscope can be an optical instrument but also and electronic instrument. There are various kind of optical microscopes, e.g confocal microscope, epifluoresence microscope) PERSON: Phillippe Rocca-Serra wikipedia microscope OBI:0400170 microscope slide PMID: 9668975.Microscope slide for enhanced analysis of DNA damage using the comet assay. a microscope slide is a device usually made of glass which is used as a solid matrix for (biological) material deposited on its surface and which is compatible for use with a microscope instrument PERSON: Phillippe Rocca-Serra OBI biomaterial branch microscope slide OBI:0400171 animal cage PMID: 18246864.Barthold SW.Effects of cage density on behavior in young adult mice. a processed material which has the function to define a bounded habitat which is amenable to keeping animals. PERSON: Phillippe Rocca-Serra laboratory cage OBI biomaterial branch animal cage OBI:0500000 study design a matched pairs study design describes criteria by which subjects are identified as pairs which then undergo the same protocols, and the data generated is analyzed by comparing the differences between the paired subjects, which constitute the results of the executed study design. A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution. Editor note: there is at least an implicit restriction on the kind of data transformations that can be done based on the measured data available. PERSON: Chris Stoeckert experimental design rediscussed at length (MC/JF/BP). 12/9/08). The definition was clarified to differentiate it from protocol. study design OBI:0500001 clinical study design PMID: 17655677.J Cardiovasc Electrophysiol. 2007 Aug;18(9):965-71.Biventricular versus right ventricular pacing in patients with AV block (BLOCK HF): clinical study design and rationale. Plan for the precise procedure to be followed in a clinical trial, including planned and actual timing of events, choice of control group, method of allocating treatments, blinding methods; assigns a subject to pass through one or more epochs in the course of a trial. Specific design elements, e.g., crossover, parallel; dose-escalation [Modified from Pocock, Clinical Trials: A Practical Approach] The definition needs to be extended to other things than simply patients PlanAndPlannedProcess Branch Clinical Research Glossary Version 4.0 CDICS glossary group clinical study design OBI:0500002 repeated measure design PMID: 10959922.J Biopharm Stat. 2000 Aug;10(3):433-45.Equivalence in test assay method comparisons for the repeated-measure, matched-pair design in medical device studies: statistical considerations. a study design which use the same individuals and exposure them to a set of conditions. The effect of order and practice can be confounding factor in such designs PlanAndPlannedProcess Branch http://www.holah.karoo.net/experimentaldesigns.htm repeated measure design OBI:0500003 cross over design PMID: 17601993-Objective: HIV-infected patients with lipodystrophy (HIV-lipodystrophy) are insulin resistant and have elevated plasma free fatty acid (FFA) concentrations. We aimed to explore the mechanisms underlying FFA-induced insulin resistance in patients with HIV-lipodystrophy. Research Design and Methods: Using a randomized placebo-controlled cross-over design, we studied the effects of an overnight acipimox-induced suppression of FFA on glucose and FFA metabolism by using stable isotope labelled tracer techniques during basal conditions and a two-stage euglycemic, hyperinsulinemic clamp (20 mU insulin/m(2)/min; 50 mU insulin/m(2)/min) in nine patients with nondiabetic HIV-lipodystrophy. All patients received antiretroviral therapy. Biopsies from the vastus lateralis muscle were obtained during each stage of the clamp. Results: Acipimox treatment reduced basal FFA rate of appearance by 68.9% (52.6%-79.5%) and decreased plasma FFA concentration by 51.6 % (42.0%-58.9%), (both, P < 0.0001). Endogenous glucose production was not influenced by acipimox. During the clamp the increase in glucose-uptake was significantly greater after acipimox treatment compared to placebo (acipimox: 26.85 (18.09-39.86) vs placebo: 20.30 (13.67-30.13) mumol/kg/min; P < 0.01). Insulin increased phosphorylation of Akt (Thr(308)) and GSK-3beta (Ser(9)), decreased phosphorylation of glycogen synthase (GS) site 3a+b and increased GS-activity (I-form) in skeletal muscle (P < 0.01). Acipimox decreased phosphorylation of GS (site 3a+b) (P < 0.02) and increased GS-activity (P < 0.01) in muscle. Conclusion: The present study provides direct evidence that suppression of lipolysis in patients with HIV-lipodystrophy improves insulin-stimulated peripheral glucose-uptake. The increased glucose-uptake may in part be explained by increased dephosphorylation of GS (site 3a+b) resulting in increased GS activity. a repeated measure design which ensures that experimental units receive, in sequence, the treatment (or the control), and then, after a specified time interval (aka *wash-out periods*), switch to the control (or treatment). In this design, subjects (patients in human context) serve as their own controls, and randomization may be used to determine the ordering which a subject receives the treatment and control Philippe Rocca-Serra (source: http://www.sbu.se/Filer/Content0/publikationer/1/literaturesearching_1993/glossary.html) cross over design OBI:0500004 n-to-1 design N-of-1 design is a cross-over design in which the same patient is repeatedly randomised to receive either the experimental treatment or its control (Senn, 1993). Philippe Rocca-Serra Adapted from http://www.childrens-mercy.org/stats/definitions/crossover.htm and source:http://symptomresearch.nih.gov/chapter_6/sec1/csss1pg1.htm) n-to-1 design OBI:0500005 matched pairs design PMID: 17288613-BSTRACT: BACKGROUND: Physicians in Canadian emergency departments (EDs) annually treat 185,000 alert and stable trauma victims who are at risk for cervical spine (C-spine) injury. However, only 0.9% of these patients have suffered a cervical spine fracture. Current use of radiography is not efficient. The Canadian C-Spine Rule is designed to allow physicians to be more selective and accurate in ordering C-spine radiography, and to rapidly clear the C-spine without the need for radiography in many patients. The goal of this phase III study is to evaluate the effectiveness of an active strategy to implement the Canadian C-Spine Rule into physician practice. Specific objectives are to: 1) determine clinical impact, 2) determine sustainability, 3) evaluate performance, and 4) conduct an economic evaluation. METHODS: We propose a matched-pair cluster design study that compares outcomes during three consecutive 12-months before, after, and decay periods at six pairs of intervention and control sites. These 12 hospital ED sites will be stratified as teaching or community hospitals, matched according to baseline C-spine radiography ordering rates, and then allocated within each pair to either intervention or control groups. During the after period at the intervention sites, simple and inexpensive strategies will be employed to actively implement the Canadian C-Spine Rule. The following outcomes will be assessed: 1) measures of clinical impact, 2) performance of the Canadian C-Spine Rule, and 3) economic measures. During the 12-month decay period, implementation strategies will continue, allowing us to evaluate the sustainability of the effect. We estimate a sample size of 4,800 patients in each period in order to have adequate power to evaluate the main outcomes. DISCUSSION: Phase I successfully derived the Canadian C-Spine Rule and phase II confirmed the accuracy and safety of the rule, hence, the potential for physicians to improve care. What remains unknown is the actual change in clinical behaviors that can be affected by implementation of the Canadian C-Spine Rule, and whether implementation can be achieved with simple and inexpensive measures. We believe that the Canadian C-Spine Rule has the potential to significantly reduce health care costs and improve the efficiency of patient flow in busy Canadian EDs. A matched pair design is a study design which use groups of individuals associated (hence matched) to each other based on a set of criteria, one member going to one treatment, the other member receiving the other treatment. Philippe Rocca-Serra http://www.holah.karoo.net/experimentaldesigns.htm matched pairs design OBI:0500006 parallel group design PMID: 17408389-Purpose: Proliferative vitreoretinopathy (PVR) is the most important reason for blindness following retinal detachment. Presently, vitreous tamponades such as gas or silicone oil cannot contact the lower part of the retina. A heavier-than-water tamponade displaces the inflammatory and PVR-stimulating environment from the inferior area of the retina. The Heavy Silicone Oil versus Standard Silicone Oil Study (HSO Study) is designed to answer the question of whether a heavier-than-water tamponade improves the prognosis of eyes with PVR of the lower retina. Methods: The HSO Study is a multicentre, randomized, prospective controlled clinical trial comparing two endotamponades within a two-arm parallel group design. Patients with inferiorly and posteriorly located PVR are randomized to either heavy silicone oil or standard silicone oil as a tamponading agent. Three hundred and fifty consecutive patients are recruited per group. After intraoperative re-attachment, patients are randomized to either standard silicone oil (1000 cSt or 5000 cSt) or Densiron((R)) as a tamponading agent. The main endpoint criteria are complete retinal attachment at 12 months and change of visual acuity (VA) 12 months postoperatively compared with the preoperative VA. Secondary endpoints include complete retinal attachment before endotamponade removal, quality of life analysis and the number of retina affecting re-operation within 1 year of follow-up. Results: The design and early recruitment phase of the study are described. Conclusions: The results of this study will uncover whether or not heavy silicone oil improves the prognosis of eyes with PVR. A parallel group design or independent measure design is a study design which uses unique experimental unit each experimental group, in other word no two individuals are shared between experimental groups, hence also known as parallel group design. Subjects of a treatment group receive a unique combination of independent variable values making up a treatment Philippe Rocca-Serra independent measure design http://www.holah.karoo.net/experimentaldesigns.htm parallel group design OBI:0500007 randomized complete block design http://www.stats.gla.ac.uk/steps/glossary/anova.html,(A researcher is carrying out a study of the effectiveness of four different skin creams for the treatment of a certain skin disease. He has eighty subjects and plans to divide them into 4 treatment groups of twenty subjects each. Using a randomised blocks& design, the subjects are assessed and put in blocks of four according to how severe their skin condition is; the four most severe cases are the first block, the next four most severe cases are the second block, and so on to the twentieth block. The four &members of each block are then randomly assigned, one to each of the four treatment groups. http://www.stats.gla.ac.uk/steps/glossary/anova.html#rbd)) A randomized complete block design is_a study design which assigns randomly treatments to block. The number of units per block equals the number of treatment so each block receives each treatment exactly once (hence the qualifier 'complete'). The design was originally devised from field trials used in agronomy and agriculture. The analysis assumes that there is no interaction between block and treatment. The method was then used in other settings So The randomised complete block design is a design in which the subjects are matched according to a variable which the experimenter wishes to control. The subjects are put into groups (blocks) of the same size as the number of treatments. The members of each block are then randomly assigned to different treatment groups. Philippe Rocca-Serra http://www.tufts.edu/~gdallal/ranblock.htm randomized complete block design OBI:0500008 balanced incomplete block design PMID: 7622388.Health Educ Q. 1995 May;22(2):201-10.Balanced incomplete block design: description, case study, and implications for practice. balanced incomplete block design is a kind of factorial design where all treatment pairs occur together within a block an equal number ?? times. ??ii' is the number of times treatment i occurs with i' Philippe Rocca-Serra http://en.wikipedia.org/wiki/Block_design and http://www.stat.psu.edu/~jglenn/stat503/05_factorial/02_factorial_IBD.html balanced incomplete block design OBI:0500009 loop design PMID: 12933549 A loop experiment design is where labeled extracts are compared in consecutive pairs. synonym: circular design Philippe Rocca-Serra on behalf of MO MO_912 loop design OBI:0500010 reference design PMID: 12933549 A reference experiment design type is where all samples are compared to a common reference. Philippe Rocca-Serra on behalf of MO MO_699 reference design OBI:0500011 latin square design PMID: 17582121-Our objective was to examine the effects of dietary cation-anion difference (DCAD) with different concentrations of dietary crude protein (CP) on performance and acid-base status in early lactation cows. Six lactating Holstein cows averaging 44 d in milk were used in a 6 x 6 Latin square design with a 2 x 3 factorial arrangement of treatments: DCAD of -3, 22, or 47 milliequivalents (Na + K - Cl - S)/100 g of dry matter (DM), and 16 or 19% CP on a DM basis. Linear increases with DCAD occurred in DM intake, milk fat percentage, 4% fat-corrected milk production, milk true protein, milk lactose, and milk solids-not-fat. Milk production itself was unaffected by DCAD. Jugular venous blood pH, base excess and HCO3(-) concentration, and urine pH increased, but jugular venous blood Cl- concentration, urine titratable acidity, and net acid excretion decreased linearly with increasing DCAD. An elevated ratio of coccygeal venous plasma essential AA to nonessential AA with increasing DCAD indicated that N metabolism in the rumen was affected, probably resulting in more microbial protein flowing to the small intestine. Cows fed 16% CP had lower urea N in milk than cows fed 19% CP; the same was true for urea N in coccygeal venous plasma and urine. Dry matter intake, milk production, milk composition, and acid-base status did not differ between the 16 and 19% CP treatments. It was concluded that DCAD affected DM intake and performance of dairy cows in early lactation. Feeding 16% dietary CP to cows in early lactation, compared with 19% CP, maintained lactation performance while reducing urea N excretion in milk and urine. Latin square design is_a study design which allows in its simpler form controlling 2 levels of nuisance variables (also known as blocking variables).he 2 nuisance factors are divided into a tabular grid with the property that each row and each column receive each treatment exactly once. Philippe Rocca-Serra Adapted from: http://www.itl.nist.gov/div898/handbook/pri/section3/pri3321.htm and latin square design OBI:0500012 graeco latin square design PMID: 6846242-Beaton et al (Am J Clin Nutr 1979;32:2546-59) reported on the partitioning of variance in 1-day dietary data for the intake of energy, protein, total carbohydrate, total fat, classes of fatty acids, cholesterol, and alcohol. Using the same food intake data and the expanded National Heart, Lung and Blood Institute food composition data base, these analyses of sources of variance have been expanded to include classes of carbohydrate, vitamin A, vitamin C, thiamin, riboflavin, niacin, calcium, iron, total ash, caffeine, and crude fiber. The analyses relate to observed intakes (replicated six times) of 30 adult males and 30 adult females obtained under a paired Graeco-Latin square design with sequence of interview, interviewer, and day of the week as determinants. Neither sequence nor interviewer made consistent contribution to variance. In females, day of the week had a significant effect for several nutrients. The major partitioning of variance was between interindividual variation (between subjects) and intraindividual variation (within subjects) which included both true day-to-day variation in intake and methodological variation. For all except caffeine, the intraindividual variability of 1-day data was larger than the interindividual variability. For vitamin A, almost all of the variance was associated with day-to-day variability. One day data provide a very inadequate estimate of usual intake of individuals. In the design of nutrition studies it is critical that the intended use of dietary data be a major consideration in deciding on methodology. There is no ideal dietary method. There may be preferred methods for particular purposes. Greco-Latin square design is a study design which relates to Latin square design Philippe Rocca-Serra Adapted from: http://www.itl.nist.gov/div898/handbook/pri/section3/pri3321.htm and only 2 articles in pubmed ->probably irrelevant graeco latin square design OBI:0500013 hyper graeco latin square design PRS to do Philippe Rocca-Serra Adapted from: http://www.itl.nist.gov/div898/handbook/pri/section3/pri3321.htm and no example found in pubmed->not in use in the community hyper graeco latin square design OBI:0500014 factorial design PMID: 17582121-Our objective was to examine the effects of dietary cation-anion difference (DCAD) with different concentrations of dietary crude protein (CP) on performance and acid-base status in early lactation cows. Six lactating Holstein cows averaging 44 d in milk were used in a 6 x 6 Latin square design with a 2 x 3 factorial arrangement of treatments: DCAD of -3, 22, or 47 milliequivalents (Na + K - Cl - S)/100 g of dry matter (DM), and 16 or 19% CP on a DM basis. Linear increases with DCAD occurred in DM intake, milk fat percentage, 4% fat-corrected milk production, milk true protein, milk lactose, and milk solids-not-fat. Milk production itself was unaffected by DCAD. Jugular venous blood pH, base excess and HCO3(-) concentration, and urine pH increased, but jugular venous blood Cl- concentration, urine titratable acidity, and net acid excretion decreased linearly with increasing DCAD. An elevated ratio of coccygeal venous plasma essential AA to nonessential AA with increasing DCAD indicated that N metabolism in the rumen was affected, probably resulting in more microbial protein flowing to the small intestine. Cows fed 16% CP had lower urea N in milk than cows fed 19% CP; the same was true for urea N in coccygeal venous plasma and urine. Dry matter intake, milk production, milk composition, and acid-base status did not differ between the 16 and 19% CP treatments. It was concluded that DCAD affected DM intake and performance of dairy cows in early lactation. Feeding 16% dietary CP to cows in early lactation, compared with 19% CP, maintained lactation performance while reducing urea N excretion in milk and urine. factorial design is_a study design which is used to evaluate two or more factors simultaneously. The treatments are combinations of levels of the factors. The advantages of factorial designs over one-factor-at-a-time experiments is that they are more efficient and they allow interactions to be detected. In statistics, a factorial design experiment is an experiment whose design consists of two or more factors, each with discrete possible values or levels, and whose experimental units take on all possible combinations of these levels across all such factors. Such an experiment allows studying the effect of each factor on the response variable, as well as the effects of interactions between factors on the response variable. Philippe Rocca-Serra http://www.stats.gla.ac.uk/steps/glossary/anova.html#facdes And from wikipedia (01/03/2007): http://en.wikipedia.org/wiki/Factorial_experiment) factorial design OBI:0500015 2x2 factorial design PMID: 17561240-The present experiment evaluates the effects of intermittent exposure to a social stimulus on ethanol and water drinking in rats. Four groups of rats were arranged in a 2x2 factorial design with 2 levels of Social procedure (Intermittent Social vs Continuous Social) and 2 levels of sipper Liquid (Ethanol vs Water). Intermittent Social groups received 35 trials per session. Each trial consisted of the insertion of the sipper tube for 10 s followed by lifting of the guillotine door for 15 s. The guillotine door separated the experimental rat from the conspecific rat in the wire mesh cage during the 60 s inter-trial interval. The Continuous Social groups received similar procedures except that the guillotine door was raised during the entire duration of the session. For the Ethanol groups, the concentrations of ethanol in the sipper [3, 4, 6, 8, 10, 12, 14, and 16% (vol/vol)] increased across sessions, while the Water groups received 0% ethanol (water) in the sipper throughout the experiment. Both Social procedures induced more intake of ethanol than water. The Intermittent Social procedure induced more ethanol intake at the two highest ethanol concentration blocks (10-12% and 14-16%) than the Continuous Social procedure, but this effect was not observed with water. Effects of social stimulation on ethanol drinking are discussed. a factorial design which has 2 experimental factors (aka independent variables) and 2 factor levels per experimental factors Philippe Rocca-Serra PMID: 17561240 2x2 factorial design OBI:0500016 fractional factorial design A fractional factorial design is_a study design in which only an adequately chosen fraction of the treatment combinations required for the complete factorial experiment is selected to be run Philippe Rocca-Serra http://www.itl.nist.gov/div898/handbook/pri/section3/pri334.htm From ASQC (1983) Glossary & Tables for Statistical Quality Control fractional factorial design OBI:0500017 dye swap design PMID: 17411393-Dye-specific bias effects, commonly observed in the two-color microarray platform, are normally corrected using the dye swap design. This design, however, is relatively expensive and labor-intensive. We propose a self-self hybridization design as an alternative to the dye swap design. In this design, the treated and control samples are labeled with Cy5 and Cy3 (or Cy3 and Cy5), respectively, without dye swap, along with a set of self-self hybridizations on the control sample. We compare this design with the dye swap design through investigation of mouse primary hepatocytes treated with three peroxisome proliferator-activated receptor-alpha (PPARalpha) agonists at three dose levels. Using Agilent's Whole Mouse Genome microarray, differentially expressed genes (DEG) were determined for both the self-self hybridization and dye swap designs. The DEG concordance between the two designs was over 80% across each dose treatment and chemical. Furthermore, 90% of DEG-associated biological pathways were in common between the designs, indicating that biological interpretations would be consistent. The reduced labor and expense for the self-self hybridization design make it an efficient substitute for the dye swap design. For example, in larger toxicogenomic studies, only about half the chips are required for the self-self hybridization design compared to that needed in the dye swap design. An experiment design type where the label orientations are reversed. exact synonym: flip dye, dye flip Philippe Rocca-Serra on behalf of MO MO_858 dye swap design OBI:0500018 replicate design A replicate experimental design type is where a series of replicates are performed to evaluate reproducibility or as a pilot study to determine the appropriate number of replicates for a subsequent experiments. Philippe Rocca-Serra on behalf of MO MO_885 replicate design OBI:0500019 self vs self design PMID: 17411393-Dye-specific bias effects, commonly observed in the two-color microarray platform, are normally corrected using the dye swap design. This design, however, is relatively expensive and labor-intensive. We propose a self-self hybridization design as an alternative to the dye swap design. In this design, the treated and control samples are labeled with Cy5 and Cy3 (or Cy3 and Cy5), respectively, without dye swap, along with a set of self-self hybridizations on the control sample. We compare this design with the dye swap design through investigation of mouse primary hepatocytes treated with three peroxisome proliferator-activated receptor-alpha (PPARalpha) agonists at three dose levels. Using Agilent's Whole Mouse Genome microarray, differentially expressed genes (DEG) were determined for both the self-self hybridization and dye swap designs. The DEG concordance between the two designs was over 80% across each dose treatment and chemical. Furthermore, 90% of DEG-associated biological pathways were in common between the designs, indicating that biological interpretations would be consistent. The reduced labor and expense for the self-self hybridization design make it an efficient substitute for the dye swap design. For example, in larger toxicogenomic studies, only about half the chips are required for the self-self hybridization design compared to that needed in the dye swap design. A study design that investigates variance and error estimates in the experimental system, and is where the same extract is compared. Philippe Rocca-Serra on behalf of MO MO_490 self vs self design OBI:0500020 time series design PMID: 14744830-Microarrays are powerful tools for surveying the expression levels of many thousands of genes simultaneously. They belong to the new genomics technologies which have important applications in the biological, agricultural and pharmaceutical sciences. There are myriad sources of uncertainty in microarray experiments, and rigorous experimental design is essential for fully realizing the potential of these valuable resources. Two questions frequently asked by biologists on the brink of conducting cDNA or two-colour, spotted microarray experiments are 'Which mRNA samples should be competitively hybridized together on the same slide?' and 'How many times should each slide be replicated?' Early experience has shown that whilst the field of classical experimental design has much to offer this emerging multi-disciplinary area, new approaches which accommodate features specific to the microarray context are needed. In this paper, we propose optimal designs for factorial and time course experiments, which are special designs arising quite frequently in microarray experimentation. Our criterion for optimality is statistical efficiency based on a new notion of admissible designs; our approach enables efficient designs to be selected subject to the information available on the effects of most interest to biologists, the number of arrays available for the experiment, and other resource or practical constraints, including limitations on the amount of mRNA probe. We show that our designs are superior to both the popular reference designs, which are highly inefficient, and to designs incorporating all possible direct pairwise comparisons. Moreover, our proposed designs represent a substantial practical improvement over classical experimental designs which work in terms of standard interactions and main effects. The latter do not provide a basis for meaningful inference on the effects of most interest to biologists, nor make the most efficient use of valuable and limited resources. Groups of assays that are related as part of a time series. Philippe Rocca-Serra on behalf of MO MO_887 time series design OBI:0500022 stopping rule PMID: 17591081-BACKGROUND/AIMS: To investigate the viral kinetics of Chinese CHC patients received pegylated interferon plus ribavirin and examine the impact of HCV genotypes and severity of liver disease. METHODOLOGY: 65 treatment-naove CHC patients who finished a 24-week therapy with peginterferon (alpha-2b (1.5 mcg/kg/week) plus ribavirin (1000-1200 mg /day) and 24 weeks of follow-up were enrolled. Hepatic fibrosis was graded by the METAVIR scoring system. Serum quantitative HCV RNA was determined by Versant HCV RNA 3.0 assay (Bayer Inc.). RESULTS: Genotype non-1 patients responded quickly and a higher percentage of them achieved undetectable HCV RNA (< 615 IU/mL) at week 4 compared with genotype 1 patients (93% vs. 69%, p = 0.018). Degree of hepatic fibrosis significantly affected end-of-treatment and sustained response (SVR). For patients who did not achieve early virological response (EVR), the negative predictive value for SVR was 100%. In genotype 1 patients, undetectable HCV RNA by week 4 was a good marker to predict treatment response, with a positive predictive value of 84% and a negative predictive value of 82%. CONCLUSIONS: EVR can be applied to Chinese patients as an early stopping rule. A 24-week duration of pegylated IFN/ribavirin might be adequate for genotype 1 patients who rapidly responded to therapy. a stopping rule (criterion) is_a *rule* which causes a *stopping process* to happen PRS PRS stopping rule OBI:0500023 compliance rule a compliance rule is a rule which ensures a compliance process occurs PRS PRS compliance rule OBI:0500024 standard compliance rule a standard compliance rule is a compliance rule which defines conformity to a representation standard PRS PRS standard compliance rule OBI:0500025 ethical standard compliance rule an ethical standard compliance rule is_a *compliance rule* which enable a *ethical compliance process* to occur PRS PRS ethical standard compliance rule OBI:0500026 eligibility criterion PMID: 17579629 -Eligibility criteria included: untreated ED-SCLC; age >/=70 and performance status 0-2, or age <70 and PS 3. an eligibility criterion (rule) is_a selection criterion which defines and states the requirements (positive or negative) for an entity to be considered as suitable for a given task or participation in a process. Person: Philippe Rocca-Serra eligibility rule Adapted from Clinical Research Glossary Version 4.0 CDICS glossary group eligibility criterion OBI:0500027 inclusion criteria PMID: 23979341-The major inclusion criterion was patients in whom severe cerebral embolism was diagnosed at age 75 or younger (more than 9 in the NIHSS score on day 7 after the onset of stroke) . an inclusion criterion (rule) is_a *eligibility criterion* which defines and states a condition which, if met, makes an entity suitable for a given task or participation in a given process. For instance, in a study protocol, inclusion criteria indicate the conditions that prospective subjects MUST meet to be eligible for participation in a study. Person: Philippe Rocca-Serra inclusion condition inclusion rule Adapted from Clinical Research Glossary Version 4.0 CDICS glossary group inclusion criteria OBI:0500028 exclusion criterion PMID: 17600285-Exclusion criteria included the use of any topical ophthalmic or topical oral medication and/or history of ocular or oral surgery within the past six months. an exclusion criterion (rule) is_a *eligibility criterion* which defines and states a condition which, if met, makes an entity unsuitable for a given task or participation in a given process. For instance, in a study protocol, exclusion criteria indicate the conditions that prospective subjects SHOULD NOT meet to be eligible for participation in a study Person: Philippe Rocca-Serra Adapted from Clinical Research Glossary Version 4.0 CDICS glossary group exclusion criterion OBI:0600000 adding substance to cell culture adding fetal calf serum to a 96 well plate containing a cell culture derived from a blood sample of a patient is process in which a material substance is added to a cell culture renamed from 'administering substance to cell culture', to reflect that administration is commonly used only for organisms Bjoern Peters IEDB adding substance to cell culture OBI:0600002 tumor grading Determination of the grade (severity/stage) of a tumor sample, used in cancer biology to describe abnormalities/qualities of tumor cells or tissues. Values can be described by terms from NCI Thesaurus. Compiled by Helen Parkinson for Transcriptomics thanks to Adam Witney grading of tumor OBI branch derived; submitted by MO tumor grading OBI:0600003 performing a clinical assessment a protocol application during which a series of tests are made of a patient leading to determination of disease state, or condition. PlanAndPlannedProcess Branch clinical diagnosis OBI branch derived (maybe CIO) performing a clinical assessment OBI:0600004 human subject enrollment enlisting familiy members of HIV patients into a study A planned process with the objective to obtain a population of human subjects to participate in an investigation by determining eligibility of subjects and obtaining informed consent. As with group assignment, should the specified output here be an organism which bears a role Bjoern Peters IEDB criteria come from plan / clinical trial branch human subject enrollment OBI:0600005 collecting specimen from organism taking a sputum sample from a cancer patient, taking the spleen from a killed mouse, collecting a urine sample from a patient a process with the objective to obtain a material entity that was part of an organism for potential future use in an investigation PERSON:Bjoern Peters IEDB collecting specimen from organism OBI:0600006 killing Terminal sacrifice of animals by cervical dislocation at the end of an investigation. A protocol application in which an organism is intentionally put to death difficult to place this properly - JG. Death process (e.g. unscheduled death) is out of scope but should be added somewhere. All killings have death process as a part, but not all death processes are part of a killing. Jennifer Fostel Philippe Rocca-Serra death status type euthanisia life termination sacrifice CEBS, Biomaterial_branch killing 1 OBI:0600007 administering substance in vivo Balb/c mice received an intracameral or subconjunctival injection of trinitrophenylated spleen cells injecting mice with 10 ug morphine intranasally, a patient taking two pills of 1 mg aspirin orally A process by which a substance is intentionally given to an organism resulting in exposure of the organism to that substance. 2009-11-10. Tracker: https://sourceforge.net/tracker/?func=detail&aid=2893050&group_id=177891&atid=886178 Different routes and means of administration should go as children underneath this Update the definition based on the discussion. Details see the tracker: https://sourceforge.net/p/obi/obi-terms/738/ needs roles such as perturber and perturbee (children of input role). Perturb is too strong. Host might be the name for one role. Others considered: Doner, Donated, Acceptor. Bjoern Peters Person:Bjoern Peters IEDB administering substance in vivo OBI:0600008 acquisition Downloading a 3D structure from the PDB. Purchasing antibodies from sigma. the planned process of gaining possession of a continuant 5/31/2012 - OBI workshop: This process is not implying ownership of the material / information. Following OBI call November 2012,5th: addition of a restriction to acquisition class to capture the need of having selection criteria Relates to the creation of a class 'selection rule' Bjoern Peters IEDB This needs to be fleshed out and logical definitions added that will allow to place the children terms automatically under acquisition acquisition OBI:0600009 exposure of material to environment Putting cells in a freezer at -80C. Cy5-labeled DNA is irradiated with a laser to excite the fluorophore. Inducing a phase transition in a material by putting it in an environment with a specific temperature. Oxygen deprivation in a chamber. a planned process in which an input material is exposed to a defined set of conditions in a controlled environment. The environment is a specified input. Bjoern Peters IEDB Alan says there will be problmes, e.g. with selection by survival exposure of material to environment OBI:0600010 material acquisition Acquiring 50 C57BL/6 mice bred in the animal facility of the institute as a service to investigators. Purchasing 1 mg of peptides synthesized by Mimotopes at 80% purity. Getting a gift of purified CD4+ specific antibodies presented by Stephen Schoenberger at LIAI. An acquisition in which possession of a material entity is gained. The assumption is that the object already exists in its current state, e.g, an available mouse strain purchased from the Jackson Lab, this is the differentia from specimen creation This excludes processes that create or change materials, such as material transformations. Bjoern Peters, Alan Ruttenberg, Helen Parkinson material procurement IEDB material acquisition OBI:0600011 acclimatization placing mice in animal facility for 2 weeks prior to an experiment to accustom them to their environment, reducing stress A protocol application in which an object is left in an environment for some period of time, until some qualities of interest are in equilibrium with that environment. Jennifer Fostel CEBS, Biomaterial_branch acclimatization OBI:0600012 environmental material collection process Taking 1 liter of surface ocean water from the San Diego Mission Bay Jetty. Capturing mice living in rural Arkansas environmental_material_collection is an acquisition where an object is taken from an environment and put into a storage container. Roles include, environment, thing collected, container, acquirer. relabel the term and add axiom connecting to EnVO:'environmental material' discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/obi-terms/779/ Bjoern Peters, Alan Ruttenberg IEDB the researcher is very interested in the location environmental material collection process OBI:0600013 information acquisition Gathering all influenza HA sequences from GenBank, Retrieveing HLA allele frequencies in the North American populations from dbMHC An acquisition in which possession of information is gained. This excludes processes that create or change information, such as assays and data transformations. Bjoern Peters data collection OBI branch derived information acquisition OBI:0600014 material component separation Using a cell sorter to separate a mixture of T cells into two fractions; one with surface receptor CD8 and the other lacking the receptor, or purification a material processing in which components of an input material become segregated in space Bjoern Peters IEDB material component separation OBI:0600015 group assignment Assigning' to be treated with active ingredient role' to an organism during group assignment. The group is those organisms that have the same role in the context of an investigation group assignment is a process which has an organism as specified input and during which a role is assigned Philippe Rocca-Serra cohort assignment study assignment OBI Plan group assignment 2 OBI:0600016 pooling specimens http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=104564; Combining spleens of 20 mice, Combining supernatant from a cell culture obtained at different time points physical combination of several instances of like material PlanAndPlannedProcess Branch sample pooling OBI branch derived like' is one of the things that you should be controling for in a well-designed experiment. The instances of material need to have the same class. pooling specimens OBI:0600017 detection of molecular label Determination of the amount of phycoerytherin label present in a cell population stained with anti-CD8-PE in order to determine the percentage of CD8+ T cells present an assay that detects the presence or a quality of a molecular label which is a proxy for the detection of the molecular target to which the label is attached PERSON:Matthew Brush OBI developer call, 3-12-12 detection of molecular label OBI:0600018 material portioning pouring 50 mL aliquots of fetal calf serum into conical tubes from a 500 mL stock a material processing in which the input substance is partitioned into a number of portions that are similar in composition. PERSON:Bjoern Peters aliquoting apportioning OBI branch derived material portioning OBI:0600019 non-specific labeling The addition of phycoerytherin label to an anti-CD8 antibody, to label all antibodies. The addition of a reagent labeling the entire input biomaterial enabling future detection of the output biomaterial PlanAndPlannedProcess Branch OBI branch derived definition blessed by Allyson, Bjoern, Jay & Randi non-specific labeling OBI:0600020 histology the counting of the number of cells with fluorescent label at their surface to determine the percentage of the population which was activated the visual examination of cells or tissue (or images of them) with an assessment regarding a quality of the cells or tissue. Parts are: staining, imaging, judgement PERSON:Compiled by Helen Parkinson for Transcriptomics thanks to Adam Witney histopathology OBI branch derived PRS:20090901: addition of alternative term = histopathology need to incorporate parts\n---\nThis is a very vague term, it should be in the same place as transcriptomics, proteomics metaboloimcs. It is the 'study' of tissues, not the process of studying tissues\n histology OBI:0600021 cell fixation http://www.tissuearray.org/CellLinesProtocolforTMA112.pdf; the treatment of CD8+ cells with methanol at -20oC; http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&amp;list_uids=16080188&dopt=AbstractPlus a protocol application to preserve defined qualities of cells or tissues (sample) which may otherwise change over time should include capturing what qualities are being preserved PERSON:Bjoern Peters OBI branch derived we could generalize this for other input materials cell fixation OBI:0600022 excision Cutting out the portion of a gel which contains a DNA fragment the use physical means to remove a portion of a substance from the rest Alan Ruttenberg, Kevin Clancy www.crohnsresource.com/glossary.jsp (via google define:resection) excision OBI:0600023 non specific enzymatic cleavage The use of agarase to digest an agar gel a protocol application to digest the fraction of input material that is susceptible to that enzyme PERSON:Kevin Clancy OBI branch derived non specific enzymatic cleavage OBI:0600024 maintaining cell culture When harvesting blood from a human, isolating T cells, and then limited dilution cloning of the cells, the maintaining_cell_culture step comprises all steps after the initial dilution and plating of the cells into culture, e.g. placing the culture into an incubator, changing or adding media, and splitting a cell culture a protocol application in which cells are kept alive in a defined environment outside of an organism. part of cell_culturing PlanAndPlannedProcess Branch OBI branch derived maintaining cell culture OBI:0600025 substance detection the detection of phycoerytherin by means of flow cytometry any protocol which results in the detection of a specified substance PERSON:Kevin Clancy OBI branch derived substance detection OBI:0600026 longitudinal mass measurement assay The comparison of the weight of vaccinated and non-vaccinated mice after infection with influenza A over 6 weeks post-infection A process in which the mass of a material is measured at two or more time points Helen Parkinson OBI branch derived longitudinal mass measurement assay OBI:0600027 artificially induced cell membrane lysis http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&amp;list_uids=16080188&dopt=AbstractPlus; The destruction of cell membranes with detergent. a material transformation to break the membranes of cells, releasing the cells contents; input=>cells; output=>cell_lysate ---\nThere is a more general 'membrane lysis', which could apply to artificial membranes etc. For this general membrane encapsulated objects would need to be defined. PlanAndPlannedProcess Branch OBI branch derived artificially induced cell membrane lysis OBI:0600028 artificially induced reverse transcription The use of M-MLV reverse transcriptase from the Moloney murine leukemia virus to transcribe an RNA sample into cDNA a protocol with the objective to transcribe single-stranded RNA into complementary DNA (cDNA) It could also be added that the reverse transcriptase is bearer of a GO:0003964 RNA-directed DNA polymerase activity, which is realized in this process. We need to indicate the relationship between the cDNA generated and the RNA that was used as a template. This may be outside of the OBI scope PERSON:Kevin Clancy OBI branch derived artificially induced reverse transcription OBI:0600029 isolation of cell culture supernatant Pouring out a portion of the fluid part of an adherant cell culture growing in a flask.; The centrifugation of a T cell culture followed by aspiration of the supernatant while the cellular pellet remains in the centrifuge tube. a protocol which results in the separation of supernatant material from a cell culture This does not apply to the case where the cells are lysed PlanAndPlannedProcess Branch OBI branch derived isolation of cell culture supernatant OBI:0600030 experimental disease induction the injection of mice with LCM virus iv to establish an LCMV infection. Witholding food from animals to induce starvation syndrome. a protocol application to induce a specific disease in an organism PlanAndPlannedProcess Branch OBI branch derived could be defined class experimental disease induction OBI:0600031 enzyme-linked immunospot assay Determination of the frequency of cells producing IFN-gamma in response to viral peptides by placing effector cells on a anti IFN-gamma coated plate, and adding antigen presenting cells pulsed with a peptide. After washing, the bound IFN-gamma is detected with a secondary antibody linked to a dye that visualizes as one spot per cell. A cytometry assay in which cells are cultured on a surface coated with a capture antibody binding a secretory material of interest which subsequently gets stained resulting in a spot for each cell producing the secretory material of interest. IEDB ELISPOT assay IEDB enzyme-linked immunospot assay OBI:0600032 artificially induced DNA repair the use of DNA repair enzymes uracil DNA glycosylase and 3-methyladenine DNA glycosylase to repair DNA strands a protocol application to repair damaged DNA molecules PlanAndPlannedProcess Branch OBI branch derived ---\nis this really a protocol?\n--> This as several other protocol applications is also a natural process. The fact that it is induced experimetnally by following a protocol makes it a protocol application. Need to make sure that labels don't conflict wi artificially induced DNA repair OBI:0600033 cell permeabilization Electroporation of HeLa cells to allow transfection with pUC19. A protocol application to permeabilize cell membranes, allowing molecules to more easily pass through the membrane than was possible prior to the protocol application need to add output cell has_quality permeable PERSON:Bjoern Peters OBI branch derived definition blessed by Jay, Alan, Randi cell permeabilization OBI:0600034 precipitation The use of ethanol to precipitate DNA molecules from a solution containing DNA a protocol application to cause a material to precipitate (becoming a solid) out of solution. Input is a solution, output is a solution plus a solid component (the precipitate) PERSON:Kevin Clancy OBI branch derived precipitation OBI:0600036 establishing cell culture a process through which a new type of cell culture or cell line is created, either through the isolation and culture of one or more cells from a fresh source, or the deliberate experimental modification of an existing cell culture (e.g passaging a primary culture to become a secondary culture or line, or the immortalization or stable genetic modification of an existing culture or line). PERSON:Matthew Brush PERSON:Matthew Brush A 'cell culture' as used here referes to a new lineage of cells in culture deriving from a single biological source.. New cultures are established through the initial isolation and culturing of cells from an organismal source, or through changes in an existing cell culture or line that result in a new culture with unique characteristics. This can occur through the passaging/selection of a primary culture into a secondary culture or line, or experimental modifications of an existing cell culture or line such as an immortalization process or other stable genetic modification. This class covers establishment of cultures of either multicellular organism cells or unicellular organisms. establishing cell culture OBI:0600037 cell culture splitting The act of taking a cell culture of high density, counting the cells, removing part of the cells, and re-seeding a select number of the cells into new flasks with fresh tissue culture media. The act of taking part of a homogeneous cell culture and creating one or more additional separate cultures of similar qualities. input: cell_culture, output cell_culture min cardinality 2. part of cell culturing PlanAndPlannedProcess Branch cell culture passaging OBI branch derived An active cell culture is typically split when it has grown to confluence in its culture dish. Cell culture splitting of a cell culture sample results in an increase in its passage number, which measures how long a sample has been propagated in vitro, and therefore how many selective or genetic changes it is likely to have undergone. cell culture splitting OBI:0600038 addition of molecular label The addition of phycoerytherin label to an anti-CD8 antibody, to label all antibodies. The addition of anti-CD8-PE to a population of cells, to label the subpopulation cells that are CD8+. a material processing technique intended to add a molecular label to some input material entity, to allow detection of the molecular target of this label in a detection of molecular label assay PERSON:Matthew Brush labeling OBI developer call, 3-12-12 addition of molecular label OBI:0600039 artificially induced methylation the use of enzymes to add methyl groups to DNA molecules A planned process of adding methyl groups to polymers PERSON:Kevin Clancy OBI branch derived artificially induced methylation OBI:0600040 synthesis making cDNA from nucleotides using RNA as a template the construction of a biomaterial from simpler biomaterials This probably needs breaking down into more specific applications. The example given is already covered in reverse_transcription PERSON:Kevin Clancy synthesize OBI branch derived synthesis OBI:0600041 concentrate Evaporation of the solution containing DNA to increase the concentration of the DNA molecules a protocol application to create an output material with an increased density of a material of interest that is part of the input material by separating other parts of the input material PERSON:Kevin Clancy OBI branch derived concentrate OBI:0600042 recombinant plasmid cloning The DNA fragment encoding the p35 gene from Mycobacterium avium complex was inserted into pcDNAII and expressed in E coli in order to study p35. the insertion of a particular DNA fragment into a plasmid in order to make copies of a biomaterial PERSON:Kevin Clancy OBI branch derived recombinant plasmid cloning OBI:0600043 genetic transformation The transduction of E. coli through the introduction of a plasmid encoding for M. avium p35 the introduction. alteration or integration of genetic material into a cell or organism PERSON:Kevin Clancy genetic modification OBI branch derived genetic transformation OBI:0600044 lavage the collection of bronchoalveolar lavage fluid (BAL) from the lungs of mice in order to study the cytokines present A protocol application to separate cells and/or cellular secretions from an anatomical space by the introduction and removal of fluid This is not washing, in which case the material of interest is not the resulting fluid PlanAndPlannedProcess Branch OBI branch derived lavage OBI:0600045 3D structure determination assay The use of X-ray crystallography to determine the 3D coordinates of atoms in a protein. An assay that determines the 3-dimensional configuration of an input material. IEDB IEDB 3D structure determination assay OBI:0600046 preparative chromatography The use of gas chromatography in order separate out from an input sample of eggs a fraction that would be enriched for pesticides. the use of a biomaterial's preferential affinity for either the mobile phase or the stationary phase to separate it from other materials of differing affinity PERSON:Kevin Clancy; Bjoern Peters OBI branch derived preparative chromatography OBI:0600047 sequencing assay The use of the Sanger method of DNA sequencing to determine the order of the nucleotides in a DNA template the use of a chemical or biochemical means to infer the sequence of a biomaterial has_output should be sequence of input; we don't have sequence well defined yet PlanAndPlannedProcess Branch OBI branch derived sequencing assay OBI:0600048 vector mediated amplification E coli expressing the gene for M avium p35 were cultured in order to produce p35. The process of creating a copy of some biological entity in cell culture PERSON:Kevin Clancy OBI branch derived vector mediated amplification OBI:0600049 DNA polymerase amplification The use of taq polymerase to amplify a DNA fragment during a PCR. DNA polymerase amplification is an enzymatic amplification which uses DNA polymerase enzyme to make copies of a DNA contained in biomaterial used as input PERSON:Kevin Clancy Philippe Rocca-Serra OBI branch derived DNA polymerase amplification OBI:0600050 specific enzymatic cleavage The use of a protease to digest a protein into peptides a protocol application to digest the fraction of input material that is susceptible to that enzyme PERSON:Kevin Clancy OBI branch derived specific enzymatic cleavage OBI:0600051 gradient separation the use of a sucrose gradient to isolate mitochondria a protocol application that uses different concentrations of materials in a defined order to create a gradient to facilitate the separation of an input material into its components with specific qualities PERSON:Kevin Clancy OBI branch derived gradient separation OBI:0600052 dialysis the use of a dialysis bag of select pore size to remove salt from collagen isolated from mouse cartilage a protocol application that uses diffusion through a semi-permeable membrane to separate an input material into two fractions of different composition PERSON:Kevin Clancy OBI branch derived dialysis OBI:0600053 electrophoresis Loading a mixture of proteins into a polyacrylamide gel and the application of an electrical current to the gel to separate the proteins by size and change. a protocol application that uses an electrical potential to move material through a defined matrix in order to separate it by its resistance to movement and its charge PERSON:Kevin Clancy OBI branch derived Need to define more terms like gel_separation, matrix,centrifugation, and the connection between the force used to separate materials and the medium or barriers. electrophoresis OBI:0600054 selection by survival The insertion of a gene for antibiotic resistance into a cell population and subsequent growth in the presence of the antibiotic to select for those cells which were successfully transfected the use of environmental conditions to select for the organism or cells that have a certain trait PERSON:Kevin Clancy OBI branch derived selection by survival OBI:0600055 DNA cleavage, restriction analysis the use of the restriction enzymes SalPI and PstI to cleave DNA into fragments, assay made up of components the use of enzymes to cut DNA molecules, the study of DNA through cleavage, mapping, and analysis of the fragments PERSON:Kevin Clancy restriction enzyme assay the use of the restriction enzymes SalPI and PstI to cleave DNA into fragments, assay made up of components DNA cleavage, restriction analysis OBI:0600056 protease cleavage the use of trypsin to cleave pepsin into peptide fragments protease cleavage is an enzymatic cleavage which relies on enzyme with protease activity to act on proteins and produce polypeptides (protein fragments). enzymatic digestion PlanAndPlannedProcess Branch OBI branch derived protease cleavage OBI:0600057 enzymatic DNA replication the use of enzymes to duplicate DNA molecules the use of enzymes to duplicate DNA molecule any process used to make additional copies of a biomaterial PERSON:Kevin Clancy OBI branch derived enzymatic DNA replication OBI:0600058 enzymatic amplification the use of a polymerase chain reaction to amplify a fragment of DNA the use of enzymes to increase the number of molecules of a biomaterial PERSON:Kevin Clancy OBI branch derived enzymatic amplification OBI:0600059 DNA transduction The transfer of a recombinant bacterial plasmid into E.coli to facilitate amplification of a specific protein a genetic transformation which relies on the use of lysogenic infection to transfer DNA sequences into an organism PERSON:Kevin Clancy OBI branch derived DNA transduction OBI:0600060 DNA transfection The use of electroporation to permeabilize a cell membrane in order to introduce a plasmid encoding for a labeled protein of interest a transfection which relies on the use of physical, electrical and chemical phenomena to introduce DNA into a cell PERSON:Kevin Clancy OBI branch derived DNA transfection OBI:0600063 vector mediated expression Construction of pRSS1327 expression vector by molecular cloning of a 1327-bp cDNA, which includes sequences of the entire coding region for RSS, into pBluescript. Expression in Escherichia coli of a functional, full-length RSS was confirmed by immunoblot analysis and enzymatic activity. vector mediated expression sis the generation of copies of biomaterial by in a cell_culture modified for this purpose by insertion of an expression vector needs defined relationship to cell culture PlanAndPlannedProcess Branch OBI branch derived vector mediated expression OBI:0600064 recombinant vector cloning a planned process with the objective to insert genetic material into a cloning vector for future replication of the inserted material pa_branch (Alan, Randi, Kevin, Jay, Bjoern) molecular cloning OBI branch derived recombinant vector cloning OBI:0600065 obsolete_defined processes Place holder class, see editor note Remove to simplify OBI release Discussed on 2012 Ann Arbor OBI wokshop PlanAndPlannedProcess Branch OBI branch derived obsolete_defined processes true OBI:0600067 specific labeling The addition of anti-CD8 antibody for an ICCS assay in order to selectively stain the CD8+ cells a labeling in which the labeling reagent used has a specificity to bind only certain components of the input material PlanAndPlannedProcess Branch OBI branch derived definition blessed by Allyson, Bjoern, Jay & Randi specific labeling OBI:0666666 RNA extraction A RNA extraction is a nucleic acid extraction where the desired output material is RNA PlanAndPlannedProcess Branch OBI branch derived requested by Helen Parkinson for MO RNA extraction OBI:0666667 nucleic acid extraction Phenol / chlorophorm extraction disolvation of protein content folllowed by ethanol precipitation of the nucleic acid fraction over night in the fridge followed by centrifugation to obtain a nucleic acid pellet. a material separation to recover the nucleic acid fraction of an input material PlanAndPlannedProcess Branch OBI branch derived requested by Helen Parkinson for MO. Could be defined class nucleic acid extraction OBI:1000023 cell culture supernatant solution containing RPMI, fetal calf sera, antibiotics, and monoclonal antibody UCHT1. Isolation of proliferation factor of immature T-cell clone in concanavalin A-stimulated splenocyte culture supernatant. Immunology. 2003 Jun;109(2):209-16. PMID: 12757615 Supernatant of a cell culture is a material entity which contains media, supplements, and secreted products of the cells and becomes the environment of cultivated cell. PERSON: Bjoern Peters GROUP: IEDB cell culture supernatant OBI:1000024 cell pellet Detection of fetal DNA in a cell pellet after centrifugation of mountant. J Forensic Sci. 2003 Jan;48(1):135-6. PMID: 12570214 A material entity which results from the aggregation of cells produced by the application of centrifugal force to a liquid containing cells in suspension PERSON: Helen Parkinson PERSON: Philippe Rocca-Serra GROUP: CEBS GROUP: OBI Biomaterial Branch cell pellet OBI:1000029 phage display library PMID: 15905471.Nucleic Acids Res. 2005 May 19;33(9):e81.Oligonucleotide-assisted cleavage and ligation: a novel directional DNA cloning technology to capture cDNAs. Application in the construction of a human immune antibody phage-display library. [Phage display library encoding fragments of human antibodies. m-rna library encoding for 9-mer peptides] a phage display library is a collection of materials in which a mixture of genes or gene fragments is expressed and can be individually selected and amplified. PERSON: Bjoern Peters PERSON: Philippe Rocca-Serra display library WEB: http://www.immuneepitope.org/home.do PRS: 22022008. class moved under population, modification of definition and replacement of biomaterials in previous definition with 'material' addition of has_role restriction phage display library OBI:1000036 cell lysate The effect of vaccination with the lysate of heat-shocked tumor cells on nitric oxide production in BALB/c mice with fibrosarcoma tumor. Cell Biol Int. 2008 Jul;32(7):835-40. PMID: 18455932 a cell lysate is a material entity which is output of a cell lysis process PRS:22-02-2008: is a material which has output_role during lysis protocol-application. old defintion: A mixture (collection) of cell components created by rupturing of the cell wall resulting from a lysis process PERSON: Susanna Sansone lysate lysed material GROUP: PSI cell lysate OBI:1000042 peptide construct Multiple Antigenic Peptide (MAP) construct containing T and B cell epitopes from p. falciparum congugated to a central glycin A novel multivalent human CTL peptide construct elicits robust cellular immune responses in HLA-A*0201 transgenic mice: implications for HTLV-1 vaccine design. Vaccine. 2003 Jun 20;21(21-22):2767-81. PMID: 12798617 a material entity synthesized to contain a number of peptides conjugated together in a non-linear fashion PERSON: Bjoern Peters IEDB peptide construct OBI:1000048 transgenic organism HLA-A*0201 transgenic mice, Vaccinia virus expressing the LCMV gp protein Possible ecological risks of transgenic organism release when transgenes affect mating success: sexual selection and the Trojan gene hypothesis. Proc Natl Acad Sci U S A. 1999 Nov 23;96(24):13853-6. PMID: 10570162 a transgenic organism is material entity which derives from an organism which has been modified to express a gene not normally part of it PRS:22-02-2008: is a organism which has output_role during genetic modification of type (KO) protocol-application PERSON: Bjoern Peters PERSON: Philippe Rocca-Serra GROUP:IEDB transgenic organism OBI:1000049 whole mount tissue A whole organism preparation resulting from a histological preparation known as whole mount preparation where the whole specimen is mounted or spread on the microscope (glass) slide PERSON: Helen Parkinson PERSON: Philippe Rocca-Serra whole mount sample GROUP: OBI PRS:22-02-2008: indicates the need to create a protocol application and distinguish it from this entity PRS:22-02-2008: is a material which has output_role during whole mount preparation protocol-application whole mount tissue OBI:1000207 assay bead Dynabeads are commercially available magnetic beads which are precoated with antibodies specific for select cellular receptors and are used to separate cell populations. A globular or round particle of defined physicochemical properties and size which can be exploited as either the primary substance for detection or as a secondary solid platform for the attachment of bioactive molecules. DS: Probably better modeled as a role. OBI bead assay bead OBI:1110001 epitope a material entity bearing the epitope role IEDB IEDB epitope OBI:1110002 obsolete_occurrence of disease An occurrence of disease is a process involving pathologic changes within an organism replaced by http://purl.obolibrary.org/obo/OGMS_0000063 'disease course' Details see https://sourceforge.net/tracker/?func=detail&aid=3515228&group_id=177891&atid=886178 IEDB IEDB obsolete_occurrence of disease true OBI:1110003 host exposure to infectious agent a process in which an infectious agent comes into physical contact with a host organism. IEDB IEDB host exposure to infectious agent OBI:1110007 administration in vivo with infectious agent is an administration of an infectious agent to a host organism IEDB IEDB administration in vivo with infectious agent OBI:1110008 occurrence of infectious disease Is an occurrence of a disease caused by an infection IEDB IEDB occurrence of infectious disease OBI:1110010 disposition to cause an allergic reaction The role borne by a material entity that is realized when it is recognized by the immune system and results in the occurrence of an allergic disease. IEDB allergenic disposition IEDB disposition to cause an allergic reaction OBI:1110011 allergic reaction an allergic reaction is an pathologic immune response by an organism to a non-self entity that is normally harmless(the allergen) IEDB IEDB allergic reaction OBI:1110012 occurrence of allergy The process of an allergic disease occurring in an organism. IEDB IEDB occurrence of allergy OBI:1110013 ELISPOT assay measuring epitope specific interleukin-2 production by T cells An assay of epitope specific interleukin-2 production by T cells that uses an ELISPOT assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-2 release|ELISPOT ELISPOT assay measuring epitope specific interleukin-2 production by T cells OBI:1110014 epitope binding by adaptive immune receptor is the process in which an adaptive immune receptor binds to a material entity (realizing its disposition). The binding affinity is significant enough to trigger an immune response. Specifically, transient non-specific binding of adaptive immune receptors occurring during immune surveillance is not considered significant binding. IEDB IEDB epitope binding by adaptive immune receptor OBI:1110015 Immunization in vivo Process of administering an object playing the role of immunogen to a living organism IEDB IEDB Immunization in vivo OBI:1110016 adaptive immune effector function A function realized as an immune response, which inheres in a T cell, B cell or antibody which derives from or is produced by a cell with prior antigen experience. IEDB IEDB adaptive immune effector function OBI:1110017 living with infected household contact a process in which a a human being lives in the same household as another human being that is known to be infected with an infectious agent IEDB IEDB living with infected household contact OBI:1110018 living in endemic area a process in which a potential host organism lives in a geographic area in which an infectious agent is present to such a degree of frequency that contact is likely IEDB IEDB living in endemic area OBI:1110019 pathogen release in laboratory accident a process in which a an infectious agent maintained in a laboratory setting is not contained as planned, leading to potential exposure of human beings to the agent IEDB IEDB pathogen release in laboratory accident OBI:1110020 Immunization in vitro Process of administering an object playing the role of immunogen to a cell culture IEDB IEDB Immunization in vitro OBI:1110021 infection process the detrimental process in which an infectious agent colonizes or replicates in a host environment IEDB IEDB infection process OBI:1110022 adaptive immune receptor is a receptor produced by cells of the adaptive immune system with the purpose of binding epitopes. IEDB IEDB adaptive immune receptor OBI:1110023 immunogen a material entity bearing the immunogen role IEDB IEDB immunogen OBI:1110024 environmental exposure to infectious agent Is a process in which an infectious agent is in direct contact with a potential host organism in its habitat. This is preceded by proximity to the infectious agent IEDB IEDB environmental exposure to infectious agent OBI:1110026 host of immune response A mouse that is vaccinated with a peptide and develops protective immunity. A human exposed to bacteria that are killed by pre-existing immune responses. An organism in which an immune response process occurs. In immune response processes in the context of infectious diseases and allergy, there are often multiple organisms involved, which requires calling out the 'host'. This terminology is expanded to allergy, cancer and transplantation. IEDB IEDB host of immune response OBI:1110028 293-T cell line A cell line derived from human embryonic kidney cells. This cell line contains the SV40 Large T-antigen, allowing episomal replication of transfected plasmids containing the SV40 origin of replication. IEDB IEDB http://www.biotech.ist.unige.it/cldb/cl5008.html 293-T cell line OBI:1110029 C1R cell line A cell line derived from human B cells. This cell line was created by EBV transformation (B-lymphoblastoid cell-line (BLCL)). IEDB IEDB C1R cell line OBI:1110030 experimental infection of cell culture is the administration of an infectious agent to a cell culture with the objective to have the agent colonize and replicate in culture IEDB IEDB experimental infection of cell culture OBI:1110031 EL-4 cell line A cell line derived from mouse (C57BL/6N) lymphoma cells. IEDB IEDB http://www.biotech.ist.unige.it/cldb/cl1160.html EL-4 cell line OBI:1110032 HeLa cell line A cell line derived from human cervical cancer cells. IEDB IEDB http://www.biotech.ist.unige.it/cldb/cl1597.html HeLa cell line OBI:1110033 JAWS II cell line A cell line derived from mouse dendritic cells. IEDB IEDB http://www.atcc.org/ATCCAdvancedCatalogSearch/ProductDetails/tabid/452/Default.aspx?ATCCNum=CRL-11904&Template=cellBiology JAWS II cell line OBI:1110034 antigen is a material entity that has the antigen role IEDB IEDB antigen OBI:1110035 Jurkat cell line A cell line derived from human T cells. IEDB IEDB http://www.biotech.ist.unige.it/cldb/cl5296.html Jurkat cell line OBI:1110036 JY cell line The JY cell line is an Epstein-Barr virus (EBV)-immortalised b cell lymphoblastoid line.(wikipedia) IEDB IEDB JY cell line OBI:1110037 assay measuring binding of a T cell epitope:MHC:TCR complex An immune epitope assay that detects T cell epitope recognition. IEDB IEDB T cell binding|any method assay measuring binding of a T cell epitope:MHC:TCR complex OBI:1110038 RMA cell line A cell line derived from a mouse lymphoma, specifically a Rauscher virus-induced tumor.This cell ine is antigen processing-defective and expresses a very low level of MHC molecules on its surface. IEDB IEDB RMA cell line OBI:1110039 T2 cell line A human T-B lymphoblastoid hybrid cell line IEDB IEDB http://www.atcc.org/ATCCAdvancedCatalogSearch/ProductDetails/tabid/452/Default.aspx?ATCCNum=CRL-1992&Template=cellBiology T2 cell line OBI:1110040 infectious disease is a disease caused by an infectious agent IEDB IEDB infectious disease OBI:1110041 lymph node cell specimen A cell specimen comprised of a mixed population of cells obtained by processing whole lymph node into individual cells, typically performed using a sieve. This population includes T cells, B cells, macrophages, and other cell types. IEDB IEDB lymph node cell specimen OBI:1110043 cultured adherent cell populaiton A mixed cell population that is characterized by its ability to bind to tissue culture flasks or plates. This population typically contains macrophages and other cells capable of playing the antigen presenting cell role. MHB 3-27-13: Following CLO alignment efforts, propose to update definition to read: "A cultured cell population comprised of cells that are able to grow attached to a solid substrate provided by tissue culture flasks or plates". The current definition seems to describe a more specific type of adherent culture of immunological origin as needed by IEDB. MHB 3-5-13: Need to review axiom on this class in light of clarification that it refers to a cell line sample, and not an entire line. Not every population of adhernet cells is the output of an isolation process. IEDB adherent cell culture sample IEDB cultured adherent cell populaiton OBI:1110044 cultured PBMC cell population A mixed cell population obtained by processing whole blood. The cells are characterized by having a similar density and are largely mononuclear cells (includes T cells, B cells, and other cell types). IEDB PBMC cell culture sample IEDB cultured PBMC cell population OBI:1110045 disposition to be bound by an adaptive immune receptor Is the disposition borne by a material entity that is realized in a process of being bound by a adaptive immune receptor. IEDB epitope disposition IEDB disposition to be bound by an adaptive immune receptor OBI:1110046 organ harvesting The process of removing an organ from its source organism IEDB IEDB organ harvesting OBI:1110047 cultured CD3+ T cell population A T cell population characterized by expressing the CD3 molecule on its surface. IEDB CD3+ T cell culture sample IEDB cultured CD3+ T cell population OBI:1110048 cultured CD3- T cell population A T cell population characterized by not expressing the CD3 molecule on its surface. IEDB CD3- T cell culture sample IEDB cultured CD3- T cell population OBI:1110049 allergy is a disease in which an abnormally strong inflammatory immune response is triggered against non-self entities, and the immune response has no protective effect IEDB IEDB allergy OBI:1110050 cultured CD4- T cell population A T cell population characterized by not expressing the CD4 molecule on its surface. IEDB CD4- T cell culture sample IEDB cultured CD4- T cell population OBI:1110051 cultured CD8- T cell population A T cell population characterized by not expressing the CD8 molecule on its surface. IEDB CD8- T cell culture sample IEDB cultured CD8- T cell population OBI:1110052 cultured CD4-/CD8- T cell population A T cell population characterized by not expressing the CD4 nor the CD8 molecule on its surface. IEDB CD4-/CD8- T cell culture sample IEDB cultured CD4-/CD8- T cell population OBI:1110053 cancer A disease characterized by abnormal and uncontrolled cell division IEDB IEDB cancer OBI:1110054 autoimmune disease Is a disease characterized by an immune response of an organism against parts of itself IEDB IEDB autoimmune disease OBI:1110055 obsolete_disease placeholder to be imported from disease ontology IEDB IEDB http://purl.obolibrary.org/obo/OGMS_0000031 obsolete_disease true OBI:1110056 epitope specific IL-2 release by T cells A biological process where T cells produce IL-2 resulting from the recognition of a T cell epitope. IEDB IEDB epitope specific IL-2 release by T cells OBI:1110057 MHC:epitope complex binding to TCR a process of an MHC molecule binding to an entity playing the role of epitope to create an MHC:epitope complex which is then bound by a TCR molecule. IEDB IEDB MHC:epitope complex binding to TCR OBI:1110059 ELISPOT assay measuring epitope specific interferon-gamma production by T cells An assay of epitope specific interferon-gamma production by T cells that uses an ELISPOT assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IFNg release|ELISPOT ELISPOT assay measuring epitope specific interferon-gamma production by T cells OBI:1110061 exposure resulting in immune reactivity a process in which an organism (host) is exposed to some material entity, which results in an immune reactivity IEDB IEDB exposure resulting in immune reactivity OBI:1110082 immunogen role any entity capable of eliciting an immune response when introduced to components of the immune system IEDB IEDB immunogen role OBI:1110083 host of immune response role is a role borne by an organism. It is realized by the organism during an immunization or an immune response taking place inside or on the surface of the organism, and in which the responding or stimulated immune system is part of the host. 03/21/2010: This sense of 'host' is used not only in infectious diseases but also allergy, cancer, transplantation, etc. which is why it is needed separately from the 'host of infectious agent' meaning, which will be imported from IDO. IEDB IEDB host of immune response role OBI:1110084 effector T cell function The function inhering in a T cell that is realized in an immune response that results from the T cell receptor binding to the MHC:epitope complex. IEDB IEDB effector T cell function OBI:1110085 antigen presentation function a function inhering in a cell that expresses MHC molecules which is realized in the process of antigen processing and presentation of antigen derived parts by MHC molecules on the cell surface. IEDB APC IEDB should add a reference to the antigen processing and presentation process. antigen presentation function OBI:1110086 restricting MHC role The role played by an MHC molecule by binding a material entity playing the role of epitope when that epitope/MHC molecule pair are recognized (bound) by a TCR molecule on the surface of a cell playing the role of effector cell. IEDB IEDB restricting MHC role OBI:1110087 donor A T cell line from a PPD(+) donor. A role which inheres in an organism or part thereof from which any part including cell, organ or tissue is removed with the intention that the donated part will be placed into another organism and/or cultured in vitro. IEDB donor role IEDB Definition modified by HP to deal with the case where an organ may be removed for donation but is not transplanted as intended. donor OBI:1110091 immune epitope carrier role A role inhering in a material entity that is covalently bound to an epitope in order to increase the epitopes immunogenicity. 03/21/2010, BP: surveying the literature, this seems to be a messy term. Need to clarify what material entities can be carriers, and if only immunogenicity (not antigenicity) is effected by their presence. IEDB IEDB immune epitope carrier role OBI:1110092 adjuvant role Adjuvant role is a role that inheres in a material entity and which is realized through a process of modifying a biological response. IEDB adjuvent role IEDB adjuvant role OBI:1110093 disposition to infect an organism Is a role borne by an agent, and realized when in contact with or inside another organism in which it is capable of replicating and causing disease IEDB IEDB disposition to infect an organism OBI:1110094 immunization Infection with influenza (the immunogen) leading to B cells producing antibodies (the effector function) against surface regions of the HA protein (the epitope). The process of an epitope that is part of or derived from an immunogen coming into contact with adaptive immune cells resulting in these cells acquiring immune effector functions specific for the epitope. IEDB IEDB immunization OBI:1110095 blood harvesting A material separation where blood is taken from an organism. IEDB IEDB blood harvesting OBI:1110099 L cell line A cell line derived from mouse fibroblasts. IEDB IEDB http://www.biotech.ist.unige.it/cldb/cl3075.html L cell line OBI:1110106 cultured antigen presenting cell population A culture of PBMCs. A culture of Hela cells. a cell culture including cells that have an antigen presentation function antigen presenting cell culture sample IEDB cultured antigen presenting cell population OBI:1110107 cultured effector T cell population A culture of cytotoxic CD8+ T cells. A cell culture including cells that have an effector T cell function culture of effector T cells effector T cell culture sample IEDB cultured effector T cell population OBI:1110108 material to be added A mixture of peptides that is being added into a cell culture. a material that is added to another one in a material combination process 10/26/09: This defined class is used as a 'macro expression' to reduce the size of the IEDB export 2010/02/24 Alan Ruttenberg: I think this might generate confusion as the common use of the term would consider something to be a specimen during the realization of the role, not only if it bears it. However having this class as a probe, or for display, or as a macro might be useful. Ideally we would mark or segregate such classes IEDB material to be added OBI:1110109 target of material addition A cell culture into which a mixture of peptides is being added. A material entity into which another is being added in a material combinatino process 10/26/09: This defined class is used as a 'macro' to reduce the size of the IEDB export. IEDB target of material addition OBI:1110111 environmental proximity to infectious agent Is a process in which an infectious agent comes close enough to a potential host organism in its habitat that a contact can result IEDB IEDB environmental proximity to infectious agent OBI:1110114 contact to pathogen carrying biological vector a process in which a vector carrying an infectious agent comes close enough to a potential host organism that a contact can result IEDB IEDB contact to pathogen carrying biological vector OBI:1110116 splenocyte specimen A cell specimen comprised of a mixed cell population obtained by processing whole spleen into individual cells, typically performed using a sieve or blender. This population includes T cells, B cells, macrophages, and other cell types. IEDB IEDB splenocyte specimen OBI:1110118 P815 cell line A cell line derived from mouse mastocytoma. IEDB IEDB http://www.biotech.ist.unige.it/cldb/cl5244.html P815 cell line OBI:1110120 assay antigen role Any molecule recognized by the adaptive immune receptors? Recognized means bound with a certain affinity? From GO ag binding:Interacting selectively with an antigen, any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen. see OBI_1110120 below IEDB IEDB assay antigen role OBI:1110122 pathologic process abnormal, harmful processes caused by or associated with a disease IEDB IEDB pathologic process OBI:1110124 assay measuring qualitiative binding of a T cell epitope:MHC:TCR complex A T cell epitope recognition assay that qualitatively detects MHC:epitope complex binding to TCR. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB qualitative binding|binding assay assay measuring qualitiative binding of a T cell epitope:MHC:TCR complex OBI:1110125 assay measuring MHC ligand processing and presentation A MHC ligand assay that determines what ligands are processed and loaded onto MHC molecules by eluting ligands and identifying them. IEDB IEDB ligand presentation|any method assay measuring MHC ligand processing and presentation OBI:1110126 assay measuring binding of a MHC:ligand complex A MHC ligand assay that detects the binding of a ligand to an MHC molecule. IEDB IEDB MHC binding|binding assay assay measuring binding of a MHC:ligand complex OBI:1110127 assay measuring binding of a B cell epitope:antibody complex An immune epitope assay that detects B cell epitope recognition. IEDB IEDB antibody binding|any method assay measuring binding of a B cell epitope:antibody complex OBI:1110128 immune epitope assay An assay that detects the binding of an epitope to an adaptive immune receptor or a immune response process resulting from such a binding event IEDB IEDB immune epitope assay immune epitope assay OBI:1110129 biological activity assay measuring epitope specific cytokine production by T cells A T cell epitope dependent biological activity assay that detects cytokine production. IEDB IEDB cytokine release|biological activity biological activity assay measuring epitope specific cytokine production by T cells OBI:1110130 biological activity assay measuring epitope specific T cell killing A T cell epitope dependent biological activity assay that detects the killing of an antigen presenting cell (APC) by a T cell whose TCR recognizes an epitope presented by the APC. IEDB IEDB cytotoxicity|biological activity biological activity assay measuring epitope specific T cell killing OBI:1110131 biological activity assay measuring epitope specific proliferation of T cells A T cell epitope dependent biological activity assay that detects T cell proliferation. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB proliferation|biological activity biological activity assay measuring epitope specific proliferation of T cells OBI:1110132 CD8 receptor A transmembrane glycoprotein that serves as a co-receptor for the T cell receptor. This term does not belong in ONTIE. It should be imported from PRO, but there seems to be no appropriate term as of 08/17/2009. CD8 WEB: http://en.wikipedia.org/wiki/CD8 CD8 receptor OBI:1110150 51 chromium assay measuring epitope specific T cell killing A T cell epitope specific killing assay performed in vitro that uses a chromium release assay. IEDB IEDB cytotoxicity|51 chromium 51 chromium assay measuring epitope specific T cell killing OBI:1110151 ELISA measuring epitope specific interferon-gamma production by T cells An assay of epitope specific interferon-gamma production by T cells that uses an ELISA. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IFNg release|ELISA ELISA measuring epitope specific interferon-gamma production by T cells OBI:1110152 ELISA measuring epitope specific interleukin-2 production by T cells An assay of epitope specific interleukin-2 production by T cells that uses an ELISA. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-2 release|ELISA ELISA measuring epitope specific interleukin-2 production by T cells OBI:1110153 ELISA measuring epitope specific interleukin-4 production by T cells An assay of epitope specific interleukin-4 production by T cells that uses an ELISA. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-4 release|ELISA ELISA measuring epitope specific interleukin-4 production by T cells OBI:1110154 ELISA measuring epitope specific interleukin-5 production by T cells An assay of epitope specific interleukin-5 production by T cells that uses an ELISA. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-5 release|ELISA ELISA measuring epitope specific interleukin-5 production by T cells OBI:1110155 ELISA measuring epitope specific tumor necrosis factor production by T cells A T cell epitope specific tumor necrosis factor production assay that uses an ELISA. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB TNFa release|ELISA ELISA measuring epitope specific tumor necrosis factor production by T cells OBI:1110156 ELISA measuring epitope specific interleukin-10 production by T cells An assay of epitope specific interleukin-10 production by T cells that uses an ELISA. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-10 release|ELISA ELISA measuring epitope specific interleukin-10 production by T cells OBI:1110157 ELISA measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells An assay of epitope specific granulocyte macrophage colony stimulating factor production by T cells that uses an ELISA. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB GM-CSF release|ELISA ELISA measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells OBI:1110158 ELISA measuring epitope specific interleukin-6 production by T cells An assay of epitope specific interleukin-6 production by T cells that uses an ELISA. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-6 release|ELISA ELISA measuring epitope specific interleukin-6 production by T cells OBI:1110159 ELISA measuring epitope specific interleukin-13 production by T cells An assay of epitope specific interleukin-13 production by T cells that uses an ELISA. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-13 release|ELISA ELISA measuring epitope specific interleukin-13 production by T cells OBI:1110160 ELISA measuring epitope specific interleukin-12 production by T cells An assay of epitope specific interleukin-12 production by T cells that uses an ELISA. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-12 release|ELISA ELISA measuring epitope specific interleukin-12 production by T cells OBI:1110161 ELISA measuring epitope specific interleukin-1 beta production by T cells An assay of epitope specific interleukin-1 beta production by T cells that uses an ELISA. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-1b release|ELISA ELISA measuring epitope specific interleukin-1 beta production by T cells OBI:1110162 ELISA measuring epitope specific interleukin-17 production by T cells An assay of epitope specific interleukin-17 production by T cells that uses an ELISA. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-17 release|ELISA ELISA measuring epitope specific interleukin-17 production by T cells OBI:1110163 ELISA measuring epitope specific interleukin-18 production by T cells An assay of epitope specific interleukin-18 production by T cells that uses an ELISA. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-18 release|ELISA ELISA measuring epitope specific interleukin-18 production by T cells OBI:1110167 ELISPOT assay measuring epitope specific interleukin-4 production by T cells An assay of epitope specific interleukin-4 production by T cells that uses an ELISPOT assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-4 release|ELISPOT ELISPOT assay measuring epitope specific interleukin-4 production by T cells OBI:1110168 ELISPOT assay measuring epitope specific tumor necrosis factor production by T cells A T cell epitope specific tumor necrosis factor production assay that uses an ELISPOT assay. IEDB IEDB TNFa release|ELISPOT ELISPOT assay measuring epitope specific tumor necrosis factor production by T cells OBI:1110170 ELISPOT assay measuring epitope specific interleukin-10 production by T cells An assay of epitope specific interleukin-10 production by T cells that uses an ELISPOT assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-10 release|ELISPOT ELISPOT assay measuring epitope specific interleukin-10 production by T cells OBI:1110171 ELISPOT assay measuring epitope specific interleukin-13 production by T cells An assay of epitope specific interleukin-13 production by T cells that uses an ELISPOT assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-13 release|ELISPOT ELISPOT assay measuring epitope specific interleukin-13 production by T cells OBI:1110172 intracellular cytokine staining assay measuring epitope specific interferon-gamma production by T cells An assay of epitope specific interferon-gamma production by T cells that uses an intracellular cytokine staining assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IFNg release|ICS intracellular cytokine staining assay measuring epitope specific interferon-gamma production by T cells OBI:1110173 intracellular cytokine staining assay measuring epitope specific interleukin-2 production by T cells An assay of epitope specific interleukin-2 production by T cells that uses an intracellular cytokine staining assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-2 release|ICS intracellular cytokine staining assay measuring epitope specific interleukin-2 production by T cells OBI:1110174 intracellular cytokine staining assay measuring epitope specific tumor necrosis factor production by T cells A T cell epitope specific tumor necrosis factor production assay that uses an intracellular cytokine staining assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB TNFa release|ICS intracellular cytokine staining assay measuring epitope specific tumor necrosis factor production by T cells OBI:1110175 intracellular cytokine staining assay measuring epitope specific interleukin-4 production by T cells An assay of epitope specific interleukin-4 production by T cells that uses an intracellular cytokine staining assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-4 release|ICS intracellular cytokine staining assay measuring epitope specific interleukin-4 production by T cells OBI:1110177 intracellular cytokine staining assay measuring epitope specific interleukin-10 production by T cells An assay of epitope specific interleukin-10 production by T cells that uses an intracellular cytokine staining assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-10 release|ICS intracellular cytokine staining assay measuring epitope specific interleukin-10 production by T cells OBI:1110178 intracellular cytokine staining assay measuring epitope specific interleukin-17 production by T cells An assay of epitope specific interleukin-17 production by T cells that uses an intracellular cytokine staining assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-17 release|ICS intracellular cytokine staining assay measuring epitope specific interleukin-17 production by T cells OBI:1110179 MHC tetramer/multimer assay measuring binding of a T cell epitope:MHC:TCR complex A T cell epitope qualitative binding assay that uses an MHC multimer staining assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB qualitative binding|multimer/tetramer MHC tetramer/multimer assay measuring binding of a T cell epitope:MHC:TCR complex OBI:1110180 3H-thymidine assay measuring epitope specific proliferation of T cells A T cell epitope specific proliferation assay performed on cells in vitro that uses a tritiated thymidine incorporation assay. IEDB IEDB proliferation|3H-thymidine 3H-thymidine assay measuring epitope specific proliferation of T cells OBI:1110181 BrdU assay measuring epitope specific proliferation of T cells A T cell epitope specific proliferation assay performed on cells in vitro that uses a BrdU incorporation assay. IEDB IEDB proliferation|BrdU BrdU assay measuring epitope specific proliferation of T cells OBI:1110182 epitope specific T cell proliferation A biological process where T cells proliferate resulting from the recognition of a T cell epitope. IEDB IEDB epitope specific T cell proliferation OBI:1110184 epitope specific GM-CSF release by T cells A biological process where T cells produce GM-CSF resulting from the recognition of a T cell epitope. IEDB IEDB epitope specific GM-CSF release by T cells OBI:1110185 epitope specific IFN-g release by T cells A biological process where T cells produce IFNg resulting from the recognition of a T cell epitope. IEDB IEDB epitope specific IFN-g release by T cells OBI:1110187 epitope specific IL-10 release by T cells A biological process where T cells produce IL-10 resulting from the recognition of a T cell epitope. IEDB IEDB epitope specific IL-10 release by T cells OBI:1110190 epitope specific IL-12 release by T cells A biological process where T cells produce IL-12 resulting from the recognition of a T cell epitope. IEDB IEDB epitope specific IL-12 release by T cells OBI:1110191 epitope specific IL-13 release by T cells A biological process where T cells produce IL-13 resulting from the recognition of a T cell epitope. IEDB IEDB epitope specific IL-13 release by T cells OBI:1110193 epitope specific IL-17 release by T cells A biological process where T cells produce IL-17 resulting from the recognition of a T cell epitope. IEDB IEDB epitope specific IL-17 release by T cells OBI:1110195 epitope specific IL-18 release by T cells A biological process where T cells produce IL-18 resulting from the recognition of a T cell epitope. IEDB IEDB epitope specific IL-18 release by T cells OBI:1110196 epitope specific IL-1b release by T cells A biological process where T cells produce IL-1b resulting from the recognition of a T cell epitope. IEDB IEDB epitope specific IL-1b release by T cells OBI:1110199 epitope specific IL-4 release by T cells A biological process where T cells produce IL-4 resulting from the recognition of a T cell epitope. IEDB IEDB epitope specific IL-4 release by T cells OBI:1110201 allergen Birch pollen is an allergen A material entity bearing the disposition to cause an allergic reaction IEDB IEDB allergen OBI:1110202 epitope specific IL-5 release by T cells A biological process where T cells produce IL-5 resulting from the recognition of a T cell epitope. IEDB IEDB epitope specific IL-5 release by T cells OBI:1110203 epitope specific IL-6 release by T cells A biological process where T cells produce IL-6 resulting from the recognition of a T cell epitope. IEDB IEDB epitope specific IL-6 release by T cells OBI:1110204 epitope specific killing by T cells A biological process where T cells lyse antigen presenting cells resulting from the recognition of a T cell epitope on MHC molecules of the antigen presenting cell. IEDB IEDB epitope specific killing by T cells OBI:1110206 epitope specific TNF release by T cells A biological process where T cells produce TNF resulting from the recognition of a T cell epitope. IEDB IEDB epitope specific TNF release by T cells OBI:1110207 assay detecting IFN-gamma production An IFN-g ELISPOT is an assay detecting ifn-gamma production an assay that determines information about the production of the cytokine interferon gamma PERSON: Bjoern Peters IEDB IFNg release assay detecting IFN-gamma production OBI:1110300 direct submission to IEDB The report on "Identification of a dominant CD4 T cell epitope in the membrane lipoprotein Tul4 from Francisella tularensis LVS. " submitted by Valentino et al to the IEDB. The content of that report on the IEDB website is here: http://iedb.org/refId/1013357 A report about experiments in an investigation that characterize immune epitopes, and was submitted directly by the authors to the Immune Epitope Database (IEDB) PERSON: Bjoern Peters IEDB direct submission to IEDB OBI:9999994 chromium release assay Autologous EBV-transformed B-LCL were used as target cells for the influenza virus-specific CTL assays. Equal volumes of target and effector cells were added to triplicate wells of 96-well tissue culture plates, and 1:2 serial dilutions of effectors were made, producing effector-to-target (E:T) ratios of 100:1, 50:1, 25:1, and 12.5:1. After a 4-h incubation of the effector cells with the target cells, supernatants were collected following brief centrifugation and transferred to polystyrene tubes to be counted with the LKB 1272 Clinigamma counter (Wallac). Percent specific killing was determined with the following equation: (experimental 51Cr release - spontaneous 51Cr release)/(maximum 51Cr release - spontaneous 51Cr release) x 100. An in vitro cell killing assay in which radioactive chromium is absorbed by cells and released into supernatant when the cells die. The amount of radioactivity measured in the supernatant is a proxy for the number of cells that have died. PlanAndPlannedProcess Branch, IEDB IEDB chromium release assay OGMS:0000015 clinical history A series of statements representing health-relevant qualities of a patient and of a patient's family. clinical history OGMS:0000023 phenotype A (combination of) quality(ies) of an organism determined by the interaction of its genetic make-up and environment that differentiates specific instances of a species from other instances of the same species. phenotype OGMS:0000031 disease A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism. disease OGMS:0000063 disease course The totality of all processes through which a given disease instance is realized. replace 'OBI:occurrence of disease', need to add logical definition The axioms of OBI occurence of disease: Equivalent classes: realizes some disease Superclasses: 'has part' some 'pathologic process' 'has participant' some (organism and ('has role' some 'host of immune response role')) biological_process realizes some 'host of immune response role' disease course OGMS:0000090 treatment A processual entity whose completion is hypothesized (by a healthcare provider) to alleviate the signs and symptoms associated with a disorder treatment PATO:0000011 age A time quality inhering in a bearer by virtue of how long the bearer has existed. age PATO:0000018 fluorescence A luminous flux quality inhering in a bearer by virtue of the bearer's emitting longer wavelength light following the absorption of shorter wavelength radiation; fluorescence is common with aromatic compounds with several rings joined together. fluorescence PATO:0000047 biological sex An organismal quality inhering in a bearer by virtue of the bearer's ability to undergo sexual reproduction in order to differentiate the individuals or types involved. biological sex PATO:0000122 length A 1-D extent quality which is equal to the distance between two points. length PATO:0000125 mass A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter. mass PATO:0000146 temperature A physical quality of the thermal energy of a system. temperature PATO:0000186 behavioral quality An organismal quality inhering in a bearer by virtue of the bearer's behavior aggregate of the responses or reactions or movements in a given situation. behavioral quality PATO:0000383 female A biological sex quality inhering in an individual or a population that only produces gametes that can be fertilised by male gametes. female PATO:0000384 male A biological sex quality inhering in an individual or a population whose sex organs contain only male gametes. male PATO:0000918 volume A 3-D extent quality inhering in a bearer by virtue of the bearer's amount of 3-dimensional space it occupies. volume PATO:0001025 pressure A physical quality that inheres in a bearer by virtue of the bearer's amount of force per unit area it exerts. pressure PATO:0001161 diluted A concentration which relatively low. diluted PATO:0001167 damaged A structural quality inhering in a bearer by virtue of the bearer being harmed or injured or spoiled, such that its functionality is impaired. damaged PATO:0001193 lateral to A spatial quality inhering in a bearer by virtue of the bearer's being located toward the side relative to another entity. lateral to PATO:0001196 ventral to A spatial quality inhering in a bearer by virtue of the bearer's being located toward the abdomen of an organism relative to another entity. ventral to PATO:0001233 dorsal to A spatial quality inhering in a bearer by virtue of the bearer's being located toward the back or upper surface of an organism relative to another entity. dorsal to PATO:0001237 quality of a single physical entity A physical object quality which inheres in a single-bearer. quality of a single physical entity PATO:0001238 quality of related physical entities A physical entity quality which exists in relation towards some other entity. quality of related physical entities PATO:0001338 mixed sex A biological sex quality inhering in a population of multiple sexes. mixed sex PATO:0001339 biomaterial purity A composition quality inhering in an bearer by virtue of the bearer's homogeneity of a biomaterial. biomaterial purity PATO:0001340 hermaphrodite A biological sex quality inhering in an organism or a population with both male and female sexual organs in one individual. hermaphrodite PATO:0001341 a mating type (yeast) A S. cerevisiae mating type cells that secrete a pheromone that in alpha haploids stimulates processes that lead to mating. a mating type (yeast) PATO:0001344 alpha mating type (yeast) A S. cerevisiae mating type cells that secrete a pheromone that stimulates a haploids. alpha mating type (yeast) PATO:0001345 h minus A S. pombe mating type determined by the mat1-Mc and mat1-Mi on the mat1 locus. h minus PATO:0001346 h plus A S. pombe mating type determined by the mat1-Pc and mat1-Pi on the mat1 locus. h plus PATO:0001347 F mating type A bacterial mating type indicating the presence of F plasmid in a bacterial cell. F mating type PATO:0001348 F minus mating type A bacterial mating type indicating the absence of F plasmid in a bacterial cell. F minus mating type PATO:0001374 ploidy A cellular quality inhering in a bearer by virtue of the bearer's number of homologous sets of chromosomes in the nucleus or primary chromosome-containing compartment of the cell, each set essentially coding for all the biological traits of the organism. ploidy PATO:0001375 haploid A ploidy quality inhering in a bearer by virtue of the bearer's containing a single set of homologous chromosomes. haploid PATO:0001377 polyploid A ploidy quality inhering in a bearer by virtue of the bearer's containing more than two homologous sets of chromosomes. polyploid PATO:0001385 aneuploid A ploidy quality inhering in a bearer by virtue of the bearer's containing a non-integral multiple of the monoploid number, due to extra or missing chromosomes. aneuploid PATO:0001394 diploid A ploidy quality inhering in a bearer by virtue of the bearer's having two copies (homologs) of each chromosome, usually one from the mother and one from the father. diploid PATO:0001396 cellular quality A monadic quality of continuant that exists at the cellular level of organisation. cellular quality PATO:0001421 alive A viability quality inhering in a bearer by virtue of the bearer's condition before death. alive PATO:0001422 dead A viability quality inhering in a bearer by virtue of the cessation of the bearer's life. dead PATO:0001546 quality of a solid A physical quality inhering in a bearer by virtue of the bearer's exhibiting the physical characteristics of an entity characterized by particles arranged such that their shape and volume are relatively stable. quality of a solid PATO:0001547 quality of a gas A physical quality inhering in a bearer by virtue of the bearer's exhibiting the physical characteristics of an entity consisting of particles that have neither a defined volume nor defined shape. quality of a gas PATO:0001548 quality of a liquid A physical quality inhering in an entity exhibiting the physical characteristics of an amorphous (non-crystalline) form of matter between a gas and a solid that has a definite volume, but no definite shape. quality of a liquid PATO:0001631 relational spatial quality A quality of related physical entities inhering in a bearer by virtue of the bearer's pertaining to or involving or having the nature of space in relation to another entity. relational spatial quality PATO:0001632 anterior to A spatial quality inhering in a bearer by virtue of the bearer's being located toward the front of an organism relative to another entity. frontal anterior to PATO:0001741 radioactive A radiation quality inhering in bearer by virtue of the bearer's exhibiting or being caused by radioactivity. radioactive PATO:0001792 left side of A spatial quality inhering in a bearer by virtue of the bearer's being located on left side of from the a another entity. left side of PATO:0001793 right side of A spatial quality inhering in a bearer by virtue of the bearer's being located on right side of a another entity. right side of PATO:0001985 frozen A quality inhering in a bearer by virtue of the bearer's being kept below its freezing point. frozen PATO:0001995 organismal quality A quality that inheres in an entire organism or part of an organism. organismal quality PATO:0002201 handedness A behavioral quality inhering ina bearer by virtue of the bearer's unequal distribution of fine motor skill between its left and right hands or feet. handedness PATO:0002202 left handedness Handedness where the organism preferentially uses the left hand or foot for tasks requiring the use of a single hand or foot or a dominant hand or foot. left handedness PATO:0002203 right handedness Handedness where the organism preferentially uses the right hand or foot for tasks requiring the use of a single hand or foot or a dominant hand or foot. right handedness PATO:0002204 ambidextrous handedness Handedness where the organism exhibits no overall dominance in the use of right or left hand or foot in the performance of tasks that require one hand or foot or a dominant hand or foot. ambidextrous handedness PATO:0002243 fluid flow rate A physical quality inhering in a fluid (liquid or gas) by virtue of the amount of fluid which passes through a given surface per unit time. fluid flow rate PR:000000001 protein antithrombin III is a protein An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA. protein PR:000001004 CD4 molecule A protein that is a translation product of the human CD4 gene or a 1:1 ortholog thereof. CD4 is an accessory protein for MHC class-II antigen/T-cell receptor interaction. It is the primary receptor for HIV-1. CD4 has four immunoglobulin-like domains in its extracellular region that share the same structure, but can differ in sequence. CD4 molecule PR:000001018 CD3 subunit with immunoglobulin domain A protein with a core domain composition consisting of an extracellular N-terminal domain that adopts an immunoglobulin fold, a transmembrane domain, and an intracellular C-terminal domain with a single copy of the Immunoreceptor tyrosine-based activation motif (Pfam:PF02189) (ITAM). It constitutes the invariant subunit of the T cell antigen receptor (TCR). TCR is a surface receptor on T cells responsible for recognizing MHC-restricted antigens and initiating the cellular immune response. CD3 subunit with immunoglobulin domain PR:000003252 antithrombin-III A serpin that is a translation product of the human SERPINC1 gene or a 1:1 ortholog thereof. antithrombin-III PR:000003745 double-stranded RNA-specific adenosine deaminase A protein that is a translation product of the human ADAR gene or a 1:1 ortholog thereof. double-stranded RNA-specific adenosine deaminase PR:000006592 deoxyribonuclease-1 A protein that is a translation product of the human DNASE1 gene or a 1:1 ortholog thereof. deoxyribonuclease-1 PR:000007928 glial cell line-derived neurotrophic factor A protein that is a translation product of the human GDNF gene or a 1:1 ortholog thereof. glial cell line-derived neurotrophic factor PR:000014060 ribonuclease T2 A protein that is a translation product of the human RNASET2 gene or a 1:1 ortholog thereof. ribonuclease T2 PR:000023089 DNA ligase A protein that is a translation product of the Escherichia coli K-12 ligA gene or a 1:1 ortholog thereof. Definition defined by OBI developers: an enzyme that covalently joins two compatible pieces of DNA through the cleavage of an ATP molecule ligase DNA ligase PR:000025402 T cell receptor co-receptor CD8 A protein complex that is a membrane-bound heterodimeric co-receptor for MHC class-I antigen/T-cell receptor interaction. T cell receptor co-receptor CD8 PR:000025467 guanyl-specific ribonuclease T1 A protein that is a translation product of the Aspergillus oryzae rntA gene or a 1:1 ortholog thereof. guanyl-specific ribonuclease T1 PR:000025471 nuclease S1 A protein that is a translation product of the Aspergillus oryzae nucS gene or a 1:1 ortholog thereof. nuclease S1 PR:000025475 ribonuclease U2 A protein that is a translation product of the Ustilago sphaerogena RNU2 gene or a 1:1 ortholog thereof. ribonuclease U2 PR:000025477 ribonuclease V1 A protein with ribonuclease activity that is a constituent of cobra venom. ribonuclease V1 PR:000025478 ribonuclease CL3 A protein with ribonuclease activity that is purified from chicken liver. ribonuclease CL3 PR:P61244 REO:0000171 molecular label role a reagent role inhering in a molecular entity intended to associate with some molecular target to serve as a proxy for the presence, abundance, or location of this target in a detection of molecular label assay. MHB (9-29-13): 'molecular label role' imported from the Reagent Ontology and replaced OBI:OBI_0000140 (label role) molecular tracer role OBI developer call, 3-12-12 molecular label role REO:0000280 molecular label a molecular reagent intended to associate with some molecular target to serve as a proxy for the presence, abundance, or location of this target in a detection of molecular label assay molecular tracer OBI developer call, 3-12-12 molecular label SO:0000001 region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. primary structure of sequence macromolecule sequence region SO:0000104 polypeptide A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation. polypeptide sequence polypeptide SO:0000148 supercontig One or more contigs that have been ordered and oriented using end-read information. Contains gaps that are filled with N's. supercontig SO:0000149 contig A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases. contig SO:0000276 miRNA Small, ~22-nt, RNA molecule that is the endogenous transcript of a miRNA gene. Micro RNAs are produced from precursor molecules (SO:0000647) that can form local hairpin structures, which ordinarily are processed (via the Dicer pathway) such that a single miRNA molecule accumulates from one arm of a hairpin precursor molecule. Micro RNAs may trigger the cleavage of their target molecules or act as translational repressors. miRNA SO:0000353 sequence_assembly A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences. sequence_assembly SO:0000988 circular A quality of a nucleotide polymer that has no terminal nucleotide residues. circular SO:0001248 assembly A region of the genome of known length that is composed by ordering and aligning two or more different regions. assembly UBERON:0000029 lymph node Any of the rounded masses of lymphoid tissue that are surrounded by a capsule of connective tissue, are distributed along the lymphatic vessels, and contain numerous lymphocytes which filter the flow of lymph. lymph node UBERON:0000105 life cycle stage A spatiotemporal region encompassing some part of the life cycle of an organism. life cycle stage UBERON:0000165 mouth The proximal portion of the digestive tract, containing the oral cavity and bounded by the oral opening. In vertebrates, this extends to the pharynx and includes gums, lips, tongue and parts of the palate. Typically also includes the teeth, except where these occur elsewhere (e.g. pharyngeal jaws) or protrude from the mouth (tusks). mouth UBERON:0000178 blood A fluid that is composed of blood plasma and erythrocytes. blood UBERON:0000955 brain The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell[WP]. brain UBERON:0001013 adipose tissue Portion of connective tissue composed of adipocytes enmeshed in areolar tissue adipose tissue UBERON:0001088 urine Excretion that is the output of a kidney urine UBERON:0001134 skeletal muscle tissue Muscle tissue that consists primarily of skeletal muscle fibers. skeletal muscle tissue UBERON:0001638 vein Any of the tubular branching vessels that carry blood from the capillaries toward the heart. vein UBERON:0001873 caudate nucleus Subcortical nucleus of telecephalic origin consisting of an elongated gray mass lying lateral to and bordering the lateral ventricle. It is divided into a head, body and tail in some species. caudate nucleus UBERON:0001874 putamen Subcortical nucleus of telencephalic , which together with the caudate nucleus, forms the striatum. The putamen lies lateral to the internal capsule and medial to the external medullary lamina, and is separated from the caudate nucleus by the fibers of the internal capsule for most of its length, except at its anterior portion. putamen UBERON:0002067 dermis The dermis is a layer of skin between the epidermis (with which it makes up the skin) and subcutaneous tissues, and is composed of two layers, the papillary and reticular dermis[WP]. dermis UBERON:0002072 hypodermis Lowermost layer of the integumentary system in vertebrates. Types of cells that are found in the hypodermis are fibroblasts, adipose cells, and macrophages. It is derived from the mesoderm, but unlike the dermis, it is not derived from the dermatome region of the mesoderm. The hypodermis is used mainly for fat storage[WP]. hypodermis UBERON:0002106 spleen the organ that functions to filter blood and to store red corpuscles and platelets spleen UBERON:0002107 liver An exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes[GO]. liver UBERON:0002358 peritoneum A serous membrane that lines the peritoneal cavity[VHOG,modified]. peritoneum UBERON:0002812 left cerebral hemisphere A cerebral hemisphere that is in the left side of a brain. left cerebral hemisphere UBERON:0002813 right cerebral hemisphere A cerebral hemisphere that is in the right side of a brain. right cerebral hemisphere UBERON:0005022 mucosa of nasopharynx A mucosa that is part of a nasopharynx [Automatically generated definition]. mucosa of nasopharynx UBERON:0005023 mucosa of oropharynx A mucosa that is part of a oropharynx [Automatically generated definition]. mucosa of oropharynx UO:0000001 length unit A unit which is a standard measure of the distance between two points. length unit UO:0000002 mass unit A unit which is a standard measure of the amount of matter/energy of a physical object. mass unit UO:0000003 time unit A unit which is a standard measure of the dimension in which events occur in sequence. time unit UO:0000005 temperature unit A unit which is a standard measure of the average kinetic energy of the particles in a sample of matter. temperature unit UO:0000006 substance unit A unit which is a standardised quantity of an element or compound with uniform composition. substance unit UO:0000051 concentration unit A unit which represents a standard measurement of how much of a given substance there is mixed with another substance. concentration unit UO:0000095 volume unit A unit which is a standard measure of the amount of space occupied by any substance, whether solid, liquid, or gas. volume unit UO:0000105 frequency unit A unit which is a standard measure of the number of repetitive actions in a particular time. frequency unit UO:0000109 pressure unit A unit which is a standard measure of the force applied to a given area. pressure unit UO:0000270 volumetric flow rate unit A unit which is a standard measure of the volume of fluid which passes through a given surface per unit time . volumetric flow rate unit UO:0000280 rate unit A unit which represents a standard measurement occurrence of a process per unit time. rate unit VO:0000001 vaccine A vaccine is a processed material with the function that when administered, it prevents or ameliorates a disorder in a target organism by inducing or modifying adaptive immune responses specific to the antigens in the vaccine. vaccine VO:0000002 vaccination a process of administering substance in vivo that involves in adding a vaccine into a host (e.g., human) in vivo with the intent to invoke a protective or therapeutic adaptive immune response. vaccination doap:Project doap:SVNRepository doap:Version oboInOwl:DbXref oboInOwl:Definition oboInOwl:ObsoleteClass Obsolete Class Obsolete Class oboInOwl:Subset oboInOwl:Synonym oboInOwl:SynonymType owl:Nothing owl:Thing example to be eventually removed example to be eventually removed failed exploratory term The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job Person:Alan Ruttenberg failed exploratory term metadata complete Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. metadata complete organizational term term created to ease viewing/sort terms for development purpose, and will not be included in a release PERSON:Alan Ruttenberg organizational term ready for release Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." ready for release metadata incomplete Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. metadata incomplete uncurated Nothing done yet beyond assigning a unique class ID and proposing a preferred term. uncurated pending final vetting All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. pending final vetting core Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes. PERSON: Alan Ruttenberg PERSON: Melanie Courtot core placeholder removed placeholder removed terms merged An editor note should explain what were the merged terms and the reason for the merge. terms merged term imported This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use. term imported term split This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created. term split other This is to be used if none of the existing instances cover the reason for obsolescence. An editor note should indicate this new reason. We expect to be able to mine these new reasons and add instances as required. other true universal Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents. Alan Ruttenberg A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf universal defined class A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal. Alan Ruttenberg defined class named class expression A named class expression is a logical expression that is given a name. The name can be used in place of the expression. named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions Alan Ruttenberg named class expression to be replaced with external ontology term Terms with this status should eventually replaced with a term from another ontology. Alan Ruttenberg group:OBI to be replaced with external ontology term requires discussion A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. Alan Ruttenberg group:OBI requires discussion Transformation-ML Transformation-ML file describing parameter transformations used in a GvHD experiment. Transformation-ML is a format standard of a digital entity that is conformant with the Transformation-ML standard.(http://wiki.ficcs.org/ficcs/Transformation-ML?action=AttachFile&do=get&target=Transformation-ML_v1.0.26.pdf) person:Jennifer Fostel web-page:http://wiki.ficcs.org/ficcs/Transformation-ML?action=AttachFile&do=get&target=Transformation-ML_v1.0.26.pdf Transformation-ML ACS d06.acs, ACS1.0 data file of well D06 of plate 2 of part 1 of a GvHD experiment. ACS is a format standard of a digital entity that is conformant with the Analytical Cytometry Standard. (http://www.isac-net.org/content/view/607/150/) person:Jennifer Fostel web-page:http://www.isac-net.org/content/view/607/150/ ACS XML RDF/XML file, OWL file, Compensation-ML file, WSDL document, SVG document XML is a format standard of a digital entity that is conformant with the W3C Extensible Markup Language Recommendation.(http://www.w3.org/XML/) person:Jennifer Fostel web-page:http://www.w3.org/XML/ XML RDF A FOAF file, a SKOS file, an OWL file. RDF is a format standard of a digital entity that is conformant with the W3C Resource Description Framework RDF/XML Syntax specification.(http://www.w3.org/RDF/) person:Jennifer Fostel web-page:http://www.w3.org/RDF/ RDF zip MagicDraw MDZIP archive, Java JAR file. zip is a format standard of a digital entity that is conformant with the PKWARE .ZIP file format specification (http://www.pkware.com/index.php?option=com_content&task=view&id=59&Itemid=103/) person:Jennifer Fostel web-page:http://www.pkware.com/index.php?option=com_content&task=view&id=59&Itemid=103/ zip tar Example.tar file. tar is a format standard of a digital entity that is conformant with the tape archive file format as standardized by POSIX.1-1998, POSIX.1-2001, or any other tar format compliant with the GNU tar specification. (http://www.gnu.org/software/tar/manual/) person:Jennifer Fostel web-page:http://www.gnu.org/software/tar/manual/ tar FCS d01.fcs, FCS3 data file of well D06 of plate 2 of part 1 of a GvHD experiment. FCS is a format standard of a digital entity that is conformant with the Flow Cytometry Data File Standard.(http://www.fcspress.com/) person:Jennifer Fostel web-page:http://www.fcspress.com/ FCS Compensation-ML compfoo.xml, Compensation-ML file describing compensation used in a GvHD experiment Compensation-ML is a format standard of a digital entity that is conformant with the Compensation-ML standard. (http://wiki.ficcs.org/ficcs/Compensation-ML?action=AttachFile&do=get&target=Compensation-ML_v1.0.24.pdf) person:Jennifer Fostel web-page:http://wiki.ficcs.org/ficcs/Compensation-ML?action=AttachFile&do=get&target=Compensation-ML_v1.0.24.pdf Compensation-ML Gating-ML foogate.xml, Gating-ML file describing gates used in a GvHD experiment. Gating-ML is a format standard of a digital entity that is conformant with the Gating-ML standard. (http://www.flowcyt.org/gating/) person:Jennifer Fostel web-page:http://www.flowcyt.org/gating/ Gating-ML OWL OBI ontology file, Basic Formal Ontology file, BIRNLex file, BioPAX file. OWL is a format standard of a digital entity that is conformant with the W3C Web Ontology Language specification.(http://www.w3.org/2004/OWL/) person:Jennifer Fostel web-page:http://www.w3.org/2004/OWL/ OWL obsolete_the supplier role of Affymetrix obsolete_the supplier role of Affymetrix true Affymetrix Affymetrix supplied microarray An organization which supplies technology, tools and protocols for use in high throughput applications Affymetrix Thermo Philippe Rocca-Serra Thermo Waters Philippe Rocca-Serra Waters BIO-RAD Philippe Rocca-Serra BIO-RAD GenePattern hierarchical clustering James Malone GenePattern hierarchical clustering Ambion Philippe Rocca-Serra Ambion Helicos Philippe Rocca-Serra Helicos Roche Philippe Rocca-Serra Roche Illumina Philippe Rocca-Serra Illumina GenePattern PCA GenePattern PCA GenePattern module SVM GenePattern module SVM is a GenePattern software module which is used to run a support vector machine data transformation. James Malone Ryan Brinkman GenePattern module SVM GenePattern k-nearest neighbors James Malone GenePattern k-nearest neighbors GenePattern LOOCV GenePattern LOOCV GenePattern k-means clustering James Malone GenePattern k-means clustering Agilent Philippe Rocca-Serra Agilent GenePattern module KMeansClustering GenePattern module KMeansClustering is a GenePattern software module which is used to perform a k Means clustering data transformation. James Malone PERSON: James Malone GenePattern module KMeansClustering GenePattern CART James Malone GenePattern CART GenePattern module CARTXValidation GenePattern module CARTXValidation is a GenePattern software module which uses a CART decision tree induction with a leave one out cross validation data transformations. GenePattern module CARTXValidation Li-Cor Philippe Rocca-Serra Li-Cor Bruker Corporation Philippe Rocca-Serra Bruker Corporation GenePattern module KNNXValidation GenePattern module KNNXValidation is a GenePattern software module which uses a k-nearest neighbours clustering with a leave one out cross validation data transformations. James Malone PERSON: James Malone GenePattern module KNNXValidation GenePattern module PeakMatch GenePattern module PeakMatch GenePattern module KNN GenePattern module KNN is a GenePattern software module which perform a k-nearest neighbors data transformation. James Malone GenePattern module KNN GenePattern module HierarchicalClustering GenePattern module HierarchicalClustering is a GenePattern software module which is used to perform a hierarchical clustering data transformation. James Malone PERSON: James Malone GenePattern module HierarchicalClustering GenePattern SVM James Malone GenePattern SVM Applied Biosystems Philippe Rocca-Serra Applied Biosystems GenePattern module PCA GenePattern module PCA is a GenePattern software module which is used to perform a principal components analysis dimensionality reduction data transformation. James Malone PERSON: James Malone GenePattern module PCA GenePattern peak matching James Malone Ryan Brinkman GenePattern peak matching Bruker Daltonics Philippe Rocca-Serra Bruker Daltonics GenePattern HeatMapViewer data visualization The GenePattern process of generating Heat Maps from clustered data. James Malone GenePattern HeatMapViewer data visualization GenePattern HierarchicalClusteringViewer data visualization The GenePattern process of generating hierarchical clustering visualization from clustered data. James Malone GenePattern HierarchicalClusteringViewer data visualization GenePattern module HeatMapViewer A GenePattern software module which is used to generate a heatmap view of data. James Malone GenePattern module HeatMapViewer GenePattern module HierarchicalClusteringViewer A GenePattern software module which is used to generate a view of data that has been hierarchically clustered. James Malone GenePattern module HierarchicalClusteringViewer Sysmex Corporation, Kobe, Japan WEB:http://www.sysmex.com/@2009/08/06 2009/09/28 Alan Ruttenberg. Fucoidan-use-case Sysmex Corporation, Kobe, Japan obsolete_the manufacturer role of Agilent obsolete_the manufacturer role of Agilent true obsolete_manufacturer role of Bruker Daltonics obsolete_manufacturer role of Bruker Daltonics true obsolete_the manufacturer role of Thermo obsolete_the manufacturer role of Thermo true obsolete_the manufacturer role of Li-Cor obsolete_the manufacturer role of Li-Cor true obsolete_the manufacturer role of Roche obsolete_the manufacturer role of Roche true obsolete_the manufacturer role of Ambion obsolete_the manufacturer role of Ambion true obsolete_the manufacturer role of BIO-RAD obsolete_the manufacturer role of BIO-RAD true obsolete_the regulator role of the FDA obsolete_the regulator role of the FDA true obsolete_the manufacturer role of Illumina obsolete_the manufacturer role of Illumina true obsolete_the manufacturer role of Helicos obsolete_the manufacturer role of Helicos true obsolete_manufacturer role of Bruker Corporation obsolete_manufacturer role of Bruker Corporation true obsolete_the manufacturer role of Waters obsolete_the manufacturer role of Waters true obsolete_manufacturer role of applied biosystems obsolete_manufacturer role of applied biosystems true U.S. Food and Drug Administration FDA U.S. Food and Drug Administration right handed right handed ambidexterous ambidexterous left handed left handed Edingburgh handedness inventory The Edinburgh Handedness Inventory is a set of questions used to assess the dominance of a person's right or left hand in everyday activities. PERSON:Alan Ruttenberg PERSON:Jessica Turner PMID:5146491#Oldfield, R.C. (1971). The assessment and analysis of handedness: The Edinburgh inventory. Neuropsychologia, 9, 97-113 WEB:http://www.cse.yorku.ca/course_archive/2006-07/W/4441/EdinburghInventory.html Edingburgh handedness inventory eBioscience A supplier of flow cytometry analyzers Karin Breuer WEB:http://www.ebioscience.com/@2011/04/11 eBioscience Cytopeia A supplier of flow cytometry analyzers Karin Breuer WEB:http://www.cytopeia.com/@2011/04/11 Cytopeia Exalpha Biological A supplier of flow cytometry analyzers Karin Breuer WEB:http://www.exalpha.com/@2011/04/11 Exalpha Biological Apogee Flow Systems A supplier of flow cytometry analyzers Karin Breuer WEB:http://www.apogeeflow.com/@2011/04/11 Apogee Flow Systems Exbio Antibodies A supplier of flow cytometry analyzers Karin Breuer WEB:http://www.exbio.cz/@2011/04/11 Exbio Antibodies Becton Dickinson (BD Biosciences) A supplier of flow cytometry analyzers Karin Breuer WEB:http://www.bdbiosciences.com/@2011/04/11 Becton Dickinson (BD Biosciences) Dako Cytomation A supplier of flow cytometry analyzers Karin Breuer WEB:http://www.dakousa.com/@2011/04/11 Dako Cytomation Millipore A supplier of flow cytometry analyzers Karin Breuer WEB:http://www.guavatechnologies.com/@2011/04/11 Millipore Antigenix A supplier of flow cytometry analyzers Karin Breuer WEB:http://www.antigenix.com/@2011/04/11 Antigenix Partec A supplier of flow cytometry analyzers Karin Breuer WEB:http://www.partec.de/@2011/04/11 Partec Beckman Coulter A supplier of flow cytometry analyzers Karin Breuer WEB:http://www.beckmancoulter.com/@2011/04/11 Beckman Coulter Advanced Instruments Inc. (AI Companies) A supplier of flow cytometry analyzers Karin Breuer WEB:http://www.aicompanies.com/@2011/04/11 Advanced Instruments Inc. (AI Companies) Miltenyi Biotec A supplier of flow cytometry analyzers Karin Breuer WEB:http://www.miltenyibiotec.com/@2011/04/11 Miltenyi Biotec AES Chemunex A supplier of flow cytometry analyzers Karin Breuer WEB:http://www.aeschemunex.com/@2011/04/11 AES Chemunex Bentley Instruments A supplier of flow cytometry analyzers Karin Breuer WEB:http://bentleyinstruments.com/@2011/04/11 Bentley Instruments Invitrogen A supplier of flow cytometry analyzers Karin Breuer WEB:http://www.invitrogen.com/@2011/04/11 Invitrogen Luminex A supplier of flow cytometry analyzers Karin Breuer WEB:http://www.luminexcorp.com/@2011/04/11 Luminex CytoBuoy A supplier of flow cytometry analyzers Karin Breuer WEB:http://www.cytobuoy.com/@2011/04/11 CytoBuoy Nimblegen An organization that focuses on manufacturing target enrichment probe pools for DNA sequencing. Person: Jie Zheng Nimblegen Pacific Biosciences An organization that supplies tools for studying the synthesis and regulation of DNA, RNA and protein. It developed a powerful technology platform called single molecule real-time (SMRT) technology which enables real-time analysis of biomolecules with single molecule resolution. Person: Jie Zheng Pacific Biosciences NanoString Technologies An organization that supplies life science tools for translational research and molecular diagnostics based on a novel digital molecular barcoding technology. The NanoString platform can provide simple, multiplexed digital profiling of single molecules. NanoString Technologies axiom holds for all times ## Elucidation This is used when the statement/axiom is assumed to hold true 'eternally' ## How to interpret (informal) First the "atemporal" FOL is derived from the OWL using the standard interpretation. This axiom is temporalized by embedding the axiom within a for-all-times quantified sentence. The t argument is added to all instantiation predicates and predicates that use this relation. ## Example Class: nucleus SubClassOf: part_of some cell forall t : forall n : instance_of(n,Nucleus,t) implies exists c : instance_of(c,Cell,t) part_of(n,c,t) ## Notes This interpretation is *not* the same as an at-all-times relation axiom holds for all times relation has no temporal argument ## Elucidation This is used when the first-order logic form of the relation is binary, and takes no temporal argument. ## Example: Class: limb SubClassOf: develops_from some lateral-plate-mesoderm forall t, t2: forall x : instance_of(x,Limb,t) implies exists y : instance_of(y,LPM,t2) develops_from(x,y) relation has no temporal argument meter A length unit which is equal to the length of the path traveled by light in vacuum during a time interval of 1/299 792 458 of a second. m meter kilogram A mass unit which is equal to the mass of the International Prototype Kilogram kept by the BIPM at Svres, France. kg kilogram second A time unit which is equal to the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the caesium 133 atom. s sec second centimeter A length unit which is equal to one hundredth of a meter or 10^[-2] m. cm centimeter millimeter A length unit which is equal to one thousandth of a meter or 10^[-3] m. mm millimeter micrometer A length unit which is equal to one millionth of a meter or 10^[-6] m. um micrometer nanometer A length unit which is equal to one thousandth of one millionth of a meter or 10^[-9] m. nm nanometer angstrom A length unit which is equal to 10 [-10] m. angstrom gram A mass unit which is equal to one thousandth of a kilogram or 10^[-3] kg. g gram milligram A mass unit which is equal to one thousandth of a gram or 10^[-3] g. mg milligram microgram A mass unit which is equal to one millionth of a gram or 10^[-6] g. ug microgram nanogram A mass unit which is equal to one thousandth of one millionth of a gram or 10^[-9] g. ng nanogram picogram A mass unit which is equal to 10^[-12] g. pg picogram degree Celsius A temperature unit which is equal to one kelvin degree. However, they have their zeros at different points. The centigrade scale has its zero at 273.15 K. C degree C degree Celsius minute A time unit which is equal to 60 seconds. min minute hour A time unit which is equal to 3600 seconds or 60 minutes. h hr hour day A time unit which is equal to 24 hours. day week A time unit which is equal to 7 days. week month A time unit which is approximately equal to the length of time of one of cycle of the moon's phases which in science is taken to be equal to 30 days. month year A time unit which is equal to 12 months which is science is taken to be equal to 365.25 days. year micromole A substance unit equal to a millionth of a mol or 10^[-6] mol. umol micromole nanomole A substance unit equal to one thousandth of one millionth of a mole or 10^[-9] mol. nmol nanomole picomole A substance unit equal to 10^[-12] mol. pmol picomole molar A unit of concentration which expresses a concentration of 1 mole of solute per liter of solution (mol/L). M molar millimolar A unit of molarity which is equal to one thousandth of a molar or 10^[-3] M. mM millimolar micromolar A unit of molarity which is equal to one millionth of a molar or 10^[-6] M. uM micromolar nanomolar A unit of molarity which is equal to one thousandth of one millionth of a molar or 10^[-9] M. nM nanomolar picomolar A unit of molarity which is equal to 10^[-12] M. pM picomolar cubic centimeter A volume unit which is equal to one millionth of a cubic meter or 10^[-9] m^[3], or to 1 ml. cc cubic centimeter milliliter A volume unit which is equal to one thousandth of a liter or 10^[-3] L, or to 1 cubic centimeter. ml milliliter liter A volume unit which is equal to one thousandth of a cubic meter or 10^[-3] m^[3], or to 1 decimeter. L liter cubic decimeter A volume unit which is equal to one thousand of a cubic meter or 10^[-3] m^[3], or to 1 L. cubic decimeter microliter A volume unit which is equal to one millionth of a liter or 10^[-6] L. ul microliter nanoliter A volume unit which is equal to one thousandth of one millionth of a liter or 10^[-9] L. nl nanoliter picoliter A volume unit which is equal to 10^[-12] L. pl picoliter hertz A frequency unit which is equal to 1 complete cycle of a recurring phenomenon in 1 second. hertz mass percentage A dimensionless concentration unit which denotes the mass of a substance in a mixture as a percentage of the mass of the entire mixture. % w/w percent weight pr weight mass percentage mass volume percentage A dimensionless concentration unit which denotes the mass of the substance in a mixture as a percentage of the volume of the entire mixture. % w/v percent vol per vol mass volume percentage volume percentage A dimensionless concentration unit which denotes the volume of the solute in mL per 100 mL of the resulting solution. % v/v percent vol per vol volume percentage gram per liter A mass unit density which is equal to mass of an object in grams divided by the volume in liters. g per L g/L gram per liter milligram per milliliter A mass unit density which is equal to mass of an object in milligrams divided by the volume in milliliters. mg per ml mg/ml milligram per milliliter pH A dimensionless concentration notation which denotes the acidity of a solution in terms of activity of hydrogen ions (H+). pH milliliter per liter A volume per unit volume unit which is equal to one millionth of a liter of solute in one liter of solution. ml per L ml/l milliliter per liter gram per deciliter A mass density unit which is equal to mass of an object in grams divided by the volume in deciliters. g/dl gram per deciliter colony forming unit per volume A concentration unit which a measure of viable bacterial numbers in a given volume. colony forming unit per volume microliters per minute A volumetric flow rate unit which is equal to one microliter volume through a given surface in one minute. microliters per minute count per nanomolar second A rate unit which is equal to one over one nanomolar second. count per nanomolar second count per molar second A rate unit which is equal to one over one molar second. count per molar second count per nanomolar A rate unit which is equal to one over one nanomolar. count per nanomolar count per molar A rate unit which is equal to one over one molar. count per molar microgram per liter A mass unit density which is equal to mass of an object in micrograms divided by the volume in liters. ng/ml ug/L microgram per liter en Advisors for this project come from the IFOMIS group, Saarbruecken and from the Co-ODE group in Manchester Alan Ruttenberg Allyson Lister Barry Smith Bill Bug Bjoern Peters Carlo Torniai Chris Mungall Chris Stoeckert Chris Taylor Christian Bolling Cristian Cocos Daniel Rubin Daniel Schober Dawn Field Dirk Derom Elisabetta Manduchi Eric Deutsch Frank Gibson Gilberto Fragoso Helen C. Causton Helen Parkinson Holger Stenzhorn James A. Overton James Malone Jay Greenbaum Jeffrey Grethe Jennifer Fostel Jessica Turner Jie Zheng Joe White John Westbrook Kevin Clancy Larisa Soldatova Lawrence Hunter Liju Fan Luisa Montecchi Matthew Brush Matthew Pocock Melanie Courtot Melissa Haendel Mervi Heiskanen Monnie McGee Norman Morrison Philip Lord Philippe Rocca-Serra Pierre Grenon Richard Bruskiewich Richard Scheuermann Robert Stevens Ryan R. Brinkman Stefan Wiemann Susanna-Assunta Sansone Tanya Gray Tina Hernandez-Boussard Trish Whetzel Yongqun He 2009-07-31 The Ontology for Biomedical Investigations (OBI) is build in a collaborative, international effort and will serve as a resource for annotating biomedical investigations, including the study design, protocols and instrumentation used, the data generated and the types of analysis performed on the data. This ontology arose from the Functional Genomics Investigation Ontology (FuGO) and will contain both terms that are common to all biomedical investigations, including functional genomics investigations and those that are more domain specific. OWL-DL An ontology for the annotation of biomedical and functional genomics experiments. Ontology for Biomedical Investigation Please cite the OBI consortium http://purl.obolibrary.org/obo/obi where traditional citation is called for. However it is adequate that individual terms be attributed simply by use of the identifying PURL for the term, in projects that refer to them. 2015-12-07 SVN $Revision: 717 $ IAO Release 2015-02-23 IAO Release 2015-02-23 SVN Revision: exported OBI Release 2015-12-07 Arbor version; 1.0.1 Person:Alan Ruttenberg has part my body has part my brain (continuant parthood, two material entities) my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) this year has part this day (occurrent parthood) a core relation that holds between a whole and its part Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. has_part has part realizes this disease course realizes this disease this investigation realizes this investigator role this shattering realizes this fragility to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process realizes preceded by An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. is preceded by preceded_by http://www.obofoundry.org/ro/#OBO_REL:preceded_by preceded by precedes precedes occurs in b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t occurs_in unfolds in unfolds_in Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant occurs in To say that each spatiotemporal region s temporally_projects_onto some temporal region t is to say that t is the temporal extension of s. (axiom label in BFO2 Reference: [080-003]) To say that spatiotemporal region s spatially_projects_onto spatial region r at t is to say that r is the spatial extent of s at t. (axiom label in BFO2 Reference: [081-003]) To say that each spatiotemporal region s temporally_projects_onto some temporal region t is to say that t is the temporal extension of s. (axiom label in BFO2 Reference: [080-003]) To say that spatiotemporal region s spatially_projects_onto spatial region r at t is to say that r is the spatial extent of s at t. (axiom label in BFO2 Reference: [081-003]) 'Max binding in MCF-7 cell': 'realized in cell' some 'MCF cell' an object property that represents a relation between a realizable entity (e.g., molecular function) and a cell type (e.g., a cell line cell). This is a shortcut relation: 'realized in' some (process and 'occurs at' some cell) Oliver He realized in cell an object property that represents a relation between a molecular function (e.g., binding) and a protein. This is a shortcut relation that equals to: 'is realized in' some ('binding process' and ('has input' some protein)) Oliver He binding by protein GAZ:00000448 geographic location A reference to a place on the Earth, by its name or by its geographical location. geographic location has measurement unit label has measurement unit label is about This document is about information artifacts and their representations is_about is a (currently) primitive relation that relates an information artifact to an entity. 7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. We will try to build it back up by elaborating the various subproperties that are more precisely defined. Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic. person:Alan Ruttenberg Smith, Ceusters, Ruttenberg, 2000 years of philosophy is about denotes A person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance "Alan" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between "Alan" and the person that is being named. denotes is a primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically 2009-11-10 Alan Ruttenberg. Old definition said the following to emphasize the generic nature of this relation. We no longer have 'specifically denotes', which would have been primitive, so make this relation primitive. g denotes r =def r is a portion of reality there is some c that is a concretization of g every c that is a concretization of g specifically denotes r person:Alan Ruttenberg Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan denotes is quality measurement of m is a quality measurement of q at t when q is a quality there is a measurement process p that has specified output m, a measurement datum, that is about q 8/6/2009 Alan Ruttenberg: The strategy is to be rather specific with this relationship. There are other kinds of measurements that are not of qualities, such as those that measure time. We will add these as separate properties for the moment and see about generalizing later From the second IAO workshop [Alan Ruttenberg 8/6/2009: not completely current, though bringing in comparison is probably important] This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details. -- From the second IAO workshop, various comments, [commented on by Alan Ruttenberg 8/6/2009] unit of measure is a quality, e.g. the length of a ruler. [We decided to hedge on what units of measure are, instead talking about measurement unit labels, which are the information content entities that are about whatever measurement units are. For IAO we need that information entity in any case. See the term measurement unit label] [Some struggling with the various subflavors of is_about. We subsequently removed the relation represents, and describes until and only when we have a better theory] a represents b means either a denotes b or a describes describe: a describes b means a is about b and a allows an inference of at least one quality of b We have had a long discussion about denotes versus describes. From the second IAO workshop: An attempt at tieing the quality to the measurement datum more carefully. a is a magnitude means a is a determinate quality particular inhering in some bearer b existing at a time t that can be represented/denoted by an information content entity e that has parts denoting a unit of measure, a number, and b. The unit of measure is an instance of the determinable quality. From the second meeting on IAO: An attempt at defining assay using Barry's "reliability" wording assay: process and has_input some material entity and has_output some information content entity and which is such that instances of this process type reliably generate outputs that describes the input. This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details. Alan Ruttenberg is quality measurement of is duration of relates a process to a time-measurement-datum that represents the duration of the process Person:Alan Ruttenberg is duration of provides_service_consumer_with The provides_service_consumer_with relation links the service to its primary process it provides for the consumer (as opposed to secondary processual parts of a service process such as payment or documentation). For example, a 'DNA sequencing service' provides_service_consumer_with 'DNA sequencing' as the essential process performed by the provider for the client. A relation between a service and the primary processual part of the service that is performed by the provider for the consumer. provides_service_consumer_with is_supported_by_data The relation between the conclusion "Gene tpbA is involved in EPS production" and the data items produced using two sets of organisms, one being a tpbA knockout, the other being tpbA wildtype tested in polysacharide production assays and analyzed using an ANOVA. The relation between a data item and a conclusion where the conclusion is the output of a data interpreting process and the data item is used as an input to that process OBI OBI Philly 2011 workshop is_supported_by_data has_specified_input see is_input_of example_of_usage A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. 8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works. PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Coutot has_specified_input has_specified_output A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Courtot has_specified_output is_manufactured_by http://www.affymetrix.com/products/arrays/specific/hgu133.affx is_manufactered_by http://www.affymetrix.com/ (if we decide to use these URIs for the actual entities) c is_manufactured_by o means that there was a process p in which c was built in which a person, or set of people or machines did the work(bore the "Manufacturer Role", and those people/and or machines were members or of directed by the organization to do this. Alan Ruttenberg Liju Fan has_make has_manufacturer is_manufactured_by is_specified_output_of A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. Alan Ruttenberg PERSON:Bjoern Peters is_specified_output_of achieves_planned_objective A cell sorting process achieves the objective specification 'material separation objective' This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process. BP, AR, PPPB branch PPPB branch derived modified according to email thread from 1/23/09 in accordince with DT and PPPB branch achieves_planned_objective has grain the relation of the cells in the finger of the skin to the finger, in which an indeterminate number of grains are parts of the whole by virtue of being grains in a collective that is part of the whole, and in which removing one granular part does not nec- essarily damage or diminish the whole. Ontological Whether there is a fixed, or nearly fixed number of parts - e.g. fingers of the hand, chambers of the heart, or wheels of a car - such that there can be a notion of a single one being missing, or whether, by contrast, the number of parts is indeterminate - e.g., cells in the skin of the hand, red cells in blood, or rubber molecules in the tread of the tire of the wheel of the car. Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. Definition take from the definition of granular parthood in the cited paper. Needs work to put into standard form PERSON: Alan Ruttenberg PAPER: Granularity, scale and collectivity: When size does and does not matter, Alan Rector, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349 has grain specifies value of A relation between a value specification and an entity which the specification is about. specifies value of has value specification A relation between an information content entity and a value specification that specifies its value. PERSON: James A. Overton OBI has value specification inheres in this fragility inheres in this vase this red color inheres in this apple a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence A dependent inheres in its bearer at all times for which the dependent exists. inheres_in inheres in bearer of this apple is bearer of this red color this vase is bearer of this fragility a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. bearer_of is bearer of bearer of has participant this blood coagulation has participant this blood clot this investigation has participant this investigator this process has participant this input material (or this output material) a relation between a process and a continuant, in which the continuant is somehow involved in the process Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. has_participant http://www.obofoundry.org/ro/#OBO_REL:has_participant has participant function of this catalysis function is a function of this enzyme a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. function_of is function of function of has function this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. has_function has function has role this person has role this investigator role (more colloquially: this person has this role of investigator) a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. has_role has role derives from this cell derives from this parent cell (cell division) this nucleus derives from this parent nucleus (nuclear division) a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'. derives_from derives from immediately preceded by David Osumi-Sutherland starts_at_end_of X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) immediately preceded by Steve Pittard Yongqun Oliver He (YH) Zhaohui Steve Qin 2016-03-13 The Epigenome Ontology (EGO) is an ontology in the domain of epigenome. Arbor version; 1.0.1 IAO_0021000-IAO_0021999 IAO_0020000-IAO_0020999