en BFO 2 Reference: BFO does not claim to be a complete coverage of all entities. It seeks only to provide coverage of those entities studied by empirical science together with those entities which affect or are involved in human activities such as data processing and planning – coverage that is sufficiently broad to provide assistance to those engaged in building domain ontologies for purposes of data annotation [17 BFO 2 Reference: BFO’s treatment of continuants and occurrents – as also its treatment of regions, rests on a dichotomy between space and time, and on the view that there are two perspectives on reality – earlier called the ‘SNAP’ and ‘SPAN’ perspectives, both of which are essential to the non-reductionist representation of reality as we understand it from the best available science [30 BFO 2 Reference: For both terms and relational expressions in BFO, we distinguish between primitive and defined. ‘Entity’ is an example of one such primitive term. Primitive terms in a highest-level ontology such as BFO are terms that 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. Adam Goldstein Alan Ruttenberg Alan Ruttenberg Albert Goldfain Albert Goldfain Anuj Shah Barry Smith Barry Smith Bill Duncan Bjoern Peters Bjoern Peters Carlo Torniai Chris Mungall Chris Mungall Chris Stoeckert Christian A. Boelling Dan Malone Darren Natale David Osumi-Sutherland David Osumi-Sutherland Fabian Neuhaus Gwen Frishkoff Holger Stenzhorn James A. Overton James A. Overton James Malone Janna Hastings Jennifer Fostel Jessica Tay-Sontheimer Jie Zheng Jie Zheng Jingjing Yu Jodi Schneider Jonathan Bona Jonathan Rees Larisa Soldatova Larry Hunter Lawrence Hunter Leonard Jacuzzo Ludger Jansen Mark Ressler Mathias Brochhausen Mathias Brochhausen Matt Brush Mauricio Almeida Melanie Courtot Melanie Courtot Michel Dumontier Paolo Ciccarese Pat Hayes Philip E. Empey Philippe Rocca-Serra Pierre Grenon Randall Dipert Randy Dipert Richard D. Boyce Robert Rovetto Ron Rudnicki Ron Rudnicki Satya Sahoo Sivaram Arabandi Stefan Schulz Thomas Bittner Werner Ceusters Werner Ceusters William Duncan William Hogan William R. Hogan Yongqun (Oliver) He Mathias Brochhausen http://creativecommons.org/licenses/by/4.0/ http://creativecommons.org/licenses/by/4.0/ An information artifact is, loosely, a dependent continuant or its bearer that is created as the result of one or more intentional processes. Examples: uniprot, the english language, the contents of this document or a printout of it, the temperature measurements from a weather balloon. For more information, see the project home page at https://github.com/information-artifact-ontology/IAO IDs allocated to related efforts: PNO: IAO_0020000-IAO_0020999, D_ACTS: IAO_0021000-IAO_0021999 IDs allocated to subdomains of IAO. pno.owl: IAO_0020000-IAO_0020999, d-acts.owl: IAO_0021000-IAO_0021999 The Drug-drug Interaction and Drug-drug Interaction Evidence Ontology (DIDEO) by the DIDEO development group is licensed under CC BY 4.0 (https://creativecommons.org/licenses/by/4.0/). The Drug-drug Interaction and Drug-drug Interaction Evidence Ontology (DIDEO) by the DIDEO development group is licensed under CC BY 4.0. You are free to share (copy and redistribute the material in any medium or format) and adapt (remix, transform, and build upon the material) for any purpose, even commercially. for any purpose, even commercially. The licensor cannot revoke these freedoms as long as you follow the license terms. You must give appropriate credit (by using the original ontology IRI for the whole ontology and original term IRIs for individual terms), provide a link to the license, and indicate if any changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. The Information Artifact Ontology (IAO) is licensed under the Creative Commons Attribution License (CC-BY) version 4.0. You are free to share (copy and redistribute the material in any medium or format) and adapt (remix, transform, and build upon the material) for any purpose, even commercially. for any purpose, even commercially. The licensor cannot revoke these freedoms as long as you follow the license terms. You must give appropriate credit (by using the original ontology IRI for the whole ontology and original term IRIs for individual terms), provide a link to the license, and indicate if any changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. For more information see http://www.obofoundry.org/docs/Citation.html The http://purl.obolibary.org/obo/bfo/classes-only.owl variant of BFO ("bfo_classes_only.owl") includes only the class hierarchy and annotations from the full OWL version of BFO 2: http://purl.obolibary.org/obo/bfo.owl ("bfo.owl"). There are no object properties or logical axioms that use the object properties in bfo_classes_only.owl. As the logical axioms in the bfo_classes_only.owl variant are limited to subclass and disjoint assertions they are much weaker than the logical axioms in bfo.owl. If you plan to use the relations that define BFO 2, you should import bfo.owl instead of bfo_classes_only.owl. To the extent that the relations are used without importing bfo.owl, be mindful that they should be used in a manner consistent with their use in bfo.owl. Otherwise if your ontology is imported by a another ontology that imports bfo.owl there may be inconsistencies. See the BFO 2 release notes for further information about BFO 2. Please note that the current release of bfo.owl uses temporal relations when the subject or object is a continuant, a major change from BFO 1. This is an early version of BFO version 2 and has not yet been extensively reviewed by the project team members. Please see the project site http://code.google.com/p/bfo/ , the bfo2 owl discussion group http://groups.google.com/group/bfo-owl-devel , the bfo2 discussion group http://groups.google.com/group/bfo-devel, the tracking google doc http://goo.gl/IlrEE, and the current version of the bfo2 reference http://purl.obolibrary.org/obo/bfo/dev/bfo2-reference.docx . This ontology is generated from a specification at http://bfo.googlecode.com/svn/trunk/src/ontology/owl-group/specification/ and with the code that generates the OWL version in http://bfo.googlecode.com/svn/trunk/src/tools/. A very early version of BFO version 2 in CLIF is at http://purl.obolibrary.org/obo/bfo/dev/bfo.clif This version of the ontology is the merge of all its imports and has added axioms inferred by an OWL reasoner DIDEO Drug-drug Interaction and Drug-drug Interaction Evidence Ontology 2024-02-13 release version 2017-11-17 https://github.com/oborel/obo-relations/wiki/ROCore 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 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 Cell line LINCS ID Cell line LINCS ID STR profile editor preferred term 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 label editor preferred term editor preferred term editor preferred term~editor preferred label example A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold. 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 has curation status definition 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 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 https://github.com/information-artifact-ontology/IAO/issues/115. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition editor definition editor term editor 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 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 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 curator note term tracker item the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/ An IRI or similar locator for a request or discussion of an ontology term. Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg The 'tracker item' can associate a tracker with a specific ontology term. term tracker item The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition. Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg The 'term requester' can credit the person, organization or project who request the ontology term. ontology term requester 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 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 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 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 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 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 id 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 has literature mining keywords MPIO user-centered definition ISA alternative term IEDB alternative term temporal interpretation https://github.com/oborel/obo-relations/wiki/ROAndTime is direct form of is indirect form of external_definition has_relational_adjective Unique Apollo Label has_rank Source Source alternative_term definition has_alternative_id has_broad_synonym database_cross_reference has_exact_synonym has_narrow_synonym has_obo_namespace has_related_synonym in_subset shorthand label see also is 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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ 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 http://purl.obolibrary.org/obo/ro.owl 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 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 x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. 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 Optional.of(http://purl.obolibrary.org/obo/obi.owl) http://purl.obolibrary.org/obo/ro.owl http://www.obofoundry.org/ro/#OBO_REL:preceded_by preceded by precedes x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. http://purl.obolibrary.org/obo/ro.owl 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 site of [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 continuant(c) and process(p) and first_time_point(p,t1) and last_time_point(p,t2) and not(exists_at(c,t1)) and exists_at(c,t2) Alan Ruttenberg https://code.google.com/p/bfo/issues/detail?id=50&colspec=ID%20Type%20Status%20Owner%20Summary%20Reporter%20Modified begins_to_exist_during there is some extended organism e & there is some temporal region tr & p occupies temporal region tr & p occurs_in e & c begins to exist during p & there is some t ( t part-of tr & c located-in e at t ) Alan Ruttenberg Mathias Brochhausen William R. Hogan organismally_begins_to_exist_during there is some extended organism e & p1 occurs_in e & p2 occurs_in e & p1 immediately precedes p2 Mathias Brochhausen for immediatly precedes please see: http://krr.meraka.org.za/~aow2010/Trentelman-etal.pdf organismally immediately precedes is organismally immediately preceded by A pharmaeutic ingredient or a metabolite X is the substrate of an enzyme E, iff E catalyzes X to M. Mathias Brochhausen is substrate of realizes substrate role true involves substrate true inhibits-catalyzes metabolism of catalyzes a Phase I or Phase II enzymatic reaction involving 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 https://github.com/information-artifact-ontology/IAO/issues/25&q=denote Alan Ruttenberg Smith, Ceusters, Ruttenberg, 2000 years of philosophy obsolete_specifically denotes true 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 see https://github.com/information-artifact-ontology/IAO/issues/25&q=denote obsolete_materially denotes true obsolete_describes true obsolete_represents true relating a cartesian spatial coordinate datum to a unit label that together with the values represent a point has coordinate unit label relates a process to a time-measurement-datum that represents the duration of the process Person:Alan Ruttenberg is duration of 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 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 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 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 relates a time stamped measurement datum to the measurement datum that was measured Alan Ruttenberg has measurement datum 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 http://purl.obolibrary.org/obo/obi.owl is_specified_input_of 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 http://purl.obolibrary.org/obo/obi.owl is_specified_output_of specifies value of A relation between a value specification and an entity which the specification is about. Optional.of(http://purl.obolibrary.org/obo/obi.owl) specifies value of 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 Optional.of(http://purl.obolibrary.org/obo/obi.owl) process is result of bearer of this apple is bearer of this red color this vase is bearer of this fragility Inverse of characteristic_of 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 characteristic 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 http://purl.obolibrary.org/obo/ro.owl participates in 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 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 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 This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. function 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 This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. quality 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 This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. role of 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 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 a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence has disposition This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. disposition of 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 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 is 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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ 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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ 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 http://www.obofoundry.org/ro/#OBO_REL:located_in located in This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. 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 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 David Osumi-Sutherland http://purl.obolibrary.org/obo/ro.owl X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) ends after David Osumi-Sutherland starts_at_end_of Optional.of(http://purl.obolibrary.org/obo/obi.owl) X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) immediately preceded by David Osumi-Sutherland ends_at_start_of meets http://purl.obolibrary.org/obo/ro.owl X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) immediately precedes x regulates y if and only if the x is the realization of a function to exert an effect on the frequency, rate or extent of y We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit Chris Mungall David Hill Tanya Berardini GO Regulation does not preclude parthood; the regulatory process may be upstream, or may be within the regulated process. http://purl.obolibrary.org/obo/ro.owl regulates (processual) false regulates x negatively regulates y if and only if the progression of x reduces the frequency, rate or extent of y Chris Mungall http://purl.obolibrary.org/obo/ro.owl negatively regulates (process to process) negatively regulates 'human p53 protein' SubClassOf some ('has prototype' some ('participates in' some 'DNA repair')) heart SubClassOf 'has prototype' some ('participates in' some 'blood circulation') x has prototype y if and only if x is an instance of C and y is a prototypical instance of C. For example, every instance of heart, both normal and abnormal is related by the has prototype relation to some instance of a "canonical" heart, which participates in blood circulation. Experimental. In future there may be a formalization in which this relation is treated as a shortcut to some modal logic axiom. We may decide to obsolete this and adopt a more specific evolutionary relationship (e.g. evolved from) This property can be used to make weaker forms of certain relations by chaining an additional property. For example, we may say: retina SubClassOf has_prototype some 'detection of light'. i.e. every retina is related to a prototypical retina instance which is detecting some light. Note that this is very similar to 'capable of', but this relation affords a wider flexibility. E.g. we can make a relation between continuants. Chris Mungall http://purl.obolibrary.org/obo/ro.owl has prototype mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974) osteoclast SubClassOf 'capable of' some 'bone resorption' A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. Chris Mungall has function realized in For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)". http://purl.obolibrary.org/obo/ro.owl RO_0000053 some (RO_0000054 only ?Y) capable of c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. Chris Mungall has function in http://purl.obolibrary.org/obo/ro.owl RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y)) capable of part of x actively participates in y if and only if x participates in y and x realizes some active role Chris Mungall agent in http://purl.obolibrary.org/obo/ro.owl actively participates in Chris Mungall Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. http://purl.obolibrary.org/obo/ro.owl https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. temporally related to Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. Chris Mungall started by http://purl.obolibrary.org/obo/ro.owl starts with x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. Chris Mungall finished by http://purl.obolibrary.org/obo/ro.owl ends with p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p. Chris Mungall consumes has input p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p. Chris Mungall produces has output a particular instances of akt-2 enables some instance of protein kinase activity Chris Mungall catalyzes executes has This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time. http://purl.obolibrary.org/obo/ro.owl enables Chris Mungall This is a grouping relation that collects relations used for the purpose of connecting structure and function http://purl.obolibrary.org/obo/ro.owl functionally related to inverse of enables Chris Mungall http://purl.obolibrary.org/obo/ro.owl enabled by inverse of regulates Chris Mungall http://purl.obolibrary.org/obo/ro.owl regulated by (processual) regulated by Chris Mungall http://purl.obolibrary.org/obo/ro.owl negatively regulated by 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 is a mereological relation between a collection and an item. SIO has member inverse of has input Chris Mungall Optional.of(http://purl.obolibrary.org/obo/ro.owl) input of inverse of has output Chris Mungall Optional.of(http://purl.obolibrary.org/obo/ro.owl) output of inverse of upstream of Chris Mungall http://purl.obolibrary.org/obo/ro.owl causally downstream of Chris Mungall directly negatively regulates http://purl.obolibrary.org/obo/ro.owl directly inhibits (process to process) directly inhibits Chris Mungall indirectly negatively regulates http://purl.obolibrary.org/obo/ro.owl indirectly inhibits This relation groups causal relations between material entities and causal relations between processes This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? * Is the influence positive or negative The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yield a cross-product of different relation types. Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. http://purl.obolibrary.org/obo/ro.owl causally related to p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain Chris Mungall http://purl.obolibrary.org/obo/ro.owl causally upstream of p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q. Chris Mungall http://purl.obolibrary.org/obo/ro.owl immediately causally upstream of p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 Chris Mungall influences (processual) http://purl.obolibrary.org/obo/ro.owl causally upstream of or within Chris Mungall http://purl.obolibrary.org/obo/ro.owl causally downstream of or within A relationship that holds between two entities in which the processes executed by the two entities are causally connected. Considering relabeling as 'pairwise interacts with' This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact. Chris Mungall Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules. http://purl.obolibrary.org/obo/ro.owl in pairwise interaction with interacts with http://purl.obolibrary.org/obo/MI_0914 https://code.google.com/p/obo-relations/wiki/InteractionRelations An interaction relationship in which the two partners are molecular entities and are executing molecular processes that are directly causally connected. Chris Mungall binds molecularly binds with http://purl.obolibrary.org/obo/ro.owl molecularly interacts with http://purl.obolibrary.org/obo/MI_0915 Holds between molecular entities a and b when the execution of a activates or inhibits the activity of b Chris Mungall http://purl.obolibrary.org/obo/ro.owl molecularly controls Holds between molecules a and b if and only if a executes a process that directly diminishes a process executed by b. Chris Mungall inhibits http://purl.obolibrary.org/obo/ro.owl molecularly decreases activity of A relationship between a material entity and a process where the material entity has some causal role that influences the process http://purl.obolibrary.org/obo/ro.owl causal agent in p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q. Chris Mungall https://docs.google.com/document/d/1WxocTXZaGVhEV1n7NB86pCF3SUcBJh8bq4vQrVCkjSU/edit# Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. http://purl.obolibrary.org/obo/ro.owl causal relation between processes The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. http://purl.obolibrary.org/obo/ro.owl causal relation between material entities Holds between materal entities a and b if the activity of a is causally upstream of the activity of b, or causally upstream of a an activity that modifies b Chris Mungall http://purl.obolibrary.org/obo/ro.owl causally influences (material entity to material entity) causally influences A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. Chris Mungall http://purl.obolibrary.org/obo/ro.owl causal relation between material entity and a process A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. http://purl.obolibrary.org/obo/ro.owl related via dependence to DEPRECATED This relation is similar to but different in important respects to the characteristic-of relation. See comments on that relation for more information. DEPRECATED inheres in true DEPRECATED bearer of true DIDEO uses this object property from the old (depracted) RO, since we need to infer parts of drug products as represented by DRON (and DRON [along with many other OBO Foundry candidate ontologies] uses this object property). http://purl.obolibrary.org/obo/ido.owl OBO_REL:0000007 relationship has_proper_part DIDEO uses this object property from the old (depracted) RO, since we need to infer parts of drug products as represented by DRON (and DRON [along with many other OBO Foundry candidate ontologies] uses this object property). http://purl.obolibrary.org/obo/ido.owl OBO_REL:0000006 relationship proper_part_of has measurement value has x coordinate value has z coordinate value has y coordinate 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 APOLLO_SV:00000032 A measurement datum that is the output of counting. Mathias Brochhausen http://purl.obolibrary.org/obo/apollo_sv/dev/apollo_sv.owl A measurement datum that is the output of counting. count count BFO:0000001 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 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 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 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 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. BFO:0000004 ic IndependentContinuant 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] A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. 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 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 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 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 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 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 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] An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. 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 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 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 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 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 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] 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. 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 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 fiat-object-part FiatObjectPart 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 fiat object part 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 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 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 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 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 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 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] 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. 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 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 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 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 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 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 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 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 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 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 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 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 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 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]) A 5-[2-(dimethylamino)ethyl]-2-(4-methoxyphenyl)-4-oxo-2,3,4,5-tetrahydro-1,5-benzothiazepin-3-yl acetate in which both stereocentres have S configuration. A calcium-channel blocker and vasodilator, it is used as the hydrochloride in the management of angina pectoris and hypertension. http://purl.obolibrary.org/obo/chebi.owl CHEBI:4602 Beilstein:3573079 ChemIDplus:42399-41-7 CiteXplore:11937779 CiteXplore:16651034 CiteXplore:19167257 CiteXplore:23687551 CiteXplore:24261918 CiteXplore:25122162 CiteXplore:8369596 DrugBank:DB00343 HMDB:HMDB14487 KEGG COMPOUND:42399-41-7 KEGG COMPOUND:C06958 KEGG DRUG:D07845 NIST Chemistry WebBook:42399-41-7 Patent:DE1805714 Patent:DE3415035 Patent:US3562257 Patent:US4552695 Reaxys:3573079 Wikipedia:Diltiazem (2S,3S)-5-[2-(dimethylamino)ethyl]-2-(4-methoxyphenyl)-4-oxo-2,3,4,5-tetrahydro-1,5-benzothiazepin-3-yl acetate DILTIAZEM Diltiazem chebi_ontology (+)-cis-5-[2-(dimethylamino)ethyl]-2,3-dihydro-3-hydroxy-2-(p-methoxyphenyl)-1,5-benzothiazepin-4(5H)-one acetate ester (2S,3S)-5-(2-(dimethylamino)ethyl)-2-(4-methoxyphenyl)-4-oxo-2,3,4,5-tetrahydrobenzo[b][1,4]thiazepin-3-yl acetate (2S-cis)-3-(acetyloxy)-5-[2-(dimethylamino)ethyl]-2,3-dihydro-2-(4-methoxyphenyl)-1,5-benzothiazepin-4(5H)-one Acetic acid (2S,3S)-5-(2-dimethylamino-ethyl)-2-(4-methoxy-phenyl)-4-oxo-2,3,4,5-tetrahydro-benzo[b][1,4]thiazepin-3-yl ester C22H26N2O4S COc1ccc(cc1)[C@@H]1Sc2ccccc2N(CCN(C)C)C(=O)[C@@H]1OC(C)=O D-cis-diltiazem InChI=1S/C22H26N2O4S/c1-15(25)28-20-21(16-9-11-17(27-4)12-10-16)29-19-8-6-5-7-18(19)24(22(20)26)14-13-23(2)3/h5-12,20-21H,13-14H2,1-4H3/t20-,21+/m1/s1 InChIKey=HSUGRBWQSSZJOP-RTWAWAEBSA-N d-cis-diltiazem diltiazem diltiazemum CHEBI:101278 diltiazem CHEBI:101278 Abbreviation for nicotinamide-adenine dinucleotide when its oxidation state is unknown or unspecified. It is used in metabolic pathways like glycolysis and citric acid cycle. http://purl.obolibrary.org/obo/chebi.owl HMDB:HMDB00902 Wikipedia:Nicotinamide_adenine_dinucleotide NAD chebi_ontology nicotinamide-adenine dinucleotide CHEBI:13389 NAD CHEBI:13389 A steroid glucosiduronic acid having 17alpha-estradiol as the steroid component. http://purl.obolibrary.org/obo/chebi.owl CHEBI:14218 CHEBI:23962 CHEBI:4863 KEGG:C04300 17alpha-hydroxyestra-1,3,5(10)-trien-3-yl beta-D-glucopyranosiduronic acid chebi_ontology 0 17alpha-estradiol 3-glucuronide 448.210 448.50610 C24H32O8 Estradiol-17alpha 3-D-glucuronoside InChI=1S/C24H32O8/c1-24-9-8-14-13-5-3-12(10-11(13)2-4-15(14)16(24)6-7-17(24)25)31-23-20(28)18(26)19(27)21(32-23)22(29)30/h3,5,10,14-21,23,25-28H,2,4,6-9H2,1H3,(H,29,30)/t14-,15-,16+,17-,18+,19+,20-,21+,23-,24+/m1/s1 MUOHJTRCBBDUOW-FNUZHIFDSA-N [H][C@]12CC[C@]3(C)[C@H](O)CC[C@@]3([H])[C@]1([H])CCc1cc(O[C@@H]3O[C@@H]([C@@H](O)[C@H](O)[C@H]3O)C(O)=O)ccc21 CHEBI:15822 17alpha-estradiol 3-glucosiduronic acid CHEBI:15822 A nucleobase-containing molecular entity with a polymeric structure comprised of a linear sequence of 13 or more nucleotide residues. http://purl.obolibrary.org/obo/chebi.owl CHEBI:13672 CHEBI:14859 CHEBI:8312 KEGG COMPOUND:C00419 Polynucleotide chebi_ontology C10H17O10PR2(C5H8O6PR)n polynucleotides CHEBI:15986 polynucleotide CHEBI:15986 NADPH is the reduced form of NADP+; used in anabolic reactions, such as lipid and nucleic acid synthesis, which require NADPH as a reducing agent. http://purl.obolibrary.org/obo/chebi.owl CHEBI:13399 CHEBI:13400 CHEBI:21904 CHEBI:44286 CHEBI:7425 Beilstein:77911 CAS:53-57-6 COMe:MOL000028 ECMDB:ECMDB04111 HMDB:HMDB00221 KEGG:C00005 KNApSAcK:C00019545 PDBeChem:NDP PMID:16884311 PMID:17371809 PMID:8627598 YMDB:YMDB00426 2'-O-phosphonoadenosine 5'-{3-[1-(3-carbamoyl-1,4-dihydropyridin-1-yl)-1,4-anhydro-D-ribitol-5-yl] dihydrogen diphosphate} NADPH chebi_ontology 0 745.091 745.42116 ACFIXJIJDZMPPO-NNYOXOHSSA-N C21H30N7O17P3 InChI=1S/C21H30N7O17P3/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(44-46(33,34)35)14(30)11(43-21)6-41-48(38,39)45-47(36,37)40-5-10-13(29)15(31)20(42-10)27-3-1-2-9(4-27)18(23)32/h1,3-4,7-8,10-11,13-16,20-21,29-31H,2,5-6H2,(H2,23,32)(H,36,37)(H,38,39)(H2,22,24,25)(H2,33,34,35)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1 NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE NC(=O)C1=CN(C=CC1)[C@@H]1O[C@H](COP(O)(=O)OP(O)(=O)OC[C@H]2O[C@H]([C@H](OP(O)(O)=O)[C@@H]2O)n2cnc3c(N)ncnc23)[C@@H](O)[C@H]1O Reduced nicotinamide adenine dinucleotide phosphate TPNH dihydronicotinamide-adenine dinucleotide phosphate reduced nicotinamide-adenine dinucleotide phosphate CHEBI:16474 NADPH CHEBI:16474 A tripeptide compound consisting of glutamic acid attached via its side chain to the N-terminus of cysteinylglycine. http://purl.obolibrary.org/obo/chebi.owl CHEBI:12402 CHEBI:14327 CHEBI:24334 CHEBI:42873 CHEBI:43049 CHEBI:5437 CAS:70-18-8 DrugBank:DB00143 Drug_Central:1312 HMDB:HMDB00125 KEGG:C00051 KEGG:D00014 KNApSAcK:C00001518 MetaCyc:GLUTATHIONE PDBeChem:GSH PMID:17439666 PMID:4200890 PMID:4745654 Reaxys:1729812 Wikipedia:Glutathione Glutathione L-gamma-glutamyl-L-cysteinylglycine chebi_ontology 0 307.084 307.32300 5-L-Glutamyl-L-cysteinylglycine C10H17N3O6S GSH Glutathione-SH InChI=1S/C10H17N3O6S/c11-5(10(18)19)1-2-7(14)13-6(4-20)9(17)12-3-8(15)16/h5-6,20H,1-4,11H2,(H,12,17)(H,13,14)(H,15,16)(H,18,19)/t5-,6-/m0/s1 N-(N-gamma-L-Glutamyl-L-cysteinyl)glycine N[C@@H](CCC(=O)N[C@@H](CS)C(=O)NCC(O)=O)C(O)=O RWSXRVCMGQZWBV-WDSKDSINSA-N Reduced glutathione gamma-L-Glutamyl-L-cysteinyl-glycine CHEBI:16856 glutathione CHEBI:16856 A coenzyme found in all living cells; consists of two nucleotides joined through their 5'-phosphate groups, with one nucleotide containing an adenine base and the other containing nicotinamide. http://purl.obolibrary.org/obo/chebi.owl CHEBI:13395 CHEBI:13396 CHEBI:21902 CHEBI:44216 CHEBI:7423 Beilstein:79324 CAS:58-68-4 COMe:MOL000027 DrugBank:DB00157 Gmelin:544241 HMDB:HMDB01487 KEGG:C00004 KNApSAcK:C00019343 PDBeChem:NAI PMID:11259315 PMID:19459318 Reaxys:79324 Wikipedia:Nicotinamide_adenine_dinucleotide NADH adenosine 5'-{3-[1-(3-carbamoyl-1,4-dihydropyridin-1-yl)-1,4-anhydro-D-ribitol-5-yl] dihydrogen diphosphate} chebi_ontology 0 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE 665.125 665.44126 BOPGDPNILDQYTO-NNYOXOHSSA-N C21H29N7O14P2 DPNH InChI=1S/C21H29N7O14P2/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(32)14(30)11(41-21)6-39-44(36,37)42-43(34,35)38-5-10-13(29)15(31)20(40-10)27-3-1-2-9(4-27)18(23)33/h1,3-4,7-8,10-11,13-16,20-21,29-32H,2,5-6H2,(H2,23,33)(H,34,35)(H,36,37)(H2,22,24,25)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1 NC(=O)C1=CN(C=CC1)[C@@H]1O[C@H](COP(O)(=O)OP(O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)n2cnc3c(N)ncnc23)[C@@H](O)[C@H]1O Reduced nicotinamide adenine dinucleotide nicotinamide adenine dinucleotide (reduced) CHEBI:16908 NADH CHEBI:16908 A UDP-sugar having alpha-D-glucuronic acid as the sugar component. http://purl.obolibrary.org/obo/chebi.owl CHEBI:13489 CHEBI:13506 CHEBI:22104 CHEBI:46309 CHEBI:9846 Beilstein:78881 CAS:2616-64-0 HMDB:HMDB00935 KEGG:C00167 KEGG:G10612 KNApSAcK:C00007238 PDBeChem:UGA PMID:11420884 PMID:13984680 PMID:14351193 Reaxys:78881 Wikipedia:Uridine_diphosphate_glucuronic_acid uridine 5'-[3-(alpha-D-glucopyranuronosyl) dihydrogen diphosphate] chebi_ontology 0 580.034 580.28538 C15H22N2O18P2 HDYANYHVCAPMJV-LXQIFKJMSA-N InChI=1S/C15H22N2O18P2/c18-5-1-2-17(15(26)16-5)12-9(22)6(19)4(32-12)3-31-36(27,28)35-37(29,30)34-14-10(23)7(20)8(21)11(33-14)13(24)25/h1-2,4,6-12,14,19-23H,3H2,(H,24,25)(H,27,28)(H,29,30)(H,16,18,26)/t4-,6-,7+,8+,9-,10-,11+,12-,14-/m1/s1 O[C@@H]1[C@@H](COP(O)(=O)OP(O)(=O)O[C@H]2O[C@@H]([C@@H](O)[C@H](O)[C@H]2O)C(O)=O)O[C@H]([C@@H]1O)n1ccc(=O)[nH]c1=O UDP-D-glucuronate UDP-alpha-D-glucuronate UDP-glucuronate UDPglucuronate URIDINE-5'-DIPHOSPHATE-GLUCURONIC ACID uridine diphosphate glucuronic acid CHEBI:17200 UDP-alpha-D-glucuronic acid CHEBI:17200 An adenosine bisphosphate having monophosphate groups at the 3'- and 5'-positions and a sulfo group attached to the phosphate at position 5'. http://purl.obolibrary.org/obo/chebi.owl CHEBI:11679 CHEBI:11680 CHEBI:1353 CHEBI:19857 CAS:482-67-7 KEGG:C00053 KNApSAcK:C00007446 PDBeChem:PPS 3'-O-phosphono-5'-adenylyl sulfate 3'-Phospho-5'-adenylyl sulfate 3'-phospho-5'-adenylyl sulfate chebi_ontology 0 3'-Phosphoadenosine 5'-phosphosulfate 3'-Phosphoadenylyl sulfate 3'-phosphoadenosine 5'-phosphosulfate 506.986 507.26552 C10H15N5O13P2S GACDQMDRPRGCTN-KQYNXXCUSA-N InChI=1S/C10H15N5O13P2S/c11-8-5-9(13-2-12-8)15(3-14-5)10-6(16)7(27-29(17,18)19)4(26-10)1-25-30(20,21)28-31(22,23)24/h2-4,6-7,10,16H,1H2,(H,20,21)(H2,11,12,13)(H2,17,18,19)(H,22,23,24)/t4-,6-,7-,10-/m1/s1 Nc1ncnc2n(cnc12)[C@@H]1O[C@H](COP(O)(=O)OS(O)(=O)=O)[C@@H](OP(O)(O)=O)[C@H]1O PAPS CHEBI:17980 3'-phospho-5'-adenylyl sulfate CHEBI:17980 A lactone having a six-membered lactone ring. http://purl.obolibrary.org/obo/chebi.owl delta-lactone chebi_ontology . 1,5-lactone 1,5-lactones delta-lactona delta-lactonas delta-lactones CHEBI:18946 delta-lactone CHEBI:18946 An organic heterocyclic compound containing a benzene ring fused to an imidazole ring. http://purl.obolibrary.org/obo/chebi.owl chebi_ontology CHEBI:22715 benzimidazoles CHEBI:22715 Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. http://purl.obolibrary.org/obo/chebi.owl molecular entity chebi_ontology . entidad molecular entidades moleculares entite moleculaire molecular entities molekulare Entitaet CHEBI:23367 molecular entity CHEBI:23367 An azole that is either one of a pair of heterocyclic organic compounds comprising three carbon atoms and two nitrogen atoms arranged in a ring. http://purl.obolibrary.org/obo/chebi.owl chebi_ontology diazoles CHEBI:23677 diazole CHEBI:23677 A 3-hydroxy steroid that is estra-1,3,5(10)-triene substituted by hydroxy groups at positions 3 and 17. http://purl.obolibrary.org/obo/chebi.owl CHEBI:42364 PMID:10696569 PMID:24084694 Wikipedia:Estradiol estra-1,3,5(10)-triene-3,17-diol chebi_ontology 0 272.178 272.38196 C18H24O2 InChI=1S/C18H24O2/c1-18-9-8-14-13-5-3-12(19)10-11(13)2-4-15(14)16(18)6-7-17(18)20/h3,5,10,14-17,19-20H,2,4,6-9H2,1H3/t14-,15-,16+,17?,18+/m1/s1 VOXZDWNPVJITMN-WKUFJEKOSA-N [H][C@]12CC[C@]3(C)C(O)CC[C@@]3([H])[C@]1([H])CCc1cc(O)ccc21 oestradiol CHEBI:23965 estradiol CHEBI:23965 CHEBI:24431 chemical entity A role played by the molecular entity or part thereof within a biological context. http://purl.obolibrary.org/obo/chebi.owl chebi_ontology biological function grouped_by_functions CHEBI:24432 biological role CHEBI:24432 A cyclic compound having as ring members atoms of carbon and at least of one other element. http://purl.obolibrary.org/obo/chebi.owl ChEBI:C03123 chebi_ontology . organic heterocycle organic heterocyclic compounds CHEBI:24532 organic heterocyclic compound CHEBI:24532 Any carboxylic acid with at least one hydroxy group. http://purl.obolibrary.org/obo/chebi.owl chebi_ontology hydroxy carboxylic acids hydroxyacids CHEBI:24669 hydroxy carboxylic acid CHEBI:24669 A five-membered organic heterocycle containing two nitrogen atoms at positions 1 and 3, or any of its derivatives; compounds containing an imidazole skeleton. http://purl.obolibrary.org/obo/chebi.owl imidazoles chebi_ontology CHEBI:24780 imidazoles CHEBI:24780 Any cyclic carboxylic ester containing a 1-oxacycloalkan-2-one structure, or an analogue having unsaturation or heteroatoms replacing one or more carbon atoms of the ring. http://purl.obolibrary.org/obo/chebi.owl lactone lactones chebi_ontology . Lacton Lakton Laktone lactona lactonas CHEBI:25000 lactone CHEBI:25000 Any intermediate or product resulting from metabolism. The term 'metabolite' subsumes the classes commonly known as primary and secondary metabolites. http://purl.obolibrary.org/obo/chebi.owl CHEBI:26619 CHEBI:35220 metabolite chebi_ontology metabolites primary metabolites secondary metabolites CHEBI:25212 metabolite CHEBI:25212 http://purl.obolibrary.org/obo/chebi.owl chebi_ontology phenoxazines CHEBI:25970 phenoxazine CHEBI:25970 An organoiodine compound that has formula C25H29I2NO3. http://purl.obolibrary.org/obo/chebi.owl Beilstein:1271711 ChemIDplus:1951-25-3 DrugBank:DB01118 KEGG COMPOUND:1951-25-3 KEGG COMPOUND:C06823 KEGG DRUG:D02910 Wikipedia:Amiodarone (2-butyl-1-benzofuran-3-yl){4-[2-(diethylamino)ethoxy]-3,5-diiodophenyl}methanone Amiodarone chebi_ontology 2-Butyl-3-(3,5-diiodo-4-(2-diethylaminoethoxy)benzoyl)benzofuran 2-Butyl-3-benzofuranyl 4-(2-(diethylamino)ethoxy)-3,5-diiodophenyl ketone 2-n-Butyl-3',5'-diiodo-4'-N-diethylaminoethoxy-3-benzoylbenzofuran C25H29I2NO3 CCCCc1oc2ccccc2c1C(=O)c1cc(I)c(OCCN(CC)CC)c(I)c1 InChI=1S/C25H29I2NO3/c1-4-7-11-22-23(18-10-8-9-12-21(18)31-22)24(29)17-15-19(26)25(20(27)16-17)30-14-13-28(5-2)6-3/h8-10,12,15-16H,4-7,11,13-14H2,1-3H3 InChIKey=IYIKLHRQXLHMJQ-UHFFFAOYSA-N CHEBI:2663 amiodarone CHEBI:2663 An organic tricyclic compound in which at least one of the rings of the tricyclic skeleton contains one or more heteroatoms. http://purl.obolibrary.org/obo/chebi.owl chebi_ontology . heterotricyclic compounds organic heterotricyclic compounds CHEBI:26979 organic heterotricyclic compound CHEBI:26979 http://purl.obolibrary.org/obo/chebi.owl chebi_ontology . heterobicyclic compounds organic heterobicyclic compounds two-ring heterocyclic compounds CHEBI:27171 organic heterobicyclic compound CHEBI:27171 An N-sulfonylurea that consists of 1-butylurea having a tosyl group attached at the 3-position. http://purl.obolibrary.org/obo/chebi.owl CHEBI:27019 CHEBI:9616 CAS:64-77-7 DrugBank:DB01124 Drug_Central:2696 KEGG:C07148 KEGG:D00380 LINCS:LSM-3907 PMID:11835228 PMID:11840346 PMID:11911494 PMID:12042355 PMID:12355256 PMID:15207658 PMID:15317941 PMID:15620874 PMID:15655519 PMID:16290322 PMID:16426753 PMID:19059420 PMID:20880646 PMID:21178111 PMID:21193530 PMID:21471135 PMID:21535124 PMID:21712613 PMID:21757329 PMID:21827497 PMID:21831467 PMID:22028182 PMID:22079696 Patent:DE1066575 Patent:GB808071 Patent:US2968158 Reaxys:1984428 Wikipedia:Tolbutamide N-[(butylamino)carbonyl]-4-methylbenzenesulfonamide Tolbutamide chebi_ontology 0 1-Butyl-3-(p-methylphenylsulfonyl)urea 1-Butyl-3-(p-tolylsulfonyl)urea 1-Butyl-3-tosylurea 1-p-Toluenesulfonyl-3-butylurea 270.104 270.34800 3-(p-Tolyl-4-sulfonyl)-1-butylurea C12H18N2O3S CCCCNC(=O)NS(=O)(=O)c1ccc(C)cc1 InChI=1S/C12H18N2O3S/c1-3-4-9-13-12(15)14-18(16,17)11-7-5-10(2)6-8-11/h5-8H,3-4,9H2,1-2H3,(H2,13,14,15) JLRGJRBPOGGCBT-UHFFFAOYSA-N N-(4-Methylbenzenesulfonyl)-N'-butylurea N-(4-Methylphenylsulfonyl)-N'-butylurea N-(Sulfonyl-p-methylbenzene)-N'-N-butylurea N-(p-Methylbenzenesulfonyl)-N'-butylurea N-Butyl-N'-(4-methylphenylsulfonyl)urea N-Butyl-N'-(p-tolylsulfonyl)urea N-Butyl-N'-p-toluenesulfonylurea N-n-Butyl-N'-tosylurea Orinase (TN) Tolylsulfonylbutylurea tolbutamida tolbutamide tolbutamidum CHEBI:27999 tolbutamide CHEBI:27999 A chromenone having the keto group located at the 2-position. http://purl.obolibrary.org/obo/chebi.owl CHEBI:101256 CHEBI:23402 CHEBI:3906 CHEBI:41552 Beilstein:383644 CAS:91-64-5 DrugBank:DB04665 Drug_Central:738 Gmelin:165222 HMDB:HMDB01218 KEGG:C05851 KEGG:D07751 KNApSAcK:C00002460 LINCS:LSM-2519 MetaCyc:COUMARIN PMID:17988284 PMID:19025869 PMID:21046436 PMID:21462332 PMID:21798343 PMID:8735869 Reaxys:383644 Wikipedia:Coumarin 2H-chromen-2-one chebi_ontology 0 1,2-Benzopyrone 146.037 146.14270 146.143 2-Propenoic acid, 3-(2-hydroxyphenyl)-, d-lactone 2-Propenoic acid, 3-(2-hydroxyphenyl)-, delta-lactone 2H-1-Benzopyran-2-one 2H-benzo[b]pyran-2-one 5,6-Benzo-2-pyrone Benzo-a-pyrone Benzo-alpha-pyrone C9H6O2 C=1C=CC=C2C1C=CC(=O)O2 Coumarine Coumarinic anhydride Cumarin InChI=1S/C9H6O2/c10-9-6-5-7-3-1-2-4-8(7)11-9/h1-6H Rattex Tonka bean camphor ZYGHJZDHTFUPRJ-UHFFFAOYSA-N cis-o-Coumarinic acid lactone o-Hydroxycinnamic acid lactone o-hydroxycinnamic acid delta-lactone CHEBI:28794 coumarin CHEBI:28794 http://purl.obolibrary.org/obo/chebi.owl Beilstein:88093 CAS:125-73-5 LINCS:LSM-36603 17-methyl-9alpha,13alpha,14alpha-morphinan-3-ol chebi_ontology (+)-3-hydroxy-N-methylmorphinan 0 257.178 257.37066 C17H23NO InChI=1S/C17H23NO/c1-18-9-8-17-7-3-2-4-14(17)16(18)10-12-5-6-13(19)11-15(12)17/h5-6,11,14,16,19H,2-4,7-10H2,1H3/t14-,16+,17+/m1/s1 JAQUASYNZVUNQP-PVAVHDDUSA-N [H][C@]12CCCC[C@]11CCN(C)[C@H]2Cc2ccc(O)cc12 d-3-hydroxy-N-methylmorphinan dextrorphan dextrorphane dextrorphanum CHEBI:29133 dextrorphan CHEBI:29133 A propanone that is propan-1-one substituted by a tert-butylamino group at position 2 and a 3-chlorophenyl group at position 1. http://purl.obolibrary.org/obo/chebi.owl Beilstein:2101062 CAS:34841-39-9 CAS:34911-55-2 DrugBank:DB01156 Drug_Central:435 HMDB:HMDB01510 KEGG:C06860 KEGG:D07591 LINCS:LSM-1267 MetaCyc:CPD-3481 PMID:12826985 PMID:15876900 Reaxys:2101062 Wikipedia:Bupropion 2-(tert-butylamino)-1-(3-chlorophenyl)propan-1-one Bupropion chebi_ontology 0 239.108 239.74086 C13H18ClNO CC(NC(C)(C)C)C(=O)c1cccc(Cl)c1 InChI=1S/C13H18ClNO/c1-9(15-13(2,3)4)12(16)10-6-5-7-11(14)8-10/h5-9,15H,1-4H3 SNPPWIUOZRMYNY-UHFFFAOYSA-N CHEBI:3219 bupropion CHEBI:3219 An assembly consisting of a central atom (usually metallic) to which is attached a surrounding array of other groups of atoms (ligands). http://purl.obolibrary.org/obo/chebi.owl coordination entities coordination entity chebi_ontology coordination compounds CHEBI:33240 coordination entity CHEBI:33240 A heteroorganic entity is an organic molecular entity in which carbon atoms or organic groups are bonded directly to one or more heteroatoms. http://purl.obolibrary.org/obo/chebi.owl chebi_ontology . heteroorganic entities organoelement compounds CHEBI:33285 heteroorganic entity CHEBI:33285 An ester of a carboxylic acid, R(1)C(=O)OR(2), where R(1) = H or organyl and R(2) = organyl. http://purl.obolibrary.org/obo/chebi.owl CHEBI:13204 CHEBI:23028 CHEBI:3408 KEGG COMPOUND:C02391 Wikipedia:Ester Carboxylic ester carboxylic esters chebi_ontology CO2R2 [*]C(=O)O[*] a carboxylic ester carboxylic acid esters CHEBI:33308 carboxylic ester CHEBI:33308 A carbon oxoacid acid carrying at least one -C(=O)OH group and having the structure RC(=O)OH, where R is any any monovalent functional group. Carboxylic acids are the most common type of organic acid. http://purl.obolibrary.org/obo/chebi.owl CHEBI:13428 CHEBI:13627 CHEBI:23027 CiteXplore:17147560 CiteXplore:18433345 carboxylic acid carboxylic acids chebi_ontology CHO2R Carbonsaeure Carbonsaeuren Karbonsaeure OC([*])=O RC(=O)OH acide carboxylique acides carboxyliques acido carboxilico acidos carboxilicos CHEBI:33575 carboxylic acid CHEBI:33575 A molecular entity containing one or more atoms from any of groups 1, 2, 13, 14, 15, 16, 17, and 18 of the periodic table. http://purl.obolibrary.org/obo/chebi.owl chebi_ontology . main group compounds main group molecular entities CHEBI:33579 main group molecular entity CHEBI:33579 http://purl.obolibrary.org/obo/chebi.owl carbon group molecular entity chebi_ontology . carbon group molecular entities CHEBI:33582 carbon group molecular entity CHEBI:33582 A p-block molecular entity is a molecular entity containing one or more atoms of a p-block element. http://purl.obolibrary.org/obo/chebi.owl chebi_ontology . p-block compounds p-block molecular entities p-block molecular entitiy CHEBI:33675 p-block molecular entity CHEBI:33675 A macromolecule formed by a living organism. http://purl.obolibrary.org/obo/chebi.owl biopolymer chebi_ontology Biopolymere biomacromolecules biopolymers CHEBI:33694 biomacromolecule CHEBI:33694 http://purl.obolibrary.org/obo/chebi.owl chebi_ontology genetically encoded biomacromolecules genetically encoded biopolymers information biomacromolecules information biopolymers information macromolecule information macromolecules CHEBI:33695 information biomacromolecule CHEBI:33695 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. http://purl.obolibrary.org/obo/chebi.owl nucleic acids chebi_ontology NA Nukleinsaeure Nukleinsaeuren acide nucleique acides nucleiques acido nucleico acidos nucleicos CHEBI:33696 nucleic acid CHEBI:33696 High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds; RNA is central to the synthesis of proteins. http://purl.obolibrary.org/obo/chebi.owl ChemIDplus:63231-63-0 ribonucleic acid ribonucleic acids chebi_ontology RNA RNS Ribonukleinsaeure pentosenucleic acids ribonucleic acids ribose nucleic acid yeast nucleic acid CHEBI:33697 ribonucleic acid CHEBI:33697 Any organic molecule that consists of atoms connected in the form of a ring. http://purl.obolibrary.org/obo/chebi.owl chebi_ontology . organic cyclic compounds CHEBI:33832 organic cyclic compound CHEBI:33832 A heterocyclic compound formally derived from an arene by replacement of one or more methine (-C=) and/or vinylene (-CH=CH-) groups by trivalent or divalent heteroatoms, respectively, in such a way as to maintain the continuous pi-electron system characteristic of aromatic systems and a number of out-of-plane pi-electrons corresponding to the Hueckel rule (4n+2). http://purl.obolibrary.org/obo/chebi.owl heteroarenes chebi_ontology . hetarenes CHEBI:33833 heteroarene CHEBI:33833 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. http://purl.obolibrary.org/obo/chebi.owl Wikipedia:Macromolecule macromolecule chebi_ontology macromolecules polymer polymer molecule polymers CHEBI:33839 macromolecule CHEBI:33839 http://purl.obolibrary.org/obo/chebi.owl magnesium coordination entity chebi_ontology magnesium coordination compounds magnesium coordination entities CHEBI:33976 magnesium coordination entity CHEBI:33976 A 17beta-hydroxy steroid that is testosterone bearing an additional hydroxy substituent at the 6beta-position. http://purl.obolibrary.org/obo/chebi.owl CHEBI:63819 CAS:62-99-7 HMDB:HMDB06259 KEGG:C14497 LIPID_MAPS_instance:LMST02020054 PMID:10574192 PMID:15203039 PMID:22822673 Reaxys:2625776 6beta,17beta-dihydroxyandrost-4-en-3-one 6beta-Hydroxytestosterone chebi_ontology (6beta,17beta)-6,17-dihydroxyandrost-4-en-3-one 0 304.204 304.42380 4-androsten-6beta,17beta-diol-3-one 6beta,17beta-Dihydroxyandrost-4-en-3-one 6beta,17beta-dihydroxy-4-androsten-3-one 6beta,17beta-dihydroxyandrost-4-en-3-one C19H28O3 InChI=1S/C19H28O3/c1-18-7-5-11(20)9-15(18)16(21)10-12-13-3-4-17(22)19(13,2)8-6-14(12)18/h9,12-14,16-17,21-22H,3-8,10H2,1-2H3/t12-,13-,14-,16+,17-,18+,19-/m0/s1 XSEGWEUVSZRCBC-ZVBLRVHNSA-N [H][C@@]12C[C@@H](O)C3=CC(=O)CC[C@]3(C)[C@@]1([H])CC[C@]1(C)[C@@H](O)CC[C@@]21[H] CHEBI:34477 6beta-hydroxytestosterone CHEBI:34477 http://purl.obolibrary.org/obo/chebi.owl Beilstein:225973 CAS:5725-91-7 KEGG:C13630 7-Ethoxyresorufin 7-ethoxy-3H-phenoxazin-3-one chebi_ontology 0 241.074 241.24208 7-Ethoxyphenoxazone C14H11NO3 CCOc1ccc2nc3ccc(=O)cc3oc2c1 CRCWUBLTFGOMDD-UHFFFAOYSA-N Ethoxyresorufin InChI=1S/C14H11NO3/c1-2-17-10-4-6-12-14(8-10)18-13-7-9(16)3-5-11(13)15-12/h3-8H,2H2,1H3 Resorufin ethyl ether CHEBI:34480 7-ethoxyresorufin CHEBI:34480 http://purl.obolibrary.org/obo/chebi.owl CAS:54340-62-4 Drug_Central:424 KEGG:C13769 Bufuralol chebi_ontology (+/-)-Bufuralol 0 261.173 261.360 C16H23NO2 CCc1cccc2cc(oc12)C(O)CNC(C)(C)C InChI=1S/C16H23NO2/c1-5-11-7-6-8-12-9-14(19-15(11)12)13(18)10-17-16(2,3)4/h6-9,13,17-18H,5,10H2,1-4H3 SSEBTPPFLLCUMN-UHFFFAOYSA-N dl-Bufuralol CHEBI:34593 Bufuralol CHEBI:34593 http://purl.obolibrary.org/obo/chebi.owl COMe:PRX000002 metalloprotein chebi_ontology metalloproteine metalloproteins CHEBI:35134 metalloprotein CHEBI:35134 http://purl.obolibrary.org/obo/chebi.owl COMe:PRX000004 iron protein chebi_ontology iron proteins iron-containing proteins CHEBI:35136 iron protein CHEBI:35136 Conjugated proteins containing heme as the prosthetic group. http://purl.obolibrary.org/obo/chebi.owl COMe:PRX000008 hemoprotein chebi_ontology Haemoprotein Haemprotein haem protein haemoprotein heme protein hemeproteins hemoproteins CHEBI:35137 hemoprotein CHEBI:35137 http://purl.obolibrary.org/obo/chebi.owl alkaline earth coordination entity chebi_ontology alkaline earth coordination compounds alkaline earth coordination entities CHEBI:35217 alkaline earth coordination entity CHEBI:35217 A substance that diminishes the rate of a chemical reaction. http://purl.obolibrary.org/obo/chebi.owl inhibitor chebi_ontology inhibidor inhibiteur inhibitors CHEBI:35222 inhibitor CHEBI:35222 http://purl.obolibrary.org/obo/chebi.owl CHEBI:22721 benzofurans chebi_ontology CHEBI:35259 benzofurans CHEBI:35259 http://purl.obolibrary.org/obo/chebi.owl chebi_ontology . triazolobenzodiazepines CHEBI:35501 triazolobenzodiazepine CHEBI:35501 http://purl.obolibrary.org/obo/chebi.owl chebi_ontology . carbon oxoacids oxoacids of carbon CHEBI:35605 carbon oxoacid CHEBI:35605 A compound formally derived from an oxoacid RkE(=O)l(OH)m (l > 0) and an alcohol, phenol, heteroarenol, or enol by linking with formal loss of water from an acidic hydroxy group of the former and a hydroxy group of the latter. http://purl.obolibrary.org/obo/chebi.owl CHEBI:23960 CHEBI:4859 KEGG COMPOUND:C00287 Ester chebi_ontology . [*]OC([*])=O esters CHEBI:35701 ester CHEBI:35701 http://purl.obolibrary.org/obo/chebi.owl chebi_ontology hydroxy acid hydroxy monocarboxylic acids CHEBI:35868 hydroxy monocarboxylic acid CHEBI:35868 http://purl.obolibrary.org/obo/chebi.owl chebi_ontology dihydroxy monocarboxylic acids CHEBI:35972 dihydroxy monocarboxylic acid CHEBI:35972 http://purl.obolibrary.org/obo/chebi.owl COMe:PRX000150 chebi_ontology haem-thiolate protein heme-thiolate proteins CHEBI:36074 heme-thiolate protein CHEBI:36074 A biological macromolecule minimally consisting of one polypeptide chain synthesized at the ribosome. http://purl.obolibrary.org/obo/chebi.owl CHEBI:13677 CHEBI:14911 proteins chebi_ontology CHEBI:36080 protein CHEBI:36080 Any molecular entity consisting of more than one atom. http://purl.obolibrary.org/obo/chebi.owl chebi_ontology polyatomic entities CHEBI:36357 polyatomic entity CHEBI:36357 A member of the class of 1,3-benzoxazoles that is 1,3-benzoxazol-2-ol in which the hydrogen atom at position 5 is substituted by chlorine. A centrally acting muscle relaxant with sedative properties, it is used for the symptomatic treatment of painful muscle spasm. http://purl.obolibrary.org/obo/chebi.owl CHEBI:47330 Beilstein:638882 CAS:95-25-0 DrugBank:DB00356 Drug_Central:626 HMDB:HMDB14500 KEGG:C07931 KEGG:D00771 LINCS:LSM-6011 PDBeChem:CLW PMID:10640318 PMID:11727787 PMID:12437348 PMID:16763012 PMID:16859676 PMID:17621748 PMID:21195386 PMID:23975871 PMID:24210069 PMID:25815637 PMID:6631711 Patent:US2895877 Reaxys:638882 Wikipedia:Chlorzoxazone 5-chloro-1,3-benzoxazol-2-ol CHLORZOXAZONE Chlorzoxazone chebi_ontology 0 168.993 169.56500 2-hydroxy-5-chlorobenzoxazole 5-chloro-2(3H)-benzoxazolone 5-chloro-2-benzoxazolinone 5-chloro-2-benzoxazolol 5-chloro-2-benzoxazolone 5-chloro-2-hydroxybenzoxazole 5-chlorobenzoxazolidone 5-chlorobenzoxazolin-2-one C7H4ClNO2 InChI=1S/C7H4ClNO2/c8-4-1-2-6-5(3-4)9-7(10)11-6/h1-3H,(H,9,10) Oc1nc2cc(Cl)ccc2o1 TZFWDZFKRBELIQ-UHFFFAOYSA-N chlorzoxane chlorzoxazona chlorzoxazone chlorzoxazonum CHEBI:3655 chlorzoxazone CHEBI:3655 A coordination entity in which the central atom to which the ligands are attached comes from groups 1, 2, 13, 14, 15, 16, 17, or 18 of the periodic table. http://purl.obolibrary.org/obo/chebi.owl chebi_ontology main group coordination compounds main-group coordination entities CHEBI:36562 main-group coordination entity CHEBI:36562 An organochalcogen compound is a compound containing at least one carbon-chalcogen bond. http://purl.obolibrary.org/obo/chebi.owl organochalcogen compound chebi_ontology . organochalcogen compounds CHEBI:36962 organochalcogen compound CHEBI:36962 An organochalcogen compound containing at least one carbon-oxygen bond. http://purl.obolibrary.org/obo/chebi.owl CiteXplore:17586126 organooxygen compound chebi_ontology . organooxygen compounds CHEBI:36963 organooxygen compound CHEBI:36963 A molecular entity consisting of two or more chemical elements. http://purl.obolibrary.org/obo/chebi.owl chebi_ontology chemical compound heteroatomic molecular entities CHEBI:37577 heteroatomic molecular entity CHEBI:37577 http://purl.obolibrary.org/obo/chebi.owl chebi_ontology organic heterotetracyclic compounds CHEBI:38163 organic heterotetracyclic compound CHEBI:38163 http://purl.obolibrary.org/obo/chebi.owl CHEBI:25429 CHEBI:38075 chebi_ontology . multi-ring heterocyclic compounds organic heteropolycyclic compounds CHEBI:38166 organic heteropolycyclic compound CHEBI:38166 http://purl.obolibrary.org/obo/chebi.owl chebi_ontology monocyclic heteroarenes CHEBI:38179 monocyclic heteroarene CHEBI:38179 A dihydroxy monocarboxylic acid that is (6E)-7-{4-(4-fluorophenyl)-2-[methyl(methylsulfonyl)amino]-6-(propan-2-yl)pyrimidin-5-yl} hept-6-enoic acid carrying two hydroxy substituents at positions 3 and 5 (the 3R,5S-diastereomer). http://purl.obolibrary.org/obo/chebi.owl Beilstein:9670765 ChemIDplus:287714-41-4 CiteXplore:17970755 CiteXplore:18509206 CiteXplore:19724024 CiteXplore:19956889 CiteXplore:23806820 CiteXplore:23881596 CiteXplore:23944632 CiteXplore:24072337 CiteXplore:24076283 CiteXplore:24076297 CiteXplore:24156555 CiteXplore:24163149 CiteXplore:24230979 CiteXplore:24253250 CiteXplore:24259612 CiteXplore:24304551 CiteXplore:24333476 CiteXplore:24353409 CiteXplore:24410968 CiteXplore:24417785 CiteXplore:24434545 CiteXplore:24440231 CiteXplore:24440960 CiteXplore:24444439 CiteXplore:24452083 CiteXplore:24456217 CiteXplore:24467235 DrugBank:DB01098 HMDB:HMDB15230 KEGG DRUG:D08492 Patent:US2013035316 Reaxys:9670765 Wikipedia:Rosuvastatin (3R,5S,6E)-7-{4-(4-fluorophenyl)-2-[methyl(methylsulfonyl)amino]-6-(propan-2-yl)pyrimidin-5-yl}-3,5-dihydroxyhept-6-enoic acid chebi_ontology (3R,5S,6E)-7-(4-(4-fluorophenyl)-6-(1-methylethyl)-2-(ethyl(methylsulfonyl)amino)-5-pyrimidinyl)-3,5-dihydroxy-6-heptenoic acid (3R,5S,6E)-7-{4-(4-fluorophenyl)-6-isopropyl-2-[methyl(methylsulfonyl)amino]pyrimidin-5-yl}-3,5-dihydroxyhept-6-enoic acid C22H28FN3O6S CC(C)c1nc(nc(-c2ccc(F)cc2)c1\C=C\[C@@H](O)C[C@@H](O)CC(O)=O)N(C)S(C)(=O)=O InChI=1S/C22H28FN3O6S/c1-13(2)20-18(10-9-16(27)11-17(28)12-19(29)30)21(14-5-7-15(23)8-6-14)25-22(24-20)26(3)33(4,31)32/h5-10,13,16-17,27-28H,11-12H2,1-4H3,(H,29,30)/b10-9+/t16-,17-/m1/s1 InChIKey=BPRHUIZQVSMCRT-VEUZHWNKSA-N rosuvastatin CHEBI:38545 rosuvastatin CHEBI:38545 http://purl.obolibrary.org/obo/chebi.owl COMe:PRX000645 cytochrome P450 chebi_ontology CYP P450 protein cytochrome P-450 CHEBI:38559 cytochrome P450 CHEBI:38559 A racemate comprising equimolar amounts of (3R,5S)- and (3S,5R)-fluvastatin. An HMG-CoA reductase inhibitor, it is used (often as the corresponding sodium salt) to reduce triglycerides and LDL-cholesterol, and increase HDL-chloesterol, in the treatment of hyperlipidaemia. http://purl.obolibrary.org/obo/chebi.owl Beilstein:9168031 ChemIDplus:93957-54-1 CiteXplore:11273020 CiteXplore:12147804 CiteXplore:18410471 CiteXplore:18413661 CiteXplore:18452779 CiteXplore:18936176 CiteXplore:23212095 CiteXplore:23846727 DrugBank:DB01095 KEGG COMPOUND:93957-54-1 KEGG COMPOUND:C07014 KEGG DRUG:D07983 Patent:US4739073 Patent:WO8402131 Wikipedia:Fluvastatin rac-(3R,5S,6E)-7-[3-(4-fluorophenyl)-1-(propan-2-yl)-1H-indol-2-yl]-3,5-dihydroxyhept-6-enoic acid chebi_ontology (+-)-fluvastatin (6E)-erythro7-[3-(4-fluorophenyl)-1-(propan-2-yl)-1H-indol-2-yl]-3,5-dihydroxyhept-6-enoic acid C24H26FNO4 Cranoc erythro-(E)-3,5-dihydroxy-7-[3'-(4''-fluorophenyl)-1'-(1''-methylethyl)indol-2'-yl]hept-6-enoic acid fluvastatin fluvastatina fluvastatine fluvastatinum rac-(3R,5S)-fluvastatin rac-(3R,5S,6E)-7-(3-(4-fluorophenyl)-1-(1-methylethyl)-1H-indol-2-yl)-3,5-dihydroxy-6-heptenoic acid CHEBI:38561 fluvastatin CHEBI:38561 http://purl.obolibrary.org/obo/chebi.owl triazole chebi_ontology C2H3N3 CHEBI:38597 triazole CHEBI:38597 A member of the class of benzofurans consisting of a 1-benzofuran skeleton and its substituted derivatives thereof. http://purl.obolibrary.org/obo/chebi.owl chebi_ontology CHEBI:38830 1-benzofurans CHEBI:38830 A dihydroxy monocarboxylic acid that is a member of the drug class known as statins, used primarily for lowering blood cholesterol and for preventing cardiovascular diseases. http://purl.obolibrary.org/obo/chebi.owl CHEBI:2910 CHEBI:39538 Beilstein:8373630 ChemIDplus:134523-00-5 CiteXplore:11693468 CiteXplore:15012735 CiteXplore:18720283 DrugBank:DB01076 HMDB:HMDB05006 KEGG COMPOUND:134523-00-5 KEGG COMPOUND:C06834 KEGG DRUG:D07474 PDBeChem:117 Patent:EP409281 Patent:US5273995 Reaxys:8373630 Wikipedia:Atorvastatin (3R,5R)-7-[3-(anilinocarbonyl)-5-(4-fluorophenyl)-4-phenyl-2-(propan-2-yl)-1H-pyrrol-1-yl]-3,5-dihydroxyheptanoic acid Atorvastatin chebi_ontology (3R,5R)-7-[2-(4-fluorophenyl)-5-(1-methylethyl)-3-phenyl-4-(phenylcarbamoyl)-1H-pyrrol-1-yl]-3,5-dihydroxyheptanoic acid (R-(R*,R*))-2-(4-Fluorophenyl)-beta,delta-dihydroxy-5-(1-methylethyl)-3-phenyl-4-((phenylamino)carbonyl)-1H-pyrrole-1-heptanoic acid 7-[2-(4-FLUORO-PHENYL)-5-ISOPROPYL-3-PHENYL-4-PHENYLCARBAMOYL-PYRROL-1-YL]- 3,5-DIHYDROXY-HEPTANOIC ACID 7-[2-(4-FLUORO-PHENYL)-5-ISOPROPYL-3-PHENYL-4-PHENYLCARBAMOYL-PYRROL-1-YL]-3,5-DIHYDROXY-HEPTANOIC ACID Atorlip C33H35FN2O5 CC(C)c1c(C(=O)Nc2ccccc2)c(-c2ccccc2)c(-c2ccc(F)cc2)n1CC[C@@H](O)C[C@@H](O)CC(O)=O InChI=1S/C33H35FN2O5/c1-21(2)31-30(33(41)35-25-11-7-4-8-12-25)29(22-9-5-3-6-10-22)32(23-13-15-24(34)16-14-23)36(31)18-17-26(37)19-27(38)20-28(39)40/h3-16,21,26-27,37-38H,17-20H2,1-2H3,(H,35,41)(H,39,40)/t26-,27-/m1/s1 InChIKey=XUKUURHRXDUEBC-KAYWLYCHSA-N atorvastatin atorvastatina atorvastatine atorvastatinum CHEBI:39548 atorvastatin CHEBI:39548 A fatty acid ester that is mevastatin carrying an additional methyl group on the carbobicyclic skeleton. It is used in as a antilipemic drug and has been found in fungal species such as Aspergillus terreus and Pleurotus ostreatus (oyster mushroom). http://purl.obolibrary.org/obo/chebi.owl CHEBI:40299 CHEBI:6544 ChemIDplus:3631989 ChemIDplus:75330-75-5 CiteXplore:11375168 CiteXplore:11389707 CiteXplore:11483865 CiteXplore:18642339 CiteXplore:24093797 DrugBank:DB00227 HMDB:HMDB14372 KEGG COMPOUND:C07074 KEGG DRUG:75330-75-5 KEGG DRUG:D00359 KNApSAcK:C00000547 PDBeChem:803 Patent:CN103172602 Patent:WO2013090461 Reaxys:4720754 Wikipedia:Lovastatin (1S,3R,7S,8S,8aR)-8-{2-[(2R,4R)-4-hydroxy-6-oxotetrahydro-2H-pyran-2-yl]ethyl}-3,7-dimethyl-1,2,3,7,8,8a-hexahydronaphthalen-1-yl (2S)-2-methylbutanoate LOVASTATIN Lovastatin chebi_ontology (1S,3R,7S,8S,8aR)-1,2,3,7,8,8a-hexahydro-3,7-dimethyl-8-(2-(2R,4R)-(tetrahydro-4-hydroxy-6-oxo-2H-pyran-2-yl)ethyl)-1-naphthalenyl (S)-2-methyl-butyrate 2beta,6alpha-dimethyl-8alpha-(2-methyl-1-oxobutoxy)-mevinic acid lactone 6alpha-methylcompactin C24H36O5 InChI=1S/C24H36O5/c1-5-15(3)24(27)29-21-11-14(2)10-17-7-6-16(4)20(23(17)21)9-8-19-12-18(25)13-22(26)28-19/h6-7,10,14-16,18-21,23,25H,5,8-9,11-13H2,1-4H3/t14-,15-,16-,18+,19+,20-,21-,23-/m0/s1 InChIKey=PCZOHLXUXFIOCF-BXMDZJJMSA-N MK-803 ML-530B Mevacor Mevinolin [H][C@]12[C@H](C[C@@H](C)C=C1C=C[C@H](C)[C@@H]2CC[C@@H]1C[C@@H](O)CC(=O)O1)OC(=O)[C@@H](C)CC CHEBI:40303 lovastatin CHEBI:40303 An organic heterotetracyclic compound that is morphinan substituted by a methoxy group at position 3 and a methyl group at position 7. It is used as an antitussive drug for suppressing cough. http://purl.obolibrary.org/obo/chebi.owl CAS:125-71-3 DrugBank:DB00514 HMDB:HMDB01920 KEGG:C06947 KEGG:D03742 PMID:17461892 PMID:18198471 PMID:24269965 Reaxys:88549 Wikipedia:Dextromethorphan 3-methoxy-17-methylmorphinan Dextromethorphan chebi_ontology 0 271.194 271.39724 C18H25NO DXM InChI=1S/C18H25NO/c1-19-10-9-18-8-4-3-5-15(18)17(19)11-13-6-7-14(20-2)12-16(13)18/h6-7,12,15,17H,3-5,8-11H2,1-2H3/t15-,17+,18+/m0/s1 MKXZASYAUGDDCJ-CGTJXYLNSA-N [H][C@@]12CCCC[C@@]11CCN(C)[C@@H]2Cc2ccc(OC)cc12 d-Methorphan delta-Methorphan CHEBI:4470 dextromethorphan CHEBI:4470 A tetracyclic diterpenoid isolated originally from the bark of the Pacific yew tree, Taxus brevifolia. It is a mitotic inhibitor used in cancer chemotherapy. Note that the use of the former generic name 'taxol' is now limited, as Taxol is a registered trade mark. http://purl.obolibrary.org/obo/chebi.owl CHEBI:45862 CHEBI:7887 CAS:33069-62-4 DrugBank:DB01229 Drug_Central:2044 KEGG:C07394 KEGG:D00491 KNApSAcK:C00002365 PDBeChem:TA1 Wikipedia:Paclitaxel 4alpha,10beta-bis(acetyloxy)-13alpha-[(2S,3S)-3-benzamido-2-hydroxy-3-phenylpropanoyloxy]-1,7beta-dihydroxy-9-oxo-5beta,20-epoxytax-11-en-2alpha-yl benzoate Paclitaxel chebi_ontology (2aR-(2aalpha,4beta,4abeta,6beta,9alpha(alpha R*,betaS*),11alpha,12alpha,12balpha))-beta-(Benzoylamino)-alpha-hydroxybenzenepropanoic acid 6,12b-bis(acetyloxy)-12-(benzoyloxy)-2a,3,4,4a,5,6,9,10,11,12,12a,12b-dodecahydro-4,11-dihydroxy-4a,8,13,13-tetramethyl-5-oxo-7,11-methano-1H-cyclodeca(3,4)benz(1,2-b)oxet-9-yl ester 0 5beta,20-Epoxy-1,2-alpha,4,7beta,10beta,13alpha-hexahydroxytax-11-en-9-one 4,10-diacetate 2-benzoate 13-ester with (2R,3S)-N-benzoyl-3-phenylisoserine 853.331 853.90618 C47H51NO14 InChI=1S/C47H51NO14/c1-25-31(60-43(56)36(52)35(28-16-10-7-11-17-28)48-41(54)29-18-12-8-13-19-29)23-47(57)40(61-42(55)30-20-14-9-15-21-30)38-45(6,32(51)22-33-46(38,24-58-33)62-27(3)50)39(53)37(59-26(2)49)34(25)44(47,4)5/h7-21,31-33,35-38,40,51-52,57H,22-24H2,1-6H3,(H,48,54)/t31-,32-,33+,35-,36+,37+,38-,40-,45+,46-,47+/m0/s1 RCINICONZNJXQF-MZXODVADSA-N TAXOL Taxol A [H][C@]12[C@H](OC(=O)c3ccccc3)[C@]3(O)C[C@H](OC(=O)[C@H](O)[C@@H](NC(=O)c4ccccc4)c4ccccc4)C(C)=C([C@@H](OC(C)=O)C(=O)[C@]1(C)[C@@H](O)C[C@H]1OC[C@@]21OC(C)=O)C3(C)C taxol CHEBI:45863 paclitaxel CHEBI:45863 A member of the class of triazoles that is propan-2-ol substituted at position 1 and 3 by 1H-1,2,4-triazol-1-yl groups and at position 2 by a 2,4-difluorophenyl group. It has been shown to exhibit antifungal activity. http://purl.obolibrary.org/obo/chebi.owl CHEBI:46079 CHEBI:5099 Beilstein:4269710 ChemIDplus:86386-73-4 CiteXplore:11366931 CiteXplore:16822276 CiteXplore:23171950 CiteXplore:23793863 DrugBank:DB00196 HMDB:HMDB14342 KEGG DRUG:D00322 PDBeChem:TPF Patent:GB2099818 Patent:US4404216 Reaxys:7311650 Wikipedia:Fluconazole 2-(2,4-difluorophenyl)-1,3-bis-(1H-1,2,4-triazol-1-yl)propan-2-ol chebi_ontology 2,4-difluoro-alpha,alpha-bis(1H-1,2,4-triazol-1-ylmethyl)benzyl alcohol 2-(2,4-DIFLUOROPHENYL)-1,3-DI(1H-1,2,4-TRIAZOL-1-YL)PROPAN-2-OL Biozole C13H12F2N6O Diflucan Elazor InChI=1S/C13H12F2N6O/c14-10-1-2-11(12(15)3-10)13(22,4-20-8-16-6-18-20)5-21-9-17-7-19-21/h1-3,6-9,22H,4-5H2 InChIKey=RFHAOTPXVQNOHP-UHFFFAOYSA-N OC(Cn1cncn1)(Cn1cncn1)c1ccc(F)cc1F Triflucan fluconazol fluconazole fluconazolum CHEBI:46081 fluconazole CHEBI:46081 A monocarboxylic acid consisting of phenylacetic acid having a (2,6-dichlorophenyl)amino group at the 2-position. http://purl.obolibrary.org/obo/chebi.owl CHEBI:4507 CHEBI:47380 Beilstein:2146636 CAS:15307-86-5 DrugBank:DB00586 Drug_Central:865 HMDB:HMDB14724 KEGG:C01690 KEGG:D07816 LINCS:LSM-2160 PDBeChem:DIF PMID:11322639 PMID:1502708 PMID:23777257 PMID:7838674 Patent:NL6604752 Patent:US3558690 Reaxys:2146636 Wikipedia:Diclofenac 2-[(2,6-dichlorophenyl)amino]benzeneacetic acid Diclofenac {2-[(2,6-dichlorophenyl)amino]phenyl}acetic acid chebi_ontology 0 2-((2,6-dichlorophenyl)amino)benzeneacetic acid 296.14900 353.022 C16H13Cl2NO4 DCOPUUMXTXDBNB-UHFFFAOYSA-N InChI=1S/C14H11Cl2NO2/c15-10-5-3-6-11(16)14(10)17-12-7-2-1-4-9(12)8-13(18)19/h1-7,17H,8H2,(H,18,19) OC(=O)Cc1ccccc1Nc1c(Cl)cccc1Cl [2-(2,6-dichloroanilino)phenyl]acetic acid diclofenac diclofenac acid diclofenaco diclofenacum CHEBI:47381 diclofenac CHEBI:47381 A N-carbonylpiperazine that has formula C26H28Cl2N4O4. http://purl.obolibrary.org/obo/chebi.owl Beilstein:634785 DrugBank:DB01026 1-acetyl-4-(4-{[2-(2,4-dichlorophenyl)-2-(1H-imidazol-1-ylmethyl)-1,3-dioxolan-4-yl]methoxy}phenyl)piperazine chebi_ontology C26H28Cl2N4O4 CC(=O)N1CCN(CC1)c1ccc(OCC2COC(Cn3ccnc3)(O2)c2ccc(Cl)cc2Cl)cc1 InChI=1S/C26H28Cl2N4O4/c1-19(33)31-10-12-32(13-11-31)21-3-5-22(6-4-21)34-15-23-16-35-26(36-23,17-30-9-8-29-18-30)24-7-2-20(27)14-25(24)28/h2-9,14,18,23H,10-13,15-17H2,1H3 InChIKey=XMAYWYJOQHXEEK-UHFFFAOYSA-N CHEBI:48339 ketoconazole CHEBI:48339 http://purl.obolibrary.org/obo/chebi.owl chebi_ontology benzothiazepines CHEBI:48684 benzothiazepine CHEBI:48684 Any molecular entity that contains carbon. http://purl.obolibrary.org/obo/chebi.owl CHEBI:25700 CHEBI:33244 chebi_ontology . organic compounds organic entity organic molecular entities organic molecules CHEBI:50860 organic molecular entity CHEBI:50860 http://purl.obolibrary.org/obo/chebi.owl chebi_ontology magnesium halides CHEBI:51234 magnesium halide CHEBI:51234 http://purl.obolibrary.org/obo/chebi.owl Beilstein:174850 CAS:635-78-9 7-hydroxy-3H-phenoxazin-3-one chebi_ontology 0 213.043 213.18892 7-Hydroxy-3H-phenoxazin-3-one 7-Hydroxyphenoxazin-3-one C12H7NO3 HSSLDCABUXLXKM-UHFFFAOYSA-N InChI=1S/C12H7NO3/c14-7-1-3-9-11(5-7)16-12-6-8(15)2-4-10(12)13-9/h1-6,14H Oc1ccc2nc3ccc(=O)cc3oc2c1 Resorufine CHEBI:51602 resorufin CHEBI:51602 A monocarboxylic acid that is the 4'-hydroxylated metabolite of diclofenac. http://purl.obolibrary.org/obo/chebi.owl Beilstein:4198042 CAS:64118-84-9 PMID:10027798 PMID:10709153 PMID:10807502 PMID:12966366 PMID:14609740 PMID:15139759 PMID:15265128 PMID:15455182 PMID:17123753 PMID:18548238 PMID:2118185 PMID:9226412 PMID:9862754 Reaxys:4198042 {2-[(2,6-dichloro-4-hydroxyphenyl)amino]phenyl}acetic acid chebi_ontology (o-(2,6-Dichloro-4-hydroxyanilino)phenyl)acetic acid 0 311.012 312.14800 4'-OH DCF 4'-hydroxy diclofenac C14H11Cl2NO3 InChI=1S/C14H11Cl2NO3/c15-10-6-9(18)7-11(16)14(10)17-12-4-2-1-3-8(12)5-13(19)20/h1-4,6-7,17-18H,5H2,(H,19,20) KGVXVPRLBMWZLG-UHFFFAOYSA-N OC(=O)Cc1ccccc1Nc1c(Cl)cc(O)cc1Cl CHEBI:59613 4'-hydroxydiclofenac CHEBI:59613 A chemical substance is a portion of matter of constant composition, composed of molecular entities of the same type or of different types. http://purl.obolibrary.org/obo/chebi.owl chebi_ontology Chemische Substanz CHEBI:59999 chemical substance CHEBI:59999 A mixture is a chemical substance composed of multiple molecules, at least two of which are of a different kind. http://purl.obolibrary.org/obo/chebi.owl chebi_ontology Mischung CHEBI:60004 mixture CHEBI:60004 A dioxolane that has formula C35H38Cl2N8O4. http://purl.obolibrary.org/obo/chebi.owl ChEMBL:17194821 ChemIDplus:84625-61-6 DrugBank:DB01167 KEGG DRUG:84625-61-6 KEGG DRUG:D00350 Wikipedia:Itraconazole 2-(butan-2-yl)-4-{4-[4-(4-{[(2R,4S)-2-(2,4-dichlorophenyl)-2-(1H-1,2,4-triazol-1-ylmethyl)-1,3-dioxolan-4-yl]methoxy}phenyl)piperazin-1-yl]phenyl}-2,4-dihydro-3H-1,2,4-triazol-3-one Itraconazole chebi_ontology C35H38Cl2N8O4 CCC(C)n1ncn(-c2ccc(cc2)N2CCN(CC2)c2ccc(OC[C@H]3CO[C@@](Cn4cncn4)(O3)c3ccc(Cl)cc3Cl)cc2)c1=O InChI=1S/C35H38Cl2N8O4/c1-3-25(2)45-34(46)44(24-40-45)29-7-5-27(6-8-29)41-14-16-42(17-15-41)28-9-11-30(12-10-28)47-19-31-20-48-35(49-31,21-43-23-38-22-39-43)32-13-4-26(36)18-33(32)37/h4-13,18,22-25,31H,3,14-17,19-21H2,1-2H3/t25?,31-,35-/m0/s1 InChIKey=VHVPQPYKVGDNFY-ZPGVKDDISA-N Itrizole (TN) Oriconazole Sporanox (TN) CHEBI:6076 itraconazole CHEBI:6076 A racemate is an equimolar mixture of a pair of enantiomers. http://purl.obolibrary.org/obo/chebi.owl chebi_ontology melange racemique racemates racemic mixture CHEBI:60911 racemate CHEBI:60911 A urea that consists of 1-butylurea having a 4-hydroxymethylbenzenesulfonyl group attached at the 3-position. http://purl.obolibrary.org/obo/chebi.owl CAS:5719-85-7 HMDB:HMDB06408 PMID:16493553 Reaxys:2867981 N-(butylcarbamoyl)-4-(hydroxymethyl)benzenesulfonamide chebi_ontology 0 1-Butyl-3-(4-hydroxymethylphenyl)sulfonylurea 286.099 286.34700 C12H18N2O4S CCCCNC(=O)NS(=O)(=O)c1ccc(CO)cc1 Hydroxymethyltolbutamide Hydroxytolbutamide InChI=1S/C12H18N2O4S/c1-2-3-8-13-12(16)14-19(17,18)11-6-4-10(9-15)5-7-11/h4-7,15H,2-3,8-9H2,1H3,(H2,13,14,16) Methylhydroxytolbutamide SJRHYONYKZIRPM-UHFFFAOYSA-N CHEBI:63799 4-hydroxytolbutamide CHEBI:63799 A sulfoxide that is omeprazole in which one of the methyl hydrogens at position 5 on the pyridine ring is substituted by a hydroxy group. http://purl.obolibrary.org/obo/chebi.owl CAS:92340-57-3 PMID:19166730 PMID:21546194 PMID:7781266 PMID:8550990 PMID:9916309 Reaxys:8439890 (4-methoxy-6-{[(5-methoxy-1H-benzimidazol-2-yl)sulfinyl]methyl}-5-methylpyridin-3-yl)methanol chebi_ontology 0 361.110 361.41500 5-Methoxy-2-(((4-methoxy-3-methyl-5-hydroxymethyl-2-pyridinyl)methyl)sulfinyl)-1H-benzimidazole C17H19N3O4S CMZHQFXXAAIBKE-UHFFFAOYSA-N COc1ccc2[nH]c(nc2c1)S(=O)Cc1ncc(CO)c(OC)c1C Hydroxyomeprazole InChI=1S/C17H19N3O4S/c1-10-15(18-7-11(8-21)16(10)24-3)9-25(22)17-19-13-5-4-12(23-2)6-14(13)20-17/h4-7,21H,8-9H2,1-3H3,(H,19,20) CHEBI:63840 5'-hydroxyomeprazole CHEBI:63840 A taxane diterpenoid that consists of paclitaxel bearing an additional hydroxy substituent at the 6alpha-position. http://purl.obolibrary.org/obo/chebi.owl CAS:153212-75-0 Reaxys:8105272 (2alpha,5beta,6alpha,7beta,10beta,13alpha)-4,10-diacetoxy-13-{[(2R,3S)-3-(benzoylamino)-2-hydroxy-3-phenylpropanoyl]oxy}-1,6,7-trihydroxy-9-oxo-5,20-epoxytax-11-en-2-yl benzoate chebi_ontology 0 6-hydroxytaxol 6alpha-hydroxypaclitaxel 6alpha-hydroxytaxol 869.326 869.90550 C47H51NO15 InChI=1S/C47H51NO15/c1-24-30(61-43(57)33(51)32(27-16-10-7-11-17-27)48-41(55)28-18-12-8-13-19-28)22-47(58)40(62-42(56)29-20-14-9-15-21-29)36-45(6,38(54)35(60-25(2)49)31(24)44(47,4)5)37(53)34(52)39-46(36,23-59-39)63-26(3)50/h7-21,30,32-37,39-40,51-53,58H,22-23H2,1-6H3,(H,48,55)/t30-,32-,33+,34-,35+,36-,37-,39+,40-,45-,46+,47+/m0/s1 NDCWHEDPSFRTDA-FJMWQILYSA-N [H][C@]12[C@H](OC(=O)c3ccccc3)[C@]3(O)C[C@H](OC(=O)[C@H](O)[C@@H](NC(=O)c4ccccc4)c4ccccc4)C(C)=C([C@@H](OC(C)=O)C(=O)[C@]1(C)[C@@H](O)[C@H](O)[C@H]1OC[C@@]21OC(C)=O)C3(C)C CHEBI:63859 6-hydroxypaclitaxel CHEBI:63859 A magnesium salt comprising of two chlorine atoms bound to a magnesium atom. http://purl.obolibrary.org/obo/chebi.owl CAS:7786-30-3 Gmelin:9305 KEGG:C07755 MolBase:1868 Reaxys:8128169 magnesium dichloride chebi_ontology 0 93.923 95.21040 Cl2Mg InChI=1S/2ClH.Mg/h2*1H;/q;;+2/p-2 Magnesium chloride Magnesium chloride anhydrous Magnesiumchlorid MgCl2 TWRXJAOTZQYOKJ-UHFFFAOYSA-L [Mg++].[Cl-].[Cl-] [MgCl2] CHEBI:6636 magnesium dichloride CHEBI:6636 Any monocyclic heteroarene consisting of a five-membered ring containing nitrogen. Azoles can also contain one or more other non-carbon atoms, such as nitrogen, sulfur or oxygen. http://purl.obolibrary.org/obo/chebi.owl Wikipedia:Azole chebi_ontology azoles CHEBI:68452 azole CHEBI:68452 http://purl.obolibrary.org/obo/chebi.owl CAS:59467-70-8 Drug_Central:1802 KEGG:C07524 KEGG:D00550 LINCS:LSM-5200 Midazolam chebi_ontology 0 325.078 325.768 C18H13ClFN3 Cc1ncc2CN=C(c3ccccc3F)c3cc(Cl)ccc3-n12 DDLIGBOFAVUZHB-UHFFFAOYSA-N InChI=1S/C18H13ClFN3/c1-11-21-9-13-10-22-18(14-4-2-3-5-16(14)20)15-8-12(19)6-7-17(15)23(11)13/h2-9H,10H2,1H3 buccolam mezolam midazolam HCl midazolam hydrochloride CHEBI:6931 Midazolam CHEBI:6931 Any molecule that consists of at least one carbon atom as part of the electrically neutral entity. http://purl.obolibrary.org/obo/chebi.owl chebi_ontology organic molecules CHEBI:72695 organic molecule CHEBI:72695 http://purl.obolibrary.org/obo/chebi.owl Beilstein:497773 CAS:21829-25-4 DrugBank:DB01115 Drug_Central:1922 KEGG:C07266 KEGG:D00437 LINCS:LSM-4176 Wikipedia:Nifedipine Nifedipine dimethyl 2,6-dimethyl-4-(2-nitrophenyl)-1,4-dihydropyridine-3,5-dicarboxylate chebi_ontology 0 346.116 346.33460 4-(2'-Nitrophenyl)-2,6-dimethyl-1,4-dihydropyridin-3,5-dicarbonsaeuredimethylester Adalat Adapine C17H18N2O6 COC(=O)C1=C(C)NC(C)=C(C1c1ccccc1[N+]([O-])=O)C(=O)OC Coracten HYIMSNHJOBLJNT-UHFFFAOYSA-N InChI=1S/C17H18N2O6/c1-9-13(16(20)24-3)15(14(10(2)18-9)17(21)25-4)11-7-5-6-8-12(11)19(22)23/h5-8,15,18H,1-4H3 Nifecard Nifecor Nifedipres Procardia nifedipine nifedipino nifedipinum CHEBI:7565 nifedipine CHEBI:7565 A racemate comprising equimolar amounts of (R)- and (S)-omeprazole. http://purl.obolibrary.org/obo/chebi.owl Beilstein:3628192 CAS:73590-58-6 DrugBank:DB00338 KEGG:C07324 KEGG:D00455 PMID:11060758 PMID:11208500 PMID:11210716 PMID:11304936 PMID:11321383 PMID:11395292 PMID:11404722 PMID:11459434 PMID:11568514 PMID:11700946 PMID:11774962 PMID:11807212 PMID:11851112 PMID:11903739 PMID:11962536 PMID:12072663 PMID:12135028 PMID:12235248 PMID:12495367 PMID:12683615 PMID:13680386 PMID:14616415 PMID:14708212 PMID:14725575 PMID:15004262 PMID:15125696 PMID:15586641 PMID:15598025 PMID:15684503 PMID:15707461 PMID:15774534 PMID:16080278 PMID:16129922 PMID:16259581 PMID:16276979 PMID:16380990 PMID:16386527 PMID:16397810 PMID:16440530 PMID:16998872 PMID:17049542 PMID:17384694 PMID:17532167 PMID:18294333 PMID:18366242 PMID:18416943 PMID:18448060 PMID:18498918 PMID:18520598 PMID:18571645 PMID:18616070 PMID:18793272 PMID:18818790 PMID:19150046 PMID:19166730 PMID:19176055 PMID:19236757 PMID:19327607 PMID:19383986 PMID:19434360 PMID:19470853 PMID:19517893 PMID:19746659 PMID:19796313 PMID:19801857 PMID:19937171 Patent:EP5129 Patent:US4255431 Patent:US5693818 Reaxys:3628192 Wikipedia:Omeprazole rac-5-methoxy-2-{[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]sulfinyl}-1H-benzimidazole chebi_ontology 5-methoxy-2-{[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]sulfinyl}-1H-benzimidazole Antra Audazol Belmazol Ceprandal Danlox Desec Elgam Emeproton Gasec Gastrimut Indurgan Inhibitron Losec OMEP OMP OMZ Olit Omapren Omebeta Prazidec Procelac Sanamidol Ulceral Ulcesep Ultop omeprazol omeprazole omeprazolum CHEBI:7772 omeprazole CHEBI:7772 A lactam that is 2,3-dihydro-1,5-benzothiazepin-4(5H)-one in which positions 2 and 3 are substituted by 4-methoxyphenyl and acetoxy, respectively, while the hydrogen attached to the nitrogen is substituted by a 2-(dimethylamino)ethyl group. http://purl.obolibrary.org/obo/chebi.owl ChemIDplus:34933-06-7 Reaxys:25644899 5-[2-(dimethylamino)ethyl]-2-(4-methoxyphenyl)-4-oxo-2,3,4,5-tetrahydro-1,5-benzothiazepin-3-yl acetate chebi_ontology 3-acetoxy-5-(2-(dimethylamino)ethyl)-2,3-dihydro-2-(4-methoxyphenyl)-1,5-benzothiazepin-4(5H)-one C22H26N2O4S COc1ccc(cc1)C1Sc2ccccc2N(CCN(C)C)C(=O)C1OC(C)=O InChI=1S/C22H26N2O4S/c1-15(25)28-20-21(16-9-11-17(27-4)12-10-16)29-19-8-6-5-7-18(19)24(22(20)26)14-13-23(2)3/h5-12,20-21H,13-14H2,1-4H3 InChIKey=HSUGRBWQSSZJOP-UHFFFAOYSA-N CHEBI:82814 5-[2-(dimethylamino)ethyl]-2-(4-methoxyphenyl)-4-oxo-2,3,4,5-tetrahydro-1,5-benzothiazepin-3-yl acetate CHEBI:82814 A fatty acid ester comprising a dihydroxyheptanoic acid unit condensed into a lactone; a partially reduced naphthalene structure; and a 2,2-dimethylbutyric acyl substituent at C17. It is used as a cholesterol-lowering and anti-cardiovascular disease drug. http://purl.obolibrary.org/obo/chebi.owl CHEBI:45577 Beilstein:4768037 ChemIDplus:79902-63-9 CiteXplore:11336576 CiteXplore:12827636 CiteXplore:14561068 CiteXplore:14973129 CiteXplore:18199328 CiteXplore:18688862 CiteXplore:18936176 DrugBank:DB00641 KEGG DRUG:79902-63-9 KEGG DRUG:D00434 PDBeChem:SIM Patent:EP33538 Patent:US4444784 Wikipedia:Simvastatin (1S,3R,7S,8S,8aR)-8-{2-[(2R,4R)-4-hydroxy-6-oxotetrahydro-2H-pyran-2-yl]ethyl}-3,7-dimethyl-1,2,3,7,8,8a-hexahydronaphthalen-1-yl 2,2-dimethylbutanoate SIMVASTATIN Simvastatin chebi_ontology (3R,5R)-7-{(1S,2S,6R,8S,8aR)-8-[(2,2-dimethylbutanoyl)oxy]-2,6-dimethyl-1,2,6,7,8,8a-hexahydronaphthalen-1-yl}-3,5-dihydroxyheptanoic acid 2,2-dimethylbutyric acid, 8-ester with (4R,6R)-6-(2-((1S,2S,6R,8S,8aR)-1,2,6,7,8,8a-hexahydro-8-hydroxy-2,6-dimethyl-1-naphthyl)ethyl)tetrahydro-4-hydroxy-2H-pyran-2-one C25H38O5 CCC(C)(C)C(=O)O[C@H]1C[C@@H](C)C=C2C=C[C@H](C)[C@H](CC[C@@H]3C[C@@H](O)CC(=O)O3)[C@@H]12 InChI=1S/C25H38O5/c1-6-25(4,5)24(28)30-21-12-15(2)11-17-8-7-16(3)20(23(17)21)10-9-19-13-18(26)14-22(27)29-19/h7-8,11,15-16,18-21,23,26H,6,9-10,12-14H2,1-5H3/t15-,16-,18+,19+,20-,21-,23-/m0/s1 InChIKey=RYMZZMVNJRMUDD-HGQWONQESA-N MK-733 Simvastatina Simvastatine Simvastatinum Zocor simvastatin CHEBI:9150 simvastatin CHEBI:9150 A triazolobenzodiazepine that has formula C17H12Cl2N4. http://purl.obolibrary.org/obo/chebi.owl Beilstein:1226643 ChemIDplus:28911-01-5 DrugBank:DB00897 KEGG DRUG:D00387 Wikipedia:Triazolam 8-chloro-6-(2-chlorophenyl)-1-methyl-4H-[1,2,4]triazolo[4,3-a][1,4]benzodiazepine chebi_ontology C17H12Cl2N4 Cc1nnc2CN=C(c3ccccc3Cl)c3cc(Cl)ccc3-n12 Halcion InChI=1S/C17H12Cl2N4/c1-10-21-22-16-9-20-17(12-4-2-3-5-14(12)19)13-8-11(18)6-7-15(13)23(10)16/h2-8H,9H2,1H3 InChIKey=JOFWLTCLBGQGBO-UHFFFAOYSA-N CHEBI:9674 triazolam CHEBI:9674 A separation method where components of a sample are separated on the basis of their density in a centrifuge according to the centrifugal force they experience. Samples are spun at >5000 rpm. http://purl.obolibrary.org/obo/chmo.owl burchh 2009-06-19T02:03:14Z high speed centrifugation CHMO:0002013 high-speed centrifugation CHMO:0002013 The process of one material (absorbate) being retained by another (absorption). http://purl.obolibrary.org/obo/chmo.owl REX:0000188 CHMO:0002914 Gold Book, somewhat modified. It goes on "The process of one material (absorbate) being retained by another (absorbent); this may be the physical solution of a gas, liquid, or solid in a liquid, attachment of molecules of a gas, vapour, liquid, or dissolved substance to a solid surface by physical forces, etc." absorption of material CHMO:0002914 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 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 Yongqun He, Matthew Brush, Sirarat Sarntivijai, Alexander Diehl, Jie Zheng, Yu Lin, Bjoern Peters http://purl.obolibrary.org/obo/clo.owl A 'cell line cell' is a part of a cell line established through the passaging/selection of a primary cultured cells or the experimental modification of an existing cell line. New types of cell line cells are established after sufficient passaging of a primary culture to establish a stable and homogenous population that qualifies as a line (typically 1-20 passages), or following some spontaneous or experimental modification that confers novel characteristics to an existing line. A cell line cell typically has mutations of five or more genes compared to the original cell that derives the cell line cell. Some gene mutations may turn on some oncogenes. Cell line cells can be in active culture, stored in a quiescent state for future use (e.g. frozen in liquid nitrogen), or applied in experimental procedures. cell line cell CLO:0000031 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 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). In the spring of 2013, a working group comprised of domain experts and representatives from CLO, OBI, CL, and ReO worked to establish a consensus model and definitions of cultured cells across these efforts. This included a careful characterization of how the term 'cell line' should be defined and applied. Notes about this work and its outcomes can be found on the CLO wiki here: http://code.google.com/p/clo-ontology/wiki/Cell_Lines MB, SS, JZ, MAH, BP, CS, YH 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 *type* of 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.). The definition provided here establishes the 'scale' of cell populations that qualify as cell lines - specifically those with a shared propagation history in culture. In this way, 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.  As defined here, 'cell line' can refer to a population of cells in active culture, applied experimentally, or stored in a quiescent state for future use. cell line CLO:0002172 LCL-1170 Caco-2 http://purl.obolibrary.org/obo/clo.owl disease: colorectal adenocarcinoma Caco-2 cell ATCC: HTB-37 CHEMBL: CHEMBL3307519 CVCL: CVCL_0025 EFO: EFO_0001099 HyperCLDB: cl618 MeSH: D018938 CLO:0002421 CHO Chinese Hamster Ovary cell http://purl.obolibrary.org/obo/clo-merged.owl CHO cell HyperCLDB: cl721 MeSH: D016466 CLO:0007331 LLC-PK subscript(1) http://purl.obolibrary.org/obo/clo.owl LLC-PK subscript(1) cell ATCC: CL-101 HyperCLDB: cl3221 MeSH: D018374 CLO:0007646 MDCK http://purl.obolibrary.org/obo/clo.owl MDCK cell HyperCLDB: cl5078 CLO:0037237 Amelogenin: X; CSF1PO: 11,12; D13S317: 12; D16S539: 9; D18S51: 18; D21S11: 28,30.2; D3S1358: 15,17; D5S818: 8,9; D7S820: 11,12; D8S1179: 12,14; FGA: 23; Penta D: 9,10; Penta E: 7,15; TH01: 7,9.3; TPOX: 11; vWA: 16,19 293 293 HEK HEK 293 HEK-293 HEK293 WEB: http://hek293.com/ WEB: http://web.expasy.org/cellosaurus/CVCL_0045 WEB: https://www.atcc.org/Products/All/CRL-1573.aspx http://purl.obolibrary.org/obo/clo-merged.owl 293-derived cell ATCC: CRL-1573 RRID: CVCL_0045 CL:0000010 cultured cell A cell in vitro that is or has been maintained or propagated as part of a cell culture. http://purl.obolibrary.org/obo/clo.owl cell Note that this class was re-labeled to 'cultured cell' instead of 'cell line cell', as it intent was clarified to cover any cultured cells of multicellular and unicellular organisms. This includes cells actively being cultured, or cells that have been cultured but are stored in a quiescent state for future use. In having been cultured, cells must establish homeostasis and often replicate in a foreign environment. Accomodation of this stress initiates a selection of cells fit for such challenges, wherein necessary adaptive biochemical and.or genetic changes can occur. These changes can set them apart from the in vivo cells from which they derive, and such changes will typically accumulate and change over increasing time in culture. cultured cell 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. http://purl.obolibrary.org/obo/clo.owl cell This class has been re-labeled to imply reference only to in vitro experimentally modified cells, similarly, the definition has been slightly updated to reflect this. 'experimentally modified cell' refers only to cells in vitro, and not modified in vivo/in environment cells. There is currently no class representing unmodified in vitro cells (other than the parent 'cell in vitro'), or a class representing modified native cells. More granular subclassing of experimentally modified cell can be found in ReO. MHB 1.12.12 experimentally modified cell in vitro DIDEO:00000000 A potential drug-drug interaction (PDDI) is an information content entity that specifies the possibility of a drug-drug interaction based on either reasonable extrapolation about drug-drug interaction mechanisms or a data item created by clinical studies, clinical observation or physiological experiment. Mathias Brochhausen potential drug-drug interaction DIDEO:00000001 the DDI mechanism, the risk of it causing a clinical effect, the clinical effect brought about by that DDI, factor's that modify the probability of it occuring An information content entity that is about a drug-drug interaction. DDI description drug-drug interaction description DIDEO:00000002 Mathias Brochhausen mechanistic assertion data item A data item that is about a biological process data item about biological process DIDEO:00000003 A data item that is about a drug-drug interaction and the creation of which was triggered by an observation outside a controlled context (e.g. a clinical trial). Mathias Brochhausen observational data item about drug-drug interaction DIDEO:00000004 A data item that is about a biological process and that is the specified output of a clinical study. physiological observation from clinical study data item DIDEO:00000005 A data item that is the output of a process of estimating, beyond the original observation range, the value of a variable on the basis of its relationship with another variable. Mathias Brochhausen https://en.wikipedia.org/w/index.php?title=Extrapolation&oldid=690284752 data item from extrapolation DIDEO:00000006 A biological process that realizes the function of the gastrointestinal system (or any organ that is a part of it.). This includes digestion of ingested substances, absorption and eliminating waste. Physiological activity and functions of the gastrointestinal system as a whole or of any of its parts, including digestion, absorption and eliminating waste. gastrointestinal functioning DIDEO:00000007 "Use only if benefit outweighs risk: “When a systemic dose of epinephrine is given to a person on one of these nonselective beta-blockers, an acute hypertensive reaction is almost certain. Systolic BPs of 250 mm/Hg are not uncommon. Most people can probably withstand a short episode of such a hypertensive reaction without permanent sequelae, but strokes have occurred in susceptible patients. Thus, it is best to avoid this reaction if possible. If a patient is likely to receive systemic epinephrine, it would be prudent to use a cardioselective beta-blocker.” (Title: Individualized Drug Interaction Alerts; Authors: Daniel C. Malone , University of Arizona; John Horn, Philip Hansten, University of Washington) No precaution: “If the NSAID is being used as an analgesic or antipyretic, it would be prudent to use an alternative such as acetaminophen. In some people, acetaminophen can increase the anticoagulant effect of warfarin, so monitor the INR if acetaminophen is used in doses over 2 g/day for a few days. For more severe pain consider short-term opioids in place of the NSAID.“ (Title: Individualized Drug Interaction Alerts; Authors: Daniel C. Malone , University of Arizona; John Horn, Philip Hansten, University of Washington) A evidence-based plan specification that specifies processes to prevent or mitigate a drug-drug interaction management option Evidence-based strategy to mitigate the potential clinical consequences of a drug-drug interaction; e.g., use only if benefit outweighs risk, assess risk and take action if necessary, no special precautions. recommended action An instance of this entity would represent an optional recommendation for the clinical management of patients who are exposed or about to be exposed to a potential DDI. Management options may be generated by expert opinion, consensus, and/or a review and synthesis of relevant evidence. drug-drug interaction management option DIDEO:00000008 A drug-drug interaction that has been the subject of a case report or study. interaction occured An instance of a drug-drug interaction that has been identified in case report or study. reported drug-drug interaction DIDEO:00000009 A data item that is the outcome of running a kinetic model and that states that drug A has some effects on the absorption, metabolism and elimination of drug B. Evidence from a kinetic model that a drug-Y has some effect on the absorption, metabolism and elimination of drug-X. pharmacokinetic interaction signal DIDEO:00000010 Bioavailability is a disposition that is borne by a drug product and is realized by the process of a proportion of the active pharmaceutical ingredient in that drug product reaching systemic circulation. Anuj Shah Mathias Brochhausen bioavailability DIDEO:00000011 An information content entity that makes a statement about a drug product being an object drug in a drug interaction. Mathias Brochhausen object drug information DIDEO:00000012 The role that inheres in a drug product or drug ingredient and that is realized by being affected by another drug pharmacokinetically or pharmacodynamically in a drug drug interaction. Daniel C. Malone Jodi Schneider Mathias Brochhausen Philip E. Empey Richard D. Boyce William R. Hogan http://www.hanstenandhorn.com/article-d-i.html object drug role DIDEO:00000013 The role that inheres in a drug product or drug ingredient that is realized by affecting another drug pharmacokinetically or pharmacodynamically in a drug drug interaction. Daniel C. Malone Jodi Schneider Mathias Brochhausen Philip E. Empey Richard C. Boyce William R. Hogan http://www.hanstenandhorn.com/article-d-i.html precipitant drug role DIDEO:00000014 An information content entity that makes a statement about a drug product being an precipitant drug in a drug interaction. Mathias Brochhausen precipitant drug information DIDEO:00000015 A potential drug drug interaction that is about a drug metabolism. Mathias Brochhausen metabolic potential drug-drug interaction DIDEO:00000016 A disposition inhering in a drug product that when realized is realized by processes that negatively affect the safety or the efficacy of the drug product, or increase its toxicity.. Mathias Brochhausen narrow therapeutic index DIDEO:00000017 A metabolism induction potential drug-drug interaction that is about an decrease of metabolic activity because of either a decreased expression of the enzyme or inference with how the enzyme contributes to the metabolic process. Mathias Brochhausen metabolism inhibition potential drug-drug interaction DIDEO:00000018 A metabolism induction potential drug-drug interaction that is about an increase of an enzyme participating in the metabolic process. Mathias Brochhausen metabolism induction potential drug-drug interaction DIDEO:00000019 A material entity that is either drug product or an ingredient thereof and that participates in a drug-drug interaction. Drug participant in drug-drug interaction A drug entity that participate in a drug-drug interaction but for which its role is not assignable as a precipitant or object. material entity participant in drug-drug interaction DIDEO:00000020 A biological process that results in a clinically meaningful change to the response of at least one co-administrated drug. DDI A clinically meaningful alteration in the exposure and/or response to a drug (object drug) that has occurred as a result of the co-administration of another drug (precipitant drug)Oates JA. Chapter 5. Goodman and Gilman 11th ed (2006):117–36; Hines. Response can refer to either precipitating an adverse event or altering the therapeutic effect of the object drug. Although some DDIs may be used for therapeutic benefit, this paper focuses on those with adverse clinical consequences. (based on the 2013 DDI conference series) / has participant some mechanism. drug-drug interaction DIDEO:00000021 A planned process of administering more than one drug to the same individual over a specific time interval. This class currently does not have a restriction. One candidate restriction is a necessary condition: 'has participant at some time' min 2 'drug product'. I was not able to find an OWL reasoner for Protege 5 that supports cardinality restrictions. An instance of this occurs when at least two or more drugs are taken in a specific time interval and the individual time interval for each drug administration overlaps with the other drug's or drugs' time interval(s). (SG1) drug co-administration DIDEO:00000022 Non-steroidal anti-inflammatory drugs (NSAIDs) have antiplatelet effects which increase the bleeding risk when combined with oral anticoagulants such as warfarin. The antiplatelet effect of NSAIDs lasts only as long as the NSAID is present in the circulation, unlike aspirin’s antiplatelet effect, which lasts for up to 2 weeks after aspirin is discontinued. Timolol is a nonselective beta-blocker, and timolol eye drops have been shown to produce systemic beta-blockade. Timolol is metabolized by CYP2D6, and patients who are deficient in CYP2D6 (PMs) have been shown to develop higher timolol plasma concentrations following timolol ophthalmic aqueous drops. An information content entity that represents a drug interaction as a directional series of molecular processes. This is an information content entity that is about a clinically measurable drug-drug interaction. drug interaction mechanism An assertion about the process or the processes by which a drug-drug interaction clinical consequence occurs. An instance of this entity would represent the biochemical process by which pharmacokinetic or pharmacodynamic DDI is thought to occur. mechanism of interaction information DIDEO:00000023 An information content entity that is about a drug co-administration and is intended to be specified input into the assessment of whether a drug-drug interaction exists or not. An instance of this type represents a information artifact used to establish knowledge for or against the existence of a drug-drug interaction. drug-drug interaction evidence DIDEO:00000024 A potential drug-drug interaction that is causally linked to an elevated risk of an adverse event that warrants a drug-drug interaction management option. Alternative definitions use the risk of harm instead of the risk of an AE. clinically relevant potential drug-drug interaction DIDEO:00000025 A scalar measurement datum that is the specified outcome of a drug bioavailability assay. Anuj Shah Mathias Brochhausen F bioavailability measurement datum DIDEO:00000026 An assay with the objective to capture information about the bioavailability of an active ingredient in a drug product. Anuj Shah Mathias Brochhausen drug bioavailability assay DIDEO:00000030 An entity that is the result of a drug-drug interaction. obsolete_drug-drug interaction effect true DIDEO:00000031 Anuj Shah Mathias Brochhausen It is a disposition that is borne by drug product and is realized by the metabolism of the active pharmaceutical ingredient in that drug product before entering systemic circulation, when ingested. first pass effect disposition DIDEO:00000032 Anuj Shah Mathias Brochhausen An assay with the objective to capture information about the first pass metabolism of an active ingredient in a drug product. drug first pass metabolism assay DIDEO:00000033 Anuj Shah Mathias Brochhausen A scalar measurement datum that is the specified outcome of a drug first pass metabolism assay. first pass metabolism measurement datum DIDEO:00000034 Anuj Shah Mathias Brochhausen Daintith J (ed.): A Dictionary of Chemistry. 2008. Oxford University Press, Oxford UK. Absorbability is a disposition that is borne by a material entity that if realized is realized by the material entity taken up by another material entity in a different state of matter. absorbability DIDEO:00000035 An assay with the objective to capture information about the absorbability of an active ingredient in a drug product. Anuj Shah Mathias Brochhausen drug absorbability assay DIDEO:00000036 A a scalar measurement datum that is the specified outcome of an drug absorbability assay. Anuj Shah Mathias Brochhausen AUC absorbability measurement datum DIDEO:00000037 Anuj Shah Mathias Brochhausen An assay that measures the maximum concentration of an active ingredient of a drug product in a specified compartment of the body of an organism after the first dose of the drug product has been administered. drug maximum concentration assay DIDEO:00000038 A scalar measurement datum that is the specified outcome of a drug maximum concentration assay. Anuj Shah Mathias Brochhausen Cmax drug maximum concentration measurement datum DIDEO:00000039 A role that is borne by the enzyme responsible for 50% or more of the active pharmaceutic ingredient or metabolite’s total clearance from the body. The role role is realized by the metabolic process of the active pharmaceutical ingredient or metabolite. Anuj Shah Mathias Brochhausen primary total clearance enzyme role DIDEO:00000040 Anuj Shah Mathias Brochhausen A role that is borne by the enzyme responsible for 50% or more of the active pharmaceutic ingredient or metabolite’s total metabolic clearance from the body. primary metabolic clearance enzyme role DIDEO:00000042 A drug-drug interaction description that is part of a drug package insert. drug-drug interaction description from drug package insert DIDEO:00000043 A drug-drug interaction description from a drug package insert for an FDA approved drug. drug-drug interaction description from FDA label information DIDEO:00000044 A document that is provided along with a medication and that gives additional information about that medication. https://en.wikipedia.org/w/index.php?title=Package_insert&oldid=699801598 drug package insert DIDEO:00000045 FDA drug label http://www.fda.gov/forpatients/other/offlabel/default.htm A drug package insert for FDA-approved drugs that gives information about the drug, including the approved doses and how it's to be given to treat the medical condition for which it was approved. U.S. Food and Drug Administration drug label DIDEO:00000046 An area under curve in a plot of concentration of granular part of a drug product in some matrix (medium) against time. pharmacokinetic area under curve DIDEO:00000047 An information content entity that is part of a drug package insert and that is about a pharmacokinetic area under the curve measurement result. Mathias Brochhausen drug package AUC information DIDEO:00000048 Mathias Brochhausen Standards Development Working Group of the "Addressing PDDI Evidence Gaps" porject. An information content entity that provides statements or data that are used to support or refute an assertion. obsolete_evidence information content entity true DIDEO:00000049 Mathias Brochhausen AUC information An information content entity that is about a pharmacokinetic area under curve. pharmacokinetic area under curve information 2 DIDEO:00000050 A pharmacokinetic area under curve information that is about at least 2 area under curve measurments and the time series shows an increase of the area under curve. Mathias Brochhausen information about increase of pharmacokinetic area under the curve 2 DIDEO:00000051 A pharmacokinetic area under curve information that is about at least 2 area under curve measurments and the time series shows a decrease of the area under curve. Mathias Brochhausen information about decrease of pharmacokinetic area under the curve DIDEO:00000052 A biological process that has as a participant a part of a drug product and includes absorption, distribution, metabolism and excretion of that substance. Mathias Brochhausen "Addressing PDDI Evidence Gaps" Standards Development Group. pharmacokinetic process DIDEO:00000053 An information content entity that is used to support or refute an assertion. Mathias Brochhausen "Addressing PDDI Evidence Gaps" Standards Development Group evidence information content entity DIDEO:00000054 An information content entity that is part of an evidence information content entity and mentions the specified input to an assay. Mathias Brochhausen "Addressing PDDI Evidence Gaps" Standards Development Group evidence material information DIDEO:00000055 Mathias Brochhausen "Addressing PDDI Evidence Gaps" Standards Development Group A data item that is part of an evidence information content entity and is the specified output of an assay. evidence data item DIDEO:00000056 An evidence information content entity that is about a clinical drug trial. Mathias Brochhausen EV_Clinical_Trial https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html evidence information from clinical study DIDEO:00000057 An evidence information content entity that is about an in vitro assay that has a part of a drug or a drug metabolite, which participate in a metabolic process, as a specified input. Mathias Brochhausen EV_EX_Met_Enz_ID https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html evidence information from drug metabolism identification experiment DIDEO:00000058 An evidence information content entity that is about an in vitro assay and that has parts of a drug or drug metabolites, which participate in a negative regulation of a metabolic process, as it's specified input. Mathias Brochhausen EV_EX_Met_Enz_Inhibit https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html evidence information from drug metabolism inhibition experiment DIDEO:00000059 An evidence information content entity that is about an assay that realizes an ex vivo design, and that has chemical substances as its specific input, which are the outcome of drug components being imported across plasma membranes. Mathias Brochhausen EV_EX_Trans_Prot_ID https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html evidence information from transport protein identification experiment DIDEO:00000060 An evidence information content entity that is about an assay that realizes an ex vivo design, and that has chemical substances as its specific input, which are the outcome of the inhibition of drug component transporter. Mathias Brochhausen EV_EX_Trans_Prot_Inhibit https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html evidence information from transport protein inhibition experiment DIDEO:00000061 An evidence information content entity that is about an assay that was triggered by an adverse drug event. Mathias Brochhausen EV_Case_Report_ADE https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html evidence information from observation-based adverse drug event report DIDEO:00000062 An evidence information content entity that is about an assay that realizes an observation design. Mathias Brochhausen EV_Observational https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html evidence information from observational study DIDEO:00000063 An evidence information content entity that is about an in vitro assay that has a part of a drug or a drug metabolite, which participate in a metabolic process that has CYP 450 as a participant, as a specified input. Mathias Brochhausen EV_EX_Met_Enz_ID_Cyp450 https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html evidence information from CYP450 drug metabolism identification experiment DIDEO:00000064 An evidence information content entity that is about an in vitro assay that has a part of a drug or a drug metabolite, which participate in a metabolic process that has CYP 450 as a participant, as a specified input, and that has a cell line as a specified input. Mathias Brochhausen EV_EX_Enz_ID_Cyp450_Hum_Recom https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html evidence information from CYP450 recombinant drug metabolism identification experiment DIDEO:00000065 An evidence information content entity that is about an in vitro assay that has a part of a drug or a drug metabolite, which participate in a metabolic process that has CYP 450 as a participant, as a specified input, and that has human tissue specimen as a specified input, and that has chemical inhibitors as a specified input. Mathias Brochhausen EV_EX_Met_Enz_ID_Cyp450_Hum_Recom_Chem https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html evidence information from CYP450 recombinant drug metabolism identification experiment using chemical inhibitors DIDEO:00000066 An evidence information content entity that is about an in vitro assay that has a part of a drug or a drug metabolite, which participate in a metabolic process that has CYP 450 as a participant, as a specified input, and that has human tissue specimen as a specified input, and that has antibody inhibitors as a specified input. Mathias Brochhausen EV_EX_Met_Enz_ID_Cyp450_Hum_Recom_Antibody https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html evidence information from CYP450 recombinant drug metabolism identification experiment using antibody inhibitors DIDEO:00000067 An evidence information content entity that is about an in vitro assay that has a part of a drug or a drug metabolite, which participate in a metabolic process that has CYP 450 as a participant, as a specified input, and that has human tissue specimen as a specified input. Mathias Brochhausen EV_EX_Met_Enz_ID_Cyp450_Hum_Microsome https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html evidence information from CYP450 human microsome drug metabolism identification experiment DIDEO:00000068 An evidence information content entity that is about an in vitro assay that has a part of a drug or a drug metabolite, which participate in a metabolic process that has CYP 450 as a participant, as a specified input, and that has human tissue specimen as a specified input, and that has chemical inhibitors as a specified input. Mathias Brochhausen EV_EX_Met_Enz_ID_Cyp450_Hum_Microsome_Chem https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html evidence information from CYP450 human microsome drug metabolism identification experiment using chemical inhibitors DIDEO:00000069 An evidence information content entity that is about an in vitro assay that has a part of a drug or a drug metabolite, which participate in a metabolic process that has CYP 450 as a participant, as a specified input, and that has human tissue specimen as a specified input, and that has antibody inhibitors as a specified input. Mathias Brochhausen EV_EX_Met_Enz_ID_Cyp450_Hum_Microsome_Antibody https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html evidence information from CYP450 human microsome drug metabolism identification experiment using antibody inhibitors DIDEO:00000070 An evidence information content entity that is about an in vitro assay and that has parts of a drug or drug metabolites, which participate in a negative regulation of a metabolic process that also involves CYP 450, as it's specified input. Mathias Brochhausen EV_EX_Met_Enz_Inhibit_Cyp450 https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html evidence information from CYP450 metabolic enzyme inhibition experiment DIDEO:00000071 An evidence information content entity that is about a clinical drug trial that has at least two drugs as its specified input. Mathias Brochhausen EV_CT_DDI https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html evidence information from drug-drug interaction clinical trial DIDEO:00000072 An evidence information content entity that is about a clinical drug trial that has at least two drugs as its specified input and does not have group randomization as a part. Mathias Brochhausen EV_PK_DDI_NR https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html evidence information from non-randomized drug-drug interaction clinical trial DIDEO:00000073 An evidence information content entity that is about a clinical drug trial that has at least two drugs as its specified input, and that does not have group randomization as a part, and that realizes a clinical study design that has parallel group design as a part. Mathias Brochhausen EV_PK_DDI_Par_Grps https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html evidence information from parallel groups drug-drug interaction clinical trial' DIDEO:00000074 An evidence information content entity that is about a clinical drug trial that has at least two drugs as its specified input and does have group randomization as a part. Mathias Brochhausen EV_PK_DDI_RCT https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html evidence information from randomized drug-drug interaction clinical trial DIDEO:00000075 An evidence information content entity that is about a clinical drug trial that focusses on pharmacokinetics. Mathias Brochhausen EV_CT_Pharmacokinetic https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html evidence information from pharmacokinetic trial DIDEO:00000076 An evidence information content entity that is about a clinical drug trial that focusses on pharmacokinetics and that has organisms as participants that participated in genotyping. Mathias Brochhausen EV_CT_PK_Genotype https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html evidence information from genotyped pharmacokinetic trial DIDEO:00000077 An evidence information content entity that is about an assay that was triggered by an occurrent. Mathias Brochhausen EV_Case_Report https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html evidence information from observation-based report DIDEO:00000078 An evidence information content entity that is about an assay that realizes an observation design and has a drug product as a specified input, and that focuses on pharmacokinetics in an organism. Mathias Brochhausen EV_PK_Observational https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html evidence information from observational pharmacokinetic study DIDEO:00000079 An evidence information content entity that is about an assay that realizes an observation design and has at least two drug products as a specified input, and that focuses on pharmacokinetics in an organism. Mathias Brochhausen EV_PK_DDI_Observational https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html evidence information from observational drug-drug interaction study DIDEO:00000080 An evidence information content entity that is about an in vitro assay and that has parts of a drug or drug metabolites, which participate in a negative regulation of a metabolic process that also involves CYP 450, as it's specified input, and that has cell lines as a specified input. Mathias Brochhausen EV_EX_Met_Enz_Inhibit_Cyp450_Hum_Recom https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html evidence information from CYP450 recombinant drug metabolism inhibition experiment DIDEO:00000081 An evidence information content entity that is about an in vitro assay and that has parts of a drug or drug metabolites, which participate in a negative regulation of a metabolic process that also involves CYP 450, as it's specified input, and that has human tissue specimens as a specified input. Mathias Brochhausen EV_EX_Met_Enz_Inhibit_Cyp450_Hum_Microsome https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html evidence information from CYP450 human microsome drug metabolism inhibition experiment DIDEO:00000082 A data set that is structured and stored on a computer and that is publicly available and contains reports of adverse events. Mathias Brochhausen public adverse event reporting database DIDEO:00000083 An evidence information content entity that is about an assay that was triggered by an adverse drug event, and that is part on a publicly accessible database for adverse event reporting. Mathias Brochhausen EV_Case_Report_ADE_Public_Reported https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html evidence information from a publicly reported observation-based adverse drug event report DIDEO:00000084 An evidence information content entity that is about an assay that was triggered by an adverse drug event following the administration of at least two drugs. Mathias Brochhausen EV_Case_Report_DI https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html evidence information from an observation-based case-report of a drug interaction DIDEO:00000087 Mathias Brochhausen A protocol that specifies methodology to assess the likelihood of a drug to be the cause for an adverse event by answering a set of questions about the drug reaction report. adverse drug reaction causality evaluation protocol DIDEO:00000088 An evidence information content entity that is about an assay that was triggered by an adverse drug event following the administration of at least two drugs, and that is the specified outcome of a adverse drug reaction causality evaluation. Mathias Brochhausen EV_Case_Report_DI_Evaluated https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html evidence information from an evaluated observation-based case-report of a drug interaction DIDEO:00000089 Mathias Brochhausen Cl A measurement datum that is the specified output of measuring the volume of plasma that is completely cleared off of a substance per unit time. clearance measurement datum DIDEO:00000091 Mathias Brochhausen A dimensionless ratio unit which describes the relation between the two numbers x and y by giving the multiplier necessary to make x equal to y. fold DIDEO:00000092 An information content entity that is part of a pharmacokinetic parameter ratio and that describes whether the relationship between the numbers of the ratio is a positive or a negative one. Mathias Brochhausen pharmacokinetic parameter ratio directionality DIDEO:00000093 Mathias Brochhausen AUC ratio A pharmacokinetic parameter ratio that describes the relation between the pharmacokinetic area under the curve (AUC) for a given active ingredient or metabolite in an organism with and without the inhibiting drug present in the organism. area under the curve ratio DIDEO:00000094 A pharmacokinetic parameter ratio that describes the relation between the measurement of the volume of blood, serum, or plasma from which an active ingredient or a metabolite is completely removed by the kidney in a given amount of time in an organism with and without the inhibiting drug present in the organism. CL_R ratio renal clearance ratio DIDEO:00000095 An information content entity that describes the relationship between the mean (arithmetic and geometric) of measurements of a pharmacokintect parameter for a given drug A in absence of another drug and the mean (arithmetic and geometric) of measurements of a pharmacokintect parameter for a given drug A coadministrated with another drug B. Mathias Brochhausen pharmacokinetic parameter ratio DIDEO:00000097 An pharmacokinetic parameter directionality that describes negative relationship between the numbers of the ratio. Mathias Brochhausen pharmacokinetic parameter ratio decrease DIDEO:00000098 An pharmacokinetic parameter directionality that describes positive relationship between the numbers of the ratio. Mathias Brochhausen pharmacokinetic parameter ratio increase DIDEO:00000099 A pharmacokinetic parameter ratio that describes the relation between the drug maximum concentration measurements for a given active ingredient or metabolite in an organism with and without the inhibiting drug present in the organism. Mathias Brochhausen Cmax ratio drug maximum concentration ratio DIDEO:00000100 A pharmacokinetic parameter ratio that describes the relation between the time it takes for half of a given active ingredient or metabolite to be removed from the system of an organism with and without the inhibiting drug present in the organism. Mathias Brochhausen t1/2 ratio half-life ratio DIDEO:00000101 A pharmacokinetic parameter ratio that describes the relation between the measurement of the volume of blood, serum, or plasma from which an active ingredient or a metabolite is completely removed by the liver in a given amount of time in an organism with and without the inhibiting drug present in the organism. Mathias Brochhausen CL_H ratio hepatic clearance ratio DIDEO:00000102 A pharmacokinetic parameter ratio that describes the relation between the measurement of the fraction of the administered dose of an unaltered drug that reaches systemic circulation in the abscene of another drug, and the the measurement of the fraction of the administered dose of an unaltered drug that reaches systemic circulation when coadministered with another drug. Mathias Brochhausen F ratio bioavailability ratio DIDEO:00000103 An evidence information content entity that is about a clinical drug trial that focusses on pharmacokinetics and that has organisms as participants that participated in phenotyping. Mathias Brochhausen EV_CT_PK_Phenotype https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html evidence information from phenotyped pharmacokinetic trial DIDEO:00000104 An evidence information content entity that is about an assay that realizes an ex vivo design, and that has chemical substances as its specific input, which are the outcome of drug components being imported across plasma membranes by involvement of P-Glycoprotein. Mathias Brochhausen EV_EX_Trans_Prot_ID_P_Glycoprotein https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html evidence information from p-glycoprotein transport protein identification experiment DIDEO:00000105 An evidence information content entity that is about an assay that realizes an ex vivo design, and that has chemical substances as its specific input, which are the outcome of drug components being imported across plasma membranes by involvement of P-Glycoprotein using bidirectional flux in Caco-2 cells. Mathias Brochhausen EV_EX_Trans_Prot_ID_P_Glycoprotein_Caco_2 https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html evidence information from p-glycoprotein transport protein identification experiment using Caco 2 cell lines DIDEO:00000106 An evidence information content entity that is about an assay that realizes an ex vivo design, and that has chemical substances as its specific input, which are the outcome of drug components being imported across plasma membranes by involvement of P-Glycoprotein using overexpressed cells. Mathias Brochhausen EV_EX_Trans_Prot_ID_P_Glycoprotein_Overexpressed_Cells https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html evidence information from p-glycoprotein transport protein identification experiment using overexpressed cell lines DIDEO:00000107 An evidence information content entity that is about an assay that realizes an ex vivo design, and that has chemical substances as its specific input, which are the outcome of drug components being imported across plasma membranes by involvement of OATP1B1. Mathias Brochhausen EV_EX_Trans_Prot_ID_OATP1B1 https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html evidence information from OATP1B1 transport protein identification experiment DIDEO:00000108 An evidence information content entity that is about an assay that realizes an ex vivo design, and that has chemical substances as its specific input, which are the outcome of drug components being imported across plasma membranes by involvement of OATP1B3. Mathias Brochhausen EV_EX_Trans_Prot_ID_OATP1B3 https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html evidence information from OATP1B3 transport protein identification experiment DIDEO:00000109 An evidence information content entity that is about an assay that realizes an ex vivo design, and that has chemical substances as its specific input, which are the outcome of drug components being imported across plasma membranes by involvement of OATP1B1 using overexpressed cells. Mathias Brochhausen EV_EX_Trans_Prot_ID_OATP1B1_Overexpressed_Cells https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html evidence information from OATP1B1 transport protein identification experiment using overexpressed cell lines DIDEO:00000110 An evidence information content entity that is about an assay that realizes an ex vivo design, and that has chemical substances as its specific input, which are the outcome of drug components being imported across plasma membranes by involvement of OATP1B3 using overexpressed cells. Mathias Brochhausen EV_EX_Trans_Prot_ID_OATP1B3_Overexpressed_Cells https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html evidence information from OATP1B3 transport protein identification experiment using overexpressed cell lines DIDEO:00000111 An evidence information content entity that is about an assay that realizes an ex vivo design, and that has chemical substances as its specific input, which are the outcome of the inhibition of P-Glycoprotein. Mathias Brochhausen EV_EX_Trans_Prot_Inhibit_P_Glycoprotein https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html evidence information from p-glycoprotein inhibition experiment DIDEO:00000112 An evidence information content entity that is about an assay that realizes an ex vivo design, and that has chemical substances as its specific input, which are the outcome of the inhibition of P-Glycoprotein, and that has Caco 2 cell lines as a specified input. Mathias Brochhausen EV_EX_Trans_Prot_Inhibit_P_Glycoprotein_Caco_2 https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html evidence information from p-glycoprotein inhibition experiment using Caco 2 cell lines DIDEO:00000113 An evidence information content entity that is about an assay that realizes an ex vivo design, and that has chemical substances as its specific input, which are the outcome of the inhibition of P-Glycoprotein, and that has overexpressed cell lines as a specified input. EV_EX_Trans_Prot_Inhibit_P_Glycoprotein_Overexpressed_Cells https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html evidence information from p-glycoprotein inhibition experiment using overexpressed cell lines DIDEO:00000114 An evidence information content entity that is about an assay that realizes an ex vivo design, and that has chemical substances as its specific input, which are the outcome of the inhibition of OATP1B1. Mathias Brochhausen EV_EX_Trans_Prot_Inhibit_OATP1B1 https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html evidence information from OATP1B1 inhibition experiment DIDEO:00000115 An evidence information content entity that is about an assay that realizes an ex vivo design, and that has chemical substances as its specific input, which are the outcome of the inhibition of OATP1B1, and that has overexpressed cell lines as a specified input. Mathias Brochhausen EV_EX_Trans_Prot_Inhibit_OATP1B1_Overexpressed_Cells https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html evidence information from OATP1B1 inhibition experiment using overexpressed cell lines DIDEO:00000116 An evidence information content entity that is about an assay that realizes an ex vivo design, and that has chemical substances as its specific input, which are the outcome of the inhibition of OATP1B3, and that has overexpressed cell lines as a specified input. Mathias Brochhausen EV_EX_Trans_Prot_Inhibit_OATP1B3_Overexpressed_Cells https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html evidence information from OATP1B3 inhibition experiment using overexpressed cell lines DIDEO:00000117 An evidence information content entity that is about an assay that realizes an ex vivo design, and that has chemical substances as its specific input, which are the outcome of the inhibition of OATP1B3. Mathias Brochhausen EV_EX_Trans_Prot_Inhibit_OATP1B3 https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html evidence information from OATP1B3 inhibition experiment DIDEO:00000118 Mathias Brochhausen Philip E. Empey amended definition from Spruill WJ, Wade WE, DiPiro JT, Blouin RA, Pruemer JM: Concepts in Clinical Pharmacology. Bethesda, MA, 2014 based on a comment by Philip E. Empey. A pharmacokinetic parameter ratio that describes the theoretical volume that would be necessary to contain the total amount of an administered drug at the same concentration that it is observed in a bodily fluid for a given active ingredient or metabolite in an organism with and without the inhibiting drug present. It is expressed as a ratio of the volume of distribution with the inhibitor present as the numerator and absent as the denominator. volume of distribution ratio DIDEO:00000119 Mathias Brochhausen Philip E. Empey Tmax ratio A pharmacokinetic parameter ratio that describes the time from dose administration until a drug reaches its maximum concentration for a given active ingredient or metabolite in an organism with and without the inhibiting drug present in the organism. It is expressed as a ratio of the Tmax with the inhibitor present as the numerator and absent as the denominator. time to maximum drug concentration ratio DIDEO:00000120 Mathias Brochhausen Philip E. Empey A pharmacokinetic parameter ratio that describes the drug transmembrane transporter activity regarding an active ingredient or a metabolite in an in vitro bi-directional transport assay. It is expressed as a ratio of the apparent permeability in the basal to apical direction as the numerator and apparent permeability in the apical-to-basolateral direction as the denominator. efflux ratio DIDEO:00000121 Mathias Brochhausen Philip E. Empey A pharmacokinetic parameter ratio that describes the drug transmembrane transporter activity regarding an active ingredient or a metabolite in an in vitro bi-directional transport assay using transporter transfected cell model. It is expressed as a ratio of the efflux ratio in cells transfected with the transporter as the numerator and efflux ratio in cells not transfected with the transporter (wild type cells) as the denominator. net flux ratio DIDEO:00000122 Mathias Brochhausen ki A measurement data that gives the concentration of an inhibiting agent to reach half of the maximum inhibition of a meabolic or transport process. inhibitory constant DIDEO:00000123 The role that inheres in a chemical substance and that, if realized, is realized by a single, specified metabolic or transport reaction, which is being affected by another chemically substance pharmacokinetically in a drug-drug interaction experiment or natural product-drug interaction. Mathias Brochhausen probe subtrate role DIDEO:00000124 An assay that is the realization of a concretization of a clinical study design. Mathias Brochhausen clinical study DIDEO:00000125 A biological process that is the result of a drug-drug interaction. Mathias Brochhausen drug-drug interaction effect DIDEO:00000126 A value specification that specifies the relationship between two numbers. Mathias Brochhausen ratio value specification DIDEO:00000127 Mathias Brochhausen A ratio value specification where the relationship between to numbers is expressed as a fraction of 100. percentage value specification DIDEO:00000149 a cultured cell population that is derived from hepatocytes isolated from a human being and that has undergone cryopreservation John Judkins Cells isolated from human liver that have been frozen and stored, usually in liquid nitrogen; an in vitro model system for human metabolism or transport; cells can be thawed and used in metabolism or transport assays cryopreserved human hepatocyte population DIDEO:00000152 a cultured cell population that is derived from hepatocytes freshly isolated from a human being John Judkins Cells isolated from human liver, never frozen; an in vitro model system for human metabolism or transport; cells can be used in metabolism or transport assays freshly isolated human hepatocyte population DIDEO:00000153 a cultured cell population that is derived from cells isolated from the liver of a transgenic organism John Judkins Cells isolated from livers of transgenic animals; an in vitro model system for human metabolism or transport transgenic animal hepatocyte population DIDEO:00000154 a cultured cell population derived from hepatocytes, in which, during the culturing process, the cells occupy a region bound by two parallel plates made of gelled collagen John Judkins sandwich cultured hepatocyte population DIDEO:00000155 a cultured cell population derived from cells isolated from human intestinal epithelium John Judkins human intestinal epithelial cell population DIDEO:00000157 an immortal human liver-derived cell line cell that is part of the HepaRG cell line John Judkins HepaRG cells are terminally differentiated human hepatocellular carcinoma cells that reproducibly express drug-metabolizing enzymes and transporters. They are commonly used for metabolism and transport evaluations in vitro, as they respond and function like primary human hepatocytes across a range of applications. HepaRG cell DIDEO:00000158 an immortal human liver-derived cell line cell that is part of the Fa2N-4 cell line John Judkins Fa2N-4 cell line was prepared by immortalizing hepatocytes from a 12 year-old Caucasian female donor with Simian virus 40 large T antigen. The donor was tested negative for CMV, HIV, HBV, and HCV. This cell line was mainly used for major CYP induction studies (including CYP3A4/5, 1A2, 2B6, and 2C9) with limitations. Hepatic transporter expression levels are low. Fa2N-4 cell DIDEO:00000159 an immortal human liver-derived cell line cell that is part of the HBG BC2 cell line John Judkins BC2 cell An Immortalized human hepatoma cell line possesses the capacities of being reversibly differentiated in vitro, and of maintaining a relatviely higher mtabolic rate in the differentiated phase. It is mainly used for repeated toxicity evaluation in vitro. HBG BC2 cell DIDEO:00000160 a processed material that has a supernatant role resulting from high-speed centrifugation of a human liver S9 fraction John Judkins Cell cytosol obtained via centrifugation of human liver cells. It is commonly used to support in vitro DMPK studies related to liver cytsolic enzymes, especially non-CYP enzymes, such as phase I enzyme aldehyde oxidase (AO), phase II enzyme SULT. human liver cytosolic fraction DIDEO:00000161 a processed material that has a supernatant role resulting from high-speed centrifugation of a human intestine S9 fraction John Judkins Cell cytosol obtained via centrifugation of human enterocytes. It is commonly used to support in vitro evaluation of intestinal cytosolic enzymes in the first-pass metabolism of orally ingested xenobitotics. human intestine cytosolic fraction DIDEO:00000162 a processed material that has a supernatant role resulting from medium-speed centrifugation of a human liver homogenate John Judkins A mixture of cell cytosol and microsomes isolated by disruption and centrifugation of human liver cells. It contains a wide range of drug-metabolizing enzymes and is commonly used for in vitro DMPK studies, including both phase I and phase II xenobiotic metabolism. human liver S9 fraction DIDEO:00000163 a processed material that has a centrifuge pellet role resulting from high-speed centrifugation of a human intestine S9 fraction, which is derived from a single donor John Judkins individual human intestinal microsomes Subcellular fractions, derived from endoplasmic reticulum that has been isolated from enterocytes from a single human donor. They contain a rich variety of metaboliz enzymes for assessing first-pass metabolism for orally ingested drugs. individual human intestinal microsomal fraction DIDEO:00000164 a processed material that has a centrifuge pellet role resulting from high-speed centrifugation of a pool of human liver S9 fractions, which is derived from multiple donors John Judkins pooled human liver microsomes Subcellular fractions, derived from endoplasmic reticulum that has been isolated from liver cells from multiple human donors. They contain a rich variety of metaboliz enzymes (e.g. CYP, UGT, FMO) for assessing drug DMPK in vitro, such as metabolic stability, CYP inhibition, CYP phenotyping, metabolite charaterization, etc. pooled human liver microsomal fraction DIDEO:00000165 a processed material that has a centrifuge pellet role resulting from high-speed centrifugation of a human liver S9 fraction, which is derived from a single donor John Judkins individual human liver microsomes Subcellular fractions, derived from endoplasmic reticulum that has been isolated from liver cells from a single human donor. They contain a rich variety of metaboliz enzymes (e.g. CYP, UGT, FMO) for assessing drug DMPK in vitro, such as metabolic stability, CYP inhibition, CYP phenotyping, metabolite charaterization, etc. individual human liver microsomal fraction DIDEO:00000166 a processed material that has a centrifuge pellet role resulting from high-speed centrifugation of a pool of human intestine S9 fractions, which is derived from multiple donors John Judkins pooled human intestinal microsomes Subcellular fractions, derived from endoplasmic reticulum that has been isolated from enterocytes of multiple human donors. They contain a rich variety of metaboliz enzymes for assessing first-pass metabolism for orally ingested drugs. pooled human intestinal microsomal fraction DIDEO:00000167 a processed material that has a supernatant role resulting from medium-speed centrifugation of a human intestine homogenate John Judkins A mixture of cell cytosol and microsomes isolated by disruption and centrifugation of human enterocytes. It contains a wide range of drug-metabolizing enzymes and is commonly used for in vitro DMPK studies, including both phase I and phase II xenobiotic metabolism. human intestine S9 fraction DIDEO:00000168 a cultured cell that is part of a culture derived from an insect and has a recombinant protein production host role John Judkins baculovirus-insect cell Insect cell-hosted viral system used to produce and express recombinant proteins/enzymes; these systems are used in metabolism studies baculovirus-insect recombinant protein production host cell DIDEO:00000169 a cultured cell of the species Escherichia coli that bears a recombinant protein production host role John Judkins Prokaryotic in vitro system used to produce and express recombinant proteins/enzymes; these systems are used in metabolism studies E. coli recombinant protein production host cell DIDEO:00000170 a measurement datum that describes the decrease in activity of a transporter or enzyme in the presence of a compound from activity in the control experiment John Judkins % inhibition Percent inhibition: the percent decrease in activity of a transporter or enzyme in the presence of a compound from activity in the control experiment percent inhibition DIDEO:00000171 a hydroxylation that has midazolam as input and 1'-hydroxymidazolam as output John Judkins Hydroxylation of midazolam at the 1' position to form 1'-hydroxymidazolam;probe substrate of CYP3A4 activity (used to measure CYP3A4 activity) midazolam 1'-hydroxylation DIDEO:00000172 a deethylation that has 7-ethoxyresorufin as input and resorufin as output John Judkins O-deethylation of 7-Ethoxyresorufin to form resorufin; probe substrate of CYP1A activity 7-ethoxyresorufin O-deethylation DIDEO:00000173 a dehydrogenation that has nifedipine as input and has dehydronifedipine as output John Judkins Dehydrogenation of nifedipine to dehydronifedipine;probe substrate of CYP3A4 activity (used to measure CYP3A4 activity) nifedipine dehydrogenation DIDEO:00000174 a hydroxylation that has bufuralol as input and 1'-hydroxybufurolol as output John Judkins 1'-hydroxylation of bufuralol to form 1'-hydroxybufurolol; probe substrate of CYP2D6 activity bufuralol 1'-hydroxylation DIDEO:00000175 a hydroxylation that has omeprazole as input and has 5-hydroxyomeprazole as output John Judkins Hydroxylation of omeprazole at the 5 position to form 5-hydroxyomeprazole; probe substrate of CYP2C19 activity omeprazole 5-hydroxylation DIDEO:00000176 a hydroxylation that has bupropion as input and 1-hydroxybupropion as output John Judkins Hydroxylation of bupropion at the 1 position to form 1-hydroxybupropion; probe substrate of CYP2B6 activity bupropion hydroxylation DIDEO:00000177 a hydroxylation that has paclitaxel as input and 6-alpha-hydroxypaclitaxel as output John Judkins Hydroxylation of paclitaxel at the 6-alpha position to form 6-alpha-hydroxypaclitaxel; probe substrate of CYP2C8 activity paclitaxel 6-alpha hydroxylation DIDEO:00000178 a deethylation that has phenacetin as input and acetaminophen as output John Judkins O-deethylation of phenacetin to form acetaminophen; probe substrate of CYP1A2 activity phenacetin O-deethylation DIDEO:00000179 a hydroxylation that has coumarin as input and has 7-hydroxycoumarin as output John Judkins Hydroxylation of coumarin at the 7 position to form 7-hydroxycoumarin; probe substrate of CYP2A6 activity coumarin 7-hydroxylation DIDEO:00000180 a hydroxylation that has testosterone as input and 6-beta-hydroxytestosterone as output John Judkins Hydroxylation of testosterone at the 6-beta position to form 6-beta-hydroxytestosterone; probe substrate of CYP3A4 activity testosterone 6-beta-hydroxylation DIDEO:00000181 a demethylation that has dextromethorphan as input and has dextrorphan as output John Judkins O-demethylation of dextromethorphan to form dextrorphan;probe substrate of CYP2C9 activity dextromethorphan O-demethylation DIDEO:00000182 a hydroxylation that has diclofenac as input and 4'-hydroxydiclofenac as output John Judkins Hydroxylation of diclofenac to form 4'-hydroxydiclofenac; probe substrate of CYP2C9 activity diclofenac 4'-hydroxylation DIDEO:00000183 a target of material addition role that is borne by a cultured cell and, if realized, is realized in recombinant protein production John Judkins An in vitro system that uses a combination of genetic pieces typically in a plasmid that is incorporated into a host cell which is used to produce the protein of interest recombinant protein production host role DIDEO:00000184 a count of administrations of a substance to an organism over a duration of 24 hours John Judkins the frequency of administration of the precipitant during the day number of doses in a day DIDEO:00000185 an immortal human liver-derived cell line cell that is part of the Hep G2 cell line John Judkins HepG2 was derived from a liver hepatocellular carcinoma of a 15 year-old Caucasian male. HepG2 cells secrete a variety of major plasma proteins. They are a suitable in vitro model system for the study of polarized human hepatocytes, with high degree of morphological and functional differentiation in vitro. It can be used for hepatic metabolism, transport, and toxicity evaluations in vitro. It was tested negative for HBV. Hep G2 cell DIDEO:00000186 a CHO cell that is a specified output of a transfection John Judkins Chinese hamster ovary cells transfected with human transporter DNA; an in vitro model used to study transporters CHO transfected cell DIDEO:00000187 a Hep G2 cell that has a target of material addition role and is a specified input of a transfection John Judkins Well characterized immortalized human liver cancer cell line used as an in vitro model system of metabolism or transport Hep G2 transfected cell DIDEO:00000188 a Caco-2 cell that is a specified output of a gene knockout that has specified input siRNA John Judkins Caco-2 cells treated with siRNA designed to down-regulate specific enzymes or transporters siRNA knockout Caco-2 cell DIDEO:00000189 a 293-derived cell that is a specified output of a transfection John Judkins HEK293 transfected cell Immortalized human kideny cells transfected/transduced with a transporter or enzyme; an in vitro model overexpressing transporter or enzyme of interest; used for transporter or metabolism assays 293 transfected cell DIDEO:00000190 a count of human beings from whom originate hepatocytes to be used in an investigation John Judkins Number of Livers Number of individual liver samples used number of liver donors DIDEO:00000191 a hydroxylation that has diclofenac as input and 4'-hydroxydiclofenac as output Hydroxylation of diclofenac to form 4'-hydroxydiclofenac; probe substrate of CYP2C9 activity diclofenac 4'-hydroxylation DIDEO:00000192 a hydroxylation that has tolbutamide as input and 4-hydroxytolbutamide as output John Judkins Methyhydroxylation of tolbutamide to form hydroxytolbutamide;probe substrate of CYP2D6 activity tolbutamide methylhydroxylation DIDEO:00000193 a glucuronosylation that has estradiol as input and has estradiol-3-glucuronide as output John Judkins Glucuronidation of estradiol to estradiol-3-glucuronide; probe substrate of UGT1A1 activity (used to measure UGT1A1 activity) estradiol glucuronosylation DIDEO:00000194 an MDCK cell that is the specified output of a transfection John Judkins Dog cells transfected with human transporter; an in vitro model used to study transporters MDCK transfected cell DIDEO:00000196 a glucuronosylation that has lamotrigine as input and has lamotrigine glucoronide as output John Judkins lamotrigine glucuronidation Glucuronidation of lamotrigine; probe substrate of UGT1A4 activity (used to measure UGT1A4 activity) lamotrigine glucuronosylation DIDEO:00000197 a hydroxylation that has chlorzoxazone as input and 6-hydroxychlorzoxazone as output John Judkins Hydroxylation of chlorzoxazone at the 6 position to form 6-hydroxychlorzoxazone; probe substrate of CYP2E1 activity chlorzoxazone 6-hydroxylation DRON:00000005 a material entity (1) containing at least one scattered molecular aggregate as part (the active ingredient) and (2) that is the bearer of a clinical drug role William Hogan http://purl.obolibrary.org/obo/dron.owl William Hogan drug product DRON:00000028 active ingredient role a role of a scattered molecular aggregate that is part of a drug product that is realized by (1) administration of the drug to an organism followed by (2) some change in the structure or functioning of some part of the organism William R. Hogan http://purl.obolibrary.org/obo/dron.owl active ingredient DRON:00000030 role of a scattered molecular aggregate a role borne by a scattered molecular aggregate and realized by its grains participating in one or more processes William R. Hogan http://purl.obolibrary.org/obo/dron.owl role of scattered molecular aggregate DRON:00000031 administration of a drug product to an organism a treatment that has as participants an extended organism and a drug product and that results in part of the drug product being located in the extended organism William R. Hogan http://purl.obolibrary.org/obo/dron.owl drug administration ERO:0000630 A primer. Reagent that is a polymer comprised of nucleotides, each of which consists of three components: a nitrogenous heterocyclic base, which is either a purine or a pyrimidine; a pentose sugar; and a phosphate group. PERSON: Melissa Haendel http://en.wikipedia.org/wiki/Nucleic_acid http://purl.obolibrary.org/obo/ero.owl Placeholder for class to be imported from the Reagent Ontology (ReO). nucleic acid reagent ERO:0000923 Characterization of the phenotype is often done in transgenic or knockout mice. An organismal assay that involves characterization of a phenotype; any observable characteristic or trait of an organism: such as its morphology, development, biochemical or physiological properties, behavior, and products of behavior (such as a bird's nest). Phenotypes result from the expression of an organism's genes as well as the influence of environmental factors and the interactions between the two. PERSON: Nicole Vasilevsky http://en.wikipedia.org/wiki/Phenotype http://purl.obolibrary.org/obo/ero.owl phenotype characterization ERO:0001202 A riboprobe. A reagent that is a polymer comprised of RNA nucleotides. PERSON: Matthew Brush PERSON: Matthew Brush http://purl.obolibrary.org/obo/ero.owl Placeholder for class to be imported from the Reagent Ontology (ReO). RNA reagent ERO:0001205 An RNA reagent consisting of a short, linear RNA polymer, typically with 100 or fewer bases. PERSON: Matthew Brush RNA oligo PERSON: Matthew Brush http://purl.obolibrary.org/obo/ero.owl Placeholder for class to be imported from the Reagent Ontology (ReO). RNA oligonucleotide ERO:0001206 An RNA interference reagent used to silence expression of a target gene in cells, through the RNA interference pathway. PERSON: Matthew Brush RNAi oligonucleotide PERSON: Matthew Brush http://purl.obolibrary.org/obo/ero.owl Placeholder for class to be imported from the Reagent Ontology (ReO). RNA interference oligonucleotide ERO:0001209 An RNA interference oligonucleotide capable of silencing expression of a target gene through the RNAi pathway. siRNAs are synthesized as single-stranded molecules, typically 19-25 nucleotides in length, and paired with complementary sequences to form duplexes that serve as substrates for cellular RNAi processing machinery. PERSON: Matthew Brush siRNA oligo MHB, http://www.sigmaaldrich.com/life-science/custom-oligos/sirna-oligos.html http://purl.obolibrary.org/obo/ero.owl Placeholder for class to be imported from the Reagent Ontology (ReO). siRNA oligonucleotide Body substance in liquid state contained in the lumen of arterial and venous trees, blood capillary and the cardiac chambers; constitutes the liquid phase of blood. http://purl.obolibrary.org/obo/fma.owl Blood plasma fma FMA:62970 Portion of plasma FMA:62970 Material anatomical entity in a gaseous, liquid, semisolid or solid state, with or without the admixture of cells and biological macromolecules; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures. Examples: saliva, semen, cerebrospinal fluid, respiratory air, urine, feces, blood, plasma, lymph. http://purl.obolibrary.org/obo/fma.owl Body substance fma FMA:9669 Portion of body substance FMA:9669 GAZ:00000448 geographic location A reference to a place on the Earth, by its name or by its geographical location. geographic location 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. http://purl.obolibrary.org/obo/go.owl GO:0005554 molecular function molecular_function GO:0003674 Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. Note that when this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code ND, no data, is used to indicate this. molecular_function GO:0003674 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. http://purl.obolibrary.org/obo/go.owl Wikipedia:Enzyme enzyme activity molecular_function GO:0003824 catalytic activity GO:0003824 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. http://purl.obolibrary.org/obo/go.owl GO:0008372 NIF_Subcellular:sao-1337158144 NIF_Subcellular:sao1337158144 cell or subcellular entity cellular component cellular_component subcellular entity GO:0005575 Note that, in addition to forming the root of the cellular component ontology, this term is recommended for use for the annotation of gene products whose cellular component is unknown. Note that when this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code ND, no data, is used to indicate this. cellular_component GO:0005575 The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein. http://purl.obolibrary.org/obo/go.owl GO:0015457 GO:0015460 small molecule transport solute:solute exchange biological_process auxiliary transport protein activity transport accessory protein activity GO:0006810 transport GO:0006810 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. http://purl.obolibrary.org/obo/obi.owl biological_process The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation. http://purl.obolibrary.org/obo/go.owl Wikipedia:Metabolism metabolism metabolic process resulting in cell growth metabolism resulting in cell growth biological_process GO:0008152 Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions. metabolic process GO:0008152 Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. http://purl.obolibrary.org/obo/go.owl down regulation of metabolic process down-regulation of metabolic process downregulation of metabolic process negative regulation of metabolism inhibition of metabolic process biological_process GO:0009892 negative regulation of metabolic process GO:0009892 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. http://purl.obolibrary.org/obo/go.owl cellular_component GO:0019814 Note that an immunoglobulin complex has the function of antigen binding if a suitable antigen is available. immunoglobulin complex GO:0019814 Any process that modulates the activity of a transporter. http://purl.obolibrary.org/obo/go.owl biological_process GO:0032409 regulation of transporter activity GO:0032409 Any process that stops or reduces the activity of a transporter. http://purl.obolibrary.org/obo/go.owl down regulation of transporter activity down-regulation of transporter activity downregulation of transporter activity inhibition of transporter activity biological_process GO:0032410 negative regulation of transporter activity GO:0032410 Any process that modulates the frequency, rate or extent of any process in which a cell, a substance, or a cellular entity is transported to, or maintained in, a specific location. http://purl.obolibrary.org/obo/go.owl regulation of localisation biological_process GO:0032879 regulation of localization GO:0032879 A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which the constituent parts function together. http://purl.obolibrary.org/obo/go.owl macromolecule complex cellular_component GO:0032991 macromolecular complex GO:0032991 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. http://purl.obolibrary.org/obo/go.owl Wikipedia:Antibody antibody cellular_component GO:0042571 Note that an immunoglobulin complex has the function of antigen binding if a suitable antigen is available. immunoglobulin complex, circulating GO:0042571 A stable 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. http://purl.obolibrary.org/obo/go.owl Wikipedia:Protein_complex protein-protein complex cellular_component GO:0043234 A protein complex in this context is meant as a stable set of interacting proteins which can be co-purified by an acceptable method, and where the complex has been shown to exist as an isolated, functional unit in vivo. Acceptable experimental methods include stringent protein purification followed by detection of protein interaction. The following methods should be considered non-acceptable: simple immunoprecipitation, pull-down experiments from cell extracts without further purification, colocalization and 2-hybrid screening. Interactions that should not be captured as protein complexes include: 1) enzyme/substrate, receptor/ligand or any similar transient interactions, unless these are a critical part of the complex assembly or are required e.g. for the receptor to be functional; 2) proteins associated in a pull-down/co-immunoprecipitation assay with no functional link or any evidence that this is a defined biological entity rather than a loose-affinity complex; 3) any complex where the only evidence is based on genetic interaction data; 4) partial complexes, where some subunits (e.g. transmembrane ones) cannot be expressed as recombinant proteins and are excluded from experiments (in this case, independent evidence is necessary to find out the composition of the full complex, if known). Interactions that may be captured as protein complexes include: 1) enzyme/substrate or receptor/ligand if the complex can only assemble and become functional in the presence of both classes of subunits; 2) complexes where one of the members has not been shown to be physically linked to the other(s), but is a homologue of, and has the same functionality as, a protein that has been experimentally demonstrated to form a complex with the other member(s); 3) complexes whose existence is accepted based on localization and pharmacological studies, but for which experimental evidence is not yet available for the complex as a whole. protein complex GO:0043234 The chemical reactions and pathways by which individual cells transform chemical substances. http://purl.obolibrary.org/obo/go.owl cellular metabolism biological_process intermediary metabolism GO:0044237 cellular metabolic process GO:0044237 Any process that activates or increases the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. http://purl.obolibrary.org/obo/go.owl GO:0043119 positive regulation of physiological process up regulation of biological process up-regulation of biological process upregulation of biological process activation of biological process stimulation of biological process biological_process GO:0048518 positive regulation of biological process GO:0048518 Any process that stops, prevents, or reduces the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. http://purl.obolibrary.org/obo/go.owl GO:0043118 down regulation of biological process down-regulation of biological process downregulation of biological process negative regulation of physiological process inhibition of biological process biological_process GO:0048519 negative regulation of biological process GO:0048519 Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. http://purl.obolibrary.org/obo/go.owl GO:0050791 regulation of physiological process biological_process GO:0050789 regulation of biological process GO:0050789 Any process that modulates the frequency, rate or extent of the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. http://purl.obolibrary.org/obo/go.owl biological_process GO:0051049 regulation of transport GO:0051049 Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. http://purl.obolibrary.org/obo/go.owl down regulation of transport down-regulation of transport downregulation of transport inhibition of transport biological_process GO:0051051 negative regulation of transport GO:0051051 Any process in which a cell, a substance, or a cellular entity, such as a protein complex or organelle, is transported, tethered to or otherwise maintained in a specific location. In the case of substances, localization may also be achieved via selective degradation. http://purl.obolibrary.org/obo/go.owl establishment and maintenance of localization establishment and maintenance of position localisation establishment and maintenance of cellular component location establishment and maintenance of substance location establishment and maintenance of substrate location biological_process GO:0051179 localization GO:0051179 Any process that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation. http://purl.obolibrary.org/obo/go.owl establishment of localisation biological_process GO:0051234 establishment of localization GO:0051234 Any process that modulates a measurable attribute of any biological process, quality or function. http://purl.obolibrary.org/obo/go.owl regulation biological_process GO:0065007 biological regulation GO:0065007 The directed movement of some substance from outside of a cell into the cytoplasmic compartment. This may occur via transport across the plasma membrane or via endocytosis. http://purl.obolibrary.org/obo/go.owl uptake biological_process GO:0098657 import into cell GO:0098657 The directed movement of some substance from outside of a cell, across the plasma membrane and into the cytosol. http://purl.obolibrary.org/obo/go.owl biological_process GO:0098739 import across plasma membrane GO:0098739 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 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 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 obsolete_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 true IAO:0000019 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 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://github.com/information-artifact-ontology/IAO/issues/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 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 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 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 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 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 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 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 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 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 _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 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 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 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 background 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 experimental experimental procedures experimental section methods 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 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 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 contributions by the authors 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 acknowledgments 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 additional information appendix supplemental information supplementary material supporting information 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 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 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 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 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 A scalar measurement datum that is the result of measurement of length quality Alan Ruttenberg length measurement datum IAO:0000409 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 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 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 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 https://github.com/information-artifact-ontology/IAO/issues/59 postal address IAO:0000429 email address Alan Ruttenberg 1/3/2012 - Provisional id, see issue at https://github.com/information-artifact-ontology/IAO/issues/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 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 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 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 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 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 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 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 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 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 IAO:0000584 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 https://github.com/information-artifact-ontology/IAO/issues/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 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 https://github.com/information-artifact-ontology/IAO/issues/80 software method IAO:0000592 A software module is software composed of a collection of software methods. PERSON: Melanei Courtot PERSON: Michel Dumontier https://github.com/information-artifact-ontology/IAO/issues/80 software module IAO:0000593 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 https://github.com/information-artifact-ontology/IAO/issues/80 software library IAO:0000594 A software application is software that can be directly executed by some processing unit. PERSON: Melanie Courtot PERSON: Michel Dumontier https://github.com/information-artifact-ontology/IAO/issues/80 software application IAO:0000595 A software script is software whose instructions can be executed using a software interpreter. PERSON: Melanie Courtot PERSON: Michel Dumontier https://github.com/information-artifact-ontology/IAO/issues/80 software script IAO:0000605 abbreviation textual entity From Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/): BAC: Bacterial artificial chromosome; CR: Calretinin; GFAP: Glial fibrillary acidic protein; MAP: Microtubule-associated protein; MRI: Magnetic resonance imaging; NSC: Neural stem cell; PDA: Patent ductus arteriosus; PMG: Polymicrogyria; PNH: Periventricular nodular heterotopia; VSD: Ventricular septal defect. A textual entity listing abbreviations and their expansions that are used in a document. PERSON: Bill Baumgartner abbreviation textual entity IAO:0000606 abbreviations section The section labelled 'abbreviations' in a typical scientific journal article. A part of a document where abbreviations and their long-forms used within the document are listed. PERSON: Bill Baumgartner abbreviations abbreviations list abbreviations used list of abbreviations list of abbreviations used abbreviations section IAO:0000607 author information section The section labelled 'author information' in a typical scientific journal article, e.g. in Takon. Ann Gen Psychiatry. 2011; 10: 25. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3204268/) A part of a document about the authors that provides biographical information and may discuss how the authors' professional experiences are relevant to the work described in the document. PERSON: Bill Baumgartner author information authors’ information author information section IAO:0000608 author information textual entity From Takon. Ann Gen Psychiatry. 2011; 10: 25. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3204268/): IT [the author] is the lead paediatrician for ADHD services in East Hertfordshire, UK, where she runs a weekly joint ADHD clinic with the Child and Adolescent psychiatrist and works within an ADHD specialist team. IT also sees children with other neurodisability issues who may have comorbid ADHD, where the presentation may be more complex and challenging to manage. IT has vast experience in managing children with complex ADHD. She has 18 years of experience in paediatrics and also has extensive experience in the use of psychopharmacologic agents in managing children with ADHD. A textual entity expression information about an author of a document. This information may include biographical information and may discuss how the authors' professional experiences are relevant to the work described in the document. PERSON: Bill Baumgartner author information textual entity IAO:0000609 author summary section The section labelled 'synopsis' in a typical scientific journal article, e.g. in Pendse et al. BMC Genomics. 2013; 14: 136. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3608171/) A part of a document, distinct from the abstract, that describes the significance and broader context of the document content. The author summary is often written in a non-technical manner and is aimed at both scientists and non-scientist readers. PERSON: Bill Baumgartner author summary summary synopsis Article submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines) author summary section IAO:0000610 author summary textual entity From Pendse et al. BMC Genomics. 2013; 14: 136. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3608171/): The search for genetic risk factors for common human diseases often relies on the use of linkage and association studies to establish correlation between genomic markers and disease risk. These studies require additional functional evaluation of candidate genes, including their possible interaction with diet and environment. The number of candidate genes is typically large and the development of appropriate genetic tools in mammalian systems is slow. By contrast, large-scale genetic screens, using widely available genetic tools, are routinely conducted in the fruit fly Drosophila melanogaster. In this study, we used Drosophila to screen candidate genes identified in human genome-wide scans as associated with risk of metabolic abnormalities such as type 2 diabetes. We show that a number of human candidate genes have fly orthologs that play an important role in Drosophila tolerance to high dietary sucrose. We further explored some of the specific metabolic abnormalities that can result when these genes’ activities are reduced in flies, focusing on a gene we call dHHEX (CG7056), the fly ortholog of human HHEX. A textual entity, distinct from the abstract, that describes the significance and broader context of the document content. The author summary is often written in a non-technical manner and is aimed at both scientists and non-scientist readers, e.g as described in the article submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines). PERSON: Bill Baumgartner Article submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines). author summary textual entity IAO:0000611 availability section The section labelled 'availability and requirements' in a typical scientific journal article, e.g. Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/). A part of a document about a resource described in the document, e.g. software, that describes where and/or how that resource can be obtained. PERSON: Bill Baumgartner availability availability section IAO:0000612 availability textual entity From Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/): Project home page:http://krux.googlecode.com A textual entity expressing the location of a resource, e.g. software, or the manner in which a resource can be obtained. PERSON: Bill Baumgartner availability textual entity IAO:0000613 case report section The section labelled 'case report' in a typical scientific journal article, e.g. in Taglia et al. Acta Myol. 2012 Dec; 31(3): 201–203. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3631801/) A part of a document about the medical history of a specific patient as it relates to the topic of the document. PERSON: Bill Baumgartner case presentation case report case report section IAO:0000614 case report textual entity Excerpt from Taglia et al. Acta Myol. 2012 Dec; 31(3): 201–203. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3631801/): The patient is a 50-year-old man. His medical history was not contributory. At the age of 37 years, he complained of persistent fatigue and dyspnoea even for modest efforts and oedema of lower limbs. The patient was examined at the department of internal medicine of the local hospital, and hospitalised with a diagnosis of dilated cardiomyopathy probably consequence of a myocarditis process. Soon after he was transferred to the cardiologic department of the regional hospital, and pharmacologically treated for heart failure and pulmonary hypertension. A textual entity that expresses a detailed account of a portion of the medical history for a specific patient. PERSON: Bill Baumgartner case report textual entity IAO:0000615 conclusion section The section labelled 'conclusion' in a typical scientific journal article. A part of a document used to summarize the findings discussed in the document. The conclusion section is typically found near the end of a document. PERSON: Bill Baumgartner concluding remarks conclusion conclusions findings summary conclusion section IAO:0000616 conflict of interest section The section labelled 'conflict of interest statement' in a typical scientific journal article. A part of a document used to declare any competing interests regarding the authors and/or funding organization for the work described in the document. PERSON: Bill Baumgartner competing interests conflict of interest conflict of interest statement declaration of competing interests disclosure of potential conflicts of interest conflict of interest section IAO:0000617 conflict of interest statement SD [an author] is a Merck employee and Merck is the sponsor of this study. [Taken from 'Effects of obstructive sleep apnoea risk on postoperative respiratory complications: protocol for a hospital-based registry study' Shin et al. 2016 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4735131/)] A textual entity that expresses a situation involving one or more of the authors, or the funding source of a document whereby the authors or funding source stand to potentially gain (typically financially) from the results reported in the document. PERSON: Bill Baumgartner conflict of interest textual entity IAO:0000618 consent section The section labelled 'consent' in a typical scientific journal article, e.g. Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/) A part of a document about the consent process that was used to enroll patients in a study. PERSON: Bill Baumgartner consent consent section IAO:0000619 consent textual entity From Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/): Written informed consent was obtained from the patient’s parents for publication of this Case report and any accompanying images. A copy of the written consent is available for review by the Editor-in chief of this journal. A textual entity that documents the consenting process used to enroll patients in a study. PERSON: Bill Baumgartner consent textual entity IAO:0000620 ethical approval section The section labelled 'ethical approval' in a typical scientific journal article. A part of a document about the governance body responsible for approving the work discussed in a document on an ethical basis. PERSON: Bill Baumgartner ethical approval ethical approval section IAO:0000621 ethical approval textual entity From McLean et al. Br J Gen Pract. 2014 Jul; 64(624): e440–e447 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4073730/): The NHS National Research Ethics Service had previously approved the use of these anonymised data for research purposes and this analysis did not require independent review. A textual entity that documents the ethical approval of some study design. PERSON: Bill Baumgartner ethical approval textual entity IAO:0000622 figures section The section labelled 'figures' in a typical scientific journal article. A part of a document that contains one or more figures. PERSON: Bill Baumgartner figures figures section IAO:0000623 funding source declaration section The section labelled 'funding' in a typical scientific journal article. A part of a document used to detail information regarding the source of funding used in support of the generation of the document content. PERSON: Bill Baumgartner funding funding information funding sources funding statement funding/support source of funding sources of funding funding source declaration section IAO:0000624 funding souce declaration textual entity From Stephan et al. Accid Anal Prev. 2011 May; 43(3): 1062–1067. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3062852/): This study was supported by the International Collaborative Research Grants Scheme with joint grants from the Wellcome Trust UK (GR071587MA) and the Australian NHMRC (268055). The funding sources played no role in study design, data collection, analysis or interpretation, writing the report, or the decision to submit the paper for publication. A textual entity documenting the source of funding that supported some study. PERSON: Bill Baumgartner funding source declaration textual entity IAO:0000625 future directions section The section labelled 'future directions' in a typical scientific journal article. A part of a document detailing extensions of the described work that may be implemented at some future point in time. PERSON: Bill Baumgartner future challenges future considerations future developments future directions future outlook future perspectives future plans future prospects future research future research directions future studies future work future directions section IAO:0000626 future directions textual entity Excerpt from Wang and Li. Acta Pharmacol Sin. 2016 Jan; 37(1): 25–33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4722976/): In the future, several questions will need to be resolved regarding the physiological assembly of KCNQ channels and their functional implications in complex neural circuits. First, we still lack sufficiently selective inhibitors and activators among the KCNQ family members. A textual entity expressing ideas regarding future work relevant to work described in a document that could be done. PERSON: Bill Baumgartner future directions textual entity IAO:0000627 genome announcement section The section labelled 'genome announcement' in a typical scientific journal article, e.g. in Kim et al. J Bacteriol. 2011 Oct; 193(19): 5537. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3187466/) A document part announcing the publication of a novel draft genome sequence. PERSON: Bill Baumgartner genome announcement genome announcement section IAO:0000628 genome announcement textual entity Excerpt from Kim et al. J Bacteriol. 2011 Oct; 193(19): 5537. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3187466/): Here we report the genome sequence of Lactobacillus malefermentans KCTC 3548, which we obtained using a whole-genome shotgun strategy (4) with Roche 454 GS (FLX Titanium) pyrosequencing (257,559 reads totaling ∼89.8 Mb; ∼45-fold coverage of the genome) at the Genome Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB). A textual entity that describes the generation and public release of a novel, draft genome sequence. PERSON: Bill Baumgartner genome announcement textual entity IAO:0000629 keyword textual entity From: Fu and Lin. Identification of gene-oriented exon orthology between human and mouse. BMC Genomics. 2012; 13(Suppl 1): S10. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3303729/): Exon orthology; alternative splicing; exon duplication; intron-exon structure. A textual entity listing keywords indicating the major theme(s) of a document. PERSON: Bill Baumgartner keyword textual entity IAO:0000630 keywords section The section labelled 'keywords' in a typical scientific journal article. A part of a document where keywords selected by the author to categorize the major theme(s) of a document are listed. PERSON: Bill Baumgartner keywords keywords section IAO:0000631 study limitations section The section labelled 'limitations' in a typical scientific journal article. A part of a document about biases or short comings related to the study design and execution. PERSON: Bill Baumgartner limitations study limitations Author guidelines published by The Society for Academic Emergency Medicine. (http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1553-2712/homepage/ForAuthors.html) study limitations section IAO:0000632 study limitations textual entity Excerpt from the Limitations section of Fermann et al 2015, Acad Emerg Med. 2015 Mar; 22(3): 299–307 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4405051/). Owing to the nature of a post hoc study, any significant values must be interpreted with caution. In the current analysis, no multiple testing was conducted and p-values remain unadjusted. Moreover, a selection bias arising from the randomized open-label design of the original EINSTEIN PE study cannot be ruled out. A textual entity addressing a shortcoming or bias of a study design or execution. PERSON: Bill Baumgartner Author guidelines published by The Society for Academic Emergency Medicine. (http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1553-2712/homepage/ForAuthors.html) study limitations textual entity IAO:0000633 materials section The section labelled 'materials' in a typical scientific journal article, e.g. Nguyen et al. BMC Bioinformatics. 2010; 11: 279. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2889936/) A part of a document about the materials required to reproduce the content of the document. PERSON: Bill Baumgartner materials materials section IAO:0000634 notes section The section labelled 'notes' in a typical scientific journal article, e.g. McLean et al. Br J Gen Pract. 2014 Jul; 64(624): e440–e447 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4073730/): A part of a document containing typically short notes about the document itself and/or the authors. Often the notes section contains subsections related to funding, competing interests, ethical approval, etc. PERSON: Bill Baumgartner footnotes notes notes section IAO:0000635 patients section The section labelled 'patients' in a typical scientific journal article, e.g. in Citak et al. Acta Orthop. 2013 Jun; 84(3): 326–327. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3715825/) A part of a document about the patients that participated in a study. PERSON: Bill Baumgartner patients section IAO:0000636 patients textual entity Excerpt from Citak et al. Acta Orthop. 2013 Jun; 84(3): 326–327. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3715825/): Between January 1996 and February 2012, we treated 4 patients with interprosthetic femoral fractures (3 of them women) (Figure 2) using a custom-made interposition device (Waldemar Link GmbH, Hamburg, Germany) (Figure 1). Mean age was 74 (59–86) years. The fractures occurred mean 18 (13–28) years after primary THA and mean 14 (10–17) years after primary TKA. At the latest follow-up, after mean 8 (0.5–16) years, revision surgery with a total femur replacement was required in 1 case due to aseptic loosening. No other complications requiring revision surgery occurred. A textual entity expressing information regarding the patients used in a study. PERSON: Bill Baumgartner patients textual entity IAO:0000637 pre-publication history section The section labelled 'pre-publication history' in a typical scientific journal article, e.g. in Xiao et al. BMC Anesthesiol. 2013; 13: 33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4016475/) A part of the document about the publication history of a document. This section typically details dates of document submission to a journal and dates of any re-submissions as well as reviewer comments and responses to reviewers by the authors. PERSON: Bill Baumgartner notice of republication pre-publication history pre-publication history section IAO:0000638 pre-publication history textual entity From Xiao et al. BMC Anesthesiol. 2013; 13: 33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4016475/): The pre-publication history for this paper can be accessed here: http://www.biomedcentral.com/1471-2253/13/33/prepub A textual entity that expresses the pre-publication history (submission dates, reviewer comments, etc) for a document, often including a hyperlink to a web page detailing the information. PERSON: Bill Baumgartner pre-publication history textual entity IAO:0000639 related work section The section labelled 'related work' in a typical scientific journal article, e.g. Žitnik and Zupan. Bioinformatics. 2015 Jun 15; 31(12): i230–i239. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4542780/) A part of a document about work in other publications that is relevant to the content of the document. PERSON: Bill Baumgartner related literature related work related work section IAO:0000640 related work textual entity Excerpt from Žitnik and Zupan. Bioinformatics. 2015 Jun 15; 31(12): i230–i239. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4542780/): Our work presented here is similar in spirit to our recently developed methodology for data fusion via collective matrix factorization (Žitnik and Zupan, 2015). A textual entity that discusses work from other publications and expresses their relevancy to the content of a document. PERSON: Bill Baumgartner related work textual entity IAO:0000641 requirements section The section labelled 'availability and requirements' in a typical scientific journal article, e.g. Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/). A part of a document about a resource described in the document, e.g. software, that describes the requirements necessary to use the resource, e.g. operating systems, hardware, etc. in the case of a software resource. PERSON: Bill Baumgartner requirements requirements section IAO:0000642 requirements textual entity From Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/): • Operating systems: Platform independent • Programming language: Matlab, R, Python • Other requirements: None • License: GNU GPL v3 • Any restrictions to use by non-academics: None A textual entity that expresses the requirements necessary to use a resource, e.g. software. PERSON: Bill Baumgartner requirements textual entity IAO:0000643 statistical analysis textual entity From Mondo et al. Cardiovasc J Afr. 2013 Mar; 24(2): 28–33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3734881/): Data were captured into EPI-DATA (version 3.1), cleaned and then exported to Stata version 10 for analysis. Continuous variables were summarised as mean (± standard deviation) and median (inter-quartile range), and presented in the tables. Categorical data were analysed using frequency and percentages, and results are presented in frequency tables and bar charts. Test of significance (p-value) was determined using the chi-square test. A p-value of less than 0.05 was considered significant. A textual entity documenting statistical analysis tools and techniques employed. PERSON: Bill Baumgartner statistical analysis textual entity IAO:0000644 statistical analysis section The section labelled 'statistical analysis' in a typical scientific journal article, e.g. Mondo et al. Cardiovasc J Afr. 2013 Mar; 24(2): 28–33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3734881/) A part of the document used to describe the statistical methodologies employed in the work presented in the document. PERSON: Bill Baumgartner statistical analysis statistical analysis section IAO:0000645 tables section The section labelled 'tables' in a typical scientific journal article. A part of a document that contains one or more tables. PERSON: Bill Baumgartner tables tables section IAO:0000650 database extract, transform, and load process A planned process which takes as input a database and fills another database by extracting concretizations of information entities from the first, transforming them, and loading the transformed concretizations into the second. Alan Ruttenberg 12/21/16: Maybe this definition instead: A planned process which takes as input a database and copies concretizations from the first, optionally transforms then copies the result to the second Alan Ruttenberg 12/21/16: We don't define database in IAO, currently, as the bare word is ambiguous. Reasonable interpretations of the word might be the material entity, an information structure, an information content entity. However this definition commits, at least, to there being some material thing which bear concretizations of information entities and that there are new concretizations created during the process. We consider the ETL process in terms of information entities rather than the concretizations. No committment is made as to whether the specified output. PERSON:Alan Ruttenberg ETL WEB:https://en.wikipedia.org/wiki/Extract,_transform,_load database extract, transform, and load process IDO:0100872 A role that inheres in a protein or a compound upon which enzyme catalyzes. It is realized in the enzymatic reaction processes, where the molecules at the beginning of the process, called substrates, are converted into different molecules, called products. enzyme substrate role INO:0000102 a biological interaction that uses the information from a gene to synthesize a functional gene product. YH, ZX http://purl.obolibrary.org/obo/in/ino.owl express, expressed, expresses, expressing, expression, expressions gene expression INO:0000114 a gene expression that has increased volume. YH, ZX increased gene expression overexpression http://purl.obolibrary.org/obo/in/ino.owl hyper-expression, hyperactivate, hyperactivated, hyperactivates, hyperactivation, hyperexpression, overexpression overexpression Formation of a covalent bond between a substrate and a glucuronosyl group. http://purl.obolibrary.org/obo/mop.owl glucuronosylation MOP:0000156 has_participant: CHEBI:24303 glucuronosylation MOP:0000156 A process in which at least one of the participants is a molecule. http://purl.obolibrary.org/obo/mop.owl MOP:0000543 TODO: needs work, formal definition, etc. molecular process MOP:0000543 An oxidation process that involves the removal of adjacent hydrogen atoms, resulting in an increase of bond order. http://purl.obolibrary.org/obo/mop.owl batchelorc 2009-06-05T04:54:48Z MOP:0000590 dehydrogenation MOP:0000590 Formation of a covalent bond between a substrate and a hydroxy group. http://purl.obolibrary.org/obo/mop.owl MOP:0000673 hydroxylation MOP:0000673 http://purl.obolibrary.org/obo/mop.owl MOP:0000779 formation of covalent bond MOP:0000779 http://purl.obolibrary.org/obo/mop.owl MOP:0000780 breaking of covalent bond MOP:0000780 Breaking of a covalent bond between a substrate and a methyl group. http://purl.obolibrary.org/obo/mop.owl MOP:0001364 has_participant: CHEBI:32875 demethylation MOP:0001364 Breaking of a covalent bond between a substrate and an ethyl group. http://purl.obolibrary.org/obo/mop.owl de-ethylation MOP:0001385 has_participant: CHEBI:37807 deethylation MOP:0001385 NCBITaxon:451864 http://purl.obolibrary.org/obo/doid.owl Dikarya NCBITaxon:562 http://purl.obolibrary.org/obo/vo.owl NCBITaxon:1637691 NCBITaxon:662101 NCBITaxon:662104 GC_ID:11 PMID:10319482 E. coli Escherichia/Shigella coli ncbi_taxonomy Bacillus coli Bacterium coli Bacterium coli commune Enterococcus coli Escherchia coli Eschericia coli Escherichia coli NCBITaxon:8355 African clawed frog Bufo laevis Xenopus laevis (Daudin, 1802) Xenopus leavis clawed frog common platanna platanna http://purl.obolibrary.org/obo/ero.owl Xenopus laevis NCBITaxon:9606 Homo sapiens human human being man http://purl.obolibrary.org/obo/obi.owl Homo sapiens OAE:0000001 a pathological bodily process that occurs after a medical intervention. An adverse event is likely caused by the medical intervention; however, such a causal association is not required to be an adverse event. adverse event OAE:0000005 an adverse event that occurs after a drug administration adverse drug event OAE:0000055 A contraindication is a disposition that increases the risk of harm involved in using a particular drug, carrying out a medical procedure, or engaging in a particular activity such that the risk of harm exceeds a threshold. An contraindication serves as a reason to withhold a certain medical treatment. http://en.wikipedia.org/wiki/Contraindication contraindication OAE:0000095 a drug adverse event that is caused by a drug adiministration. Here a causal effect is established between the drug administration and the adverse event. causal adverse drug event OAE:0000631 serious adverse event is an adverse event that requires in-patient hospitalization, or prolongation of existing hospitalization, or that causes congenital malformation, or that results in persistent or significant disability or incapacity, or that is life threatening or results in death. severe adverse event OBI:0000011 planned process A processual entity that realizes a plan which is the concretization of a plan specification. planned process 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; http://purl.obolibrary.org/obo/obi.owl centrifuge pellet 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 http://purl.obolibrary.org/obo/obi.owl supernatant role 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 http://purl.obolibrary.org/obo/obi.owl processed material OBI:0000066 investigation a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s). 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. http://purl.obolibrary.org/obo/obi.owl evaluant 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 http://purl.obolibrary.org/obo/obi.owl study assay any method assay 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 http://purl.obolibrary.org/obo/obi.owl material processing 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 http://purl.obolibrary.org/obo/obi.owl microtiter plate 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) http://purl.obolibrary.org/obo/obi.owl study protocol protocol 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 http://purl.obolibrary.org/obo/obi.owl enzyme 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 http://purl.obolibrary.org/obo/obi.owl target of material addition role OBI:0000471 study design execution a planned process that carries out a study design study design execution 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 http://purl.obolibrary.org/obo/obi.owl manufacturer role OBI:0000576 scattered molecular aggregate the sodium and chloride ions in a glass of salt water A scattered molecular aggregate is 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 http://purl.obolibrary.org/obo/dron.owl scattered molecular aggregate 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 http://purl.obolibrary.org/obo/obi.owl specimen collection process 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 http://purl.obolibrary.org/obo/obi.owl 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. http://purl.obolibrary.org/obo/obi.owl 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 http://purl.obolibrary.org/obo/obi.owl dose specification 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 http://purl.obolibrary.org/obo/obi.owl gene knock out 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 http://purl.obolibrary.org/obo/obi.owl transfection 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 http://purl.obolibrary.org/obo/obi.owl half maximal effective concentration (EC50) 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 http://purl.obolibrary.org/obo/obi.owl half maximal inhibitory concentration (IC50) 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 http://purl.obolibrary.org/obo/obi.owl ex vivo design 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 http://purl.obolibrary.org/obo/obi.owl in vitro design 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 http://purl.obolibrary.org/obo/obi.owl tissue specimen OBI:0001929 mass value specification A value specification that specifies the mass of some thing. PERSON:Bjoern Peters http://purl.obolibrary.org/obo/obi.owl mass value specification OBI:0001931 scalar value specification A value specification that consists of two parts: a numeral and a unit label PERSON:Bjoern Peters http://purl.obolibrary.org/obo/obi.owl scalar value specification 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 http://purl.obolibrary.org/obo/obi.owl value specification 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 http://purl.obolibrary.org/obo/obi.owl organism 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 http://purl.obolibrary.org/obo/obi.owl specimen 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 http://purl.obolibrary.org/obo/obi.owl 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: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 http://purl.obolibrary.org/obo/obi.owl observation design 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 http://purl.obolibrary.org/obo/obi.owl centrifugation 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. http://purl.obolibrary.org/obo/obi.owl 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 http://purl.obolibrary.org/obo/obi.owl clinical study 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 http://purl.obolibrary.org/obo/obi.owl parallel group design 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 http://purl.obolibrary.org/obo/obi.owl 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 http://purl.obolibrary.org/obo/obi.owl group assignment 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 http://purl.obolibrary.org/obo/obi.owl genetic transformation 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 http://purl.obolibrary.org/obo/obi.owl cell pellet OGMS:0000060 Albert Goldfain creation date: 2009-06-23T11:53:49Z http://purl.obolibrary.org/obo/ogms.owl bodily process OGMS:0000061 A bodily process that is clinically abnormal. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:54:29Z http://purl.obolibrary.org/obo/ogms.owl pathological bodily process OGMS:0000090 A processual entity whose completion is hypothesized (by a healthcare provider) to alleviate the signs and symptoms associated with a disorder Albert Goldfain http://code.google.com/p/ogms/issues/detail?id=35 creation date: 2010-03-31T04:51:11Z http://purl.obolibrary.org/obo/dron.owl treatment 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 PR:000001891 p-glycoprotein multidrug resistance protein 1 A protein that is a translation product of the human POR gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/pr.owl P450R POR protein CPR CYPOR PR:000013030 Category=gene. NADPH--cytochrome P450 reductase PR:000013030 A solute carrier organic anion transporter family member that is a translation product of the human SLCO1B1 gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/pr/pr-non-classified.owl LST-1 liver-specific organic anion transporter 1 OATP-2 OATP-C SLCO1B1 solute carrier family 21 member 6 protein LST1 OATP2 OATPC SLC21A6 sodium-independent organic anion-transporting polypeptide 2 PR:000015223 Category=gene. solute carrier organic anion transporter family member 1B1 PR:000015223 A solute carrier organic anion transporter family member that is a translation product of the human SLCO1B3 gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/pr/pr-non-classified.owl PR:000015969 LST-1 liver-specific organic anion transporter 1 LST-2 OATP-8 SLC21A6 SLCO1B3 liver-specific organic anion transporter 2 organic anion transporter 8 organic anion-transporting polypeptide 8 solute carrier family 21 member 10 solute carrier family 21 member 8 protein LST2 OATP8 SLC21A8 Slc21a10 Slco1b2 PR:000015224 Category=gene. solute carrier organic anion transporter family member 1B3 PR:000015224 STATO:0000209 PMID:12892658 "Two formulas for computation of the area under the curve represent measures of total hormone concentration versus time-dependent change." Area under curve is a measurement datum which corresponds to the surface define by the x-axis and bound by the line graph represented in a 2 dimensional plot resulting from an integration or integrative calculus. The interpretation of this measurement datum depends on the variables plotted in the graph PRS: submit 'integral calculus' as a kind of data transformation in OBI:DT branch Orlaith Burke, Philippe Rocca-Serra, Alejandra Gonzalez-Beltran area under curve Anatomical entity that has mass. http://purl.obolibrary.org/obo/uberon.owl AAO:0010264 AEO:0000006 BILA:0000006 CARO:0000006 EHDAA2:0003006 FBbt:00007016 FMA:67165 HAO:0000006 TAO:0001836 TGMA:0001826 VHOG:0001721 uberon UBERON:0000465 material anatomical entity UBERON:0000465 Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function. http://purl.obolibrary.org/obo/uberon.owl system AAO:0000007 AEO:0000011 BILA:0000011 BSA:0000049 CALOHA:TS-2088 CARO:0000011 EHDAA2:0003011 EHDAA:392 EMAPA:16103 EV:0100000 FBbt:00004856 FMA:7149 HAO:0000011 MA:0000003 OpenCyc:Mx4rCWM0QCtDEdyAAADggVbxzQ TAO:0001439 TGMA:0001831 UMLS:C0460002 VHOG:0001725 WBbt:0005746 WBbt:0005763 XAO:0003002 ZFA:0001439 galen:AnatomicalSystem body system connected anatomical system organ system uberon anatomical systems UBERON:0000467 anatomical system UBERON:0000467 http://www.ebi.ac.uk/efo/efo.owl An anatomical system consisting of the alimentary canal and digestive glands responsible for intake, absorption, digestion and excretion of food.[AAO] digestive AAO:0000129 BILA:0000082 BTO:0000058 CALOHA:TS-1293 EFO:0000793 EV:0100056 FBbt:00005055 FMA:7152 GAID:278 MAT:0000018 MA:0002431 MESH:A03 MIAA:0000018 NCI_Thesaurus:Digestive_System SNOMEDCT:278859004 TADS:0000170 TAO:0000339 WBbt:0005748 Wikipedia:Digestive_system XAO:0000125 ZFA:0000339 alimentary system alimentary tract gastrointestinal system gut Anatomical system that has as its parts the organs devoted to the ingestion, digestion, and assimilation of food and the discharge of residual wastes. galen:DigestiveSystem uberon UBERON:0001007 digestive system UBERON:0001007 A unit of measurement is a standardized quantity of a physical quality. http://purl.obolibrary.org/obo/uo.owl george gkoutos unit.ontology UO:0000000 unit UO:0000000 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 A unit which is a standard measure of physical quantity consisting of only a numerical number without any units. http://purl.obolibrary.org/obo/uo.owl george gkoutos unit.ontology UO:0000186 dimensionless unit UO:0000186 A dimensionless ratio unit which denotes numbers as fractions of 100. http://purl.obolibrary.org/obo/uo.owl george gkoutos % unit.ontology UO:0000187 percent UO:0000187 A dimensionless unit which denotes an amount or magnitude of one quantity relative to another. http://purl.obolibrary.org/obo/uo.owl george gkoutos unit.ontology UO:0000190 ratio UO:0000190 An information content entity that specifies how a dose is quantified in a dose administration. http://purl.obolibrary.org/obo/PDRO/PDRO.owl This part of a prescription usually specifies a fixed amount (like '50 mg' or '500 mL'), but may instead specify a rate in some situations, e.g., in ongiong IV perfusions, where the total dose that will be administered in a single dose is unkown until the administration has ended. In either situation, the dose quantification specification is what enables the calculation of the quantity of active ingredient or drug product in the dose that is administered dose quantification specification A dose quantification specification that quantifies a dose by referring to the quantity of active ingredient administered in a dose administration. http://purl.obolibrary.org/obo/PDRO/PDRO.owl active ingredient quantification specification A dose quantification specification that quantifies a dose by referring to the quantity of drug product administered in a dose administration. http://purl.obolibrary.org/obo/PDRO/PDRO.owl drug product quantification specification http://purl.org/obo/owl/go_xp_all GO:0005554 molecular_function Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. Note that when this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code ND, no data, is used to indicate this. molecular_function http://purl.org/obo/owl/go_xp_all molecular_function catalytic activity http://purl.org/obo/owl/go_xp_all GO:0008151 GO:0050875 biological_process cellular process http://purl.org/obo/owl/go_xp_all biological_process drug metabolic process efo:EFO_0000750 http://www.ebi.ac.uk/efo/efo.owl Genotyping NCIt:C45447 An assay in which variation in the genome is analysed ArrayExpress production team James Malone genotyping oboInOwl:DbXref oboInOwl:Definition oboInOwl:ObsoleteClass Obsolete Class oboInOwl:Subset oboInOwl:Synonym oboInOwl:SynonymType owl:Thing example to be eventually removed 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 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 term created to ease viewing/sort terms for development purpose, and will not be included in a release organizational term 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 Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. metadata incomplete Nothing done yet beyond assigning a unique class ID and proposing a preferred term. uncurated 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 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 An editor note should explain what were the merged terms and the reason for the merge. terms merged 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 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 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 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 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 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 Terms with this status should eventually replaced with a term from another ontology. Alan Ruttenberg group:OBI to be replaced with external ontology term 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 ## 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 ## 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 en Adam Goldstein Alan Ruttenberg Albert Goldfain Barry Smith Bjoern Peters Carlo Torniai Chris Mungall Chris Stoeckert Christian A. Boelling Darren Natale David Osumi-Sutherland Gwen Frishkoff Holger Stenzhorn James A. Overton James Malone Jennifer Fostel Jie Zheng Jonathan Rees Larisa Soldatova Lawrence Hunter Mathias Brochhausen Matt Brush Melanie Courtot Michel Dumontier Paolo Ciccarese Pat Hayes Philippe Rocca-Serra Randy Dipert Ron Rudnicki Satya Sahoo Sivaram Arabandi Werner Ceusters William Duncan William Hogan Yongqun (Oliver) He http://creativecommons.org/licenses/by/4.0/ An information artifact is, loosely, a dependent continuant or its bearer that is created as the result of one or more intentional processes. Examples: uniprot, the english language, the contents of this document or a printout of it, the temperature measurements from a weather balloon. For more information, see the project home page at https://github.com/information-artifact-ontology/IAO IDs allocated to related efforts: PNO: IAO_0020000-IAO_0020999, D_ACTS: IAO_0021000-IAO_0021999 IDs allocated to subdomains of IAO. pno.owl: IAO_0020000-IAO_0020999, d-acts.owl: IAO_0021000-IAO_0021999 The Information Artifact Ontology (IAO) is licensed under the Creative Commons Attribution License (CC-BY) version 4.0. You are free to share (copy and redistribute the material in any medium or format) and adapt (remix, transform, and build upon the material) for any purpose, even commercially. for any purpose, even commercially. The licensor cannot revoke these freedoms as long as you follow the license terms. You must give appropriate credit (by using the original ontology IRI for the whole ontology and original term IRIs for individual terms), provide a link to the license, and indicate if any changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. For more information see http://www.obofoundry.org/docs/Citation.html This version of the ontology is the merge of all its imports and has added axioms inferred by an OWL reasoner true release version 2017-11-17 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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ 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 http://purl.obolibrary.org/obo/obi.owl has part o-has-part hasOccurrentPart [copied from inverse property 'part of occurrent'] Mary’s 5th birthday occurrent_part_of Mary’s life [copied from inverse property 'part of occurrent'] The process of a footballer’s heart beating once is an occurrent part but not a temporal_part of a game of football. [copied from inverse property 'part of occurrent'] the first set of the tennis match occurrent_part_of the tennis match. b has_occurrent_part c = Def. c occurrent_part_of b. (axiom label in BFO2 Reference: [007-001]) [copied from inverse property 'part of occurrent'] BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion. [copied from inverse property 'part of occurrent'] BFO2 Reference: occurrent http://purl.obolibrary.org/obo/bfo.owl [copied from inverse property 'part of occurrent'] b occurrent_part_of c =Def. b is a part of c & b and c are occurrents. (axiom label in BFO2 Reference: [003-002]) (iff (hasOccurrentPart a b) (occurrentPartOf b a)) // axiom label in BFO2 CLIF: [007-001] has occurrent part 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]) has measurement unit label 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 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 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 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 has value specification A relation between an information content entity and a value specification that specifies its value. PERSON: James A. Overton OBI http://purl.obolibrary.org/obo/obi.owl has value specification 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] http://purl.obolibrary.org/obo/obi.owl group randomization inheres in this fragility inheres in this vase this fragility is a characteristic of this vase this red color inheres in this apple this red color is a characteristic of this apple a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. 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 http://purl.obolibrary.org/obo/obi.owl Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. characteristic of inheres in 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://purl.obolibrary.org/obo/dron.owl http://www.obofoundry.org/ro/#OBO_REL:has_participant http://www.obofoundry.org/ro/#OBO_REL:has_participant has participant 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 BFO 2 Reference: BFO does not claim to be a complete coverage of all entities. It seeks only to provide coverage of those entities studied by empirical science together with those entities which affect or are involved in human activities such as data processing and planning – coverage that is sufficiently broad to provide assistance to those engaged in building domain ontologies for purposes of data annotation [17 BFO 2 Reference: BFO’s treatment of continuants and occurrents – as also its treatment of regions, rests on a dichotomy between space and time, and on the view that there are two perspectives on reality – earlier called the ‘SNAP’ and ‘SPAN’ perspectives, both of which are essential to the non-reductionist representation of reality as we understand it from the best available science [30 BFO 2 Reference: For both terms and relational expressions in BFO, we distinguish between primitive and defined. ‘Entity’ is an example of one such primitive term. Primitive terms in a highest-level ontology such as BFO are terms that 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. Alan Ruttenberg Albert Goldfain Barry Smith Bill Duncan Bjoern Peters Chris Mungall David Osumi-Sutherland Fabian Neuhaus James A. Overton Janna Hastings Jie Zheng Jonathan Bona Larry Hunter Leonard Jacuzzo Ludger Jansen Mark Ressler Mathias Brochhausen Mauricio Almeida Melanie Courtot Pierre Grenon Randall Dipert Robert Rovetto Ron Rudnicki Stefan Schulz Thomas Bittner Werner Ceusters The http://purl.obolibary.org/obo/bfo/classes-only.owl variant of BFO ("bfo_classes_only.owl") includes only the class hierarchy and annotations from the full OWL version of BFO 2: http://purl.obolibary.org/obo/bfo.owl ("bfo.owl"). There are no object properties or logical axioms that use the object properties in bfo_classes_only.owl. As the logical axioms in the bfo_classes_only.owl variant are limited to subclass and disjoint assertions they are much weaker than the logical axioms in bfo.owl. If you plan to use the relations that define BFO 2, you should import bfo.owl instead of bfo_classes_only.owl. To the extent that the relations are used without importing bfo.owl, be mindful that they should be used in a manner consistent with their use in bfo.owl. Otherwise if your ontology is imported by a another ontology that imports bfo.owl there may be inconsistencies. See the BFO 2 release notes for further information about BFO 2. Please note that the current release of bfo.owl uses temporal relations when the subject or object is a continuant, a major change from BFO 1. This is an early version of BFO version 2 and has not yet been extensively reviewed by the project team members. Please see the project site http://code.google.com/p/bfo/ , the bfo2 owl discussion group http://groups.google.com/group/bfo-owl-devel , the bfo2 discussion group http://groups.google.com/group/bfo-devel, the tracking google doc http://goo.gl/IlrEE, and the current version of the bfo2 reference http://purl.obolibrary.org/obo/bfo/dev/bfo2-reference.docx . This ontology is generated from a specification at http://bfo.googlecode.com/svn/trunk/src/ontology/owl-group/specification/ and with the code that generates the OWL version in http://bfo.googlecode.com/svn/trunk/src/tools/. A very early version of BFO version 2 in CLIF is at http://purl.obolibrary.org/obo/bfo/dev/bfo.clif Anuj Shah Dan Malone Jessica Tay-Sontheimer Jingjing Yu Jodi Schneider Philip E. Empey Richard D. Boyce William R. Hogan Mathias Brochhausen http://creativecommons.org/licenses/by/4.0/ The Drug-drug Interaction and Drug-drug Interaction Evidence Ontology (DIDEO) by the DIDEO development group is licensed under CC BY 4.0 (https://creativecommons.org/licenses/by/4.0/). The Drug-drug Interaction and Drug-drug Interaction Evidence Ontology (DIDEO) by the DIDEO development group is licensed under CC BY 4.0. You are free to share (copy and redistribute the material in any medium or format) and adapt (remix, transform, and build upon the material) for any purpose, even commercially. for any purpose, even commercially. The licensor cannot revoke these freedoms as long as you follow the license terms. You must give appropriate credit (by using the original ontology IRI for the whole ontology and original term IRIs for individual terms), provide a link to the license, and indicate if any changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. DIDEO Drug-drug Interaction and Drug-drug Interaction Evidence Ontology release version 2017-11-17 IAO_0021000-IAO_0021999 IAO_0020000-IAO_0020999 2024-02-13 https://github.com/oborel/obo-relations/wiki/ROCore