Elisabetta Manduchi Emily Greenfest-Allen Chris Stoeckert Jie Zheng The ontology is built based on OBI release 2015-04-13 This file is based on checkout of our SVN repository revision $Revision: 204$ https://github.com/obi-bcgo/bcgo BFO OWL specification label Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification. Really of interest to developers only BFO OWL specification label BFO CLIF specification label Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2 Person:Alan Ruttenberg Really of interest to developers only BFO CLIF specification label editor preferred label 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 term editor preferred term example example of usage A phrase describing how a class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms, examples for low level terms (e.g., Affymetrix HU133 array) are not PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> example of usage has curation status PERSON:Alan Ruttenberg PERSON:Bill Bug PERSON:Melanie Courtot OBI_0000281 has curation status definition definition The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. 2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition definition textual definition editor note An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. PERSON:Daniel Schober GROUP:OBI:<http://purl.obfoundry.org/obo/obi> IAO:0000116 uberon editor_note 1 editor_note 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 http://code.google.com/p/information-artifact-ontology/issues/detail?id=115. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> term editor alternative term An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent) PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> alternative term definition source formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 PERSON:Daniel Schober Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition source has obsolescence reason Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification. PERSON:Alan Ruttenberg PERSON:Melanie Courtot has obsolescence reason curator note An administrative note of use for a curator but of no use for a user PERSON:Alan Ruttenberg IAO:0000232 uberon curator_notes 1 curator_notes curator note curator notes 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 imported from expand expression to expand expression to expand assertion to first order logic expression elucidation person:Alan Ruttenberg Person:Barry Smith Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms elucidation has associated axiom(nl) Person:Alan Ruttenberg Person:Alan Ruttenberg An axiom associated with a term expressed using natural language has associated axiom(nl) has associated axiom(fol) Person:Alan Ruttenberg Person:Alan Ruttenberg An axiom expressed in first order logic using CLIF syntax has associated axiom(fol) has axiom label term replaced by Add as annotation triples in the granting ontology Use on obsolete terms, relating the term to another term that can be used as a substitute Person:Alan Ruttenberg Person:Alan Ruttenberg term replaced by ISA alternative term An alternative term used by the ISA tools project (http://isa-tools.org). Requested by Alejandra Gonzalez-Beltran https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891&atid=886178 Person: Alejandra Gonzalez-Beltran Person: Philippe Rocca-Serra ISA tools project (http://isa-tools.org) ISA alternative term NIAID GSCID-BRC alternative term An alternative term used by the National Institute of Allergy and Infectious Diseases (NIAID) Genomic Sequencing Centers for Infectious Diseases (GSCID) and Bioinformatics Resource Centers (BRC). PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group NIAID GSCID-BRC alternative term IEDB alternative term An alternative term used by the IEDB. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IEDB alternative term temporal interpretation temporal interpretation https://code.google.com/p/obo-relations/wiki/ROAndTime Abnormal/normal slim Attribute slim cell_quality Disposition slim Pathology slim Relational slim: types of quality that require an additional entity in order to exist Scalar slim Value slim abstract upper-level terms not directly useful for analysis Description may include but is not limited to: an abstract, table of contents, reference to a graphical representation of content or a free-text account of the content. An account of the content of the resource. Description Description The present resource may be derived from the Source resource in whole or in part. Recommended best practice is to reference the resource by means of a string or number conforming to a formal identification system. A reference to a resource from which the present resource is derived. Source Source subset_property 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 strain a has genetic backgroud as strain b is that strain a is derived from strain b and genetic make-up (all its alleles at all loci) of strain a is same to strain b except the mutated gene of interest and a very small amount of other genetic material, generally from one or two other strains. For example, the genetic background of the mutant strains NOD.129S7(B6)-Rag1tm1Mom/J (003729) and NOD.Cg-Rag1tm1Mom Prf1tm1Sdz/SzJ (004848) is NOD. Person: Jie Zheng has_genetic_background_of a produces_no b if some process that occurs_in a and has_no_output b, where a and b are material entities. Person: Jie Zheng not_produce relates an entity to a person or an organization that can be contacted for information regarding the entity. has contact relates an entity to the information about it in an external database. has external resource relates an entity to an identifier assigned by an external resource which denotes the entity. has external identifier a instance-level relation between a person or an organization to an email address the person or organization has. Person: Jie Zheng has email address shortcut relation of a planned process realizes or concretizes some plan specification executes relates an investigation to an experimental factor which is a study independent variable specified in a study design. An experimental factor can be a material entity (such as treated and untreated specimen), a quality (such as sex of an organism), a process (such as developmental stage of an organism), or an information about a process (such as duration of a treatment), etc. has experimental factor relates experimental factor (could be anything that a study independent variable specification is about) to its values For example, biological sex can be a study independent variable, potential values can be male or female. has experimental factor value relates experimental factor values to its factor type (could be anything that a study independent variable specification is about) For example, male/female could be values for biological sex, 0, 0.01, 0.02 mg/L for glucose concentation, 1,5,20 minutes for treatment duration, etc. value of experimental factor relates an invesitigation to any biologically-related entity that is examined as part of that process, such as a protein, a biological process, etc. examines Person: Jie Zheng a instance-level relation between an entity to a PubMed ID that denotes a publication associated with the entity. associated PubMed ID relates an information artifact to the species of an organism that it is about. Person: Jie Zheng is about organism species is denoted by is an instance-level, relation obtaining between an entity to an information content entity that is created to specifically refer to something. It is the inverse relation of 'denotes'. Person: Jie Zheng is denoted by relates an information artifact to the genotype of an organism that it is about. Person: Jie Zheng is about genotype relates an information artifact to the type of a cell that it is about. Person: Jie Zheng is about cell type relates an information artifact to the cell line that it is about. Person: Jie Zheng is about cell line relates an information artifact to the tissue of an organism that it is about. Person: Jie Zheng is about tissue relates the member (a data item) of a gene list (a data set) to the gene that it is about. has gene member relates an information artifact to the strain of an organism that it is about. is about strain relates an information artifact to the phenotype born by an organism that it is about. is about phenotype relates an information artifact to the development stage of an organism that it is about. is about development stage relates an information artifact to the treatment that it is about. For specimens in an assay, the treatment referred to was performed prior to specimen collection. is about treatment relates a process to a time-measurement-datum that represents the duration of the process has duration relates a molecular entity to its concentration measurement datum that is the measurement of its concentration quality has concentration relates a gene that has protein binding to the biological context in which that binding was identified. binding context relates a gene that is differentially expressed to the biological context in which that differential expression was identified. differential expression context relates a biological context (e.g., cell, developmental stage, etc.) to a gene whose protein binding was identified in this specific context. context of differential expression relates the context to a gene that protein binding is identified in this specific context context of binding 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 https://code.google.com/p/obo-relations/wiki/ROAndTime Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. part_of part of http://www.obofoundry.org/ro/#OBO_REL:part_of realized in this disease is realized in this disease course this fragility is realized in this shattering this investigator role is realized in this investigation is realized by realized_in [copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process realized in 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 Jie Zheng, Yongqun He, Yu Lin, Allen Xiang has disease has measurement unit label has measurement unit label denotes A person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance "Alan" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between "Alan" and the person that is being named. denotes is a primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically 2009-11-10 Alan Ruttenberg. Old definition said the following to emphasize the generic nature of this relation. We no longer have 'specifically denotes', which would have been primitive, so make this relation primitive. g denotes r =def r is a portion of reality there is some c that is a concretization of g every c that is a concretization of g specifically denotes r person:Alan Ruttenberg Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan denotes is duration of relates a process to a time-measurement-datum that represents the duration of the process Person:Alan Ruttenberg is duration of is_manufactured_by http://www.affymetrix.com/products/arrays/specific/hgu133.affx is_manufactered_by http://www.affymetrix.com/ (if we decide to use these URIs for the actual entities) c is_manufactured_by o means that there was a process p in which c was built in which a person, or set of people or machines did the work(bore the "Manufacturer Role", and those people/and or machines were members or of directed by the organization to do this. Alan Ruttenberg Liju Fan has_make has_manufacturer is_manufactured_by supplies A relation between an organisation or person and a material entity who owned or has license to the material entity and there was a legal transfer of ownership or licensing of the material entity to the current owner. GROUP: Relations branch supplies has_supplier A relation between a material entity and an organisation or person who owned or has license to the material entity and there was a legal transfer of ownership or licensing of the material entity to the current owner. PERSON: Alan Rutternberg PERSON: Cristian Cocos PERSON: Frank Gibson PERSON: Melanie Courtot has_supplier objective_achieved_by This relation obtains between a a objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process. OBI OBI objective_achieved_by is member of organization Relating a legal person or organization to an organization in the case where the legal person or organization has a role as member of the organization. 2009/10/01 Alan Ruttenberg. Barry prefers generic is-member-of. Question of what the range should be. For now organization. Is organization a population? Would the same relation be used to record members of a population JZ: Discussed on May 7, 2012 OBI dev call. Bjoern points out that we need to allow for organizations to be members of organizations. And agreed by the other OBI developers. So, human and organization were specified in 'Domains'. The textual definition was updated based on it. Person:Alan Ruttenberg Person:Helen Parkinson Person:Alan Ruttenberg Person:Helen Parkinson 2009/09/28 Alan Ruttenberg. Fucoidan-use-case is member of organization 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 red color is a quality of this apple a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence A quality inheres in its bearer at all times for which the quality exists. is quality of quality_of quality of this investigator role is a role of this person a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. is role of role_of role of 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 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 https://code.google.com/p/obo-relations/wiki/ROAndTime location_of location of located in my brain is located in my head this rat is located in this cage a relation between two independent continuants, the target and the location, in which the target is entirely within the location Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime located_in http://www.obofoundry.org/ro/#OBO_REL:located_in located in 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 ends_at_start_of meets X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) immediately precedes x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y Chris Mungall David Osumi-Sutherland Melissa Haendel Terry Meehan This is the transitive form of the develops from relation develops from '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. Chris Mungall 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) has prototype x actively participates in y if and only if x participates in y and x realizes some active role agent in actively participates in 'heart development' has active development some Shh protein x has participant y if and only if x realizes some active role that inheres in y This may be obsoleted and replaced by the original 'has agent' relation has agent has active participant move to BFO? Allen A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. temporal relation 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 x has the potential to develop into y iff x develops into y or if x is capable of developing into y has potential to develop into a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix. Melissa Haendel Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue. produces Melissa Haendel produced by Inverse of translation _of. kareneilbeck Wed Aug 19 00:11:53 PDT 2009 Example: codon translates_to amino_acid. translates_to X is translation of Y if X is translated by ribosome to create Y. kareneilbeck Wed Aug 19 00:09:59 PDT 2009 Example: Polypeptide translation_of CDS. translation_of q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. quality different_in_magnitude_relative_to different_in_magnitude_relative_to has NCBI gene id differential expression pattern has measurement value has measurement 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 Called Family Name in vCard has last name called Given Name invCard first name BCGO:0000002 Mus musculus that is bred to have some uniform behavioral, morphological, physiological, or genetic characteristics with similarly bred organism. Person: Jie Zheng mouse strain BCGO:0000003 Rattus norvegicus that is bred to have some uniform behavioral, morphological, physiological, or genetic characteristics with similarly bred organism. Person: Jie Zheng rat strain BCGO:0000004 a cell that expresses a gene for insulin. insulin expressing cell BCGO:0000010 A data transformation that attaches quantified values to specific sequence features, e.g. transcript, exon, etc. Person: Chris Stoeckert, Jie Zheng, Elisabetta Manduchi UPenn Group sequence feature quantification BCGO:0000011 a data transformation that aligns sequencing reads to reference sequence. Person: Chris Stoeckert, Jie Zheng EFO_0004917 high throughput sequence alignment protocol high throughput sequence alignment BCGO:0000012 A mouse strain containing a transgene in which EGFP (transgene) is driven by the Ins1 promoter (NCBI Gene ID: 16333). Hemizygous mice show expression of EGFP in beta lineage cells of the pancreas. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler MIP-GFP mouse strain RES188 mouse strain STOCK Tg(Ins1-EGFP/GH1)14Hara/Mmmh mouse strain Tg(Ins1-EGFP/GH1)14Hara Vanderbilt University Medical Center Tg(Ins1-EGFP/GH1)14Hara mouse strain BCGO:0000013 A mouse strain that is a laboratory mouse generated from long inbreeding with nearly identical genotype. C57BL/6 mouse has a dark brown, nearly black coat, and an easily irritable temperament. It has a good reproductive performance and is the most widely used "genetic background" for genetically modified mice for use as models of human disease. Person:Jie Zheng C57 C57 black 6 black 6 http://en.wikipedia.org/wiki/C57BL/6 C57BL/6 mouse strain BCGO:0000014 A cell that has all features and genetic signatures as functional beta cell. It may not be part of pancreas. functional beta cell like cell BCGO:0000016 A mouse strain in which part or all of the targeted gene, SRY-box containing gene 17 (NCBI Gene ID: 20671) is replaced to create Sox17{GFPCre} using the Loxed Cassette Acceptor allele Sox17{tm1(LCA)}). Using an RMCE strategy, we inserted a GFP-Cre (Green fluorescent protein-Cre-recombinase) fusion protein into a Sox17 LCA allele thereby replacing Sox17 coding sequences. The Sox17{GFPCre} mice may be used to track Sox17-expressing cells and their early progeny, or to conditionally inactivate genes in Sox17-expressing cells. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler RES1681 mouse strain STOCK Sox17tm2(EGFP/cre)Mgn/Mmnc mouse strain Sox17tm1.3(Cre.GFP)Mgn mouse strain Sox17{(GFPCre)Mgn} Vanderbilt University Medical Center Sox17{(GFPCre)Mgn} mouse strain BCGO:0000017 A mouse strain in which part or all of the targeted gene, pancreatic and duodenal homeobox 1 (NCBI Gene ID: 18609) is replaced to create Pdx1{tm1.2(CFP)} using the Loxed Cassette Acceptor allele Pdx1{tm1(LCA)}). This mouse contains a cyan fluorescent protein (CFP, Cerulean), tagged with 3 copies of an SV40 NLS knocked into the endogenous Pdx1 gene. This mouse strain enables pre-pancreatic endoderm to be easily identified in the developing mouse embryo and the isolation of Pdx1(+) cells by FACS. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler B6.129S6-Pdx1tm2Mgn/Mmnc mouse strain Pdx1CFP mouse strain Pdx1{(CFP)Mgn} RES1301 mouse strain Vanderbilt University Medical Center Pdx1{(CFP)Mgn} mouse strain BCGO:0000018 A mouse strain in which part or all of the targeted gene, pancreas specific transcription factor, 1a (NCBI Gene ID: 19213) is replaced to create ptf1a{tm1.1(YFP)} using the Loxed Cassette Acceptor allele Ptf1a{tm1(LCA)}). <p>Ptf1a{YFP} mice may be used to visualize yellow fluorescent protein (YFP) expression from the ptf1a allele. Ptf1a is expressedin pancreatic buds beginning at E9.5 andplays a vital role in the growth and lineage specification of pancreatic multipotent progenitor cells (MPCs). Ptf1a is also expressed in the neuronal precursors of the cerebellum, spinal cord, and retina where it also performs fate determining roles.</p> Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Ptf1a{tm1Mgn} RES236 mouse strain STOCK Ptf1atm1.1Mgn/Mmmh mouse strain ptf1aYFP mouse strain Vanderbilt University Medical Center Ptf1a{tm1Mgn} mouse strain BCGO:0000019 A mouse strain in which the targeted gene, Neurogenin 3 (NCBI Gene ID: 11925), has been modified (allele type: Gene Replacement) to targeted mutation 1, Klaus H Kaestner (MGI ID: Neurog3{tm1(EGFP)Khk}). A targeted mutation at the Neurogenin 3 locus where EGFP replaces entire coding region of Neurogenin3. The basic phenotype is EGFP expression in developing endocrine cells of pancreas and in glandular regions of the stomach. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler B6.129S-Neurog3tm1(EGFP)Khk/Mmcd mouse strain B6.129S-Neurog3{tm1(EGFP)Khk}/Mmcd RES176 mouse strain ngn3-EGFP mouse strain Vanderbilt University Medical Center B6.129S-Neurog3{tm1(EGFP)Khk}/Mmcd mouse strain BCGO:0000020 A mouse strain contains a GFP-Cre fusion protein which replaces the Insm1 coding sequence. These mice express green fluorescent protein (GFP) under control of the Insm1 gene locus. Insm1 is expressed in pancreatic primordium starting at E9.5. Insm1 is also expressed in neural precursor cells and tumors of may be used for lineage tracing of Insm1-positive cells in both wild-type and Insm1-null mice. http://www.betacell.org/resource/view/resource_id/661/ provide the definition of 'Insm1tm1.1Mgn mouse strain' which might be the early version of 'Insm1tm2Mgn mouse strain'. However, we are not clear the difference between two strains. We borrowed the definition of 'Insm1tm1.1Mgn mouse strain'. In the webpage, it has strain name 'Mouse Strain RES661' and common name 'lnsm1GFP.Cre mouse strain'. We added 'lnsm1GFP.Cre mouse strain' as alternative term which is true to 'Insm1tm2Mgn mouse strain' too . Person: Jie Zheng, Chris Stoeckert Insm1GFP.Cre mouse strain RES661 mouse strain http://www.betacell.org/resource/view/resource_id/661/ Insm1tm2Mgn mouse strain BCGO:0000021 Person: Jie Zheng MIP-GFP mouse strain RES188 mouse strain http://www.betacell.org/resource/view/resource_id/188/ http://purl.obolibrary.org/obo/BCGO_0000012 A mouse strain which is hemizygous and shows expression of EGFP in beta lineage cells of the pancreas. obsolete_STOCK Tg(Tnpo1-EGFP)6729Hara/Mmmh mouse strain true BCGO:0000028 A mouse strain that is a laboratory mouse generated from inbreeding. It has white-bellied, pink-eyed, light chinchilla (off-white) or albino or white-bellied, pink-eyed, light chinchilla (light tan). It has a good reproductive performance and is widely used in the production of targeted mutations due to the availability of multiple embryonic stem cell lines derived from them. Person:Jie Zheng 129/SvJ 129X1 http://www.informatics.jax.org/mgihome/nomen/strain_129.shtml http://jaxmice.jax.org/strain/000691.html 129X1/SvJ mouse strain BCGO:0000030 A mouse strain that Inbred from F130 to F170 depending on substrain original generated from a cross of a Bagg albino female and a DBA male by Strong in 1920. It has Agouti coat color. Most substrains have a good reproductive performance. It is widely used in a wide variety of research areas including cancer, immunology and inflammation, sensorineural, and cardiovascular biology. Person:Jie Zheng http://www.informatics.jax.org/external/festing/mouse/docs/C3H.shtml http://www.criver.com/EN-US/PRODSERV/BYTYPE/RESMODOVER/RESMOD/Pages/C3HMouse.aspx C3H mouse strain BCGO:0000031 Person: Jie Zheng black swiss mouse strain BCGO:0000046 an endodermal cell that is part of the definitive endoderm and expresses a gene for SOX-17 Person: Chris Stoeckert, Jie Zheng Sox17 expressing cell from the embryo body proper Chris Stoeckert Sox17-expressing definitive endodermal cell BCGO:0000047 an epithelial cell that is part of the ventral pancreatic bud, expresses a gene for SOX-17 and has Epcam in the plasma membrane. Person: Chris Stoeckert, Jie Zheng Sox17 expressing cell in ventral pancreatic bud Chris Stoeckert Sox17-expressing Epcam+ pancreatic epithelial cell BCGO:0000048 an endodermal cell that is part of the foregut endoderm and expresses the gene for pancreas/duodenum homeobox protein 1 Person: Chris Stoeckert, Jie Zheng Pdx1-expressing endoderm cell Chris Stoeckert Pdx1-expressing foregut endodermal cell BCGO:0000049 a non-terminally differentiated cell that is part of the pancreatic bud, participates in pancreas development and expresses the gene for pancreas transcription factor 1 subunit alpha. Person: Chris Stoeckert, Jie Zheng Ptf1a-expressing cell Chris Stoeckert Ptf1a-expressing multipotent pancreatic cell BCGO:0000050 a non-terminally differentiated cell that is part of the pancreatic bud but lacks pancreas transcription factor 1 subunit alpha. Person: Chris Stoeckert, Jie Zheng Ptf1a-null cell Chris Stoeckert Ptf1a-lacking pancreatic progenitor cell BCGO:0000051 a non-terminally differentiated cell that participates in endocrine pancreas developement and expresses the gene for neurogenin-3. Person: Chris Stoeckert, Jie Zheng Ngn3-expressing cell Chris Stoeckert neurogenin-3-expressing endocrine progenitor cell BCGO:0000052 a non-terminally differentiated cell that is part of the pancreas, participates in pancreas development and lacks neurogenin-3. Person: Chris Stoeckert, Jie Zheng Ngn3-null cell Chris Stoeckert neurogenin-3-lacking pancreatic progenitor cell BCGO:0000053 a non-terminally differentiated cell that participates in endocrine pancreas development and expresses a gene for insulinoma-associated protein 1 Person: Chris Stoeckert, Jie Zheng Insm1 expressing pancreatic endocrine cell Chris Stoeckert Insm1-expressing endocrine progenitor cell BCGO:0000054 a non-terminally differentiated cell that is part of the endocrine pancreas and lacks insulinoma-associated protein 1 Person: Chris Stoeckert, Jie Zheng Non-functional Insm1 expressing pancreatic endocrine cell Chris Stoeckert Insm1-lacking endocrine progenitor cell BCGO:0000055 a type B pancreatic cell that is immature and expresses a gene for insulin Person: Chris Stoeckert, Jie Zheng insulin-expressing nascent beta cells Chris Stoeckert insulin-expressing immature beta cell BCGO:0000056 a type B pancreatic cell that is mature and expresses a gene for insulin Person: Chris Stoeckert, Jie Zheng insulin-expressing mature beta cells Chris Stoeckert insulin-expressing mature beta cell BCGO:0000057 A Insm1-expressing endocrine progenitor cell that expresses the gene for pancreas/duodenum homeobox protein 1 at a high level. Person: Jie Zheng, Chris Stoeckert Insm1-expressing Pdx1 high-positive pancreatic endocrine progenitor cell BCGO:0000058 A Insm1-expressing endocrine progenitor cell that expresses the gene for pancreas/duodenum homeobox protein 1 at a low level. Person: Jie Zheng, Chris Stoeckert Insm1-expressing Pdx1 low-positive pancreatic endocrine progenitor cell BCGO:0000059 A mouse strain that is the result of mating between a Insm1GFPCre/+ mouse and a Pdx1CFP/+ mouse both on a CD-1 background Person: Chris Stoeckert, Anna Osipovich Insm1tm2(GFP.Cre)Mgn/Pdx1tm2(CFP)Mgn mouse strain BCGO:0000060 A software implementing a higher level analysis protocol of type differential expresssion. GBCO differential expression software BCGO:0000061 A mouse strain that is genetically modified expressing Enhanced Green Fluorescent Protein (EGFP) under the control of the mouse insulin 1 promoter. Fluorescence is detected in tissues where insulin I is normally expressed; fluorescent protein expression in pancreatic beta-cells is evident from embryonic day (E)13.5 through adulthood. The fluorescence expression pattern is similar to the patterns seen in two other strains STOCK Tg(Ins1-Cerulean)24Hara/J and STOCK Tg(Ins1-DsRed*T4)32Hara/J. This mutant mouse strain exhits normal glucose tolerance and pancreatic insulin levels and may be useful in studies of diabetes and pancreatic beta islet cell biology. Person: Jie Zheng http://jaxmice.jax.org/strain/006864.html B6.Cg-Tg(Ins1-EGFP)1Hara/J mouse strain BCGO:0000068 A CRID symbol assigned by ArrayExpress to uniquely identify a study in ArrayExpress ArrayExpress ID BCGO:0000069 A CRID symbol assigned by Gene Expression Omnibus (GEO) to uniquely identify a study in GEO. GEO ID BCGO:0000070 A gene expression that produces cellular surface proteins that can be used to identify and isolate specific cells. Person: Chris Stoeckert, Jie Zheng Penn Group Beta Cell Biology Consoritum cellular marker expression BCGO:0000071 A material entity that could be whole pancreas, part of pancreas (including a single cell type (e.g., beta cell), or precursor to pancreas. Person: Chris Stoeckert, Jie Zheng Penn Group Beta Cell Biology Consoritum pancreatic material BCGO:0000076 A cellular feature identification objective that aims to examine or characterize cell development or differentiation. Person: Chris Stoeckert, Jie Zheng Penn group Beta Cell Biology Consoritum characterization of cell differentiation objective BCGO:0000077 A characterization of cell differentiation objective that aims to examine the influence of specific protocols with regard to generating insulin-producing cells from putative progenitors or other mechanisms (e.g., transdifferentiation). Person: Chris Stoeckert, Jie Zheng Penn group Beta Cell Biology Consoritum characterization of differentiation of insulin-producing cells objective BCGO:0000078 A characterization of cell stimulation or injury objective that aims to address the effects of compounds, hormones, or cell manipulations on the ability of islets and/or beta-cells to secrete insulin or respond to glucose levels. Person: Chris Stoeckert, Jie Zheng Penn group Beta Cell Biology Consoritum characterization of islet/beta-cell stimulation/injury objective BCGO:0000079 A biological feature identification objective that aims to examine changes in gene expression and/or epigenome during pancreas development or regeneration. Person: Chris Stoeckert, Jie Zheng Penn group Beta Cell Biology Consoritum characterization of pancreas development and growth objective BCGO:0000080 A cellular feature identification objective that aims to address the effects of compounds, hormones, or cell manipulations on the ability of tissues or specific cell types to perform their normal functions or respond to insult. Person: Chris Stoeckert, Jie Zheng Penn group Beta Cell Biology Consoritum characterization of cell stimulation or injury objective BCGO:0000081 A molecular feature identification objective that aims to identify genes and processes regulated by transcription factors, co-activators, and other types of transcriptional regulators. Person: Chris Stoeckert, Jie Zheng Penn group Beta Cell Biology Consoritum targets and roles of transcriptional regulators objective BCGO:0000082 A biological feature identification objective that aims to address the question of what genes are expressed in a given tissue or cell type or the expression of genes across multiple cells and tissues. Person: Chris Stoeckert, Jie Zheng Penn group Beta Cell Biology Consoritum tissue expression survey objective BCGO:0000083 A biological process of generating epigenetic modifications, such as DNA methylation and histone modifications. Person: Chris Stoeckert, Jie Zheng Penn Group Beta Cell Biology Consoritum epigenetic modification process BCGO:0000084 A planned process that aims to expand islets in culture and redifferentiate them to insulin producing cells. Person: Chris Stoeckert, Jie Zheng Penn Group Beta Cell Biology Consoritum islet expansion in vitro BCGO:0000085 islet of Langerhans that is part of a person who has diabetes. Person: Chris Stoeckert, Jie Zheng Penn Group Will add following axiom after import 'has disease' from CLO 'is part of' some ('Homo sapiens' and 'has disease' some 'diabetes mellitus') Beta Cell Biology Consoritum islets in diabetes BCGO:0000086 A ncRNA which is transcribed, non-protein coding, and longer than 200 nucleotides. Person: Chris Stoeckert, Jie Zheng lncRNA http://en.wikipedia.org/wiki/Long_non-coding_RNA Beta Cell Biology Consoritum long non-coding RNA BCGO:0000087 Person: Chris Stoeckert, Jie Zheng Penn Group Beta Cell Biology Consoritum stress and apoptosis in islets or beta cells BCGO:0000088 An assay that uses chromatin immunoprecipitation combined with serial analysis of chromatin occupancy (SACO) to identify binding sites for transcription factors. Person: Chris Stoeckert, Jie Zheng TF Binding SACO Penn group Beta Cell Biology Consoritum transcription factor binding site identification by SACO assay BCGO:0000089 An assay that aims to measure abundance of transcripts using high-quality RNA isolated from cells following intracellular antibody staining and fluorescence-activated cell sorting (FACS). Person: Chris Stoeckert, Jie Zheng MARIS http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0089459 Beta Cell Biology Consoritum transcriptional profiling by MARIS assay BCGO:0000095 A data item of age. It could be measurement datum like 10 weeks, 2 years, or categorical datum like young, adult. age datum BCGO:0000097 A data item of how much of a given substance there is mixed with another substance.Annotations. It could be measurement datum like 10 mM, or categorical datum like low, high concentration. concentration datum BCGO:0000105 Person: Jie Zheng, Chris Stoeckert BTBR PMID: 25034792, Nephron Exp Nephrol. 2014;126(4):191-5. doi: 10.1159/000363300. "Recent advances in animal models of diabetic nephropathy." A mouse strain that is deficient for the leptin receptor (ob/ob) which is naturally insulin resistant and develops many of the pathological features of human Diabetic nephropathy. Black and tan, brachyury mouse strain BCGO:0000106 Person: Chris Stoeckert large duct cell http://www.sciencedirect.com/science/article/pii/S1357272504002717 A pancreatic ductal cell of the large pancreatic duct. large pancreatic ductal cell BCGO:0000107 Person: Chris Stoeckert small duct cell http://www.sciencedirect.com/science/article/pii/S1357272504002717 A pancreatic ductal cell of a small interlobular pancreatic duct. small pancreatic ductal cell' BCGO:0000108 Person: Jie Zheng, Chris Stoeckert ES (Tet-On/Ngn3) Penn Group An embryonic stem cell line that contains a ‘tet-on’ operon system and expresses Ngn3 in the presence of Tetracycline. Tet-On/Ngn3 embryonic stem cell BCGO:0000109 Person: Jie Zheng, Chris Stoeckert GKP2 BCBC (http://www.betacell.org/resource/view/resource_id/1038) An immortal animal cell line cell which was derived from an insulinoma and expresses insulin and pdx1. GKP2 cell BCGO:0000110 Person: Jie Zheng, Chris Stoeckert GKP4 BCBC (http://www.betacell.org/resource/view/resource_id/1038) An immortal animal cell line cell which was derived from a periductal tumor that did not express insulin or pdx1 but expressed genes of the endocrine lineage, such as Isl1 and Nkx2.2. GKP4 cell BCGO:0000111 Person: Jie Zheng, Chris Stoeckert BCBC (http://www.betacell.org/resource/view/resource_id/4216) A H9 cell that expresses Sox17. Sox17 expressiong H9 cell BCGO:0000112 Person: Jie Zheng, Chris Stoeckert PMID:17185391 An INS-1 cell which is poorly responsive to glucose. It is a mixture of INS-1 (832/1) and INS-1 (832/2). INS-1 (832/1 and 832/2) BCGO:0000113 Person: Jie Zheng, Chris Stoeckert PMID:17185391 An INS-1 cell which is poorly responsive to glucose. INS-1 (832/1) cell BCGO:0000114 Person: Jie Zheng, Chris Stoeckert PMID:17185391 An INS-1 cell which is highly responsive to glucose. It is a mixture of INS-1 (832/13) and INS-1 (832/15). INS-1 (832/13 and 833/15) BCGO:0000115 Person: Jie Zheng, Chris Stoeckert PMID:17185391 An INS-1 cell which is highly responsive to glucose. INS-1 (832/13) cell BCGO:0000116 Person: Jie Zheng, Chris Stoeckert PMID:17185391 An INS-1 cellwhich is poorly responsive to glucose. INS-1 (832/2) cell BCGO:0000117 Person: Jie Zheng, Chris Stoeckert BCBC An INS-1 cell which is cytokine resistant. INS-1 (833/117) cell BCGO:0000118 Person: Jie Zheng, Chris Stoeckert BCBC An INS-1 cell which is cytokine resistant and highly glucose-responsive. INS-1 (833/15) cell BCGO:0000119 Person: Jie Zheng, Chris Stoeckert BCBC An INS-1 cell which is cytokine sensitive. INS-1 (834/40) cell BCGO:0000120 Person: Jie Zheng, Chris Stoeckert PMID: 10037448 An INS-1 cell which has high insulin secretion in responses to glucose. INS-1E BCGO:0000121 Person: Jie Zheng, Chris Stoeckert mPAC L20 PMID: 15340143 An immortal animal cell line cell which is a pancreatic duct cell and contains an Ngn3-expressing adenovirus. mPAC L20 cell BCGO:0000122 Person: Jie Zheng, Chris Stoeckert PANC-1 http://www.sigmaaldrich.com/catalog/product/sigma/87092802 An immortal animal cell line cell which was established from a pancreatic carcinoma of ductal origin from a 56-year-old Caucasian male. The cell possesses the type B phenotype for G6PD. PANC-1 cell BCGO:0000123 Person: Jie Zheng, Chris Stoeckert R7T1 PMID: 19164755 An immortal animal cell line cell that is a rat beta-cell line. R7T1 cell BCGO:9000177 A mouse strain containing a transgene in which Cre (transgene) is driven by the Gcg promoter (NCBI Gene ID: 14526). <p>A transgenic alteration consisting of a SacI fragment containing the glucagon promoter, inserted at SacI of pBS-beta globin-Cre, resulting in Cre expression in pancreatic lineage cells.</p> Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler B6.CBA-{Tg(Gcg-cre)1Herr}/Mmnc Vanderbilt University Medical Center B6.CBA-{Tg(Gcg-cre)1Herr}/Mmnc mouse strain BCGO:9000178 A mouse strain containing a transgene in which EGFP (transgene) is driven by the Ipf1 promoter (NCBI Gene ID: 18609). This strain allows Expression of EGFP in pancreatic precursor populations. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler B6.CBA-{Tg(Ipf1-EGFP)1Herr}/Mmnc Vanderbilt University Medical Center B6.CBA-{Tg(Ipf1-EGFP)1Herr}/Mmnc mouse strain BCGO:9000179 A mouse strain containing a transgene in which Cre (transgene) is driven by the Ins1 promoter (NCBI Gene ID: 24505). This strain relies on the recombination of floxed DNA in insulin-producing beta cells. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler B6;D2-Tg(Ins-cre)23Herr Vanderbilt University Medical Center B6;D2-Tg(Ins-cre)23Herr mouse strain BCGO:9000180 A mouse strain containing a transgene in which Cre (transgene) is driven by the Neurog3 promoter (NCBI Gene ID: 11925). <p>All islet endocrine cells inherit a recombination event, if a segment of DNA is loxP-flanked. Transgene encoding Cre recombinase under the control of a human Neurogenin3 promoter.</p> Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler B6;D2-Tg(NEUROG3-cre)1Herr Vanderbilt University Medical Center B6;D2-Tg(NEUROG3-cre)1Herr mouse strain BCGO:9000181 A mouse strain containing a transgene in which LacZ-Neo (transgene) is driven by the Neurod1 promoter (NCBI Gene ID: 18012). Homozygous phenotype: Postnatal lethal due to neonatal diabetes Pancreas--5% insulin production, no islet formation Gut--no CCK or secretin production Inner ear defects resulting in deafness--no cochlear ganglia and poor vestibular ganglia formation Cerebellar defect resulting in ataxia-- >90% depletion of cerebellar granule cells Hippocampal defects--no dentate gyrus. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler BX129-Neurod1{tmAK71(lacZ)Jle/Mmcd} Vanderbilt University Medical Center BX129-Neurod1{tmAK71(lacZ)Jle/Mmcd} mouse strain BCGO:9000182 A mouse strain in which the targeted gene, insulin promoter factor 1, homeodomain transcription factor (NCBI Gene ID: 18609), has been modified (allele type: Global Null) to targeted mutation 1, Christopher V E Wright (MGI ID: Ipf1{tm1Cvw}). Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler STOCK Ipf1{tm1Cvw} Vanderbilt University Medical Center STOCK Ipf1{tm1Cvw} mouse strain BCGO:9000183 A mouse strain in which the targeted gene, insulin promoter factor 1, homeodomain transcription factor (NCBI Gene ID: 18609), has been modified (allele type: Gene Replacement) to insulin promoter factor 1, homeodomain transcription factor / targeted mutation 2, Christopher V E Wright (MGI ID: Ipf1{tm2Cvw}). The homozygous phenotype of these animals show growth retardation and dehydration with lack of gastric emptying; ie. a-pancreatic. Heterozygous phenotype includes expression of beta-galactosidase in developing stomach, bile duct and cystic ducts and early pancreatic buds. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler STOCK Ipf1{tm2Cvw}/Mmnc Vanderbilt University Medical Center STOCK Ipf1{tm2Cvw}/Mmnc mouse strain BCGO:9000184 A mouse strain in which the targeted gene, pancreas specific transcription factor, 1a (NCBI Gene ID: 19213), has been modified (allele type: Gene Replacement) to targeted mutation 1.1, Christopher VE Wright (MGI ID: Ptf1a{tm1.1(cre)Cvw}). <p>Homozygous phenotype is altered pancreatic development with loss of exocrine acini.</p> Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler STOCK Ptf1a{tm1(cre)Cvw} Vanderbilt University Medical Center STOCK Ptf1a{tm1(cre)Cvw} mouse strain BCGO:9000185 A mouse strain containing a transgene in which Cre (transgene) is driven by the Foxa3 promoter (NCBI Gene ID: 15377). Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler STOCK Tg(Foxa3-cre)1Khk Vanderbilt University Medical Center STOCK Tg(Foxa3-cre)1Khk mouse strain BCGO:9000186 A mouse strain containing a transgene in which Cre (transgene) is driven by the Ipf1 promoter (NCBI Gene ID: 18609). Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler STOCK Tg(Ipf1-cre/Esr1)1Dam/Mmcd Vanderbilt University Medical Center STOCK Tg(Ipf1-cre/Esr1)1Dam/Mmcd mouse strain BCGO:9000189 A mouse strain containing a transgene in which Cre (transgene) is driven by the Ipf1 promoter (NCBI Gene ID: 18609). Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler STOCK-Tg(Ipf1-cre)89.1Dam/Mmcd Vanderbilt University Medical Center STOCK-Tg(Ipf1-cre)89.1Dam/Mmcd mouse strain BCGO:9000190 A mouse strain containing a transgene in which Cre (transgene) is driven by the Neurog3 promoter (NCBI Gene ID: 11925). Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler STOCK Tg(Neurog3-cre)1Dam/Mmcd Vanderbilt University Medical Center STOCK Tg(Neurog3-cre)1Dam/Mmcd mouse strain BCGO:9000191 A mouse strain in which the targeted gene, Glucokinase (NCBI Gene ID: 103988), has been modified (allele type: Global Mutation) to targeted mutation 3 (MGI ID: Gck{tm3Mgn}). This line of mice provides a model for Persistant Hyperinsulinemic Hypoglycemia of Infancy, or PHHI-GK, a rare genetic disease of humans. A gk{A456V} mutation, originally identified in a human pedigree with PHHI-GK, was introduced into these mice by gene knock-in. These mice may be useful for studies of sustained hypoglycemia. The mutation has been bred into a C57BL/6J strain thereby facilitating direct comparisons to both wild type C57BL/6J animals and to animals with a gk{K414E} mutation. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Gck{tm3Mgn} Vanderbilt University Medical Center Gck{tm3Mgn} mouse strain BCGO:9000192 A mouse strain in which the targeted gene, Glucokinase (NCBI Gene ID: 103988), has been modified (allele type: Global Mutation) to targeted mutation 2 (MGI ID: Gck{tm2Mgn}). This line of mice contains a gk{K414E} point mutation that was introduced by gene knock-in. This point mutation wasidentified in aMODY-GK pedigree. These mice will be useful for studies of sustained hyperglycemia since they contain only a single mutation and are congenic with the C57BL/6J strain. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Gck{tm2Mgn} Vanderbilt University Medical Center Gck{tm2Mgn} mouse strain BCGO:9000193 A mouse strain in which the targeted gene, Glucokinase (NCBI Gene ID: 103988), has been modified (allele type: Conditional Null) to targeted mutation 1.1 (MGI ID: Gck{tm1.1Mgn}). Gk{lox} mice may be used to generate cell specific knock-outs of glucokinase, depending which cre-expressing transgenic mouse is used. In humans, glucokinase gene mutations cause maturity onset diabetes of the young (MODY-GK), a disease that is characterized by early onset and persistent hyperglycemia. Thus, these mice are useful in determining how diminished experssion of glucokinase in specific cells causes hyperglycemia. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Gck{tm1.1Mgn} Vanderbilt University Medical Center Gck{tm1.1Mgn} mouse strain BCGO:9000194 A mouse strain in which the targeted gene, phosphoenolpyruvate carboxykinase 1 (NCBI Gene ID: 18534), has been modified (allele type: Conditional Null) to targeted mutation 1.1, Mark A Magnuson (MGI ID: Pck1{tm1.1Mgn} ). These mice may be used to study tissue-specific functions of phosphoenolpyruvate carboxykinase (Pck1). This enzyme is essential for gluconeogenesis and also is important for regulating anapleurosis/catapleurosis of TCA cycle intermediates. By generating mice that are homozygous for the pck{lox} allele and that contain a tissue-specific Cre transgene, Pck1 can be deleted from various sites. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler pck{tm1.1Mgn} Vanderbilt University Medical Center pck{tm1.1Mgn} mouse strain BCGO:9000195 A mouse strain in which the targeted gene, Rictor (NCBI Gene ID: 78757), has been modified (allele type: Global Null) to targeted mutation 1.3 (MGI ID: 4921505C17Rik{tm2Mgn}). Rictor is an essential part of mTOR complex 2 (mTORC2). mTORC2 phosphorylates Ser473 of Akt/PKB. Eliminating this gene disrupts the function of mTORC2, thereby preventing growth factor mediated activation of Akt/PKB. Thus, these mice have utility for studying both the sites of expression and function of rictor. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Rik{tm1.3Mgn} Vanderbilt University Medical Center Rik{tm1.3Mgn} mouse strain BCGO:9000196 A mouse strain in which the targeted gene, Rictor (NCBI Gene ID: 78757), has been modified (allele type: Conditional Null) to targeted mutation 1.1 (MGI ID: 4921505C17Rik{tm1.1Mgn}). These mice carrya conditional allele for Rictor, a component mTOR complex 2 (mTORC2). Disruption of the Rictor gene attenuates phosphorylation ofSer473 of Akt/PKB, which is important for a normal response to growth factor stimulation acting through the PI3-kinase signaling pathway. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Rik{tm1.1Mgn} Vanderbilt University Medical Center Rik{tm1.1Mgn} mouse strain BCGO:9000197 A mouse strain in which the targeted gene, Peroxisome proliferator-activated receptor gamma (NCBI Gene ID: 19016), has been modified (allele type: Conditional Null) to targeted mutation 1.1Mgn (MGI ID: Pparg{tm1.1Mgn}). These mice carry a conditional allele for PPARgamma that can be used in combination with various cre-expressing transgenes. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Pparg{tm1.1Mgn} Vanderbilt University Medical Center Pparg{tm1.1Mgn} mouse strain BCGO:9000198 A mouse strain in which the targeted gene, ATP-binding cassette, sub-family C (CFTR/MRP), member 8 (NCBI Gene ID: 20927), has been modified (allele type: Global Null) to targeted mutation 1.1Mgn (MGI ID: Sur1{neotm1.1Mgn}). These mice contain a global knock-out of the sulfonylurea receptor (Sur1), which is part of the ATP-dependent potassium channel. In humans, mutations in Sur1 cause persistent hyperinsulinemic hypoglycemia of infancy (PHHI). Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler B6.129X1-Abcc8{tm1.1Mgn} Vanderbilt University Medical Center B6.129X1-Abcc8{tm1.1Mgn} mouse strain BCGO:9000199 A mouse strain containing a transgene in which Neurog3-ER (transgene) is driven by the Pdx1 promoter (NCBI Gene ID: 18609). The transgene is driven by the Pdx1 promoter whcih targets it in pancreas progenitor during development. These mice express a fusion protein between the pro-endocrine transcription factor Ngn3 and the tamoxifen responsive estrogen receptor. An IRES site allows GFP to be co-expressed with Ngn3-ER. The protein is active only upon tamoxifen injection. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Tg(Pdx1-Neurog3-ER)1Agb Vanderbilt University Medical Center Tg(Pdx1-Neurog3-ER)1Agb mouse strain BCGO:9000203 A mouse strain containing a transgene in which rtTA (transgene) is driven by the Gcg promoter (NCBI Gene ID: 14562). These mice expresses the rtTA (tetracycline transactivator) in islet alpha cells upon treatment with doxicycline. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Glucagon:rtta Vanderbilt University Medical Center Glucagon:rtta mouse strain BCGO:9000204 A mouse strain in which the targeted gene, hypoxanthine guanine phosphoribosyl transferase 1 (NCBI Gene ID: 15452), has been modified (allele type: Gene Replacement) to (MGI ID: ). C57/CBAJ-Hprt{tm3(Ins2-HBEGF)Ugfm} carries a transgene encoding the human diphtheria toxin receptor under the control of rat insulin II promoter, was inserted by homologous recombination at the Hprt locus of the X chromosome. It provides a model for depletion of 50% of beta cells using Diphtheria toxin. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler C57/CBAJ-Hprt{tm3(Ins2-HBEGF)Ugfm} Vanderbilt University Medical Center C57/CBAJ-Hprt{tm3(Ins2-HBEGF)Ugfm} mouse strain BCGO:9000205 A mouse strain in which the targeted gene, Nkx6.1 (NCBI Gene ID: 18096), has been modified (allele type: Global Null) to targeted mutation (MGI ID: Nkx6.1{tm1(DsRed2)}). An IRES-DsRed2 cassette was introduced into exon 1 of the Nkx6.1 genomic sequence. The insertion generates a null allele. DsRed2 expression is not detected in these mice. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler B6-Nkx6-1{tm1Msan} Vanderbilt University Medical Center B6-Nkx6-1{tm1Msan} mouse strain BCGO:9000206 A mouse strain containing a transgene in which CreER (transgene) is driven by the Ins promoter (NCBI Gene ID: 16333). A transgenic mouse expression tamoxifen-inducible Cre recombinase under rat insulin promoter. Upon the injection of tamoxifen, loxP-flanked DNA sequences in beta cells will be deleted. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Tg(RIP-Cre/ESR1){Ydor} Vanderbilt University Medical Center Tg(RIP-Cre/ESR1){Ydor} mouse strain BCGO:9000207 A mouse strain in which part or all of the targeted gene, pancreas specific transcription factor, 1a (NCBI Gene ID: 19213) is replaced to create Ptf1a{tTA} using the Loxed Cassette Acceptor allele Ptf1a{tm1(LCA)}). Mice heterozygous for the tTA replacement of the Ptf1a gene are viable, fertile, of normal size, and do not display any behavioral abnormalities. The replacement places the expression of tTAoff (Gossen &amp; Bujard, PNAS 89:5547, 1992) under the control of the regulatory sequences of the endogenous Ptf1a gene. This mouse was initially designed to be mated to a mouse (see BCBC #M461) bearing a bicistronic Ptf1a-lacZ transgene driven by the tetracycline-regulatory element (TRE: 7 copies of tetO with the CMV minimal promoter). For offspring homozygous for the tTA allele of Ptf1a and hemi- or homozygous for the transgene, the production of PTF1a is due solely to tTA-activation of the transgene, which is repressed by administration of tetracycline/doxycycline. This strategy allows embryonic developmental arrest at desired stages or cessation of gene function in adult mice for the pancreas (similar to that for Pdx1 described in Holland et al., PNAS 99:12236, 2002) and also for the cerebellum, retina, dorsal spinal cord and possibly hypothalamus. This transgenic mouse may be useful in studies of pancreatic endocrine/exocrine development and function, diabetes, and certain defects of the CNS. This tissue-specific expresser of tTA can also be bred with strains bearing other TRE-transgenes for organ-specific conditional expression analyses. Nearly all of the Ptf1a transcription unit has been replaced by a tTAoff coding sequence with accessory translational and RNA-processing signals, as follows, from 5' to 3': the Ptf1a gene transcriptional start and 49-bp of its 5'UTR; the Xenopus laevis beta-globin 5'UTR with Kozak initiator codon; the tTA coding sequence; and a 990-bp rabbit beta-globin gene fragment encoding the last 14-bp of its second exon, the 573-bp second intron, and the 364-bp last exon including a 98-bp 3'UTR with the polyA addition signal and addition site, and 39-bp of 3' beta-globin gene flanking sequence. The Ptf1a locus was modified by recombination-mediated cassette exchange using the cassette exchange allele in Ptf1a-LCA ES cells (Burlison et al., submitted). Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Ptf1a{tm1(tTAoff)Macd} Vanderbilt University Medical Center Ptf1a{tm1(tTAoff)Macd} mouse strain BCGO:9000209 A mouse strain containing a transgene in which DTR (transgene) is driven by the RIP promoter (NCBI Gene ID: ). NOD-Prkdc{scid} IL2rg{null}Tg(Ins2-HBEGF){6832Ugfm} mice are deficient in mature lymphocytes and NK cells, survive beyond 16 months of age, and even after sublethal irradiation resist lymphoma development. They can be induced to become hypoglycemic when Diphtheria toxin is used. 100% of beta cells will be depleted upon administration of diphtheria toxin. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler NOD.Cg-Prkdc{scid} Il2rg{tm1Wjl} Tg(Ins2-HBEGF){6832Ugfm}/Sz Vanderbilt University Medical Center NOD.Cg-Prkdc{scid} Il2rg{tm1Wjl} Tg(Ins2-HBEGF){6832Ugfm}/Sz mouse strain BCGO:9000210 A mouse strain containing a transgene in which DTR (transgene) is driven by the RIP promoter (NCBI Gene ID: ). NOD-scid IL2rg{null}Hprt{tm3(Ins2-HBEGF)Ugfm} mice are deficient in mature lymphocytes and NK cells, survive beyond 16 months of age, and even after sublethal irradiation resist lymphoma development. They can be induced to become hypoglycemic when Diphtheria toxin is used. 50% of beta cells will be depleted after diphtheria toxin administration. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler NOD.Cg-Prkdc{scid} Il2rg{tm1Wjl}Hprt{tm3(Ins2-HBEGF)Ugfm}/Sz Vanderbilt University Medical Center NOD.Cg-Prkdc{scid} Il2rg{tm1Wjl}Hprt{tm3(Ins2-HBEGF)Ugfm}/Sz mouse strain BCGO:9000211 A mouse strain in which the targeted gene, recombination activating gene 1 (NCBI Gene ID: 19373), has been modified (allele type: Global Null) to (MGI ID: ). The NOD-Rag1{null} Prf1{null} Ins2{Akita} mouse is the first immunodeficient, spontaneously hyperglycemic mouse strain described that is based on the Ins2{Akita} mutation. This strain is suitable as hosts for human islet and human beta stem and progenitor cell transplantation in the absence of the need for pharmacological induction of diabetes. This strain of mice also has low levels of innate immunity and can be engrafted with a human immune system for the study of human islet allograft rejection. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler NOD.Cg-Rag1{tm1Mom} Ins2{Akita} Prf1{tm1Sdz}/Sz Vanderbilt University Medical Center NOD.Cg-Rag1{tm1Mom} Ins2{Akita} Prf1{tm1Sdz}/Sz mouse strain BCGO:9000212 A mouse strain in which the targeted gene, interleukin 2 receptor, gamma chain (NCBI Gene ID: 16186), has been modified (allele type: Global Null) to (MGI ID: Il2rg{tm1Wjl}). Backcrossing of the Rag1 null allele onto the NOD/Lt strain background (NOD-Rag1{null} mice) provided a radio-resistant and longer-lived model for human-cell engraftment. Mutations in X-chromosome-linked Il2rg gene cause X-linked severe combined immunodeficiency (XSCID). Immunodeficient NOD-Rag1{null} IL2rg {null}mice tolerated much higher levels of irradiation conditioning than did NOD-Prkdc{scid} IL2rg {null} mice. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler NOD.Cg-Rag1{tm1Mom} Il2rg{tm1Wjl}/Sz Vanderbilt University Medical Center NOD.Cg-Rag1{tm1Mom} Il2rg{tm1Wjl}/Sz mouse strain BCGO:9000214 A mouse strain in which the targeted gene, interleukin 2 receptor, gamma chain (NCBI Gene ID: 16186), has been modified (allele type: Global Null) to targeted mutation 1 (MGI ID: Il2rg{tm1Wjl}). NOD.Cg-Prkdc{scid}Il2rg{tm1Wjl}Tg(Ins1-EGFP/GH1){14Hara}/Sz is a immunodeficient mouse carries a GFP transgene under the control of mouse insulin promoter 1, which leads to expression of eGFP in the beta cells. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler NOD.Cg-Prkdc{scid} Il2rg{tm1Wjl} Tg(Ins1-EGFP/GH1){14Hara}/Sz Vanderbilt University Medical Center NOD.Cg-Prkdc{scid} Il2rg{tm1Wjl} Tg(Ins1-EGFP/GH1){14Hara}/Sz mouse strain BCGO:9000215 A mouse strain in which the targeted gene, Neurogenin 3 (NCBI Gene ID: 11925), has been modified (allele type: Other) to targeted mutation 1 (MGI ID: Ngn3{EYFP/+}). A targeting construct was designed to insert an IRES-EYFP and a floxed puro downstream of the coding sequence. Crossing with mice expressing Cre in the germ line excised the puromycin resistance gene. Coding region for Ngn3 is kept intact consequentely homozygous mice express Ngn3 protein , do not develop diabetes and behave like wild-types. in these mice, Ngn3-positive progenitors express EYFP and can be purified by FACS. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Neurog3{tm1Ggr} Vanderbilt University Medical Center Neurog3{tm1Ggr} mouse strain BCGO:9000216 A mouse strain containing a transgene in which bicistronic Ptf1a-lacZ (transgene) is driven by the TRE promoter (NCBI Gene ID: ). Mice hemi- or homozygous for the transgene are viable, fertile, normal size, and do not display any behavioral abnormalities. Expression of the bicistronic transgene is directed by a heptameric tetO repeat linked to the CMV minimal promoter (collectively the tetracycline-response element). The mice do not express lacZ until a tetracycline-gransactivator (tTA) protein is produced; thereafter Ptf1a and lacZ genes are highly expressed. This mouse was designed to be mated to an apancreatic targeted mutant with tTAoff in place of the Ptf1a coding sequence (see BCBC strain M321). The combined genetic alterations provide normal pancreatic development and function until doxycycline-administration render the mice conditionally null of Ptf1a. This approach allows embryonic developmental arrest at desired stages or cessation of gene function in adult mice for the pancreas, cerebellum, retina, dorsal spinal cord and possibly hypothalamus. This transgenic mouse may be useful in studies of pancreatic endocrine/exocrine development and function, diabetes, and and certain defects of the CNS. This transgenic can also be bred with other tTA strains for conditional mutation analysis. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Tg(tetO-Ptf1a,lacZ)Macd Vanderbilt University Medical Center Tg(tetO-Ptf1a,lacZ)Macd mouse strain BCGO:9000218 A mouse strain in which part or all of the targeted gene, pancreas specific transcription factor, 1a (NCBI Gene ID: 19213) is replaced to create Ptf1a{tm2(W298A)} using the Loxed Cassette Acceptor allele Ptf1a{tm1(LCA)}). This mouse strain has a 2-bp site-directed mutation in the endogenous Ptf1a locus that changes codon 298 from tryptophan to alanine. The mutation disrupts the ability of the PTF1a protein to bind RBPJ. Mice heterozygous for the mutation are viable, fertile, of normal size, and do not display any behavioral abnormalities. Mice homozygous for the mutation phenocopy the homozygous Ptf1a-null. Newborn homozygotes are apancreatic, devoid of the dI4 and dILA GABAergic dorsal interneurons, have an incomplete cerebellum, and die shortly after birth. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Ptf1a{tm2(W298A)Macd} Vanderbilt University Medical Center Ptf1a{tm2(W298A)Macd} mouse strain BCGO:9000219 A mouse strain in which the targeted gene, Recombination signal binding protein for immunoglobulin kappa J region-like (NCBI Gene ID: 19668), has been modified (allele type: Global Mutation) to Rbpjl{tm1Macd} (MGI ID: Rbpjl{tm1(lacZ)}). This mouse strain has the Rbpjl gene region spanning exons 7, 8, and 9 replaced with lacZ in-frame. A pgk-neo resistance cassette has been removed by Cre-loxP deletion from the founder. Mice heterozygous and homozygous for the lacZ replacement are viable, fertile, of normal size, and do not display any behavioral abnormalities. In mature mice, the pancreas is one-third smaller than normal, due to less acinar tissue. Expression of the lacZ, measured by bet-galactosidase histostaining is very low. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Rbpjl{tm1(lacZ)Macd} Vanderbilt University Medical Center Rbpjl{tm1(lacZ)Macd} mouse strain BCGO:9000220 A mouse strain in which the targeted gene, Pancreatic and duodenal homeobox 1 (NCBI Gene ID: 18609), has been modified (allele type: Gene Replacement) to targeted mutation 1 (MGI ID: Pdx1{tmd1Macd}). Mice homozygous for the targeted mutation fail to develop a pancreas. Heterozygous mice have normal pancreatic development, but have partially impaired glucose tolerance in adulthood. The substitution of the targeted Ipf1/Pdx1 gene with tTAoff inactivates the endogenous allele and places tTAoff expression under the control of the endogenous transcriptional regulatory sequences of the Pdx1 locus. Identical to the endogenous allele, mutant locus expression is detectable in the pancreas and adjacent duodenum but not in other visceral organs or salivary glands. This mutant may be useful to direct tetracycline-regulated expression of responder transgenes in studies of pancreatic endocrine/exocrine development and function and diabetes. This mutant can also be bred with other tetO/TRE strains for pancreas-specific applications. This mutant was originally designed to be mated with mice engineered with a heptameric tetracycline operator (tetO)-controlled bicistronic transgene coding for a normal PDX1 protein and with a beta-galactosidase or EGFP reporter (see BCBC mouse M561). The combined modifications allow normal pancreatic development and function until doxycycline-administration renders the mouse conditionally null of the Pdx1 gene. This configuration for conditional expression of Pdx1is most effective when the transgene locus is homozygous. This allows embryonic developmental arrest at desired stages or cessation of function in adult mice by tetracycline administration. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler STOCK Pdx1{tm1Macd}/J Vanderbilt University Medical Center STOCK Pdx1{tm1Macd}/J mouse strain BCGO:9000221 A mouse strain containing a transgene in which bicistronic Pdx1-lacZ (transgene) is driven by the TRE promoter (NCBI Gene ID: ). Mice hemizygous and homozygous for the transgenic insert are viable, fertile, of normal size, and do not display any behavioral abnormalities. Expression of the bicistronic transgene is directed by a heptameric tetO repeat fused to a minimal promoter (collectively the tetracycline-response element, or TRE). Transgenic mice do not express lacZ until a tetracycline-transactivator (tTA) protein is introduced; thereafter Pdx1 and lacZ from the transgene are expressed. All cells expressing transgenic Pdx1 coexpress the reporter. Further, mRNA levels of the transgene and endogenous Pdx1 fluctuate in concert during development. This mouse was originally designed to be mated to an apancreatic targeted mutant with the coding sequence of the Pdx1 locus replaced with that for tTAoff (see BCBC #M541). The combined mutations allow normal pancreatic development and function until doxycycline treatments render the mouse conditionally null of the endogenous gene. For this configuration, rescue of pancreatic development is most effective when the transgene locus is homozygous. This allows embryonic developmental arrest at desired stages or cessation of function in adult mice by administration of tetracycline/doxycycline. This transgenic strain may be useful in studies of pancreatic development and endocrine/exocrine function and diabetes. This strain can also be bred with other tTA strains for regulating Pdx1 expression in other contexts. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler STOCK Tg(tetO-Pdx1,lacZ)958.1Macd Vanderbilt University Medical Center STOCK Tg(tetO-Pdx1,lacZ)958.1Macd mouse strain BCGO:9000222 A mouse strain in which the targeted gene, Neurogenin 3 (NCBI Gene ID: 11925), has been modified (allele type: Other) to targeted mutation 2 (MGI ID: Neurog3{tm2(EGFP)Ggr). A targeting construct was designed to insert an IRES-EGFP and a floxed puro downstream of the coding sequence. Crossing with mice expressing Cre in the germ line excised the puromycin resistance gene. Homozygous mice express Ngn3 protein, do not develop diabetes and behave like wild-types. Ngn3-positive cells are labeled with EGFP and can be purified by FACS. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Neurog3{tm2(EGFP)Ggr} Vanderbilt University Medical Center Neurog3{tm2(EGFP)Ggr} mouse strain BCGO:9000223 A mouse strain containing a transgene in which LacZ (transgene) is driven by the Neurog3 promoter (NCBI Gene ID: 11925). Transgenic mice where Ngn3-positive cell are labeled with beta-galactosidase. Due to the stability of beta-galactosidase protein, the early descendants of Ngn3-positve cells are also labeled. To generate the Ngn3 promoter::LacZ construct, a 6.86 kb XbaI-XhoI fragment (6696 bp of 5' genomic and untranslated region sequences and 176 bp of ngn3 coding region) of mouse ngn3 genomic DNA was cloned upstream of the IRES-NLS-LacZ-pA sequence in pBS-INL vector resulting in plasmid pngn3(6.8)-INL. The 10.6 kb Ngn3-IRES-NLS-LacZ insert was released by NotI digestion and microinjected into murine oocyte pronuclei, and transgenic line was generated and maintained by crossing into a CD1 outbred background. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Tg(Neurog3-IRES-NLS-LacZ)1Ggr Vanderbilt University Medical Center Tg(Neurog3-IRES-NLS-LacZ)1Ggr mouse strain BCGO:9000224 A mouse strain containing a transgene in which mRFP (transgene) is driven by the Ins1 promoter (NCBI Gene ID: 1633). These transgenic mice express the monomeric red fluorescent protein under the control of Ins1 gene (BAC) regulatory elements. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Tg(Ins1-mRFP)2Ggr Vanderbilt University Medical Center Tg(Ins1-mRFP)2Ggr mouse strain BCGO:9000225 A mouse strain in which the targeted gene, Arx (NCBI Gene ID: 11878), has been modified (allele type: Gene Replacement) to targeted mutation 1 (MGI ID: Arx{tm1Pgr}). These mice were created by insertion of the LacZ gene (with nuclear localization signal) into the Arx locus by homologous recombination in embryonic stem cells. The Arx gene is localized on the X chromosome. Knockout mice die after birth with due to hypoglycemia. Therefore male mice die at day 2 past birth. The colony has to be propagated with female mice. Arx-deficient mice do not produce alpha cells in the islets of Langerhans. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Arx{tm1Pgr} Vanderbilt University Medical Center Arx{tm1Pgr} mouse strain BCGO:9000228 A mouse strain in which the targeted gene, v-maf musculoaponeurotic fibrosarcoma oncogene family, protein A (avian) (NCBI Gene ID: 378435), has been modified (allele type: Conditional Null) to targeted mutation 1.1 (MGI ID: Mafa{tm1.1(lox)}). Mafa is a basic leucine-zipper containing member of the large Maf transcription factor family.It is part of the RIPE3b1 activator complex and functions as a key activator of insulin and pdx-1 gene transcription. Mafa{lox} mice may be used to generate both global and cell-specific Mafa null mice, depending on which cre-expressing transgenic mouse is used. Removal of Mafa gene might have a profound effect on beta cell function; thus we can closely monitor the expression of islet hormones, transcription functions and the glucose sensing machinery immunohistochemically. The experiment will provide us with the information about the role of Mafa plays in vivo in islet beta cells and the developing pancreas, thus helping us to understand how transcription activator contribute to the pathogenesis and the treatment of diabetes. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Mafa{tm1.1Rwst} Vanderbilt University Medical Center Mafa{tm1.1Rwst} mouse strain BCGO:9000229 A mouse strain in which the targeted gene, Myt1 (myelin transcriptioin factor 1) (NCBI Gene ID: 1100535 ), has been modified (allele type: Conditional Null) to targeted mutation 1.1 (MGI ID: Myt1{tm1.1Ggu}). Two loxP sites flank exon 6 of Myt1b. The allele behaves as wild type allele without Cre-mediated deletion. Cre-mediated deletion creates null Myt1 allele. The homozygous null is neonatal lethal. Myt1 null pancreas has abnormal islet cell differentiation, ie. single cells produce multiple hormones. Pancreatic-specific Myt1 deletion results in glucose intolerance in males. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Myt1{tm1.1Ggu} Vanderbilt University Medical Center Myt1{tm1.1Ggu} mouse strain BCGO:9000230 A mouse strain in which the targeted gene, Onecut1 (NCBI Gene ID: 15379), has been modified (allele type: Conditional Null) to targeted mutation 1.1 (MGI ID: OC-1{tm1.1Mga}). This line of mice allows for conditional inactivation of the OC-1 (HNF6) gene using Cre recombinase. Thus, HNF6 function can be assessed in the different tissues in which it is expressed. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler OC-1{tm1.1Mga} Vanderbilt University Medical Center OC-1{tm1.1Mga} mouse strain BCGO:9000231 A mouse strain in which part or all of the targeted gene, NK2 transcription factor related, locus 2 (NCBI Gene ID: 18088) is replaced to create Nkx2.2(TNmut) using the Loxed Cassette Acceptor allele Nkx2.2{tm1(LCA)}). These mice contain mutations in the central core of the Nkx2.2 TN domain (putative groucho-interaction domain). Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Nkx2-2{tm3Suss} Vanderbilt University Medical Center Nkx2-2{tm3Suss} mouse strain BCGO:9000232 A mouse strain in which part or all of the targeted gene, NK2 transcription factor related, locus 2 (NCBI Gene ID: 18088) is replaced to create Nkx2.2:rtTA using the Loxed Cassette Acceptor allele Nkx2.2{tm1(LCA)}). The reverse tetracycline transactivator (rtTA) is knocked into the Nkx2.2 coding region, effectively knocking out one Nkx2.2 allele. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Nkx2-2{tm2Suss} Vanderbilt University Medical Center Nkx2-2{tm2Suss} mouse strain BCGO:9000233 A mouse strain containing a transgene in which Diphtheria Toxin Receptor (transgene) is driven by the Gcg promoter (NCBI Gene ID: 14526). Transgenic strain (generated by pronuclear microinjection) of a transgene containing the rat glucagon promoter (1.6kb fragment) upstream of a rabbit beta-globin intron and the coding sequence of the human diphtheria toxin receptor (heparin-binding epidermal growth factor, membrane form). Downstream, there is a rabbit beta-globin stop codon and the polyadenylation signal. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler C57/CBAJ-TgN(Glucagon- hHB EGF)Ugfm Vanderbilt University Medical Center C57/CBAJ-TgN(Glucagon- hHB EGF)Ugfm mouse strain BCGO:9000234 A mouse strain containing a transgene in which rtTA (transgene) is driven by the Gcg promoter (NCBI Gene ID: 14526). Transgenic strain (generated by pronuclear microinjection) of a transgene containing the rat glucagon promoter (1.6kb fragment) upstream of the coding region of the reverse transactivator doxycycline-dependent. The rtTA is flanked by a rabbit beta-globin intron and downstream there is a stop and polyA signal from the same rabbit beta-globin gene. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler C57/CBAJ-TgN(Glucagon- rtTA)Ugfm Vanderbilt University Medical Center C57/CBAJ-TgN(Glucagon- rtTA)Ugfm mouse strain BCGO:9000235 A mouse strain containing a transgene in which DTR (transgene) is driven by the Ins promoter (NCBI Gene ID: 16333). Transgenic mice generated by pronuclear microinjection of a transgene encoding the human diphtheria toxin receptor (heparin binding epidermal growth factor, also termed DTR) under the control of the rat insulin II gene promoter (0.6kb-long fragment). The DTR coding sequence is flanked by the rabbit beta-globin intron and stop/polyA sequences. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler C57/CBAJ-Tg(Ins2- HBEGF){6832Ugfm} Vanderbilt University Medical Center C57/CBAJ-Tg(Ins2- HBEGF){6832Ugfm} mouse strain BCGO:9000237 A mouse strain containing a transgene in which Luc (transgene) is driven by the MIP promoter (NCBI Gene ID: 16333). We generated a transgenic mouse expressing the luciferase optical reporter under control of the mouse insulin I promoter (MIP-Luc-VU) and characterized this model in mice with increased or decreased beta-cell mass and after islet transplantation. MIP-Luc-VU mice emitted strong and consistent bioluminescence emanating exclusively from beta-cells of the pancreatic islet. MIP-Luc-VU islets had normal islet architecture and secreted insulin normally in vivo and in vitro. By tracking changes in &beta; cell mass using bioluminescence imaging (BLI) and post-mortem metrics, streptozotocin-induced, diabetic MIP-Luc-VU mice had a progressive decline in bioluminescence that correlated with a decrease in pancreatic insulin content and beta-cell mass. MIP-Luc-VU animals fed a high fat diet displayed a progressive increase in bioluminescence that reflected an immunohistochemically verified increase in beta-cell mass. MIP-Luc-VU islets transplanted beneath the renal capsule or into the liver emitted bioluminescence proportional to the number of islets transplanted and graft insulin content and could be imaged for more than a year. Since bioluminescence in the MIP-Luc-VU mouse model is proportional to beta-cell mass in the setting of increased and decreased beta-cell mass and after transplantation, this approach should be useful for non-invasively assessing beta-cell mass in pre-clinical mouse models of glucose homeostasis, beta-cell growth and regeneration, and diabetes. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler FVB/NJ-Tg(MIP-Luc-VU)3Pwrs/J Vanderbilt University Medical Center FVB/NJ-Tg(MIP-Luc-VU)3Pwrs/J mouse strain BCGO:9000238 A mouse strain in which the targeted gene, ROSA26 (NCBI Gene ID: 14910), has been modified (allele type: Conditional Activating) to ROSA26-loxp-STOP-loxp-Myt1 (MGI ID: Not yet available). Targeted insertion of a LoxP-STOP-LoxP-Myt1 casette into the ROSA26 locus. The presence of Cre recombinase will lead to activation of the 7 zinc finger isoform of Myt1. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Gt(ROSA)26Sor{tm1(Myt1*)Hri} Vanderbilt University Medical Center Gt(ROSA)26Sor{tm1(Myt1*)Hri} mouse strain BCGO:9000239 A mouse strain in which the targeted gene, Neurogenin 3 (NCBI Gene ID: 11925), has been modified (allele type: Gene Replacement) to Ngn3 tTA knockin (MGI ID: Ngn3tTA). The mouse contains a Ngn3 knock-in allele. IRES-tTA-rabbit beta globin polyA signal replaced the entire Ngn3 cDNA coding sequence. This is therefore also a Ngn3 null allele. Ngn3 is a bHLH transcription factor that is required for the differentiation of endocrine islet and some neuronal cells. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Ngn3{tm1(tTA)Hri} Vanderbilt University Medical Center Ngn3{tm1(tTA)Hri} mouse strain BCGO:9000240 A mouse strain in which part or all of the targeted gene, NK2 transcription factor related, locus 2 (NCBI Gene ID: 18088) is replaced to create Nkx2.2:LacZ using the Loxed Cassette Acceptor allele Nkx2.2{tm1(LCA)}). The lacZ gene has been knocked in to the Nkx2.2 genomic locus using RMCE, effectively replacing the two coding exons. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Nkx2-2{tm1Suss} Vanderbilt University Medical Center Nkx2-2{tm1Suss} mouse strain BCGO:9000241 A mouse strain in which part or all of the targeted gene, NK2 transcription factor related, locus 2 (NCBI Gene ID: 18088) is replaced to create Nkx2.2-NK2 mutation using the Loxed Cassette Acceptor allele Nkx2.2{tm1(LCA)}). The strain carries a mutant Nkx2.2 allele in which conserved residues of the NK2 domain are mutated to alanines. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Nkx2-2{tm4Suss} Vanderbilt University Medical Center Nkx2-2{tm4Suss} mouse strain BCGO:9000242 A mouse strain in which part or all of the targeted gene, pancreatic and duodenal homeobox 1 (NCBI Gene ID: 18609) is replaced to create Pdx1{AIId} using the Loxed Cassette Acceptor allele Pdx1{tm1(LCA)}). This is a targeted deletion of Area II 5' cis-regulatory region of Pdx1. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Pdx1{tm6Cvw} Vanderbilt University Medical Center Pdx1{tm6Cvw} mouse strain BCGO:9000243 A mouse strain in which the targeted gene, Pancreatic and Duodenal homeobox 1 (NCBI Gene ID: 18609), has been modified (allele type: Conditional Null) to targeted mutation 4 (MGI ID: Pdx1{tm4(E2)}). This is a conditional null allele of Pdx1. LoxP sites for Cre recombinase were inserted to flank exon 2 of the gene. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Pdx1{tm4Cvw} Vanderbilt University Medical Center Pdx1{tm4Cvw} mouse strain BCGO:9000244 A mouse strain in which part or all of the targeted gene, pancreas specific transcription factor, 1a (NCBI Gene ID: 19213) is replaced to create Ptf1a{tm2(cre/ESR1)} using the Loxed Cassette Acceptor allele Ptf1a{tm1(LCA)}). CreER knock-in into Ptf1a locus replacing part of the exon1 at the translation initiator ATG position using RMCE method. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Ptf1a{tm2(cre/ESR1)Cvw} Vanderbilt University Medical Center Ptf1a{tm2(cre/ESR1)Cvw} mouse strain BCGO:9000245 A mouse strain in which the targeted gene, Pancreatic and Duodenal homeobox 1 (NCBI Gene ID: 18609), has been modified (allele type: Other) to targeted mutation 5 (MGI ID: Pdx1{tm5(AI-II-III)}). LoxP sites for cre recombinase were inserted to flank Area I-II-III, a conserved 5' cis-regulatory region of Pdx1. This allele was shown to be a conditional hypomorph by Fujitani et al. (2006) (PMID 16418487). Pdx1{tm3Cvw} (Pdx1{deltaI-II-III}) is generated by Cre-mediated recombination in the germline of this allele. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Pdx1{tm5Cvw} Vanderbilt University Medical Center Pdx1{tm5Cvw} mouse strain BCGO:9000246 A mouse strain in which the targeted gene, Delta-like 1 (NCBI Gene ID: 13388), has been modified (allele type: Conditional Null) to targeted mutation 1 (MGI ID: Dll1{tm1Hri}). This is a targeted mutation of the Notch ligand Dll1, introducing two loxP sites flanking the exons encoding the DSL domain. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Dll1{tm1Hri} Vanderbilt University Medical Center Dll1{tm1Hri} mouse strain BCGO:9000247 A mouse strain in which the targeted gene, Pancreatic and Duodenal homeobox 1 (NCBI Gene ID: 18609), has been modified (allele type: Global Mutation) to targeted mutation 3 (MGI ID: Pdx1{tm3(deltaI-II-III)). Area I-II-III, a conserved 5' cis-regulatory region of Pdx1, was removed by Cre mediated recombination in the germline of Pdx1{tm5Cvw} (Pdx1{Flox123}) by crossing to deleter Cre mice. This allele was shown to be a hypomorph. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Pdx1{tm3Cvw} Vanderbilt University Medical Center Pdx1{tm3Cvw} mouse strain BCGO:9000248 A mouse strain in which the targeted gene, Pancreas Specific Transcription Factor, 1a (NCBI Gene ID: 19213), has been modified (allele type: Cassette Acceptor) to Targeted Mutation 3 (MGI ID: Ptf1a{tm3Cvw}). This mouse strain is a conditional null allele of Ptf1a. LoxP sites flanking exon 1 and 2 (entire coding region of Ptf1a). Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Ptf1a{tm3Cvw} Vanderbilt University Medical Center Ptf1a{tm3Cvw} mouse strain BCGO:9000253 A mouse ESC line in which the targeted gene, pancreas specific transcription factor, 1a (NCBI Gene ID: 19213), has been modified (allele type: Cassette Acceptor) to targeted mutation 1 (MGI ID: Ptf1a{tm1(LCA)}). This ES cell line contains a loxed cassette acceptor (LCA) allele in which a 4.1 kb region of this gene (including the proximal promoter and both exons 1 and 2) was replaced with a loxP site, an inverted loxP site, and both positive and negative selectable markers. This enables the use of Recombinase-Mediated Cassette Exchange (RMCE) to easily insert various reporter genes or to make other modifications of the Ptf1a gene locus. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Ptf1a{LCA} mouse ESC line BCGO:9000254 A mouse ESC line in which part or all of the targeted gene, pancreas specific transcription factor, 1a (NCBI Gene ID: 19213) is replaced to create Ptf1a{LCA} using the Loxed Cassette Acceptor allele Ptf1a{tm1.1(YFP)}). This ES cell line contains YFP inserted into a Ptf1a{LCA} allele by recombinase mediated cassette exchange. These cells may be useful for identifying pancreatic progenitor cells in cultures that have been stimulated to differentiate towards endodermal and pancreatic fates. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Ptf1a{YFP} mouse ESC line BCGO:9000255 A mouse ESC line in which the targeted gene, glucokinase (NCBI Gene ID: 19213), has been modified (allele type: Cassette Acceptor) to targeted mutation 4 (MGI ID: gk{tm4(LCA)}). This ES cell line contains a loxed cassette acceptor (LCA) allele that may be utilized for the exchange of DNAs of interest into the glucokinase locus by recombinase mediated cassette exchange (RMCE). This LCA uses a loxP/inverted loxP strategy for RMCE and allows sequences between - 6 kb and + 5 kb (relevative to the hepatic-specific promoter) to be manipulated. This enables a variety of different types of experiments to be performed using a range of cassette designs. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Gck{LCA} mouse ESC line BCGO:9000256 A mouse ESC line in which the targeted gene, insulinoma-associated 1 (NCBI Gene ID: 53626), has been modified (allele type: Cassette Acceptor) to targeted mutation 1 (MGI ID: Insm1{tm1(LCA)}). This ES cell line contains a loxed cassette acceptor(LCA)allele that may be utilized for the exchange of DNAs of interest into the Insm1 gene locus by recombinase mediated cassette exchange (RMCE). This LCA uses a lox 66/71 and lox 2272 strategy for RMCE and allows a ~5.2 kb region of this single exon gene to be manipulated. This enables a variety of different types of experiments to be performed using a range of cassette designs. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Insm1{LCA} mouse ESC line BCGO:9000257 A mouse ESC line in which the targeted gene, NK2 transcription factor related, locus 2 (NCBI Gene ID: 18088), has been modified (allele type: Cassette Acceptor) to targeted mutation 1 (MGI ID: Nkx2.2{tm1(LCA)}). This ES cell line contains a loxed cassette acceptor (LCA) allele that may be utilized for the exchange of DNAs of interest into the Nkx2.2 locus by recombinase mediated cassette exchange (RMCE). This LCA uses a Lox71/66 and Lox2272 strategy for RMCE and allows for manipulation of a 5.1 kb region of the gene (contains promoter, exon 1, and exon 2). This leads to a variety of experiments that can be performed using a wide range of cassette designs. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Nkx2.2{LCA} mouse ESC line BCGO:9000260 A mouse ESC line containing a transgene in which Gfp (transgene) is driven by the Ins1 promoter (NCBI Gene ID: 16333). New ESC line derived from MIP-GFP mice (Hara et al. 2003,Am J Physiol Endocrinol Metab. 284: E177-83). Genetic background is C57Bl6/J. When injected into E3.5 mouse blastocysts this line contributes to chimeras and Insulin+/GFP+ double positive cells are found in E14.5 embryonic pancreas. No GFP+ cells are seen outside the pancreas. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center MIP-GFP mouse ESC line BCGO:9000261 A mouse ESC line containing a transgene in which Gfp (transgene) is driven by the Neurog3 promoter (NCBI Gene ID: 11925). Mouse ESC line derived from Ngn3-GFP transgenic mice (Gradwohl et al. unpublished). Genetic background is CD1. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Ngn3-GFP mouse ESC line BCGO:9000262 A mouse ESC line in which the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910), has been modified (allele type: Cassette Acceptor) to targeted mutation 1 (MGI ID: Rosa26{tm1(LCA)}). This ES cell line contains a loxed cassette acceptor (LCA) allele in which a 5.17 kb region of the gene has been replaced by a Lox66 site, a puromycin-(delta)-thymidine kinase fusion gene driven by the mouse phosphoglycerol kinase promoter, a kanamycin resistance gene driven by the bacterial EM7 promoter, and a Lox2272 site. These features enable use of Recombinase-Mediated Cassette Exchange for the rapid insertion of various DNAs into the Rosa26 gene locus. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Rosa26{LCA} mouse ESC line BCGO:9000263 A mouse ESC line in which the targeted gene, SRY-box containing gene 17 (NCBI Gene ID: 20671), has been modified (allele type: Cassette Acceptor) to targeted mutation 1 (MGI ID: Sox17{tm1(LCA)}). This mouse ES cell line contains a loxed cassette acceptor (LCA) allele that may be utilized for the exchange of DNAs of interest into the Sox17 gene locus by recombinase mediated cassette exchange (RMCE). A 3.79 kb region of the gene (exons 3-5) was replaced by tandemly oriented lox66 and lox2272 sites as well as both positive and negative selectable markers. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Sox17{LCA} mouse ESC line BCGO:9000266 A polyclonal antibody raised in rabbit that targets the rat "IAPP" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal rat IAPP raised in rabbit BCGO:9000267 A polyclonal antibody raised in rabbit that targets the rat "C-peptide 2" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal rat C-peptide 2 raised in rabbit BCGO:9000268 A polyclonal antibody raised in rabbit that targets the rat "C-peptide 1" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal rat C-peptide 1 raised in rabbit BCGO:9000269 A polyclonal antibody raised in rabbit that targets the mouse "C-peptide 1" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal mouse C-peptide 1 raised in rabbit BCGO:9000270 A monoclonal antibody raised in mouse that targets the human "Insulin" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal human Insulin raised in mouse BCGO:9000271 A polyclonal antibody raised in rabbit that targets the rat "PDX1" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal rat PDX1 raised in rabbit BCGO:9000272 A polyclonal antibody raised in rabbit that targets the rat "PDX1" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal rat PDX1 raised in rabbit BCGO:9000273 A polyclonal antibody raised in rabbit that targets the rat "Nkx6.1" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal rat Nkx6.1 raised in rabbit BCGO:9000274 A polyclonal antibody raised in goat that targets the human "Nkx2.2" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal human Nkx2.2 raised in goat BCGO:9000275 A polyclonal antibody raised in goat that targets the human "ghrelin" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal human ghrelin raised in goat BCGO:9000276 A polyclonal antibody raised in rabbit that targets the mouse "Pax6" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal mouse Pax6 raised in rabbit BCGO:9000277 A polyclonal antibody raised in goat that targets the human "b-catenin" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal human b-catenin raised in goat BCGO:9000278 A monoclonal antibody raised in mouse that targets the mouse "smooth muscle actin" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal mouse smooth muscle actin raised in mouse BCGO:9000279 A polyclonal antibody raised in rabbit that targets the human "amylase" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal human amylase raised in rabbit BCGO:9000280 A polyclonal antibody raised in rabbit that targets the human "c-myc" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal human c-myc raised in rabbit BCGO:9000281 A polyclonal antibody raised in rabbit that targets the rat "Glut-2" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal rat Glut-2 raised in rabbit BCGO:9000282 A polyclonal antibody raised in rabbit that targets the bovine "Carboxypeptidase A" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal bovine Carboxypeptidase A raised in rabbit BCGO:9000283 A polyclonal antibody raised in rabbit that targets the human "Chromogranin A" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal human Chromogranin A raised in rabbit BCGO:9000284 A monoclonal antibody raised in mouse that targets the human "Chromogranin A" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal human Chromogranin A raised in mouse BCGO:9000285 A monoclonal antibody raised in mouse that targets the human "Cytokeratin 7" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal human Cytokeratin 7 raised in mouse BCGO:9000286 A monoclonal antibody raised in mouse that targets the human "PECAM-1" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal human PECAM-1 raised in mouse BCGO:9000287 A polyclonal antibody raised in rabbit that targets the aequorea victoria "Green Fluorescent Protein" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal aequorea victoria Green Fluorescent Protein raised in rabbit BCGO:9000288 A monoclonal antibody raised in mouse that targets the chicken "Nkx2.2" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal chicken Nkx2.2 raised in mouse BCGO:9000289 A polyclonal antibody raised in rabbit that targets the rat "ghrelin" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal rat ghrelin raised in rabbit BCGO:9000290 A monoclonal antibody raised in mouse that targets the chicken "Islet-1" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal chicken Islet-1 raised in mouse BCGO:9000291 A polyclonal antibody raised in rabbit that targets the human "GATA-4" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal human GATA-4 raised in rabbit BCGO:9000292 A polyclonal antibody raised in rabbit that targets the mouse "PDX1" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal mouse PDX1 raised in rabbit BCGO:9000294 A polyclonal antibody raised in chicken that targets the mouse "PDX1" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal mouse PDX1 raised in chicken BCGO:9000295 A monoclonal antibody raised in mouse that targets the human "Glucagon" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal human Glucagon raised in mouse BCGO:9000296 A monoclonal antibody raised in mouse that targets the human "Somatostatin" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal human Somatostatin raised in mouse BCGO:9000297 A monoclonal antibody raised in mouse that targets the rat "Pancreatic Ducts" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal rat Pancreatic Ducts raised in mouse BCGO:9000298 A monoclonal antibody raised in mouse that targets the rat "Pancreatic Ducts" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal rat Pancreatic Ducts raised in mouse BCGO:9000299 A monoclonal antibody raised in rat that targets the rat "Islet Delta Cells" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal rat Islet Delta Cells raised in rat BCGO:9000300 A monoclonal antibody raised in rat that targets the rat "Pancreatic Ducts" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal rat Pancreatic Ducts raised in rat BCGO:9000301 A monoclonal antibody raised in mouse that targets the human "Pro-Insulin" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal human Pro-Insulin raised in mouse BCGO:9000302 A polyclonal antibody raised in rabbit that targets the mouse "Ngn3" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal mouse Ngn3 raised in rabbit BCGO:9000303 A polyclonal antibody raised in rabbit that targets the mouse "Ngn3" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal mouse Ngn3 raised in rabbit BCGO:9000304 A monoclonal antibody raised in mouse that targets the mouse "Ngn3" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal mouse Ngn3 raised in mouse BCGO:9000305 A monoclonal antibody raised in mouse that targets the mouse "Ngn3" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal mouse Ngn3 raised in mouse BCGO:9000307 A monoclonal antibody raised in mouse that targets the rat "Nkx6.1" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal rat Nkx6.1 raised in mouse BCGO:9000308 A monoclonal antibody raised in mouse that targets the rat "Nkx6.1" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal rat Nkx6.1 raised in mouse BCGO:9000309 A monoclonal antibody raised in mouse that targets the rat "Nkx6.1" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal rat Nkx6.1 raised in mouse BCGO:9000310 A monoclonal antibody raised in mouse that targets the rat "Nkx6.1" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal rat Nkx6.1 raised in mouse BCGO:9000311 A polyclonal antibody raised in rabbit that targets the human "HNF6" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal human HNF6 raised in rabbit BCGO:9000312 A polyclonal antibody raised in goat that targets the mouse "PDX1" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal mouse PDX1 raised in goat BCGO:9000313 A polyclonal antibody raised in guinea pig that targets the mouse "PDX1" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal mouse PDX1 raised in guinea pig BCGO:9000314 A polyclonal antibody raised in rabbit that targets the human "ghrelin" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal human ghrelin raised in rabbit BCGO:9000315 A polyclonal antibody raised in rabbit that targets the human "ghrelin" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal human ghrelin raised in rabbit BCGO:9000316 A monoclonal antibody raised in mouse that targets the rat "PDX1" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal rat PDX1 raised in mouse BCGO:9000317 A monoclonal antibody raised in mouse that targets the rat "PDX1" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal rat PDX1 raised in mouse BCGO:9000318 A monoclonal antibody raised in mouse that targets the rat "PDX1" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal rat PDX1 raised in mouse BCGO:9000321 A polyclonal antibody raised in rabbit that targets the human "Sox2" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal human Sox2 raised in rabbit BCGO:9000322 A polyclonal antibody raised in goat that targets the mouse "FoxA2" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal mouse FoxA2 raised in goat BCGO:9000323 A monoclonal antibody raised in mouse that targets the human "E-cadherin" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal human E-cadherin raised in mouse BCGO:9000324 A polyclonal antibody raised in rabbit that targets the human "Sox17" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal human Sox17 raised in rabbit BCGO:9000325 A polyclonal antibody raised in rabbit that targets the human "Sox17" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal human Sox17 raised in rabbit BCGO:9000326 A monoclonal antibody raised in mouse that targets the human "Pancreatic endocrine cells" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal human Pancreatic endocrine cells raised in mouse BCGO:9000327 A monoclonal antibody raised in mouse that targets the human "Pancreatic endocrine cells" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal human Pancreatic endocrine cells raised in mouse BCGO:9000328 A monoclonal antibody raised in mouse that targets the human "Pancreatic endocrine cells" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal human Pancreatic endocrine cells raised in mouse BCGO:9000329 A monoclonal antibody raised in mouse that targets the human "Pancreatic endocrine cells" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal human Pancreatic endocrine cells raised in mouse BCGO:9000330 A monoclonal antibody raised in mouse that targets the human "Pancreatic endocrine cells" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal human Pancreatic endocrine cells raised in mouse BCGO:9000331 A polyclonal antibody raised in goat that targets the human "Sox17" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal human Sox17 raised in goat BCGO:9000332 A polyclonal antibody raised in goat that targets the mouse "Shh" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal mouse Shh raised in goat BCGO:9000333 A polyclonal antibody raised in chicken that targets the e. coli "beta Galactosidase" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal e. coli beta Galactosidase raised in chicken BCGO:9000334 A monoclonal antibody raised in mouse that targets the aequorea victoria "Green Fluorescent Protein" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal aequorea victoria Green Fluorescent Protein raised in mouse BCGO:9000335 A polyclonal antibody raised in rabbit that targets the mouse "Ptf1a" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal mouse Ptf1a raised in rabbit BCGO:9000336 A polyclonal antibody raised in rabbit that targets the mouse "IA1 (Insm-1)" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal mouse IA1 (Insm-1) raised in rabbit BCGO:9000337 A monoclonal antibody raised in mouse that targets the human "Pancreatic duct cells" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal human Pancreatic duct cells raised in mouse BCGO:9000338 A monoclonal antibody raised in mouse that targets the human "Pancreatic duct cells" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal human Pancreatic duct cells raised in mouse BCGO:9000339 A monoclonal antibody raised in mouse that targets the human "Pancreatic exocrine cells" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal human Pancreatic exocrine cells raised in mouse BCGO:9000340 A monoclonal antibody raised in mouse that targets the human "Pancreatic exocrine cells" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal human Pancreatic exocrine cells raised in mouse BCGO:9000341 A monoclonal antibody raised in mouse that targets the human "Pancreatic endocrine cells" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal human Pancreatic endocrine cells raised in mouse BCGO:9000342 A monoclonal antibody raised in mouse that targets the human "Alpha cells" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal human Alpha cells raised in mouse BCGO:9000343 A monoclonal antibody raised in mouse that targets the human "Alpha cells" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal human Alpha cells raised in mouse BCGO:9000344 A monoclonal antibody raised in rat that targets the mouse "Mo ES-Derived Definitive Endoderm" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal mouse Mo ES-Derived Definitive Endoderm raised in rat BCGO:9000345 A monoclonal antibody raised in rat that targets the mouse "Mo ES-Derived Definitive Endoderm" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal mouse Mo ES-Derived Definitive Endoderm raised in rat BCGO:9000346 A polyclonal antibody raised in goat that targets the human "T (Brachyury)" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal human T (Brachyury) raised in goat BCGO:9000347 A polyclonal antibody raised in rabbit that targets the mouse "Laminin" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal mouse Laminin raised in rabbit BCGO:9000348 A monoclonal antibody raised in mouse that targets the chicken "Pax6" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal chicken Pax6 raised in mouse BCGO:9000602 A mouse ESC line in which part or all of the targeted gene, SRY-box containing gene 17 (NCBI Gene ID: 20671) is replaced to create Sox17{Cre-GFP} using the Loxed Cassette Acceptor allele Sox17{tm1(LCA)}). Using an RMCE strategy, we inserted a Cre-GFP (Green fluorescent protein) fusion protein into a Sox17[LCA] allele thereby replacing Sox17 coding sequences. The Sox17-CreGFP ESCs may be used to track Sox17-expressing cells and their progeny, or to conditionally inactivate genes in Sox17-expressing cells. Mark the expression of Sox17 with both Cre and GFP. Cre will enable lineage tracing using reporter alleles that are activated by cre recombination. GFP will enable direct visualization of Sox17 gene expression. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Sox17{GFPCre} mouse ESC line BCGO:9000661 A mouse strain in which part or all of the targeted gene, insulinoma-associated 1 (NCBI Gene ID: 53626) is replaced to create Insm1{tm1.1(GFP-Cre)} using the Loxed Cassette Acceptor allele Insm1{tm1(LCA)}). <p>Insm1{GFPCre} mice contain a GFP-Cre fusion protein which replaces the Insm1 coding sequence. These mice express green fluorescent protein (GFP) under control of theInsm1gene locus. Insm1 is expressed in pancreatic primordium starting at E9.5. Insm1 is also expressed in neural precursor cells and tumors of may be used for lineage tracing of Insm1-positive cells in both wild-type and Insm1-null mice.</p> Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Insm1{tm1.1Mgn} Vanderbilt University Medical Center Insm1{tm1.1Mgn} mouse strain BCGO:9000721 A mouse ESC line in which the targeted gene, Ghrelin (NCBI Gene ID: 58991), has been modified (allele type: Cassette Acceptor) to targeted mutation (MGI ID: Ghrl{LCA}). ES cells were modified by homologous recombination to replace a 6.912 kb region of the Ghrelin (GHRL) gene from 2.7 kb upstream of exon 1 to 0.5 kb downstream of exon 5 with tandemly oriented lox71 and lox2272 sites as well as both positive and negative selectable markers. The gene was replaced by tandemly oriented lox71 and lox2272 sitesas well as both positive and negative selectable markers. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Ghrl{LCA} mouse ESC line BCGO:9000761 A mouse ESC line in which part or all of the targeted gene, Ghrelin (NCBI Gene ID: 58991) is replaced to create Ghrl{Cre-eGFP} using the Loxed Cassette Acceptor allele Ghrl{LCA}). Recombinase mediated cassette exchange (RMCE) was used to insert the Cre-eGFP fusion protein into the ghrelin locus using ES cells containing the Ghrl{LCA} allele. The Cre-eGFP protein uses the endogenous AUG start codon and polyadenylation sequence. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Ghrl{Cre-eGFP} mouse ESC line BCGO:9000821 A monoclonal antibody raised in mouse that targets the mouse "BetaTC6" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal mouse BetaTC6 raised in mouse BCGO:9000842 A mouse strain containing a transgene in which GCK (transgene) is driven by the ROSA26 promoter (NCBI Gene ID: 14910). Glucokinase containing the Y214C activating mutation, causing severe persistent hyperinsulinemic hypoglycemia (Diabetes 53:2164-2168, 2004) was targeted to the ROSA26 locus, preceded by a lox-stop-lox sequence and followed by IRES-EGFP. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Gt(ROSA)26Sor{tm1(GCK*)Ydor} Vanderbilt University Medical Center Gt(ROSA)26Sor{tm1(GCK*)Ydor} mouse strain BCGO:9000861 A polyclonal antibody raised in rabbit that targets the rat "CART" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal rat CART raised in rabbit BCGO:9000901 A monoclonal antibody raised in rat that targets the mouse "Mo ES-Derived Early Endoderm" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal mouse Mo ES-Derived Early Endoderm raised in rat BCGO:9000903 A monoclonal antibody raised in rat that targets the mouse "Mo ES-Derived Early Endoderm" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal mouse Mo ES-Derived Early Endoderm raised in rat BCGO:9000904 A monoclonal antibody raised in rat that targets the mouse "Mo ES-Derived Early Endoderm" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal mouse Mo ES-Derived Early Endoderm raised in rat BCGO:9000905 A monoclonal antibody raised in rat that targets the mouse "Mo ES-Derived Early Endoderm" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal mouse Mo ES-Derived Early Endoderm raised in rat BCGO:9000906 A monoclonal antibody raised in rat that targets the mouse "Mo ES-Derived Early Endoderm" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal mouse Mo ES-Derived Early Endoderm raised in rat BCGO:9000907 A monoclonal antibody raised in rat that targets the mouse "Mo ES-Derived Early Endoderm" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal mouse Mo ES-Derived Early Endoderm raised in rat BCGO:9000908 A monoclonal antibody raised in rat that targets the mouse "Mo ES-Derived Early Endoderm" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal mouse Mo ES-Derived Early Endoderm raised in rat BCGO:9000921 A monoclonal antibody raised in mouse that targets the human "Hu ES-Derived Early Endoderm" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal human Hu ES-Derived Early Endoderm raised in mouse BCGO:9000922 A monoclonal antibody raised in mouse that targets the human "Hu ES-Derived Early Endoderm" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal human Hu ES-Derived Early Endoderm raised in mouse BCGO:9000941 A monoclonal antibody raised in mouse that targets the human "Hu ES-Derived Early Endoderm" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal human Hu ES-Derived Early Endoderm raised in mouse BCGO:9000942 A monoclonal antibody raised in rat that targets the mouse "Pancreatic duct cells" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal mouse Pancreatic duct cells raised in rat BCGO:9000943 A monoclonal antibody raised in rat that targets the mouse "Pancreatic duct and acinar cells" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal mouse Pancreatic duct and acinar cells raised in rat BCGO:9000945 A monoclonal antibody raised in rat that targets the mouse "Endothelial cells" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal mouse Endothelial cells raised in rat BCGO:9000961 A monoclonal antibody raised in mouse that targets the mouse "BetaTC6" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal mouse BetaTC6 raised in mouse BCGO:9000962 A monoclonal antibody raised in mouse that targets the mouse "BetaTC6" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal mouse BetaTC6 raised in mouse BCGO:9000964 A monoclonal antibody raised in mouse that targets the human "Disp2" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal human Disp2 raised in mouse BCGO:9000965 A monoclonal antibody raised in mouse that targets the human "Disp2" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal human Disp2 raised in mouse BCGO:9000966 A polyclonal antibody raised in rabbit that targets the mouse "Lrp11" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal mouse Lrp11 raised in rabbit BCGO:9000967 A polyclonal antibody raised in rabbit that targets the mouse "Sez6l2" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal mouse Sez6l2 raised in rabbit BCGO:9000968 A polyclonal antibody raised in rabbit that targets the mouse "Sez6l2" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal mouse Sez6l2 raised in rabbit BCGO:9000969 A polyclonal antibody raised in goat that targets the human "DDR1" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal human DDR1 raised in goat BCGO:9000970 A monoclonal antibody raised in mouse that targets the human "DDR1" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal human DDR1 raised in mouse BCGO:9000971 A polyclonal antibody raised in rabbit that targets the mouse "Gpr39-1a" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal mouse Gpr39-1a raised in rabbit BCGO:9000972 A polyclonal antibody raised in rabbit that targets the rat "CART" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal rat CART raised in rabbit BCGO:9000974 A monoclonal antibody raised in mouse that targets the rat "CART" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal rat CART raised in mouse BCGO:9000981 A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{R26-60-DR5-TA-Cerulean} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). In these cells Rosa26 gene sequences from -60 to +81 were replaced by a retinoic acid response element (DR5) fused to a TATA-Cerulean (CFP) reporter. These ESCs may be useful for assess retinoic acid responsiveness. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Rosa26{R26-60-DR5-TA-Cerulean} mouse ESC line BCGO:9000982 A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Roas26{R26-228-DR5-TA-Cerulean} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). In these cells Rosa26 gene sequences from -228 to +81 were replaced by a retinoic acid response element (DR5) fused to a TATA-Cerulean (CFP) reporter. These ESCs may be useful for assess retinoic acid responsiveness. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Rosa26{R26-228-DR5-TA-Cerulean} mouse ESC line BCGO:9001001 A mouse strain in which part or all of the targeted gene, pancreas specific transcription factor, 1a (NCBI Gene ID: 19213) is replaced to create Ptf1a{tm3Macd} using the Loxed Cassette Acceptor allele Ptf1a{tm1(LCA)}). Modified allele of Ptf1a with a biotinylation Tag sequence attached to the amino terminus of Ptf1a. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Ptf1a{tm3Macd} Vanderbilt University Medical Center Ptf1a{tm3Macd} mouse strain BCGO:9001101 A mouse strain in which part or all of the targeted gene, SRY-box containing gene 17 (NCBI Gene ID: 20671) is replaced to create Sox17{CreERT2} using the Loxed Cassette Acceptor allele Sox17{tm1(LCA)}). Sox17{CreERT2} mice may be used either to track Sox17-expressing cells or their progeny or to conditionally inactivate genes in Sox17-expressing cells at specific time points by tamoxifen injection. This line is complementary to Sox17-CreGFP and may avoid possible interferences of expression in the extra-embryonic visceral endoderm. We plan to analyze the effects of a direct activation/deletion of the Wnt pathway in the endoderm by crossing the Sox17-CreERT2 with the gain- and loss-of-function of beta-catenin. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Sox17{tm1.2Mgn} Vanderbilt University Medical Center Sox17{tm1.2Mgn} mouse strain BCGO:9001161 A polyclonal antibody raised in goat that targets the mouse "Carboxypeptidase A1 (CPA1)" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal mouse Carboxypeptidase A1 (CPA1) raised in goat BCGO:9001162 A polyclonal antibody raised in rabbit that targets the human "Muc1" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal human Muc1 raised in rabbit BCGO:9001163 A polyclonal antibody raised in rabbit that targets the human "Cleaved Notch1" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal human Cleaved Notch1 raised in rabbit BCGO:9001164 A polyclonal antibody raised in goat that targets the human "Jagged1" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal human Jagged1 raised in goat BCGO:9001181 A mouse ESC line in which part or all of the targeted gene, pancreatic and duodenal homeobox 1 (NCBI Gene ID: 18609) is replaced to create Pdx1{CFP} using the Loxed Cassette Acceptor allele Pdx1{tm1(LCA)}). This ES cell line contains cyan fluorescent protein (CFP, Cerulean variant) inserted into a Pdx1{LCA} allele by recombinase mediated cassette exchange. These cells may be useful for identifying pancreatic progenitor cells in cultures that have been stimulated to differentiate towards endodermal and pancreatic fates. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Pdx1{CFP} mouse ESC line BCGO:9001221 A mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{(Ccnd1T286A)} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This strain expresses both mutant cyclin D1{T286A} and a cherry reporter under the regulation of a tetracycline-responsive bi-directional minimal CMV promoter (TRE-Tight; tetO). The cyclin D1-T286A mutant cannot be phosphorylated by GSK-3beta and is resistant to polyubiquitination. Therefore, cyclin D1-T286A remains nuclear throughout the cell cycle and has an extended half-life relative to wild-type cyclin D1. This strain represents an effective tool for generating inducible tissue-specific cyclin D1{T286A} mutants with a cherry reporter. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Gt(ROSA)26Sor{tm1(Ccnd1T286A)Stang} Vanderbilt University Medical Center Gt(ROSA)26Sor{tm1(Ccnd1T286A)Stang} mouse strain BCGO:9001241 A mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{tm1.1(R26-DR5-TA-Cerulean)} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). These mice were generated using RMCE to insert an exchange vector containing a modified Rosa26 promoter linked to a Cerulean fluorescent protein (CFP) reporter gene into mESCs containing a Loxed Cassette Acceptor (LCA) allele within the Rosa26 gene locus. The Rosa26 promoter in this mouse was altered by replacing DNA sequences from -60 to +81 with a multimerized retinoic acid response element (DR5) fused to a TATA box. This mouse will facilitate studies of retinoic acid signaling in an intact animal. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Rosa26{tm1.1(R26-60-DR5-TA-Cerulean)Mgn} Vanderbilt University Medical Center Rosa26{tm1.1(R26-60-DR5-TA-Cerulean)Mgn} mouse strain BCGO:9001261 A mouse strain in which the targeted gene, recombination activating gene 1 (NCBI Gene ID: 19373), has been modified (allele type: Global Null) to (MGI ID: Rag1{tm1Mom}). Backcrossing of the Rag1 null allele onto the NOD/Lt strain background (NOD-Rag1{null} mice) provided a radio-resistant and longer-lived model for human-cell engraftment. Mutations in X-chromosome-linked Il2rg gene cause X-linked severe combined immunodeficiency (XSCID). Immunodeficient NOD-Rag1{null} IL2rg nullmice tolerated much higher levels of irradiation conditioning than did NOD-Prkdcscid IL2rg{null} mice. This immunodeficient mouse also develops spontaneous hyperglycemia based on the Ins2{Akita} mutation. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler NOD.Cg-Rag1{tm1Mom}Ins2{Akita}Il2rg{tm1Wjl}/Sz Vanderbilt University Medical Center NOD.Cg-Rag1{tm1Mom}Ins2{Akita}Il2rg{tm1Wjl}/Sz mouse strain BCGO:9001262 A mouse strain in which the targeted gene, interleukin 2 receptor, gamma chain (NCBI Gene ID: 16186), has been modified (allele type: Global Null) to targeted mutation 1 (MGI ID: Il2rg{tm1Wjl}). NOD-scid IL2rg{null} mice are deficient in mature lymphocytes and NK cells, survive beyond 16-month of age, and even after sublethal irradiation resist lymphoma development. Moreover, cytokine-mobilized human peripheral blood stem cells engraft at high levels in NOD-scid IL2rg{null} mice and develop into human CD3+CD4+ and CD3+CD8+ T cells, Ig+B cells, myeloid cells, NK cells and plasmacytoid dentritic cells. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler NOD.Cg-Prkdc{scid}Il2rg{tm1Wjl}/Sz Vanderbilt University Medical Center NOD.Cg-Prkdc{scid}Il2rg{tm1Wjl}/Sz mouse strain BCGO:9001281 A mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{tm1.2((R26-228-DR5-Cerulean) using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). These mice were generated using RMCE to insert an exchange vector containing a modified Rosa26 promoter linked to a Cerulean fluorescent protein (CFP) reporter gene into mESCs containing a Loxed Cassette Acceptor (LCA) allele within the Rosa26 gene locus. The Rosa26 promoter in this mouse was altered by replacing DNA sequences from -228 to +81 with a multimerized retinoic acid response element (DR5) fused to a TATA box. This mouse will facilitate studies of retinoic acid signaling in an intact animal. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Rosa26{tm1.2(R26-228-DR5-TA-Cerulean)Mgn} Vanderbilt University Medical Center Rosa26{tm1.2(R26-228-DR5-TA-Cerulean)Mgn} mouse strain BCGO:9001321 A mouse strain in which the targeted gene, Nkx2.2 (NCBI Gene ID: 18088), has been modified (allele type: Global Null) to Null (MGI ID: Nkx2.2{tm5(null)}). These mice contain a deletion of the Nkx2.2 coding region to create a null allele. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Nkx2-2{tm5(null)Suss} Vanderbilt University Medical Center Nkx2-2{tm5(null)Suss} mouse strain BCGO:9001342 A mouse strain in which the targeted gene, Nk6 Homeobox 1 (NCBI Gene ID: 18096), has been modified (allele type: Conditional Null) to targeted mutation 1.1 (MGI ID: Nkx6.1{tm1.1Msan}). A conditional allele for nkx6.1 is necessary to study the function of Nkx6.1 in adult mice. A homozygous nkx6.1 null allele results in neonatal lethality due to a paralytic state, which is a direct result of Nkx6.1 function in the development of motor neurons. Conditional loss of Nkx6.1 is achieved through Cre mediated recombination of a floxed exon II of nkx6.1. Our use for a conditional nkx6.1 allele is to study its function in beta cells of the adult pancreas. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Nkx6-1{tm2(flox)Msan} Vanderbilt University Medical Center Nkx6-1{tm2(flox)Msan} mouse strain BCGO:9001421 A mouse strain in which the targeted gene, Perforin 1 (Pore forming protein) (NCBI Gene ID: 18646), has been modified (allele type: Global Null) to (MGI ID: ). Mice that are homozygous for both targeted mutations are viable, fertile, normal in size and do not display any gross physical or behavioral abnormalities when housed under specific pathogen free conditions. These double homozygote mutant mice have no mature T or B lymphocytes, no detectable NK cell cytotoxic activity, and lack serum immunoglobulin. The number of nucleated spleen cells is significantly reduced in double mutant mice, when compared to the single homozygote, NOD.129S7(B6)-Rag1tm1Mom/J (Stock No. 003729). Although an increased number of DX5+CD122+ NK cells are found in the spleens of double mutants, these NK cells have impaired cytotoxic activity. The disruption of Prf1 ablates NK cell cytotoxic activity resulting in increased engraftment levels over that observed with Stock No. 003729. All mutant mice develop thymic lymphomas. This double mutant mouse strain may be useful in studies involving engraftment of human hematolymphoid cells. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler NOD.Cg-Rag1{tm1Mom}Prf1{tm1Sdz}/SzJ Vanderbilt University Medical Center NOD.Cg-Rag1{tm1Mom}Prf1{tm1Sdz}/SzJ mouse strain BCGO:9001701 A mouse strain in which part or all of the targeted gene, forkhead box O1 (NCBI Gene ID: 56458) is replaced to create Foxo1{DBD} using the Loxed Cassette Acceptor allele Foxo1{tm1(LCA)}). <p>This line contains a DNA binding-deficient mutant of Foxo1. The mutation may be useful for assessing the contribution of DNA co-activation in the function of Foxo1.</p> Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Foxo1{tm1(DBD)Dac} Vanderbilt University Medical Center Foxo1{tm1(DBD)Dac} mouse strain BCGO:9001961 A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{Ccnd1} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). ES cells express mutant cyclin D1-T286A and a cherry reporter under the regulation of a tetracycline-responsive bi-directional minimal CMV promoter (TRE-Tight; tetO) targeted to the ROSA26 locus. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Rosa26{tm1(Ccnd1)} mouse ESC line BCGO:9002001 A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{R26-60-IBRE4-TA-Cerulean} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). In these cells Rosa26 gene sequences from -60 to +81 were replaced by a BMP response element (IBRE4) fused to a TATA-Cerulean (CFP) reporter. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Rosa26{R26-60-IBRE4-TA-Cerulean} mouse ESC line BCGO:9002002 A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{R26-228-IBRE4-TA-Cerulean} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). In these cells Rosa26 gene sequences from -228 to +81 were replaced by a BMP response element (IBRE4) fused to a TATA-Cerulean (CFP) reporter. These ESCs may be useful for assess BMP responsiveness. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Rosa26{R26-228-IBRE4-TA-Cerulean} mouse ESC line BCGO:9002061 A mouse strain in which part or all of the targeted gene, forkhead box O1 (NCBI Gene ID: 56458) is replaced to create Foxo1{GFP} using the Loxed Cassette Acceptor allele Foxo1{tm1(LCA)}). A GFP cDNA has been knocked into the Foxo1 locus at the 3' end of the endogenous Foxo1 cDNA to generate a Foxo1-gfp fusion protein that can be used to study Foxo1 translocation in vivo. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Foxo1{tm1(GFP)Dac} Vanderbilt University Medical Center Foxo1{tm1(GFP)Dac} mouse strain BCGO:9002201 A polyclonal antibody raised in goat that targets the mouse "DNER" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal mouse DNER raised in goat BCGO:9002222 A monoclonal antibody raised in mouse that targets the rat "Shh" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal rat Shh raised in mouse BCGO:9002223 A monoclonal antibody raised in mouse that targets the chicken "Chick HNF3Beta" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal chicken Chick HNF3Beta raised in mouse BCGO:9002241 A mouse ESC line in which the targeted gene, pancreatic and duodenal homeobox 1 (NCBI Gene ID: 18609), has been modified (allele type: Cassette Acceptor) to targeted mutation 1 (MGI ID: Pdx1{tm1(LCA)}). This mouse ES cell line contains a loxed cassette acceptor (LCA) allele that may be utilized for the exchange of DNAs of interest into the Pdx1 gene locus by recombinase mediated cassette exchange (RMCE). An 8.62 kb region of the gene was replaced by tandemly oriented Lox66 and Lox2272 sites flanking both positive (puromycin) and negative (HSV-TK)selectable markers. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Pdx1{LCA} mouse ESC line BCGO:9002263 A polyclonal antibody raised in guinea pig that targets the mouse "Pax4" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal mouse Pax4 raised in guinea pig BCGO:9002281 A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{EN-Cherry-Neo} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This ES cell line expresses mCherry, a red fluorescent protein, under control of the endogenous Rosa26gene. A cassette containing mCherry and other sequences to assure efficient expression were inserted into the Rosa26[LCA] allele by recombinase mediated cassette exchange. These cells will be used to identify an optimal combination of regulatory elements for fluorescent protein expression from a single gene copy and as a reference cell line for fluorescent cell sorting. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Rosa26{EN-Cherry-Neo} mouse ESC line BCGO:9002301 A mouse strain in which the targeted gene, Neurogenin 3 (NCBI Gene ID: 11925), has been modified (allele type: Gene Replacement) to Ngn3{nCre} (MGI ID: Neurog3{nCre}). A nCre-iRES (n-terminal half of Cre followed by internal ribosomal entry site) was inserted after Ngn3ATG. This allele is confirmed to express both nCre and Ngn3 (no visible phenotype in homozygous animals). Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Neurog3{tm1.1(nCre)Ggu} Vanderbilt University Medical Center Neurog3{tm1.1(nCre)Ggu} mouse strain BCGO:9002401 A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{LCA} using the Loxed Cassette Acceptor allele Rosa26{tm1.8(Non-EN-CFP)}). This ES cell line contains CFP (Cerulean) inserted into a Rosa26{LCA} allele by recombinase mediated cassette exchange. These cells were used to identifythe optimal arrangement of regulatory elements for fluorescent protein expression from a single genomic copy. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Rosa26{Non-EN-CFP-Neo} mouse ESC line BCGO:9002482 A polyclonal antibody raised in goat that targets the mouse "Ngn3" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal mouse Ngn3 raised in goat BCGO:9002502 A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{EN.CFP} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This ES cell line contains CFP (Cerulean) inserted into a Rosa26 LCA allele by recombinase mediated cassette exchange. These cells were used to identify the optimal arrangement of regulatory elements for fluorescent protein expression from a single genomic copy. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Rosa26{EN-CFP-Neo} mouse ESC line BCGO:9002522 A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{CFP.SV40} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This ES cell line contains CFP (Cerulean) inserted into a Rosa26 LCA allele by recombinase mediated cassette exchange. These cells were used to identify the optimal arrangement of regulatory elements for fluorescent protein expression from a single genomic copy. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Rosa26{EN.CFP.SV40.Neo} mouse ESC line BCGO:9002542 A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{EN.GFP} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This ES cell line contains eGFP inserted into the Rosa26 gene locus. These cells were used to identify an optimal combination of regulatory elements for fluorescent protein expression from a single genomic copy and can serve as a reference cell line for fluorescent cell sorting. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Rosa26{EN-GFP-Neo} mouse ESC line BCGO:9002562 A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{CFP} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This ES cell line contains CFP (Cerulean) inserted into a Rosa26{LCA} allele by recombinase mediated cassette exchange. These cells were used to identify an optimal combination of regulatory elements for fluorescent protein expression from single a genomic copy. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Rosa26{EN-CFP-bGpA-Neo} mouse ESC line BCGO:9002582 A mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{Ngn3-CFP} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This mouse contains a bidirectional TetO-regulated fusion gene that has been inserted into a disabled Rosa26 locus. In one direction the tetO/CMV promoter drives expression of CFP (Cerulean). In the other direction it drives Ngn3. Mice containing this allelecan be used to drive the expression of Ngn3 under control of both doxycycline and either an rtTA or tTA transgene. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Rosa26{(Ngn3.CFP)Mgn} Vanderbilt University Medical Center Rosa26{(Ngn3.CFP)Mgn} mouse strain BCGO:9002702 A mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{MafA-Cherry} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This mouse contains a bidirectional Tet0-regulated fusion gene that has been inserted into adisabled Rosa26 loxed cassette acceptor allele by RMCE. In one direction the tetO/CMV promoter drives expression of a red fluorescent protein (Cherry) while in the other direction it drives MafA expression. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Rosa26{tm1.4(MafA-Cherry)Mgn} Vanderbilt University Medical Center Rosa26{tm1.4(MafA-Cherry)Mgn} mouse strain BCGO:9002742 A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{(R26-60-CNotch-TA-Cerulean)} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). The Rosa26 gene sequences from -228 to +81 were replaced with a repeat of alternating 32-bp C-elements and 31-bp Rbpj-binding sites (i.e.,C-R-C-R-C-R). The 31 base-pair region is derived from the CBF1/Rbpj binding region of the C-promoter of EBV (cataaattTTTTCCCACGgcgtgtttacacc; uppercase letters are the consensus Rbpj binding sequence within the 31-bp element) (Hsieh, MCB 16:952, 1996). The 32-bp C-element is from the Ela1 enhancer (Kruse et al., MCB 15:4385, 1995). Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Rosa26{R26-60-3XCNotch-TA-Cerulean} mouse ESC line BCGO:9002762 A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{R26-60-AR8-TA-mCherry} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). In these cells Rosa26 gene sequences from -60 to +81 were replaced by an Activin response element (AR8) fused to a TATA-mCherry reporter Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Rosa26{R26-60-AR8-TA-mCherry} mouse ESC line BCGO:9002782 A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{tm2.2(R26-228-AR8-TA-mCherry)} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). In these cells Rosa26 gene sequences from -228 to +81 were replaced by an Activin response element (AR8) fused to a TATA-mCherry reporter. These ESCs may be usefulto assess Activin, Nodal, and TGFbeta responsiveness. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Rosa26{R26-228-AR8-TA-mCherry} mouse ESC line BCGO:9002802 A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26(R26-60-6XNotch-TA-Cerulean) using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). The binding site for Rbpj, the transcriptional mediator of Notch signaling was inserted into the Rosa 26 locus replacing nucleotides -60 to -228.The complete insert contains the Rbpj cis element in a series of six repeats. Each repeat includes a 31 base-pair region derived from the CBF1/Rbpj binding region of the C-promoter of EBV (cataaattTTTTCCCACGgcgtgtttacacc). Uppercase letters are the consensus Rbpj binding sequence within the 31-bp element) (Hsieh et al., MCB 16:952, 1996). Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Rosa26{R26-60-6XNotch-TA-Cerulean} mouse ESC line BCGO:9002822 A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26(R26-228-3XCNotch-TA-Cerulean) using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). The Rosa26 gene sequences from -60 to -228 were replaced with a repeat of alternating 32-bp C-elements and 31-bp Rbpj-binding sites (i.e.,C-R-C-R-C-R). The 31 base-pair region is derived from the CBF1/Rbpj binding region of the C-promoter of EBV (cataaattTTTTCCCACGgcgtgtttacacc; uppercase letters are the consensus Rbpj binding sequence within the 31-bp element) (Hsieh, MCB 16:952, 1996). The 32-bp C-element is from the Ela1 enhancer (Kruse et al., MCB 15:4385, 1995). Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Rosa26{-228.3XCNotch.TA.Cerulean} mouse ESC line BCGO:9002842 A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26(Rbpj(R26-228-6XNotch-TA-Cerulean)) using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). The binding site for Rbpj, the transcriptional mediator of Notch signaling was inserted into the Rosa 26 locus replacing nucleotides -60 to -228.The complete insert contains the Rbpj cis element in a series of six repeats. Each repeat includes a 31 base-pair region derived from the CBF1/Rbpj binding region of the C-promoter of EBV (cataaattTTTTCCCACGgcgtgtttacacc). Uppercase letters are the consensus Rbpj binding sequence within the 31-bp element) (Hsieh et al., MCB 16:952, 1996). Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Rosa26{-228.6XNotch.TA.Cerulean} mouse ESC line BCGO:9003022 A polyclonal antibody raised in rabbit that targets the mouse "Irx2" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal mouse Irx2 raised in rabbit BCGO:9003023 A polyclonal antibody raised in rabbit that targets the mouse "Arx" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal mouse Arx raised in rabbit BCGO:9003042 A mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{Nkx2.2/CFP} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). In this strain both CFP and myc-tagged Nkx2.2 were inserted into a ROSA26 LCA allele under control of a bidirectional tetO/CMV promoter element. The mouse line will allow us to explore the contribution of Nkx2.2 to progenitor cell population competency by allowing for the manipulation of Nkx2.2 gene expression within the developing pancreas. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler ROSA26{(Nkx2.2.CFP)Suss} Vanderbilt University Medical Center ROSA26{(Nkx2.2.CFP)Suss} mouse strain BCGO:9003102 A polyclonal antibody raised in guinea pig that targets the mouse "mArx" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal mouse mArx raised in guinea pig BCGO:9003185 A monoclonal antibody raised in rat that targets the human "C-peptide" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal human C-peptide raised in rat BCGO:9004012 A mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{tm2.1(R26-60-IBRE4-TA-Cerulean)} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This mouse contains aBMP reporter element withina modified ROSA26 promoter followed by a CFP reporter. This mouse is identical to the -228 variant except for the amount of ROSA26 DNA. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Rosa26{(-60.IBRE4.TACerulean)Hri} Vanderbilt University Medical Center Rosa26{(-60.IBRE4.TACerulean)Hri} mouse strain BCGO:9004015 A mouse ESC line in which part or all of the targeted gene, pancreas specific transcription factor, 1a (NCBI Gene ID: 19213) is replaced to create Ptf1a{rtTA} using the Loxed Cassette Acceptor allele Ptf1a{tm1(LCA)}). These mESCs contain the reverse tetracycline transactivator (rtTA) under control of the Ptf1a regulatory sequences. rtTA is a transcriptional activator, which can inducibly (in the presence of the tetracycline analog doxycycline) activate the genes under Tet-O activator/promoter element. The rtTA sequences were introduced in to Ptf1a[LCA] by Recombinase-Mediated Cassette Exchange using standard methods.These cells were made in order togenerate a mouse line that express rtTA under control of the Ptf1a gene locus. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Ptf1a{rtTA} mouse ESC line BCGO:9004016 A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Nepn-Cherry using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This ES cell line was generated by RMCE usingthe Rosa26.LCA allele. To create a Nepn reporter allele, a 9kb promoter region of the Nepn gene is inserted upstream of the red fluorescent protein mCherry-pA sequence. Since Nepn is expressed during endoderm development, this cell line can be used for visualisation and sorting of endodermal cell populations. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Rosa26{Nepn.Cherry} mouse ESC line BCGO:9004017 A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{YFP} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). These mESCs contain yellow fluorescent protein (YFP, Citrine) under control of the ROSA26 gene locus. They were made as part of a study to quantify variables that affect fluorescent protein expression levels in mESCs. TheYFP sequences are flanked by a translational enhancer and beta-globin splice/polyA sequences. The cassette containing the YFP was inserted intoa ROSA26 LCA allel using Recombinase-Mediated Cassette Exchange. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Rosa26{EN.YFP.bGsplicepA.Neo} mouse ESC line BCGO:9004018 A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{EN.Apple.bGspliceA.neo} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). To better quantify protein expression levels via confocal microscopy, flow sorting and western blot analysis this cell line contains a 4kb R26 promoter element, Apple (a red fluorescent protein) with an upstream enhancer element, a splicing beta-globin polyA tail and the neomycin gene as a selection agent. Through Recombinase-Mediated Cassette Exchange this construct was inserted into the Rosa26 locus. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Rosa26{Apple.bGsplicepA.Neo} mouse ESC line BCGO:9004019 A mouse ESC line in which part or all of the targeted gene, Gt(ROSA)26Sor gene trap ROSA 26, Philippe Soriano [ Mus musculus ] (NCBI Gene ID: 14910) is replaced to create Rosa26 LCA using the Loxed Cassette Acceptor allele ). Recombinase mediated cassette exchange was performed to introduce a bidirectional tetO-regulated cassette containing coding sequences for transcription factors MafA and Ngn3 into Rosa26 LCA mESCs. ThismESC line can be used to generate mice that will simultaneously overexpress MafA and Ngn3 using tet-inducible activation with rtTA. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Rosa26{Ngn3.Mafa} mouse ESC line BCGO:9004020 A mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{EN-Cherry-Neo} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This mouse line expresses mCherry, a red fluorescent protein, under control of the endogenous ROSA26 gene locus. This mouse was generated as part of a study to identify the optimal combination of regulatory elements for fluorescent protein expression from a single gene copy. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Rosa26{tm2Mgn} Vanderbilt University Medical Center Rosa26{tm2Mgn} mouse strain BCGO:9004021 A mouse strain in which part or all of the targeted gene, pancreas specific transcription factor, 1a (NCBI Gene ID: 19213) is replaced to create Ptf1a{tm1.2(rtTA)Mgn} using the Loxed Cassette Acceptor allele Ptf1a{tm1(LCA)}). This mouse line expresses the reverse tetracycline transactivator (rtTA) under control of the Ptf1a regulatory sequences. This mouseisuseful for activating expression of various TetO-regulated genes in sites where Ptf1a is normally expressed. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Ptf1a{tm2(rtTA)Mgn} Vanderbilt University Medical Center Ptf1a{tm2(rtTA)Mgn} mouse strain BCGO:9004022 A mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26[Nepn.Cherry] using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). Nephrocan (Nepn) has been shown to be expressed specifically during early endoderm development. A Nepn promoter driven reporter (Cherry) has been inserted in the Rosa26LCA locus by recombinase mediated cassette exchange. This mouse line will be useful in visualizing whether Nepn can be used as a specific DE marker for beta-cell development. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Rosa26{(Nepn.Cherry)Mgn} Vanderbilt University Medical Center Rosa26{(Nepn.Cherry)Mgn} mouse strain BCGO:9004023 A mouse ESC line in which part or all of the targeted gene, Gt(ROSA)26Sor gene trap ROSA 26, Philippe Soriano [ Mus musculus ] (NCBI Gene ID: 14910) is replaced to create Rosa26 LCA using the Loxed Cassette Acceptor allele Rosa26{tm1.1(mlre1.WT.Cherry)FerozPapa}). This mESC line contains a bidirectional Tet0-regulated fusion gene that has been inserted into a disabled Rosa26 loxed cassette acceptor allele by RMCE. In one direction the tetO/CMV promoter drives expression of a red fluorescent protein (Cherry) while in the other direction it drives the wild type form of mlre1. mlre1 is an endoplasmic reticulum (ER) membrane kinase response to unfolded protein response (UPR). Activated mlre1 endonucleases leads to the splicing of XBP-1 (a transcription factor which is upregulated in times of ER stress) which transcriptionally increases the expression of ER chaperones and alleviates UPR. This cell line should be useful for studying the role of mlre1 in the response to ER stress. By generating mice with this allele Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Rosa26{mIre1.WT.Cherry} mouse ESC line BCGO:9004024 A mouse ESC line in which part or all of the targeted gene, Gt(ROSA)26Sor gene trap ROSA 26, Philippe Soriano [ Mus musculus ] (NCBI Gene ID: 14910) is replaced to create Rosa26 LCA using the Loxed Cassette Acceptor allele Rosa26{tm1.1(mlre1.IG.Cherry)FerozPapa}). This mESC line contains a bidirectional Tet0-regulated fusion gene that has been inserted into a disabled Rosa26 loxed cassette acceptor allele by RMCE. In one direction the tetO/CMV promoter drives expression of a red fluorescent protein (Cherry) while in the other direction it drives a mutant version of mlre1. mlre1 is an endoplasmic reticulum (ER) membrane kinase response to unfolded protein response (UPR). Activated mlre1 endonucleases leads to the splicing of XBP-1 (a transcription factor which is upregulated in times of ER stress) which transcriptionally increases the expression of ER chaperones and alleviates UPR. This cell line should be useful for studying the role of mlre1 in the response to ER stress. By generating mice with this allele t Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Rosa26{mIre1.IG.Cherry} mouse ESC line BCGO:9004025 A mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{mlre1.WT-Cherry} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This mouse line contains a bidirectional Tet0-regulated fusion gene that has been inserted into a disabled Rosa26 loxed cassette acceptor allele by RMCE. In one direction the tetO/CMV promoter drives expression of a red fluorescent protein (Cherry) while in the other direction it drives a wild type mlre1. mlre1 is an endoplasmic reticulum (ER) membrane kinase response to unfolded protein response (UPR). Activated mlre1 endonucleases leads to the splicing of XBP-1 (a transcription factor which is upregulated in times of ER stress) which transcriptionally increases the expression of ER chaperones and alleviates UPR. These mice may be useful for studying the role of mlre1 in the response to ER stress in the setting of diet induced obesity and insulin resistance. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Rosa26{(mlre1.WT.Cherry)Fpa} Vanderbilt University Medical Center Rosa26{(mlre1.WT.Cherry)Fpa} mouse strain BCGO:9004026 A mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{mlre1.IG-Cherry} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This mouse line contains a bidirectional Tet0-regulated fusion gene that has been inserted into a disabled Rosa26 loxed cassette acceptor allele by RMCE. In one direction the tetO/CMV promoter drives expression of a red fluorescent protein (Cherry) while in the other direction it drives a mutant mlre1. mlre1 is an endoplasmic reticulum (ER) membrane kinase response to unfolded protein response (UPR). Activated mlre1 endonucleases leads to the splicing of XBP-1 (a transcription factor which is upregulated in times of ER stress) which transcriptionally increases the expression of ER chaperones and alleviates UPR. These mice may be usefulfor studying the role of mlre1 in the response to ER stress in the setting of diet induced obesity and insulin resistance. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Rosa26{(mlre1.IG.Cherry)Fpa} Vanderbilt University Medical Center Rosa26{(mlre1.IG.Cherry)Fpa} mouse strain BCGO:9004027 A mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{R26-228-IBRE4-TA-Cerulean} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). These mice were generated by performing recombinase mediated cassette exchange on the Rosa26 LCA. The sequence from -228 to +81 of the Rosa26 gene was replaced with a BMP responsive element (IBRE4) fused to a TATA-Cerulean (CFP) reporter. These mice may be useful in visualizing BMP responsiveness. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Rosa26{(R26-228-IBRE4-TA-Cerulean)Hri} Vanderbilt University Medical Center Rosa26{(R26-228-IBRE4-TA-Cerulean)Hri} mouse strain BCGO:9004029 A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Sox9/mCherry using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This ES line contains bidirectional TetO-regulated genes inserted into the Rosa26.LCA allele by RMCE. In one direction the TetO/CMV promoter drives the expression of transcription factor Sox9. In the other direction it drives the expression of red fluorescent protein mCherry. This ES cell line can be used to simultaneously over-express Sox9 and mCherry upon administration of doxycyline when the effector protein rtTA is expressed. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Rosa26{Sox9.Cherry} mouse ESC line BCGO:9004030 A mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Sox9 using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This mouse line contains bidirectional TetO-regulated genes inserted into the Rosa26{LCA} allele by RMCE. In one direction, the TetO/CMV promoter drives the expression of the transcription factor Sox9. In the other direction, it drives the expression of the red fluorescent protein mCherry. In this mouse line, when the effector protein rtTA is expressed, Sox9 and mCherry will be over-expressed simultaneously upon administration of doxycyline. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Rosa26{(TetO.Sox9)Msan} Vanderbilt University Medical Center Rosa26{(TetO.Sox9)Msan} mouse strain BCGO:9004031 A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create NRSF using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This cell line contains bidirectional TetO-regulated genes inserted into the Rosa26{LCA} allele by RMCE. In one direction, the TetO/CMV promoter drives expression of the transcription factor NRSF/REST. In the other direction, it drives the expression of the red fluorescent protein mCherry. In this cell line, when the effector protein rtTA is expressed, NRSF and mCherry are simultaneously over-expressed upon administration of doxycyline. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Rosa26{TetO.NRSF} mouse ESC line BCGO:9004032 A mouse ESC line in which part or all of the targeted gene, pancreas specific transcription factor, 1a (NCBI Gene ID: 19213) is replaced to create Ptf1a{td.TOM} using the Loxed Cassette Acceptor allele Ptf1a{tm1(LCA)}). Recombinase mediated cassette exchange was performed using the Ptf1aLCA. This cell line expresses both tdTOM (a red fluorescent protein) and an N-terminal epitope tagged Strep/Flag (NSF) fusion of ptf1a in the adult pancreas. These cells will be useful in a variety of applications such as FACS sorting of ptf1a expressing cells, chromatin immunoprecipitation and proteomic analyses. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Ptf1a{tdTOM} mouse ESC line BCGO:9004040 A polyclonal antibody raised in rabbit that targets the human "TSPAN7" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal human TSPAN7 raised in rabbit BCGO:9004041 A monoclonal antibody raised in mouse that targets the human "FXYD2" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal human FXYD2 raised in mouse BCGO:9004047 A polyclonal antibody raised in rabbit that targets the mouse "Sez6l2" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal mouse Sez6l2 raised in rabbit BCGO:9004048 A polyclonal antibody raised in rabbit that targets the human "Lrp11" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal human Lrp11 raised in rabbit BCGO:9004052 A polyclonal antibody raised in guinea pig that targets the mouse "Onecut1" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal mouse Onecut1 raised in guinea pig BCGO:9004054 A mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create CFP using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This mouse line was made by RMCE in the Rosa26[LCA] allele and has a cyan fluorescent protein (CFP, Cerulean) expressed under the control of the ROSA26 promoter. The CFP sequence is preceded by a translational enhancer and followed by intron-containing rabbit beta-globin polyA sequences. This mouse has ubiquitously expressed CFP protein and can be used for transplantation and other experiments where tracing of source cells is required. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Rosa26{tm3Mgn} Vanderbilt University Medical Center Rosa26{tm3Mgn} mouse strain BCGO:9004055 A mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create YFP using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This mouse line was made by RMCE in the Rosa26[LCA] allele and has yellow fluorescent protein (YFP, Citrine) expressed under control of the ROSA26 promoter. The YFP sequence is preceded by a translational enhancer and followed by intron-containing rabbit beta-globin polyA sequences. This mouse has ubiquitously expressed YFP protein and can be used for transplantation and other experiments where tracing of source cells is required. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Rosa26{tm4Mgn} Vanderbilt University Medical Center Rosa26{tm4Mgn} mouse strain BCGO:9004056 A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Setd5/GFP using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This ES cell line was generated by RMCE in the Rosa26{LCA} allele. A coding sequence for green fluorescent protein (GFP) was inserted into the first exon of the Setd5 gene. This exon is located upstream of the Rosa26 transcribed sequence and is transcribed in an opposite orientation. The GFP-polyA cassette, transcribed from the Setd5 promoter, knocks out Setd5 transcription and provides a reporter for Setd5 gene expression. The purpose of this cell line is to study the molecular function of the Setd5 gene. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Rosa26{Setd5.GFP} mouse ESC line BCGO:9004058 A mouse strain in which part or all of the targeted gene, pancreatic and duodenal homeobox 1 (NCBI Gene ID: 18609) is replaced to create Pdx1{H2B.Apple} using the Loxed Cassette Acceptor allele Pdx1{tm1(LCA)}). This mouse contains a coding sequence for the mApple-H2B fusion protein in order to tag cells expressing Pdx1 with a red fluorescent protein. The generation of a Pdx-1 red fluorescent marker will enable the isolation of pancreatic lineage progenitors by FACS. The presence of the H2B sequences may also be useful in allowing the plane of cell division to be analyzed. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Pdx1{(H2B.Apple)Mgn} Vanderbilt University Medical Center Pdx1{(H2B.Apple)Mgn} mouse strain BCGO:9004059 A mouse ESC line in which the targeted gene, Neurogenin 3 (NCBI Gene ID: 11925), has been modified (allele type: Cassette Acceptor) to (MGI ID: ). This ES cell line was made by gene targeting and designed to express an HA-tagged version of the transcription factor Ngn3. The Lox71 and Lox2272 sites were inserted flanking the Ngn3 coding sequence. Within the flanked region an HA-tag was placed at the N-terminus of the Ngn3 protein. This allele can be used to study chromatin and protein-protein interactions of Ngn3. Additionally, the Lox71 and Lox2272 sites allow for manipulations of the flanked region by RMCE. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Ngn3{HA.LCA} mouse ESC line BCGO:9004060 A mouse ESC line in which the targeted gene, Forkhead box M1 (NCBI Gene ID: 14235), has been modified (allele type: Gene Replacement) to (MGI ID: ). This ES cell line was made by gene targeting and is designed to serve as a cassette acceptor allele at the Foxm1 locus. The portion of genomic DNA containing exons 2-4 of Foxm1 was flanked with Lox71 and Lox2272 sites and replaced with a selection marker. This line allows for modification of the flanked sequences through RMCE. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Foxm1{LCA} mouse ESC line BCGO:9004061 A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Pdx1/YFP using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This ES cell line contains bidirectional TetO-regulated genes inserted into the Rosa26{LCA} allele by RMCE. In one direction, the tetO/CMV promoter will drive expression of Pdx1. In the other direction, it will drive the expression of yellow fluorescent protein (YFP). In this cell line, when the effector protein rtTA is expressed, Pdx1 and YFP will be over-expressed simultaneously upon administration of doxycyline. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Rosa26{Pdx1.YFP} mouse ESC line BCGO:9004062 A mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Pdx1/YFP using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This mouse line contains bidirectional TetO-regulated genes inserted into the Rosa26[LCA] allele by RMCE. In one direction, the TetO/CMV promoter will drive expression of Pdx1. In the other direction, it will drive the expression of yellow fluorescent protein (YFP). In this mouse line, when the effector protein rtTA is expressed, Pdx1 and YFP will be over-expressed simultaneously upon administration of doxycyline. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Rosa26{(Pdx1.YFP)Mgn} Vanderbilt University Medical Center Rosa26{(Pdx1.YFP)Mgn} mouse strain BCGO:9004072 A mouse ESC line in which part or all of the targeted gene, insulinoma-associated 1 (NCBI Gene ID: 53626) is replaced to create Pdx1/YFP using the Loxed Cassette Acceptor allele Insm1{tm1(LCA)}). This ES cell line contains bidirectional TetO-regulated genes inserted into the Insm1{LCA} allele by RMCE. In one direction, the TetO/CMV promoter drives the expression of the transcription factor Pdx1. In the other direction, it drives the expression of yellow fluorescent protein (YFP). In this cell line, when the effector protein rtTA is expressed, Pdx1 and YFP will be over-expressed simultaneously upon administration of doxycyline. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Insm1{Pdx1.YFP} mouse ESC line BCGO:9004074 A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create mCherry/MafA/Pdx1/Ngn3 using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This ES cell line contains bidirectional TetO-regulated genes inserted into the Rosa26{LCA} allele by RMCE. In one direction, the TetO/CMV promoter drives the expression of a polycistronic mRNA with transcription factors MafA, Pdx1, and Ngn3 linked by 2A peptide cleavage sequences. In the other direction, it drives the expression of the red fluorescent protein mCherry. In this cell line, when the effector protein rtTA is expressed, all three transcription factors and mCherry will be over-expressed simultaneously upon administration of doxycyline. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Rosa26{3TF.Cherry} mouse ESC line BCGO:9004075 A mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create mCherry/MafA/Pdx1/Ngn3 using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This mouse line contains bidirectional TetO-regulated genes inserted into the Rosa26[LCA] by RMCE. In one direction, the TetO/CMV promoter drives expression of a polycistronic mRNA with transcription factors MafA, Pdx1, and Ngn3 linked by 2A peptide cleavage sequences. In the other direction, it drives the expression of red fluorescent protein mCherry. In this mouse line, when the effector protein rtTA is expressed, all three transcription factors and mCherry will be over-expressed simultaneously upon administration of doxycyline. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Rosa26{(3TF.Cherry)Mgn} Vanderbilt University Medical Center Rosa26{(3TF.Cherry)Mgn} mouse strain BCGO:9004076 A mouse ESC line in which part or all of the targeted gene, pancreatic and duodenal homeobox 1 (NCBI Gene ID: 18609) is replaced to create Pdx1{aIVd} using the Loxed Cassette Acceptor allele Pdx1{tm1(LCA)}). In this ES cell line, Area IV of the Pdx1 enhancer (-2168/-1913 relative to the primary transcription start site) was deleted using RMCE in the Pdx1{LCA} allele. This cell line allows for assessment of the role of these DNA sequences in the regulation and function of Pdx1. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Pdx1{AIVd} mouse ESC line BCGO:9004077 A mouse strain in which part or all of the targeted gene, pancreatic and duodenal homeobox 1 (NCBI Gene ID: 18609) is replaced to create Pdx1{area IV deletion} using the Loxed Cassette Acceptor allele Pdx1{tm1(LCA)}). In this mouse line, Area IV of the Pdx1 enhancer (-2168/-1913 relative to the primary transcription start site) was deleted using RMCE in the Pdx1[LCA] allele. This mouse line allows for assessment of the role of these DNA sequences in the regulation and function of Pdx1. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Pdx1{(AIVd)Rwst} Vanderbilt University Medical Center Pdx1{(AIVd)Rwst} mouse strain BCGO:9004078 A mouse ESC line in which part or all of the targeted gene, NK2 transcription factor related, locus 2 (NCBI Gene ID: 18088) is replaced to create Nkx2.2{Cre} using the Loxed Cassette Acceptor allele Nkx2.2{tm1(LCA)}). In this ES cell line, the sequence for one of the two bi-partite Cre molecules (cCre) and the IRES sequence were knocked into a site directly upstream of the Nkx2.2 start codon using RMCE in the Nkx2.2{LCA} allele. The presence of the IRES sequence allows for the transcription of cCre and Nkx2.2 from the native Nkx2.2 locus at the same time. This results in the labeling of pancreatic epithelium cells that co-express high levels of Ngn3 and Nkx2.2 during mouse embryonic development. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Nkx2.2{cCre-Knock-in} mouse ESC line BCGO:9004079 A mouse strain in which part or all of the targeted gene, NK2 transcription factor related, locus 2 (NCBI Gene ID: 18088) is replaced to create Nkx2.2{Cre-knock-in)} using the Loxed Cassette Acceptor allele Nkx2.2{tm1(LCA)}). In this mouse line, one of the two bi-partite Cre molecules, cCre, together with the IRES sequence was knocked into the site directly upstream of the Nkx2.2 start codon using RMCE in the Nkx2.2[LCA] allele. The presence of the IRES sequence allows for transcription of cCre and Nkx2.2 from the native Nkx2.2 locus at the same time. This mouse line allows the labeling of pancreatic epithelium cells that co-express high levels of Ngn3 and Nkx2.2 during mouse embryonic development. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Nkx2.2{(Cre-Knock-in)} Vanderbilt University Medical Center Nkx2.2{(Cre-Knock-in)} mouse strain BCGO:9004080 A mouse ESC line in which part or all of the targeted gene, NK2 transcription factor related, locus 2 (NCBI Gene ID: 18088) is replaced to create Nkx2.2{3XHA-Nkx2.2} using the Loxed Cassette Acceptor allele Nkx2.2{tm1(LCA)}). In this cell line RMCE in the Nkx2.2.LCA allele was used to introduce a triple HA tag in frame at the N-terminus of the transcription factor Nkx2.2. This allows for efficient immunoprecipitation of HA-tagged Nkx2.2 protein from mouse tissues to perform ChIP and protein-protein interaction studies. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Nkx2.2{3XHA.Nkx2.2} mouse ESC line BCGO:9004086 A mouse strain in which part or all of the targeted gene, NK2 transcription factor related, locus 2 (NCBI Gene ID: 18088) is replaced to create Nkx2.2{3XHA-Nkx2.2} using the Loxed Cassette Acceptor allele Nkx2.2{tm1(LCA)}). In this mouse line, RMCE in the Nkx2.2{LCA} allele was used to introduce a triple HA tag in frame at the N-terminus of the transcription factor Nkx2.2. This allows for efficient immunoprecipitation of HA-tagged Nkx2.2 protein from mouse tissues to perform ChIP and protein-protein interaction studies. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Nkx2.2{(3XHA.Nkx2.2)Suss} Vanderbilt University Medical Center Nkx2.2{(3XHA.Nkx2.2)Suss} mouse strain BCGO:9004087 A mouse ESC line in which part or all of the targeted gene, NK2 transcription factor related, locus 2 (NCBI Gene ID: 18088) is replaced to create Nkx2.2{Cre-EGFP} using the Loxed Cassette Acceptor allele Nkx2.2{tm1(LCA)}). In this ES cell line, a coding portion of the transcription factor Nkx2.2 was replaced with a Cre-EGFP cassette, in frame to the Nkx2.2 ATG. This allows for sites of Nkx2.2 gene expression to be identified in mice using direct immunofluorescence, FACS purification of Nkx2.2 expressing cells, and lineage tracing using Nkx2.2 driven Cre expression. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Nkx2.2{Cre.EGFP} mouse ESC line BCGO:9004088 A mouse strain in which part or all of the targeted gene, pancreatic and duodenal homeobox 1 (NCBI Gene ID: 18609) is replaced to create Pdx1/cre-ER using the Loxed Cassette Acceptor allele Pdx1{tm1(LCA)}). In this mouse line, the first exon of the transcription factor Pdx1 was replaced with the coding sequence for a Cre-ER fusion protein using RMCE in the Pdx1[LCA] allele. Pdx1-promoter driven Cre-ER expressing mice enable tamoxifen-inducible Cre-LoxP manipulation of pancreatic lineage cells. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Pdx1{(Cre-ER)} Vanderbilt University Medical Center Pdx1{(Cre-ER)} mouse strain BCGO:9004093 A mouse ESC line in which part or all of the targeted gene, NK2 transcription factor related, locus 2 (NCBI Gene ID: 18088) is replaced to create Cherry using the Loxed Cassette Acceptor allele Nkx2.2{tm1(LCA)}). In this ES cell, 1.956 kb of the native Nkx2.2 gene, containing a portion of exon 1 (all but the first 214 bp) and all of exon 2, was replaced by the mCherry cassette in frame to the Nkx2.2 ATG. This allows for sites of Nkx2.2 gene expression in the mouse to be identified using direct immunofluorescence and FACS purification of Nkx2.2 expressing cells. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Nkx2.2{Cherry} mouse ESC line BCGO:9004113 A polyclonal antibody raised in guinea pig that targets the enterobacteria phage p1 "Cre" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal enterobacteria phage p1 Cre raised in guinea pig BCGO:9004123 A mouse ESC line in which the targeted gene, paired box 4 (NCBI Gene ID: 18506), has been modified (allele type: Cassette Acceptor) to targeted mutation 1 (MGI ID: Pax4{tm1(LCA)Ggu}). This ES cell line is made by gene targeting and is designed to express an HA-tagged version of the transcription factor Pax4. Lox71 and Lox2272 sites are inserted, flanking the last coding exon of the Pax4 gene. In the flanked region, an HA-tag was placed at the C-terminus of the PAX4 protein. This allele can be used to study chromatin and protein-protein interactions of PAX4. Additionally, the Lox71 and Lox2272 sites allow for future manipulations of the flanked region by RMCE. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Pax4{HA.LCA} mouse ESC line BCGO:9004125 A polyclonal antibody raised in goat that targets the human "CDCP1" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal human CDCP1 raised in goat BCGO:9004126 A polyclonal antibody raised in goat that targets the human "CD-200" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal human CD-200 raised in goat BCGO:9004127 A polyclonal antibody raised in goat that targets the human "Coagulation factor 3(rhF3)" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal human Coagulation factor 3(rhF3) raised in goat BCGO:9004129 A polyclonal antibody raised in sheep that targets the human "Ngn3" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal human Ngn3 raised in sheep BCGO:9004130 A monoclonal antibody raised in mouse that targets the mouse "Pax4" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal mouse Pax4 raised in mouse BCGO:9004131 A monoclonal antibody raised in mouse that targets the mouse "Pax4" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal mouse Pax4 raised in mouse BCGO:9004132 A monoclonal antibody raised in mouse that targets the mouse "Pax4" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal mouse Pax4 raised in mouse BCGO:9004133 A monoclonal antibody raised in mouse that targets the human "CD142" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal human CD142 raised in mouse BCGO:9004134 A monoclonal antibody raised in rat that targets the rat "Beta cell, IC2" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal rat Beta cell, IC2 raised in rat BCGO:9004135 A polyclonal antibody raised in goat that targets the human "CD-200" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal human CD-200 raised in goat BCGO:9004142 A mouse strain in which the targeted gene, protein kinase, DNA activated, catalytic polypeptide (NCBI Gene ID: 19090), has been modified (allele type: Other) to severe combined immunodeficiency (MGI ID: Prkdc{scid}). The NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ mice, commonly known as NOD scid gamma (NSG), do not express the Prkdc gene nor the X-linked Il2rg gene. NSG mice are viable, fertile, normal in size and do not display any gross physical or behavioral abnormalities. Histological examination of lymphoid tissues reveals absence of lymphoid cells and some cystic structures in the thymus, an absence of follicles in the spleen and markedly diminished celluarity of lymph nodes. NSG mice are deficient in mature lymphocytes, serum Ig is not detectable and natural killer (NK) cell cytotoxic activity is extremely low. These mice are resistant to lymphoma development even after sublethal irradiation treatment. These mutant mice have been shown to readily support engraftment of human CD34+ hematopoietic stem cells and represent a superior, long-lived model suitable for studies employing xenotransplantation strategies. Please note that the NSG carries the true null interleukin-2 receptor gamma chain mutation and should not be confused with other strains that express a truncated interleukin-2 receptor gamma chain as described in: "Modulation of hematopoiesis in mice with a truncated mutant of the interleukin-2 receptor gamma chain". Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler NOD.Cg-Prkdc{scid} Il2rg{tm1Wjl}/SzJ Vanderbilt University Medical Center NOD.Cg-Prkdc{scid} Il2rg{tm1Wjl}/SzJ mouse strain BCGO:9004143 A mouse strain in which the targeted gene, insulin II (NCBI Gene ID: 16334), has been modified (allele type: Other) to Akita (MGI ID: Ins2{Akita}). NRG-Akita mice, which are homozygous for the Rag1tm1Mom and the Il2rgtm1Wjl alleles (males are hemizygous for the X-linked Il2rgtm1Wjl allele) and heterozygous for the Ins2Akita allele, develop spontaneous hyperglycermia. No mature T, B or NK cells are detected in flow cytometric analysis of splenocytes from NRG-Akita mutant mice. Granulocyte and macrophage populations are similar to those seen in NRG mice. NRG-Akita mice develop hyperglycemia between 3 and 5 weeks of age. Histological examination at 3 weeks of age reveals normal pancreas morphology, and routine insulin and glucagon staining. By approximately 32 weeks of age, NRG-Akita mice display disorganized, condensed pancreatic islet architecture, with loss of insulin-positive cells. Euglycemia is restored by subrenal transplantation of mouse or human islets or intrapancreatic transplantation of dissociated mouse islet cells. NRG-Akita mice engrafted with human hematopoietic stem cells (HSC) develop humanized immune systems. Approximately 60% of the human HSC engrafted NRG-Akita mice reject human islet allografts. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler NOD.Cg-Rag1{tm1Mom}Ins2{Akita}Il2rg{tm1Wjl}/SzJ Vanderbilt University Medical Center NOD.Cg-Rag1{tm1Mom}Ins2{Akita}Il2rg{tm1Wjl}/SzJ mouse strain BCGO:9004144 A mouse ESC line in which part or all of the targeted gene, pancreatic and duodenal homeobox 1 (NCBI Gene ID: 18609) is replaced to create Pdx1/cre-ER using the Loxed Cassette Acceptor allele Pdx1{tm1(LCA)}). In this cell line, the first exon of the transcription factor Pdx1 was replaced with the coding sequence for a Cre-ER fusion protein using RMCE in the Pdx1{LCA} allele. Pdx1-promoter driven Cre-ER expressing mice enable tamoxifen-inducible Cre-LoxP manipulation of pancreatic lineage cells. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Pdx1{Cre.ER} mouse ESC line BCGO:9004145 A mouse strain in which the targeted gene, Neurogenin 3 (NCBI Gene ID: 11925), has been modified (allele type: Cassette Acceptor) to (MGI ID: ). This mouse line was made by gene targeting and designed to express an HA-tagged version of the transcription factor Ngn3. The Lox71 and Lox2272 sites were inserted flanking the Ngn3 coding sequence. Within the flanked region an HA-tag was placed at the N-terminus of the Ngn3 protein. This allele can be used to study chromatin and protein-protein interactions of Ngn3. Additionally, the Lox71 and Lox2272 sites allow for manipulations of the flanked region by RMCE. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Ngn3{(HA.LCA)} Vanderbilt University Medical Center Ngn3{(HA.LCA)} mouse strain BCGO:9004146 A mouse strain in which the targeted gene, paired box 4 (NCBI Gene ID: 18506), has been modified (allele type: Cassette Acceptor) to targeted mutation 1 (MGI ID: Pax4{tm1(LCA)Ggu}). This mouse line was made by gene targeting and designed to express an HA-tagged version of the transcription factor Pax4. The Lox71 and Lox2272 sites were inserted flanking the last coding exon of the Pax4 gene. Within the flanked region an HA-tag was placed at the C-terminus of the PAX4 protein. This allele can be used to study chromatin and protein-protein interactions of PAX4. Additionally, the Lox71 and Lox2272 sites allow for manipulations of the flanked region by RMCE in the future. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Pax4{(HA.LCA)Ggu} Vanderbilt University Medical Center Pax4{(HA.LCA)Ggu} mouse strain BCGO:9004147 A mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Setd5/GFP using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This mouse line was generated by RMCE in the Rosa26[LCA] allele. A coding sequence for green fluorescent protein (GFP) was inserted into the first exon of the Setd5 gene. This exon is located upstream of the Rosa26 transcribed sequence and is transcribed in an opposite orientation. The GFP-polyA cassette, transcribed from the Setd5 promoter, knocks out Setd5 transcription and provides a reporter for Setd5 gene expression. The purpose of this mouse line is to study the molecular function of the Setd5 gene. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Rosa26{(Setd5.GFP)Mgn} Vanderbilt University Medical Center Rosa26{(Setd5.GFP)Mgn} mouse strain BCGO:9004148 A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create 7xTcf/Lef binding site using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This ES cell line was generated by RMCE in the Rosa26{LCA} allele. The Rosa26 gene sequence (from -228 to +81) was replaced by a Wnt response element (7xTcf/Lef binding site) fused to a TATA-Cerulean (CFP) reporter. This ES cell line may be useful for assessing canonical Wnt responsiveness. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Rosa26{228.TOP.CFP} mouse ESC line BCGO:9004149 A mouse strain in which part or all of the targeted gene, pancreas specific transcription factor, 1a (NCBI Gene ID: 19213) is replaced to create Ptf1a{td.TOM} using the Loxed Cassette Acceptor allele Ptf1a{tm1(LCA)}). This mouse cell line was generated by RMCE in the Ptf1a[LCA] allele. Pancreata of this mouse line express both td.Tomato (a red fluorescent protein) and an N-terminal epitope tagged Strep/Flag (NSF) fusion of the transcription factor Ptf1a. This line may be used in a variety of applications such as FACS sorting of Ptf1a expressing cells, chromatin immunoprecipitation, and proteomic analyses. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Ptf1a{(tdTomato)} Vanderbilt University Medical Center Ptf1a{(tdTomato)} mouse strain BCGO:9004150 A mouse strain in which part or all of the targeted gene, NK2 transcription factor related, locus 2 (NCBI Gene ID: 18088) is replaced to create Nkx2.2{Cre-EGFP} using the Loxed Cassette Acceptor allele Nkx2.2{tm1(LCA)}). In this mouse, a coding portion of the transcription factor Nkx2.2 was replaced with a Cre-EGFP cassette, in frame to the Nkx2.2 ATG. This allows for sites of Nkx2.2 gene expression to be identified in mice using direct immunofluorescence, FACS purification of Nkx2.2 expressing cells, and lineage tracing using Nkx2.2 driven Cre expression. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Nkx2.2{(Cre.EGFP)Suss} Vanderbilt University Medical Center Nkx2.2{(Cre.EGFP)Suss} mouse strain BCGO:9004152 A mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create NRSF using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This mouse line contains bidirectional TetO-regulated genes inserted into the Rosa26[LCA] allele by RMCE. In one direction, the TetO/CMV promoter drives the expression of the transcription factor NRSF/REST. In the other direction, it drives the expression of red fluorescent protein mCherry. In this mouse line, when the effector protein rtTA is expressed, NRSF and mCherry will be simultaneously over-expressed upon administration of doxycyline. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Rosa26{(TetO.NRSF)Msan} Vanderbilt University Medical Center Rosa26{(TetO.NRSF)Msan} mouse strain BCGO:9004153 A mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{(R26-228-AR8-TA-mCherry)} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This mouse line was generated by RMCE in the Rosa26[LCA] allele. In this mouse line, the Rosa26 gene sequence (-228 to +81) was replaced by the Foxh1/Smad2-dependent, Mix2-derived Activin response element (AR8) fused to a TATA-mCherry reporter. These mice may be useful to assess Activin, Nodal, and TGFbeta responsiveness. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Gt(ROSA)26Sor{tm2.1(mix1b-mCherry)Mgn} Vanderbilt University Medical Center Gt(ROSA)26Sor{tm2.1(mix1b-mCherry)Mgn} mouse strain BCGO:9004154 A mouse ESC line in which the targeted gene, Nephrocan (NCBI Gene ID: 66650), has been modified (allele type: Global Null) to (MGI ID: Neph(mCherry)). This ES cell line was made by gene targeting and was designed to express red fluorescent protein (mCherry) from the Nepn promoter thereby disrupting the expression of Nepn. The FP coding sequence was inserted dowstream of the Nepn start codon, in front of the Nepn first exon. This cell line is used to study the function and expression of Nepn. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Nepn{Cherry} mouse ESC line BCGO:9004156 A mouse ESC line in which the targeted gene, Insulin 2 (NCBI Gene ID: 20671), has been modified (allele type: Cassette Acceptor) to (MGI ID: Ins2{(apple.LCA)}). This ES cell line was made by gene targeting and designed to express a H2B-Apple fusion protein (nuclear red fluorescent protein) from the Ins2 promoter. The FP coding sequence is downsteam of the Ins2 start codon (replacing exon 2 of Ins2) and is flanked by Lox66/Lox2272 sites to allow for future manipulations of the flanked region by RMCE. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Ins2{Apple.LCA} mouse ESC line BCGO:9004157 A mouse ESC line in which part or all of the targeted gene, pancreatic and duodenal homeobox 1 (NCBI Gene ID: 18609) is replaced to create Pdx1{rTTA} using the Loxed Cassette Acceptor allele Pdx1{tm1(LCA)}). In this cell line, thefirst exon of Pdx1 was replaced with the coding sequence for rTTA protein, using RMCE in the Pdx1{LCA} allele. Generation of Pdx1-promoter driven rTTA expressing mice will enable tetracycline-inducible manipulation of pancreatic lineage cells. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Pdx1{rTTA} mouse ESC line BCGO:9004158 A mouse ESC line in which part or all of the targeted gene, pancreatic and duodenal homeobox 1 (NCBI Gene ID: 18609) is replaced to create Pdx1/cre using the Loxed Cassette Acceptor allele Pdx1{tm1(LCA)}). In this cell line, thefirst exon of Pdx1 was replaced with the coding sequence for Cre-recombinase using RMCE in the Pdx1{LCA} allele. Generation of Pdx1-promoter driven Cre-expressing cells will enable Cre-LoxP manipulation of pancreatic lineage cells. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Pdx1{Cre} mouse ESC line BCGO:9004159 A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create 3TF.GFP-Cre using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This cell line contains TetO-regulated genes inserted into the Rosa26{LCA} allele by RMCE. The TetO/miniCMV promoter was placed (at -228) upstream of the putative ROSA26 transcription start site and drives the expression of a polycistronic mRNA with transcription factors MafA, Pdx1, and Ngn3 together with a GFP-Cre fusion protein. The sequences are linked by 2A peptide cleavage sequences. In this cell line, when the effector protein rtTA is expressed, all three transcription factors and GFP-Cre will be over-expressed simultaneously upon administration of doxycyline. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Rosa26{228.3TF.GFP.Cre} mouse ESC line BCGO:9004160 A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{mIre1.N906A.Cherry} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This ES line contains bidirectional TetO-regulated genes inserted into the Rosa26{LCA} allele by RMCE. In one direction the TetO/CMV promoter drives the expression of point mutant(N906A) of IRE1, an ER transmenbrane kinase response to unfolded protein response (UPR). In the other direction it drives the expression of red fluorescent protein mCherry. This ES cell line can be used to simultaneously over-express Ire1(N906A) and mCherry upon administration of doxycyline when the effector protein rtTA is expressed. This line can be used to study the roles of IRE1 in the response to ER stress, diet induced obesity and insulin resistance. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Rosa26{mIre1.N906A.Cherry} mouse ESC line BCGO:9004256 A polyclonal antibody raised in rabbit that targets the human "HIP-14 ZDHHC17" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal human HIP-14 ZDHHC17 raised in rabbit BCGO:9004278 A mouse strain in which part or all of the targeted gene, Ghrelin (NCBI Gene ID: 58991) is replaced to create Ghrl Cre-eGFP CEV using the Loxed Cassette Acceptor allele Ghrl{LCA}). Ghrl{Cre-eGGP} mice contain a Cre-eGFP fusion protein which replaces the Ghrelin coding sequence. These mice expressc Cre-eGFP phusion protein under control of the Ghrelin gene locus. The Ghrl{Cre-eGGP} mice may be used to track ghrelin-expressing cells progeny,or to conditionally inactivate genes in ghrelin-expressing cells. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Ghrl{tm1(Cre-eGFP)Suss} Vanderbilt University Medical Center Ghrl{tm1(Cre-eGFP)Suss} mouse strain BCGO:9004305 A monoclonal antibody raised in mouse that targets the human "Cd31 (PECAM1)" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal human Cd31 (PECAM1) raised in mouse BCGO:9004306 A polyclonal antibody raised in rabbit that targets the cow "GFAP" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal cow GFAP raised in rabbit BCGO:9004307 A polyclonal antibody raised in rabbit that targets the human "Glucagon (GCG)" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal human Glucagon (GCG) raised in rabbit BCGO:9004308 A polyclonal antibody raised in guinea pig that targets the human "Glucagon (GCG)" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal human Glucagon (GCG) raised in guinea pig BCGO:9004309 A polyclonal antibody raised in guinea pig that targets the pig "Insulin" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal pig Insulin raised in guinea pig BCGO:9004310 A polyclonal antibody raised in rabbit that targets the human "Ki67" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal human Ki67 raised in rabbit BCGO:9004311 A polyclonal antibody raised in rabbit that targets the human "MafA" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal human MafA raised in rabbit BCGO:9004312 A polyclonal antibody raised in rabbit that targets the human "MafB" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal human MafB raised in rabbit BCGO:9004313 A polyclonal antibody raised in rabbit that targets the human "Pancreatic Polypeptide (PPY)" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal human Pancreatic Polypeptide (PPY) raised in rabbit BCGO:9004315 A polyclonal antibody raised in sheep that targets the human "Somatostatin (Sst)" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal human Somatostatin (Sst) raised in sheep BCGO:9004316 A monoclonal antibody raised in rabbit that targets the rat "Tuj1 (TUBB3)" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal rat Tuj1 (TUBB3) raised in rabbit BCGO:9004317 A polyclonal antibody raised in goat that targets the rat "VEGFA" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal rat VEGFA raised in goat BCGO:9004318 A polyclonal antibody raised in goat that targets the mouse "Foxa2 (HNF3b)" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal mouse Foxa2 (HNF3b) raised in goat BCGO:9004319 A monoclonal antibody raised in hamster (armenian) that targets the human "Muc1" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal human Muc1 raised in hamster (armenian) BCGO:9004320 A polyclonal antibody raised in goat that targets the human "HNF-1β" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal human HNF-1β raised in goat BCGO:9004321 A polyclonal antibody raised in rabbit that targets the human "Sox9" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal human Sox9 raised in rabbit BCGO:9004322 A polyclonal antibody raised in goat that targets the human "CDCP1" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal human CDCP1 raised in goat BCGO:9004323 A polyclonal antibody raised in rabbit that targets the human "α-Amylase (AMY2A)" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal human α-Amylase (AMY2A) raised in rabbit BCGO:9004324 A polyclonal antibody raised in guinea pig that targets the cow "Insulin" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal cow Insulin raised in guinea pig BCGO:9004325 A polyclonal antibody raised in guinea pig that targets the human "Insulin" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal human Insulin raised in guinea pig BCGO:9004326 A polyclonal antibody raised in goat that targets the human "Insulin" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal human Insulin raised in goat BCGO:9004327 A polyclonal antibody raised in rabbit that targets the human "Glucagon" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal human Glucagon raised in rabbit BCGO:9004328 A polyclonal antibody raised in goat that targets the human "Somatostatin (Sst)" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal human Somatostatin (Sst) raised in goat BCGO:9004329 A polyclonal antibody raised in rabbit that targets the rat "Synaptophysin (SYP)" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal rat Synaptophysin (SYP) raised in rabbit BCGO:9004489 A mouse ESC line in which part or all of the targeted gene, Neurogenin 3 (NCBI Gene ID: 11925) is replaced to create Ngn3{T2A.nCre} using the Loxed Cassette Acceptor allele ). In this mouse ES cell line, one of the two bi-partite Cre molecules, nCre, was knocked in upstream of Ngn3 coding sequence by RMCE in Ngn3.HA.LCA ES cell line. nCre sequence is expressed from policistronic mRNA linked by 2a peptide to Ngn3 coding sequence allowing for simultanious expression of both proteins from Ngn3 promoter. This mouse line, in combination with Nkx2.2-cCre mouse line, allows to label pancreatic epithelium cells that co-express high levels of Ngn3 and Nkx2.2 during mouse embryonic development. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Ngn3{T2A.nCre} mouse ESC line BCGO:9004527 A mouse ESC line in which part or all of the targeted gene, NK2 transcription factor related, locus 2 (NCBI Gene ID: 18088) is replaced to create Nkx2.2{T2A.cCre} using the Loxed Cassette Acceptor allele Nkx2.2{tm1(LCA)}). In this line, one of the two bi-partite Cre molecules, cCre, is inserted downstream of Nkx2.2 coding sequence fused with 2a peptide using RMCE in the Nkx2.2{LCA}allele. The presence of the T2A sequence allows for transcription of Nkx2.2 and cCre from the native Nkx2.2 locus at the same time. Mouse lines obtained from these ES cells allow the labeling of pancreatic epithelium cells that co-express high levels of Ngn3 and Nkx2.2 during mouse embryonic development. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Nkx2.2{T2A.cCre} mouse ESC line BCGO:9004529 A mouse ESC line containing a transgene in which Cre (transgene) is driven by the Neurog3 promoter (NCBI Gene ID: 11925). This line has a single copy of Neurog3.Cre-ER.LCA BAC transgene inserted in a genome. The transgene is designed to express Cre-ER under control of Neurog 3 promoter and will allow inducible tracking or gene inactivation in the Ngn3-LOW and Ngn3-HIGH populations of pre-endocrine cells. Additionally, the lox66 and lox2272 sites will allow the BAC transgene to serve as a loxed cassette acceptor (LCA) in ES cells for future recombinase-mediated cassette exchange (RMCE). Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Neurog3{Cre-ER.BAC} mouse ESC line BCGO:9004533 A mouse strain in which part or all of the targeted gene, pancreatic and duodenal homeobox 1 (NCBI Gene ID: 18609) is replaced to create Pdx1{Cre} using the Loxed Cassette Acceptor allele Pdx1{tm1(LCA)}). In this mouse strain, the first exon of Pdx1 is replaced with coding sequence for Cre recombinase using RMCE in the Pdx1{LCA} allele. Generation of Pdx-promoter driven Cre expressing mice will enable Cre-LoxP manipulation of pancreatic lineage cells. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Pdx1{CreMgn} Vanderbilt University Medical Center Pdx1{CreMgn} mouse strain BCGO:9004534 A mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{228.TOP.CFP} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). In this mouse strain the Rosa26 gene sequence from -228 to +81 was replaced by a Wnt response element (7xTcf/Lef binding site) fused to a TATA-Cerulean (CFP) reporter. These mice may be useful in assessing Canonical Wnt responsiveness. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Rosa26{228.TOP.CFPHri} Vanderbilt University Medical Center Rosa26{228.TOP.CFPHri} mouse strain BCGO:9004536 A mouse ESC line containing a transgene in which RG (transgene) is driven by the Neurog3 promoter (NCBI Gene ID: 11925). This line has a single copy of Neurog3.RG.LCA BAC transgene inserted in the genome. The transgene is designed to express an H2B-mCherry fusion protein in the nucleus and a membrane anchored EGFP (via GPI), both under the control of the Neurog3 promoter. This will allow for live-cell imaging of mitotic nuclear/chromosome dynamics and membrane protrusive behavior in endocrine progenitors. Additionally, Lox71 and Lox2272 sites flanking the transgene will allow for manipulations by RMCE in the future. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Neurog3{RG.BAC} mouse ESC line BCGO:9004537 A mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create ROSA26{228.3TF.GFP-Cre} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This mouse strain contains TetO-regulated genes inserted into the Rosa 26{LCA} allele by RMCE. TetO/miniCMV promoter is placed at -228 position upstream of putative ROSA26 transcription start site and drives the expression of a polycistronic mRNA with transcription factors MafA, Pdx1, and Ngn3 together with GFP-Cre fusion protein linked by 2A peptide cleavage sequences. These mice will be able to simultaneously over-express all three transcription factors and GFP-Cre upon administration of doxycyline when the effector protein rtTA is expressed. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Rosa26{228.3TF.GFP-CreMgn} Vanderbilt University Medical Center Rosa26{228.3TF.GFP-CreMgn} mouse strain BCGO:9004538 A mouse strain in which part or all of the targeted gene, Neurogenin 3 (NCBI Gene ID: 11925) is replaced to create Ngn3{T2A.nCre} using the Loxed Cassette Acceptor allele ). In this mouse line, one of the two bi-partite Cre molecules, nCre, was knocked in upstream of Ngn3 coding sequence by RMCE in Ngn3{HA.LCA} ES cell line. nCre sequence is expressed from policistronic mRNA linked by 2a peptide to Ngn3 coding sequence allowing for simultanious expression of both proteins from the Ngn3 promoter. This mouse line, in combination with Nkx2.2{cCre} mouse line, allows for the labeling of pancreatic epithelium cells that co-express high levels of Ngn3 and Nkx2.2 during mouse embryonic development. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Ngn3{T2A.nCreGgu} Vanderbilt University Medical Center Ngn3{T2A.nCreGgu} mouse strain BCGO:9004539 A mouse ESC line in which part or all of the targeted gene, pancreatic and duodenal homeobox 1 (NCBI Gene ID: 18609) is replaced to create Pdx1{H2B.Neptune} using the Loxed Cassette Acceptor allele Pdx1{tm1(LCA)}). In this line, the first exon of Pdx1 is replaced with coding sequence for mNeptune (a far red fluorescent protein) using RMCE in the Pdx1 LCA allele. Generation of a Pdx-promoter driven mNeptune fluorescent allele will enable the isolation of pancreatic lineage cells by FACS and broaden the possibilities for combinatorial sorting with other fluorescent alleles. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Pdx1{H2B.Neptune} mouse ESC line BCGO:9004545 A mouse ESC line in which the targeted gene, Somatostatin (NCBI Gene ID: 20604), has been modified (allele type: Cassette Acceptor) to Sst.rTTA loxed cassette acceptor (MGI ID: Sst.rTTA{LCA}). This allelle is designed to express a tet-inducible reverse-transactivator under control of the somatostatin promoter. Lox66 and Lox2272 sites are inserted flanking 500bp of Sst promoter region, Sst exons I and II and Sst poly A site. The rTTA-beta-globin poly A cassete replaces Sst coding exons (I and II). The allele can be used to drive tet-inducible expression in somatostatin expressing cells (Delta-cells). Additionally, the Lox66 and Lox2272 sites allow for manipulations of the flanked region by RMCE in the future. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Sst.rTTA.LCA mouse ESC line BCGO:9004547 A mouse ESC line in which the targeted gene, forkhead box A2 (NCBI Gene ID: 15376), has been modified (allele type: Cassette Acceptor) to Forkhead box A2 loxed cassette acceptor (MGI ID: Foxa2{LCA}). This ES cell line contains a loxed cassette acceptor (LCA) allele that may be utilized for the exchange of DNAs of interest into the Foxa2 locus by recombinase mediated cassette exchange (RMCE). This LCA uses a Lox66/71 and Lox2272 strategy for RMCE and allows for manipulation of a 4.7 kb region of the gene (contains a promoter and all exons: exon 1, 2 and 3). This leads to a variety of experiments that can be performed using a wide range of cassette designs. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Foxa2{LCA} mouse ESC line BCGO:9004548 A polyclonal antibody raised in chicken that targets the mouse "Ngn3" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal mouse Ngn3 raised in chicken BCGO:9004549 A polyclonal antibody raised in chicken that targets the mouse "Ngn3" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal mouse Ngn3 raised in chicken BCGO:9004550 A polyclonal antibody raised in chicken that targets the mouse "Nkx6.1" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal mouse Nkx6.1 raised in chicken BCGO:9004551 A polyclonal antibody raised in chicken that targets the mouse "Nkx6.1" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal mouse Nkx6.1 raised in chicken BCGO:9004552 A polyclonal antibody raised in chicken that targets the mouse "PDX1" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal mouse PDX1 raised in chicken BCGO:9004553 A polyclonal antibody raised in chicken that targets the mouse "PDX1" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal mouse PDX1 raised in chicken BCGO:9004554 A polyclonal antibody raised in chicken that targets the mouse "Prox1" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal mouse Prox1 raised in chicken BCGO:9004555 A polyclonal antibody raised in chicken that targets the mouse "Prox1" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Polyclonal mouse Prox1 raised in chicken BCGO:9004556 A mouse strain in which part or all of the targeted gene, NK2 transcription factor related, locus 2 (NCBI Gene ID: 18088) is replaced to create Nkx2.2{T2A.cCre} using the Loxed Cassette Acceptor allele Nkx2.2{tm1(LCA)}). In this line, one of the two bi-partite Cre molecules, cCre, is placed downstream of Nkx2.2 coding sequence fused with 2a peptide using RMCE in the Nkx2.2[LCA] allele. The presence of the T2A sequence allows for transcription of Nkx2.2 and cCre from the native Nkx2.2 locus at the same time. This mouse line allows the labeling of pancreatic epithelium cells that co-express high levels of Ngn3 and Nkx2.2 during mouse embryonic development. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Nkx2.2{T2A.cCreGgu} Vanderbilt University Medical Center Nkx2.2{T2A.cCreGgu} mouse strain BCGO:9004560 A mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26.mIre1.N906A.Cherry using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This mouse contains bidirectional TetO-regulated genes inserted into the Rosa26.LCA allele by RMCE. In one direction the TetO/CMV promoter drives the expression of point mutant (N906A) of IRE1, an ER transmembrane kinase response to unfolded protein response (UPR). In the other direction it drives the expression of red fluorescent protein mCherry. This mouse can be used to simultaneously over-express Ire1 (N906A) and mCherry upon administration of doxycyline when the effector protein rtTA is expressed. This line can be used to study the roles of IRE1 in the response to ER stress, diet induced obesity and insulin resistance. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Rosa26{mIre1.N906A.CherryMgn} Vanderbilt University Medical Center Rosa26{mIre1.N906A.CherryMgn} mouse strain BCGO:9004561 A mouse strain in which the targeted gene, Somatostatin (NCBI Gene ID: 20604), has been modified (allele type: Gene Replacement) to (MGI ID: Sst{rTTA.LCA}). TheSst.rTTA.LCA mice are designed to express a tet-inducible reverse-transactivator under control of somatostatin promoter. Lox66 and Lox2272 sites are inserted flanking 500bp of Sst promoter region, Sst exons I and II and Sst poly A site. The rTTA-beta-globin poly A cassete is put in place of Sst coding exons (I and II). The mice can be used to drive tet-inducible expression in somatostatin expressing cells (Delta-cells). Additionally, the Lox66 and Lox2272 sites allow for manipulations of the flanked region by RMCE in the future. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Sst{rTTA.LCA.Mgn} Vanderbilt University Medical Center Sst{rTTA.LCA.Mgn} mouse strain BCGO:9004563 A monoclonal antibody raised in mouse that targets the human "ghrelin" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal human ghrelin raised in mouse BCGO:9004573 A monoclonal antibody raised in mouse that targets the human "Gallbladder mucosal epithelium" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal human Gallbladder mucosal epithelium raised in mouse BCGO:9004574 A monoclonal antibody raised in mouse that targets the human "Gallbladder mucosal epithelium" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal human Gallbladder mucosal epithelium raised in mouse BCGO:9004575 A monoclonal antibody raised in mouse that targets the human "Gallbladder mucosal epithelium" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal human Gallbladder mucosal epithelium raised in mouse BCGO:9004576 A monoclonal antibody raised in mouse that targets the human "Gallbladder mucosal epithelium" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal human Gallbladder mucosal epithelium raised in mouse BCGO:9004597 A monoclonal antibody raised in mouse that targets the human "Alpha cells" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal human Alpha cells raised in mouse BCGO:9004598 A monoclonal antibody raised in mouse that targets the human "Pancreatic duct cells" antigen. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler Vanderbilt University Medical Center Monoclonal human Pancreatic duct cells raised in mouse BCGO:9004611 A mouse strain that is immunodeficient and express human HLA class 1 heavy and light chains. This strain may be useful as a human hematopoietic engraftment host that supports the maturation of human T cells with transplantation http://jaxmice.jax.org/strain/014570.html. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler NOD.Cg-Prkdc{scid} Il2rg{tm1Wjl} Tg(HLA-A/H2-D/B2M)1Dvs/SzJ Vanderbilt University Medical Center NOD.Cg-Prkdc{scid} Il2rg{tm1Wjl} Tg(HLA-A/H2-D/B2M)1Dvs/SzJ mouse strain BCGO:9004612 A mouse strain that lacks expression of the murine Prkdc gene, the X-linked Il2rg gene, and MHC class II, but express the human leukocyte antigen DR4 gene. These mice may be useful for targeting human CD4{+} T cells in transplantation studies in the absence of xeno-GVHD.More details are available at http://jaxmice.jax.org/strain/017637.html. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartailler NOD.Cg-Prkdc{scid} Il2rg{tm1Wjl} H2-Ab1{tm1Gru} Tg(HLA-DRB1)31Dmz/SzJ Vanderbilt University Medical Center NOD.Cg-Prkdc{scid} Il2rg{tm1Wjl} H2-Ab1{tm1Gru} Tg(HLA-DRB1)31Dmz/SzJ mouse strain 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 Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. per discussion with Barry Smith Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] BFO:0000004 ic IndependentContinuant a chair a heart a leg a molecule a spatial region an atom an orchestra. an organism the bottom right portion of a human torso the interior of your mouth A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] independent continuant b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] BFO:0000005 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] 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] 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 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 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] 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]) BTO:0000632 A cell of a usually benign tumor of the insulin-secreting cells of the pancreas. insulinoma cell BTO:0000773 Human cell line from tissue infected with Epstein-Barr virus, resembling a lymphoblast. lymphoblastoid cell line BTO:0001581 embryonic stem cell line BTO:0003081 pancreatic ductal adenocarcinoma cell BTO:0003560 CCE is a mouse embryonic stem cell line derived from 129/Sv mouse strain and has been provided for research use only. CCE cell CARO:0001008 gross anatomical part Anatomical structure that is part of a multicellular organism and is at the gross anatomical level, e.g. above the level of a cell. Included are portions of organism substances such as blood, multi-cell-part structures such as axon tracts, acellular anatomical structures such as hair, and organism subdivisions such as head. Excluded is the whole organism and more granular parts of the organism, such as atoms, molecules, macromolecular complexes and cells. gross anatomical part CHEBI:15956 biotin An organic heterobicyclic compound that consists of 2-oxohexahydro-1H-thieno[3,4-d]imidazole having a valeric acid substituent attached to the tetrahydrothiophene ring. The parent of the class of biotins. biotin CHEBI:15986 polynucleotide A nucleobase-containing molecular entity with a polymeric structure comprised of a linear sequence of 13 or more nucleotide residues. polynucleotide CHEBI:16670 peptide Amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from alpha-amino acids, but it includes those derived from any amino carboxylic acid. X = OH, OR, NH2, NHR, etc. peptide CHEBI:16991 deoxyribonucleic acid High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms. deoxyribonucleic acid CHEBI:17137 hydrogensulfite A sulfur oxoanion that has formula HO3S. hydrogensulfite CHEBI:18154 polysaccharide A biomacromolecule consisting of large numbers of monosaccharide residues linked glycosidically. This term is commonly used only for those containing more than ten monosaccharide residues. polysaccharide CHEBI:18274 2'-deoxyribonucleoside 2'-deoxyribonucleoside CHEBI:19255 pyrimidine 2'-deoxyribonucleoside pyrimidine 2'-deoxyribonucleoside CHEBI:21731 N-glycosyl compound A glycosyl compound arising formally from the elimination of water from a glycosidic hydroxy group and an H atom bound to a nitrogen atom, thus creating a C-N bond. N-glycosyl compound CHEBI:22728 benzopyrrole benzopyrrole CHEBI:23367 molecular entity Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. molecular entity CHEBI:23636 deoxyribonucleoside deoxyribonucleoside CHEBI:24431 chemical entity A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances. chemical entity CHEBI:24532 organic heterocyclic compound A cyclic compound having as ring members atoms of carbon and at least of one other element. organic heterocyclic compound CHEBI:24651 hydroxides Hydroxides are chemical compounds containing a hydroxy group or salts containing hydroxide (OH(-)). hydroxides CHEBI:24828 indoles Any compound containing an indole skeleton. indoles CHEBI:24870 ion A molecular entity having a net electric charge. ion CHEBI:2511 agarose agarose CHEBI:25367 molecule Any polyatomic entity that is an electrically neutral entity consisting of more than one atom. molecule CHEBI:25693 organic heteromonocyclic compound organic heteromonocyclic compound CHEBI:25741 oxide An oxide is a chemical compound of oxygen with other chemical elements. oxide CHEBI:25806 oxygen molecular entity oxygen molecular entity CHEBI:26440 pyrimidine nucleoside pyrimidine nucleoside CHEBI:26835 sulfur molecular entity sulfur molecular entity CHEBI:26912 oxolanes Any oxacycle having an oxolane (tetrahydrofuran) skeleton. oxolanes CHEBI:27171 organic heterobicyclic compound organic heterobicyclic compound CHEBI:28659 phosphorus atom A pnictogen that has formula P. phosphorus atom CHEBI:33250 atom A chemical entity constituting the smallest component of an element having the chemical properties of the element. atom CHEBI:33256 primary amide A derivative of an oxoacid RkE(=O)l(OH)m (l =/= 0) in which an acidic hydroxy group has been replaced by an amino or substituted amino group. primary amide CHEBI:33261 organosulfur compound An organosulfur compound is a compound containing at least one carbon-sulfur bond. organosulfur compound CHEBI:33273 polyatomic anion An anion consisting of more than one atom. polyatomic anion CHEBI:33285 heteroorganic entity A heteroorganic entity is an organic molecular entity in which carbon atoms or organic groups are bonded directly to one or more heteroatoms. heteroorganic entity CHEBI:33304 chalcogen molecular entity Any p-block molecular entity containing a chalcogen. chalcogen molecular entity CHEBI:33318 main group element atom An atom belonging to one of the main groups (found in the s- and p- blocks) of the periodic table. main group element atom CHEBI:33424 sulfur oxoacid derivative sulfur oxoacid derivative CHEBI:33482 sulfur oxoanion sulfur oxoanion CHEBI:33551 organosulfonic acid An organic derivative of sulfonic acid in which the sulfo group is linked directly to carbon. organosulfonic acid CHEBI:33575 carboxylic acid 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. carboxylic acid CHEBI:33579 main group molecular entity 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. main group molecular entity CHEBI:33595 cyclic compound Any molecule that consists of a series of atoms joined together to form a ring. cyclic compound CHEBI:33659 organic aromatic compound organic aromatic compound CHEBI:33670 heteromonocyclic compound heteromonocyclic compound CHEBI:33671 heteropolycyclic compound heteropolycyclic compound CHEBI:33672 heterobicyclic compound A bicyclic compound in which at least one of the rings contains at least one skeletal heteroatom. heterobicyclic compound CHEBI:33675 p-block molecular entity A p-block molecular entity is a molecular entity containing one or more atoms of a p-block element. p-block molecular entity CHEBI:33694 biomacromolecule A macromolecule formed by a living organism. biomacromolecule CHEBI:33696 nucleic acid A macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid. nucleic acid CHEBI:33697 ribonucleic acid High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds; RNA is central to the synthesis of proteins. ribonucleic acid CHEBI:33832 organic cyclic compound Any organic molecule that consists of atoms connected in the form of a ring. organic cyclic compound CHEBI:33833 heteroarene 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). heteroarene CHEBI:33838 nucleoside An N-glycosyl compound that has both a nucleobase, normally adenine, guanine, xanthine, thymine, cytosine or uracil, and either a ribose or deoxyribose as functional parents. nucleoside CHEBI:35352 organonitrogen compound Any heteroorganic entity containing at least one carbon-nitrogen bond. organonitrogen compound CHEBI:35406 oxoanion An oxoanion is an anion derived from an oxoacid by loss of hydron(s) bound to oxygen. oxoanion CHEBI:35605 carbon oxoacid carbon oxoacid CHEBI:36357 polyatomic entity Any molecular entity consisting of more than one atom. polyatomic entity CHEBI:36358 polyatomic ion An ion consisting of more than one atom. polyatomic ion CHEBI:36586 carbonyl compound Any compound containing the carbonyl group, C=O. The term is commonly used in the restricted sense of aldehydes and ketones, although it actually includes carboxylic acids and derivatives. carbonyl compound CHEBI:36962 organochalcogen compound An organochalcogen compound is a compound containing at least one carbon-chalcogen bond. organochalcogen compound CHEBI:36963 organooxygen compound An organochalcogen compound containing at least one carbon-oxygen bond. organooxygen compound CHEBI:37577 heteroatomic molecular entity A molecular entity consisting of two or more chemical elements. heteroatomic molecular entity CHEBI:37622 carboxamide An amide of a carboxylic acid, having the structure RC(=O)NR2. The term is used as a suffix in systematic name formation to denote the -C(=O)NH2 group including its carbon atom. carboxamide CHEBI:37960 cyanine dye Cyanine dyes are synthetic dyes with the general formula R2N[CH=CH]nCH=N(+)R2 <-> R2N(+)=CH[CH=CH]nNR2 (n is a small number) in which the nitrogen and part of the conjugated chain usually form part of a heterocyclic system, such as imidazole, pyridine, pyrrole, quinoline and thiazole. cyanine dye CHEBI:37972 phosphorus-32 atom The radioactive isotope of phosphorus with relative atomic mass 31.973907 and half-life of 14.26 days. phosphorus-32 atom CHEBI:37973 phosphorus-33 atom The radioactive isotope of phosphorus with relative atomic mass 32.971725, half-life of 25.34 days and nuclear spin (1)/2. phosphorus-33 atom CHEBI:37987 Cy3 dye Cy3 dye CHEBI:37989 Cy5 dye Cy5 dye CHEBI:38101 organonitrogen heterocyclic compound Any organonitrogen compound containing a cyclic component with nitrogen and at least one other element as ring member atoms. organonitrogen heterocyclic compound CHEBI:38104 oxacycle Any organic heterocyclic compound containing at least one ring oxygen atom. oxacycle CHEBI:38106 organosulfur heterocyclic compound organosulfur heterocyclic compound CHEBI:38164 organic heteropentacyclic compound organic heteropentacyclic compound CHEBI:38166 organic heteropolycyclic compound organic heteropolycyclic compound CHEBI:38295 azabicycloalkane azabicycloalkane CHEBI:38297 thiabicycloalkane thiabicycloalkane CHEBI:38313 diazines Any organic heterocyclic compound containing a benzene ring in which two of the C-H fragments have been replaced by isolobal nitrogens (the diazine parent structure). diazines CHEBI:4705 double-stranded DNA double-stranded DNA CHEBI:472552 5-bromo-2'-deoxyuridine A pyrimidine 2'-deoxyribonucleoside compound having 5-bromouracil as the nucleobase. 5-bromo-2'-deoxyuridine CHEBI:50860 organic molecular entity Any molecular entity that contains carbon. organic molecular entity CHEBI:51143 nitrogen molecular entity nitrogen molecular entity CHEBI:51570 biotins Compounds containing a biotin (5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoic acid) skeleton. biotins CHEBI:51756 Alexa Fluor 532 An organosulfonic acid that has formula C34H33N3O11S2. Alexa Fluor 532 CHEBI:51760 Alexa Fluor 546 An organic heteropentacyclic compound that has formula C44H46Cl3N4NaO14S3. Alexa Fluor 546 CHEBI:5686 heterocyclic compound A cyclic compound having as ring members atoms of at least two different elements. heterocyclic compound CHEBI:61120 nucleobase-containing molecular entity Any compound that has a nucleobase as a part. nucleobase-containing molecular entity CHEBI:68472 pyrimidine deoxyribonucleoside A deoxyribonucleoside containing a pyrimidine base. pyrimidine deoxyribonucleoside CHEBI:72695 organic molecule Any molecule that consists of at least one carbon atom as part of the electrically neutral entity. organic molecule CHEBI:78616 carbohydrates and carbohydrate derivatives Any organooxygen compound that is a polyhydroxy-aldehyde or -ketone, or a compound derived from one. Carbohydrates contain only carbon, hydrogen and oxygen and usually have an empirical formula Cm(H2O)n; carbohydrate derivatives may contain other elements by substitution or condensation. carbohydrates and carbohydrate derivatives CLO:0000001 A cultured cell that is part of a cell line - a stable and homogeneous population of cells with a common biological origin and propagation history in culture cell line cell CLO:0000019 A cell line cell that is expected to be capable of an unlimited number of divisions, and is thus able to support indefinite propagation in vitro as part of an immortal cell line. immortal cell line cell CLO:0000031 A cultured cell population that represents a genetically stable and homogenous population of cultured cells that shares a common propagation history (i.e. has been successively passaged together in culture). cell line CLO:0000044 a cell line that is derived from stem cell immortal stem cell line cell CLO:0000081 a immortal electrically responsive cell line cell that is derived from neuron immortal neuron cell line cell CLO:0000128 a immortal eukaryotic cell line that is derived from animal cell immortal animal cell line cell CLO:0000147 a immortal animal cell line that is derived from hematopoietic cell immortal hematopoietic cell line cell CLO:0000156 a immortal animal cell line that is derived from neural cell immortal neural cell line cell CLO:0000166 a cell line that is derived from somatic cell immortal somatic cell line cell CLO:0000503 An immortal embryo-derived cell line cell that derives from mouse. immortal mouse embryo-derived cell line cell CLO:0001352 3T3-L1 cell CLO:0001690 Ainv15 cell CLO:0001932 BETA-TC-3 cell CLO:0002405 CGR8 cell CLO:0002708 Daudi cell CLO:0003612 H9 cell CLO:0007043 JURKAT cell CLO:0007050 K 562 cell CLO:0008734 Raji cell CLO:0009218 SW480 cell CLO:0009828 A cell line that is expected to be capable of indefinite propagation in an vitro culture. immortal cell line CL:0000000 A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. CALOHA:TS-2035 FMA:68646 GO:0005623 KUPO:0000002 VHOG:0001533 WBbt:0004017 XAO:0003012 cell The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one). cell CL:0000001 A cultured cell that is freshly isolated from a organismal source, or derives in culture from such a cell prior to the culture being passaged. BTO:0002290 primary cell culture cell unpassaged cultured cell cell primary cell line cell Covers cells actively being cultured or stored in a quiescent state for future use. primary cultured cell CL:0000003 A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment). CARO:0000013 cell in vivo cell To accommodate unicellular organisms better, 'cell in vivo' has been re-labeled 'native cell' to better represent its intended meaning - that is, that it is a cell in the context of a multicellular organism or in a natural environment. 'Native' is intended to contrast with 'in vitro', which refers to cells or other biological entities that have been intentionally placed in a controlled, non-natural setting for the purpose of study or manipulation. (MAH 1.12.12). native cell CL:0000010 A cell in vitro that is or has been maintained or propagated as part of a cell culture. 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:0000021 Female germ cell is a germ cell that supports female gamete production. MA:0000388 VHOG:0001530 ncithesaurus:Egg cell female germ cell CL:0000023 A female germ cell that has entered meiosis. BTO:0000964 CALOHA:TS-0711 FBbt:00004886 FMA:18644 WBbt:0006797 cell oogonium oocyte CL:0000034 A relatively undifferentiated cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells. CALOHA:TS-2086 FMA:63368 cell stem cell CL:0000037 A stem cell from which all cells of the lymphoid and myeloid lineages develop, including blood cells and cells of the immune system. Hematopoietic stem cells lack cell markers of effector cells (lin-negative). Lin-negative is defined by lacking one or more of the following cell surface markers: CD2, CD3 epsilon, CD4, CD5 ,CD8 alpha chain, CD11b, CD14, CD19, CD20, CD56, ly6G, ter119. BTO:0000725 CALOHA:TS-0448 FMA:70337 FMA:86475 VHOG:0001485 HSC blood forming stem cell hemopoietic stem cell cell colony forming unit hematopoietic Markers differ between species, and two sets of markers have been described for mice. HSCs are reportedly CD34-positive, CD45-positive, CD48-negative, CD150-positive, CD133-positive, and CD244-negative. hematopoietic stem cell CL:0000038 A progenitor cell committed to the erythroid lineage. BTO:0004911 cell BFU-E CFU-E blast forming unit erythroid burst forming unit erythroid colony forming unit erythroid erythroid stem cell erythroid progenitor cell CL:0000039 A cell that is within the developmental lineage of gametes and is able to pass along its genetic material to offspring. cell Originally this term had some plant germ line cell children. germ line cell CL:0000040 A myeloid progenitor cell committed to the monocyte lineage. This cell is CD11b-positive, has basophilic cytoplasm, euchromatin, and the presence of a nucleolus. CALOHA:TS-1195 FMA:83553 cell CFU-M colony forming unit macrophage colony forming unit monocyte monocyte stem cell Morphology: mononuclear cell, diameter 12-20 _M, non-granular, N/C ratio 3/1 - 4/1; markers: CD11b (shared with many other myeloid cells); location: Adult: bone marrow; fetal: liver, Yolk Sac; role or process: hematopoiesis, monocyte development; lineage: hematopoietic, myeloid. monoblast CL:0000048 A stem cell that can give rise to multiple lineages of cells. FMA:84789 multi-fate stem cell multifate stem cell multipotent cell multipotent stem cell cell multi fate stem cell CL:0000049 A progenitor cell committed to myeloid lineage, including the megakaryocyte and erythroid lineages. BTO:0004730 CMP common myeloid precursor cell CFU-GEMM CFU-S colony forming unit granulocyte, erythrocyte, macrophage, and megakaryocyte multipotential myeloid stem cell myeloid stem cell pluripotent stem cell (bone marrow) This cell type is intended to be compatible with any vertebrate common myeloid progenitor. For mammalian CMP known to be CD34-positive, please use the term 'common myeloid progenitor, CD34-positive' (CL_0001059). common myeloid progenitor CL:0000050 A progenitor cell committed to the megakaryocyte and erythroid lineages. CFU-EM CFU-MegE MEP Meg/E progenitor colony forming unit erythroid megakaryocyte megakaryocyte/erythrocyte progenitor megakaryocyte/erythroid progenitor cell cell MEPs are reportedly CD19-negative, CD34-negative, CD45RA-negative, CD110-positive, CD117-positive, and SCA1-negative and reportedly express the transcription factors GATA-1 and NF-E2. megakaryocyte-erythroid progenitor cell CL:0000051 A oligopotent progenitor cell committed to the lymphoid lineage. CL:0000044 CLP common lymphocyte precursor common lymphocyte progenitor common lymphoid precursor cell ELP committed lymphopoietic stem cell early lymphocyte progenitor lymphoid stem cell lymphopoietic stem cell CLP are CD7-positive, CD10-positive, CD19-negative, CD34-positive, CD45RA-positive, CD79a-negative, CD127-positive, AA4.1-positive, RAG-negative, Sca-1-low, sIgM-negative, sIgD-negative, TdT-negative, Vpre-B-negative, and pre-BCR-negative. Expression of transcription factors include E2A-positive, EBF-positive, Ikaros-negative, PU.1-negative, and Pax5-negative. common lymphoid progenitor CL:0000055 A precursor cell with a limited number of potential fates. BTO:0000125 FMA:84782 blast cell cell define using PATO mulit-potent or oligopotent? non-terminally differentiated cell CL:0000056 A cell that is commited to differentiating into a muscle cell. Embryonic myoblasts develop from the mesoderm. They undergo proliferation, migrate to their various sites, and then differentiate into the appropriate form of myocytes. Myoblasts also occur as transient populations of cells in muscles undergoing repair. BTO:0000222 CALOHA:TS-0650 FBbt:00005083 FMA:70335 VHOG:0001529 cell myoblast CL:0000057 A connective tissue cell which secretes an extracellular matrix rich in collagen and other macromolecules. Flattened and irregular in outline with branching processes; appear fusiform or spindle-shaped. BTO:0000452 CALOHA:TS-0362 FMA:63877 VHOG:0001482 cell These cells may be vimentin-positive, fibronectin-positive, fsp1-positive, MMP-1-positive, collagen I-positive, collagen III-positive, and alpha-SMA-negative. fibroblast CL:0000066 A cell that is usually found in a two-dimensional sheet with a free surface. The cell has a cytoskeleton that allows for tight cell to cell contact and for cell polarity where apical part is directed towards the lumen and the basal part to the basal lamina. BTO:0000414 CALOHA:TS-2026 CARO:0000077 FBbt:00000124 FMA:66768 WBbt:0003672 epitheliocyte cell epithelial cell CL:0000068 cell duct epithelial cell CL:0000069 cell branched duct epithelial cell CL:0000071 An endothelial cell that lines the vasculature. cuboidal endothelial cell of vascular tree cell blood vessel endothelial cell CL:0000076 CALOHA:TS-1249 cell squamous epithelial cell CL:0000081 A cell found predominately in the blood. FMA:62844 cell blood cell CL:0000083 An epithelial cell of the pancreas. BTO:0000028 pancreas epithelial cell pancreatic epithelial cell cell epithelial cell of pancreas CL:0000084 A type of lymphocyte whose defining characteristic is the expression of a T cell receptor complex. CL:0000804 CL:0000812 BTO:0000782 CALOHA:TS-1001 FMA:62870 VHOG:0001479 T lymphocyte T-cell T-lymphocyte cell immature T cell mature T cell T cell CL:0000094 A leukocyte with abundant granules in the cytoplasm. BTO:0000539 BTO:0001026 CALOHA:TS-0422 FMA:62854 granular leucocyte granular leukocyte polymorphonuclear leukocyte cell granulocyte CL:0000115 An endothelial cell comprises the outermost layer or lining of anatomical structures and can be squamous or cuboidal. In mammals, endothelial cell has vimentin filaments and is derived from the mesoderm. BTO:0001176 CALOHA:TS-0278 FMA:66772 endotheliocyte cell From FMA: 9.07.2001: Endothelial cell has always been classified as a kind of epithelial cell, specifically a squamous cell but that is not true. First, endothelial cell can either be squamous or cuboidal (e.g. high-endothelial cell) and secondly, it has different embryological derivation (mesodermal) than a true epithelial cell (ectodermal and endodermal). The basis for present classification is the fact that it comprises the outermost layer or lining of anatomical structures (location-based) but a better structural basis for the differentia is the cytoskeleton of the cell. Endothelial cell has vimentin filaments while an epithelial cell has keratin filaments. [Onard]. endothelial cell CL:0000133 Ectoderm destined to be nervous tissue. neurectoderm cell cell neurectodermal cell CL:0000134 A connective tissue cell that normally gives rise to other cells that are organized as three-dimensional masses. This cell type is CD73-positive, CD90-positive, CD105-positive, CD45-negative, CD34-negative, and MHCII-negative. They may further differentiate into osteoblasts, adipocytes, myocytes, neurons, or chondroblasts in vitro. Originally described as residing in the bone marrow, this cell type is now known to reside in many, if not all, adult organs. CL:0002452 BTO:0002625 BTO:0003298 FMA:70546 BMSC bone marrow stromal cells colony-forming unit-fibroblast marrow stromal cells cell CFU-F MSC mesenchymal precursor cell mesenchymal progenitor cells mesenchymal stem cell mesenchymal stromal cell mesenchymal stromal cells stem cells, mesenchymal Many but not all mesenchymal cells derive from the mesoderm. MSCs are reportedly CD3-negative, CD4-negative, CD5-negative, CD8-negative, CD11a-negative, CD11b-negative, CD14-negative, CD19-negative, CD29-positive, CD31-negative, CD34-negative, CD38-negative, CD40-negative, CD44-positive, CD45-negative, CD49-positive, CD54-positive, CD66b-negative, CD79a-negative, CD80-negative, CD102-positive, CD106-positive, CD117-positive, CD121a-positive, CD121b-positive, CD123-positive, CD124-positive, CD133-negative, CD146-positive, CD166-positive, CD271-positive, B220-negative, Gr1-negative, MHCI-positive, MHCII-negative, SSEA4-negative, sca1-positive, Ter119-negative, and glycophorin A-negative. Cultured MSCs are capable of producing stem cell factor, IL7, IL8, IL11, TGF-beta, cofilin, galectin-1, laminin-receptor 1, cyclophilin A, and MMP-2. mesenchymal stem cell CL:0000136 A fat-storing cell found mostly in the abdominal cavity and subcutaneous tissue of mammals. Fat is usually stored in the form of triglycerides. CL:0000450 BTO:0000443 CALOHA:TS-0012 FMA:63880 adipocyte adipose cell cell fat cell CL:0000147 A pigment cell is a cell that contains pigment granules. VHOG:0001678 chromatocyte chromatophore cell pigment cell CL:0000148 A pigment cell derived from the neural crest. Contains melanin-filled pigment granules, which gives a brown to black appearance. CL:0000572 BTO:0000847 CALOHA:TS-0613 FMA:70545 VHOG:0001679 melanophore cell melanocyte CL:0000150 A specialized epithelial cell that is capable of synthesizing and secreting certain biomolecules. CALOHA:TS-2085 FMA:86494 cell glandular epithelial cell CL:0000151 A cell that specializes in controlled release of one or more substances. BTO:0003659 FMA:86916 cell secretory cell CL:0000152 A cell of an exocrine gland; i.e. a gland that discharges its secretion via a duct. FMA:16014 cell exocrine cell CL:0000154 cell protein secreting cell CL:0000163 A cell of an endocrine gland, ductless glands that secrete substances which are released directly into the circulation and which influence metabolism and other body functions. FMA:83809 endocrinocyte cell endocrine cell CL:0000164 An endocrine cell that is located in the epithelium of the gastrointestinal tract or in the pancreas. BTO:0003865 FMA:62930 cell enteroendocrine cell CL:0000167 cell peptide hormone secreting cell CL:0000168 BTO:0000783 cell insulin secreting cell CL:0000169 A cell that secretes insulin and is located towards the center of the islets of Langerhans. beta cell BTO:0000783 EV:0200009 FMA:70586 MA:0002419 ncithesaurus:Beta_Cell B-cell of pancreatic islet beta cell of pancreatic islet insulin-secreting cell pancreatic B cell pancreatic B-cell pancreatic beta cell pancreatic islet core type B enteroendocrine cell cell beta cell islet Pancreatic beta cells are also reportedly CD284-positive. Upon activation, they upregulate their CD14 expression. type B pancreatic cell CL:0000170 A cell that secretes glucagon. FMA:84045 glucagon-secreting cell cell glucagon secreting cell CL:0000171 A type of enteocrine cell found in the periphery of the islets of Langerhans that secretes glucagon. BTO:0000990 FMA:70585 alpha cell of iselt of Langerhans pancreatic alpha cell cell pancreatic A cell CL:0000172 cell somatostatin secreting cell CL:0000173 A D cell located in the pancreas. Peripherally placed within the islets like type A cells; contains somatostatin. BTO:0000803 FMA:70587 D-cell of pancreatic islet delta cell of islet delta cell of pancreatic islet pancreatic D-cell pancreatic delta cell somatostatin-secreting pancreatic cell cell pancreatic D cell CL:0000181 A cell whose primary function is intermediary metabolism. cell metabolising cell CL:0000182 The main structural component of the liver. They are specialized epithelial cells that are organized into interconnected plates called lobules. Majority of cell population of liver, polygonal in shape, arranged in plates or trabeculae between sinusoids; may have single nucleus or binucleated. BTO:0000575 CALOHA:TS-0454 FMA:14515 cell Hepatocytes are reportedly MHC Class I-positive and MHC Class II-positive. hepatocyte CL:0000183 A cell whose primary function is to shorten. cell contractile cell CL:0000187 A mature contractile cell, commonly known as a myocyte. This cell has as part of its cytoplasm myofibrils organized in various patterns. BTO:0000888 BTO:0000902 CALOHA:TS-2032 FBbt:00005074 FMA:67328 WBbt:0003675 muscle fiber myocyte cell muscle cell CL:0000211 A cell whose function is determined by the generation or the reception of an electric signal. cell electrically active cell CL:0000213 A cell within an epithelial cell sheet whose main function is to act as an internal or external covering for a tissue or an organism. boundary cell cell lining cell CL:0000215 A cell whose primary function is to prevent the transport of stuff across compartments. cell barrier cell CL:0000219 A cell that moves by its own activities. cell motile cell CL:0000221 A cell of the outer of the three germ layers of the embryo. FMA:72549 ectoderm cell cell ectodermal cell CL:0000222 A cell of the middle germ layer of the embryo. FMA:72554 mesoblast mesoderm cell cell mesodermal cell CL:0000223 A cell of the inner of the three germ layers of the embryo. FMA:72555 endoderm cell cell endodermal cell CL:0000225 A cell that lacks a nucleus. FMA:68647 non-nucleated cell cell anucleate cell CL:0000226 A cell with a single nucleus. cell single nucleate cell CL:0000232 A red blood cell. In mammals, mature erythrocytes are biconcave disks containing hemoglobin whose function is to transport oxygen. BTO:0000424 CALOHA:TS-0290 FMA:81100 RBC red blood cell cell erythrocyte CL:0000233 A non-nucleated disk-shaped cell formed by extrusion from megakaryocytes, found in the blood of all mammals, and mainly involved in blood coagulation. BTO:0000132 CALOHA:TS-0803 FMA:62851 anucleate thrombocyte blood platelet enucleate thrombocyte cell Platelets are reportedly CCR1-positive, CCR2-negative, CCR3-positive, CCR4-positive, CCR5-negative, CCR6-negative, CCR7-negative, CCR8-negative, CCR9-negative, CCR10-negative, CD16-positive, CD23-positive, CD32-positive, CD40-positive, CD41-positive CD42-positive, CD61-positive, CD62P-positive, CD64-positive, CD89-positive, CD102-positive, CD147-positive (activated platelets), CD154-positive (activated platelets), CD162-positive, CD209, CD282-positive, CD284-positive, CD289-positive, CD181-negative, CD182-negative, CD183-negative, CD184-positive, CLEC2-positive, GPVI-positive, JAMC-positive, PAR1-positive, PAR2-negative, PAR3-positive, PAR4-positive, TSP1-positive, and TXA2R-positive. Platelets can reportedly produce CCL2, CCL3, CCL5, CCL7, CCL17, CD40L, CXCL1, CXCL4, CXCL4L1, CXCL5, CXCL7, CXCL8, CXCL12, EGF, factor V, factor VII, factor XI, factor XIII, bFGF, histamine, IGF-1, IL-1beta, PAI-1, PDGF, plasminogen, protein S, serotonin, TGF-beta, TFPI, VEGF, and vWF. platelet CL:0000236 A lymphocyte of B lineage with the phenotype CD19-positive, CD20-positive, and capable of B cell mediated immunity. BTO:0000776 CALOHA:TS-0068 FMA:62869 VHOG:0001480 B lymphocyte B-cell B-lymphocyte cell B cell CL:0000255 cell eukaryotic cell CL:0000325 A cell that is specialised to accumulate a particular substance(s). cell stuff accumulating cell CL:0000329 cell oxygen accumulating cell CL:0000333 A cell derived from the specialized ectoderm flanking each side of the embryonic neural plate, which after the closure of the neural tube, forms masses of cells that migrate out from the dorsal aspect of the neural tube to spread throughout the body. FMA:86667 cell migratory neural crest cell CL:0000393 A cell whose function is determined by its response to an electric signal. cell electrically responsive cell CL:0000412 A cell whose nucleus, or nuclei, each contain more than two haploid genomes. cell polyploid cell CL:0000417 cell endopolyploid cell CL:0000448 Fat cells with light coloration and few mitochondria. They contain a scant ring of cytoplasm surrounding a single large lipid droplet or vacuole. CALOHA:TS-1119 FMA:83434 white adipose cell white fat cell cell white adipocyte white fat cell CL:0000451 A cell of hematopoietic origin, typically resident in particular tissues, specialized in the uptake, processing, and transport of antigens to lymph nodes for the purpose of stimulating an immune response via T cell activation. These cells are lineage negative (CD3-negative, CD19-negative, CD34-negative, and CD56-negative). BTO:0002042 CALOHA:TS-0194 FMA:83036 cell interdigitating cell veiled cell dendritic cell CL:0000457 cell biogenic amine secreting cell CL:0000458 A cell type that secretes 5-Hydroxytryptamine (serotonin). 5-HT secreting cell 5-Hydroxytryptamine secreting cell cell serotonin secreting cell CL:0000502 A cell found throughout the gastrointestinal tract and in the pancreas. They secrete somatostatin in both an endocrine and paracrine manner. Somatostatin inhibits gastrin, cholecystokinin, insulin, glucagon, pancreatic enzymes, and gastric hydrochloric acid. A variety of substances which inhibit gastric acid secretion (vasoactive intestinal peptide, calcitonin gene-related peptide, cholecystokinin, beta-adrenergic agonists, and gastric inhibitory peptide) are thought to act by releasing somatostatin. FMA:62935 D cell cell type D enteroendocrine cell CL:0000513 A precursor cell destined to differentiate into cardiac muscle cell. CL:0000714 FMA:84797 cell cardiac muscle myoblast CL:0000541 A cell that originates from the neural crest and differentiates into a pigment cell. BTO:0003217 FMA:83377 cell Derived from UBERON:0002342 neural crest. melanoblast CL:0000542 A lymphocyte is a leukocyte commonly found in the blood and lymph that has the characteristics of a large nucleus, a neutral staining cytoplasm, and prominent heterochromatin. BTO:0000775 CALOHA:TS-0583 FMA:62863 VHOG:0001535 cell Editors note: consider adding taxon constraint to vertebrata (PMID:18025161) lymphocyte CL:0000547 An immature, nucleated erythrocyte occupying the stage of erythropoeisis that follows formation of erythroid progenitor cells. This cell is CD71-positive, has both a nucleus and a nucleolus, and lacks hematopoeitic lineage markers. FMA:83518 rubriblast cell pronormoblast proerythroblast CL:0000548 cell animal cell CL:0000549 A nucleated immature erythrocyte, having cytoplasm generally similar to that of the earlier proerythroblast but sometimes even more basophilic, and usually regular in outline. The nucleus is still relatively large, but the chromatin strands are thicker and more deeply staining, giving a coarser appearance; the nucleoli have disappeared. This cell is CD71-positive and lacks hematopoeitic lineage markers. FMA:83505 basophilic normoblast early erythroblast early normoblast prorubricyte cell basophilic erythroblast CL:0000550 A nucleated, immature erythrocyte in which the nucleus occupies a relatively smaller part of the cell than in its precursor, the basophilic erythroblast. The cytoplasm is beginning to acquire hemoglobin and thus is no longer a purely basophilic, but takes on acidophilic aspects, which becomes progressively more marked as the cell matures. The chromatin of the nucleus is arranged in coarse, deeply staining clumps. This cell is CD71-positive and lacks hematopoeitic lineage markers. FMA:83506 intermediate erythroblast intermediate normoblast polychromatic erythroblast polychromatic normoblast polychromatophilic normoblast rubricyte cell polychromatophilic erythroblast CL:0000552 The final stage of the nucleated, immature erythrocyte, before nuclear loss. Typically the cytoplasm is described as acidophilic, but it still shows a faint polychromatic tint. The nucleus is small and initially may still have coarse, clumped chromatin, as in its precursor, the polychromatophilic erythroblast, but ultimately it becomes pyknotic, and appears as a deeply staining, blue-black, homogeneous structureless mass. The nucleus is often eccentric and sometimes lobulated. FMA:84646 acidophilic erythroblast eosinophilic erythroblast late erythoblast orthochromatic normoblast pyknotic eto enrythroblast cell orthochromatic erythroblast CL:0000553 The earliest cytologically identifiable precursor in the thrombocytic series. This cell is capable of endomitosis and lacks expression of hematopoieitic lineage markers (lin-negative). BTO:0001164 CALOHA:TS-0610 FMA:84235 CFU-Meg Meg-CFC MkP colony-forming unit-megakaryocyte megacaryoblast megacaryocyte progenitor cell megakaryoblast megakaryocytic progenitor cell cell promegacaryocyte promegakaryocyte Lineage negative is described here as CD2-negative, CD3-negative, CD4-negative, CD5-negative, CD8a-negative, CD14-negative, CD19-negative, CD20-negative, CD56-negative, Ly6g-negative, and Ter119-negative. megakaryocyte progenitor cell CL:0000556 A giant cell 50 to 100 micron in diameter, with a greatly lobulated nucleus, found in the bone marrow; mature blood platelets are released from its cytoplasm. BTO:0000843 CALOHA:TS-0611 FMA:83555 megacaryocyte megalocaryocyte megalokaryocyte cell Megakaryocytes are reportedly CD181-positive and CD182-positive. megakaryocyte CL:0000557 A hematopoietic progenitor cell that is committed to the granulocyte and monocyte lineages. These cells are CD123-positive, and do not express Gata1 or Gata2 but do express C/EBPa, and Pu.1. CFU-C , Colony forming unit in culture CFU-GM GMP colony forming unit granulocyte macrophage granulocyte-macrophage progenitor granulocyte/monocyte precursor granulocyte/monocyte progenitor cell Originally described in the dendritic cell ontology (DC_CL:0000042)(PMID:19243617). GMPs are reportedly CD16-positive, CD32-positive, CD34-positive, CD38-positive, CD45RA-positive, CD110-negative, CD117-positive, CD123-positive, and SCA1-negative. granulocyte monocyte progenitor cell CL:0000558 An immature erythrocyte that changes the protein composition of its plasma membrane by exosome formation and extrusion. The types of protein removed differ between species though removal of the transferrin receptor is apparent in mammals and birds. BTO:0001173 CALOHA:TS-0864 cell reticulocyte CL:0000559 A precursor in the monocytic series, being a cell intermediate in development between the monoblast and monocyte. This cell is CD11b-positive and has fine azurophil granules. BTO:0004657 FMA:83551 cell Morphology: Mononuclear cell, diameter 14-18 _M, fine azurophilic granules; markers: CD11b (shared with many other myeloid cells); location: Adult: bone marrow; Fetal: Liver, Yolk Sac; role or process: hematopoiesis, monocyte development; lineage: hematopoietic, myeloid. promonocyte CL:0000566 A mesenchymal stem cell capable of developing into blood vessel endothelium. angioblast chondroplast cell These cells are reportedly CD31-positive, CD34-positive, CD144-positive, CD309-positive, and TAL1-positive. angioblastic mesenchymal cell CL:0000576 Myeloid mononuclear recirculating leukocyte that can act as a precursor of tissue macrophages, osteoclasts and some populations of tissue dendritic cells. BTO:0000876 CALOHA:TS-0638 FMA:62864 cell Morphology: Mononuclear cell, diameter, 14 to 20 _M, N/C ratio 2:1-1:1. Nucleus may appear in variety of shapes: round, kidney, lobulated, or convoluted. Fine azurophilic granules present; markers: CD11b (shared with other myeloid cells), human: CD14, mouse: F4/80-mid,GR1-low; location: Blood, but can be recruited into tissues; role or process: immune & tissue remodelling; lineage: hematopoietic, myeloid. monocyte CL:0000578 A cell in vitro that has undergone physical changes as a consequence of a deliberate and specific experimental procedure. 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 CL:0000586 The reproductive cell in multicellular organisms. BTO:0000535 VHOG:0001534 WBbt:0006796 cell germ cell CL:0000622 A secretory cell that is grouped together with other cells of the same type to form grape shaped clusters known as acini (singular acinus). FMA:83625 acinic cell acinous cell cell acinar cell CL:0000623 A lymphocyte that can spontaneously kill a variety of target cells without prior antigenic activation via germline encoded activation receptors and also regulate immune responses via cytokine release and direct contact with other cells. large granular lymphocyte null cell BTO:0000914 BTO:0004716 CALOHA:TS-0664 FMA:63147 FMA:83601 VHOG:0001697 NK cell cell natural killer cell CL:0000680 cell muscle precursor cell CL:0000696 A cell that stores and secretes pancreatic polypeptide hormone. FMA:62938 FMA:83409 type F enteroendocrine cell cell PP cell CL:0000723 A stem cell that can give rise to cell types of the body other than those of the germ-line. CALOHA:TS-2086 FMA:63368 cell somatic stem cell CL:0000737 Muscle cell which has as its direct parts myofilaments organized into sarcomeres. BTO:0002916 CALOHA:TS-2157 FMA:86936 cell striated muscle cell CL:0000738 An achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue. BTO:0000751 CALOHA:TS-0549 FMA:62852 immune cell leucocyte white blood cell cell leukocyte CL:0000746 Cardiac muscle cells are striated muscle cells that are responsible for heart contraction. In mammals, the contractile fiber resembles those of skeletal muscle but are only one third as large in diameter, are richer in sarcoplasm, and contain centrally located instead of peripheral nuclei. FMA:83808 cardiocyte BTO:0001539 CALOHA:TS-0115 FMA:14067 cardiac muscle fiber cardiac myocyte cardiomyocyte heart muscle cell cell This class encompasses the muscle cells responsible for heart* contraction in both vertebrates and arthropods. The ultrastucture of a wide range of arthropod heart cells has been examined including spiders, horseshoe crabs, crustaceans (see Sherman, 1973 and refs therein) and insects (see Lehmacher et al (2012) and refs therein). According to these refs, the cells participating in heart contraction in all cases are transversely striated. Insects hearts additionally contain ostial cells, also transversely striated muscle cells, but which do not participate in heart contraction. cardiac muscle cell CL:0000763 A cell of the monocyte, granulocyte, mast cell, megakaryocyte, or erythroid lineage. BTO:0001441 CALOHA:TS-0647 cell myeloid cell CL:0000764 A immature or mature cell in the lineage leading to and including erythrocytes. CL:0002156 CALOHA:TS-0290 FMA:62845 FMA:83516 erythropoietic cell cell Note that in FMA erythropoietic cells are types of nucleated erythrocytes and thus don't include erythrocytes. erythroid lineage cell CL:0000765 A nucleated precursor of an erythrocyte that lacks hematopoietic lineage markers. BTO:0001571 CALOHA:TS-0289 FMA:83504 normoblast cell erythroblast CL:0000766 A cell of the monocyte, granulocyte, or mast cell lineage. cell myeloid leukocyte CL:0000767 Any of the immature or mature forms of a granular leukocyte that in its mature form has an irregularly shaped, pale-staining nucleus that is partially constricted into two lobes, and with cytoplasm that contains coarse, bluish-black granules of variable size. Basophils contain vasoactive amines such as histamine and serotonin, which are released on appropriate stimulation. A basophil is CD123-positive, CD193-positive, CD203c-positive, and FceRIa-positive. polymorphonuclear leucocyte polymorphonuclear leukocyte BTO:0000129 CALOHA:TS-0073 FMA:62862 basophilic leucocyte basophilic leukocyte cell Matures in the bone marrow and account for <1% of leukocytes in the peripheral blood, spleen, and bone marrow. Basophils are described as being CD11a-positive, CD11b-positive, CD13-positive, CD15-positive, CD18-positive, CD21-positive, CD25-positive, CD29-positive, CD35-positive, CD40-positive, CD40L-positive, CD44-positive, CD45R-negative, CD46-positive, CD49a-positive, CD49b-positive, CD49d-positive, CD55-positive, CD59-positive, CD62L-positive, CD63-positive, CD69-positive, CD90-negative, CD116-positive, CD117-negative, CD124-positive, CD125-positive, CD131-positive, CD161-positive, CD184-positive, CD191-positive, CD192-positive, CD197-positive, CD200R3-positive, CD218-positive, CD282-positive, CD284-positive, CD289-positive, CD290-positive, CD294-positive, natural killer cell receptor 2B4-positive, smad1-positive, CD3-negative, CD4-negative, CD7-negative, CD8-negative, CD14-negative, CD15-negative, CD16-negative, CD19-negative, CD20-negative, CD34-negative, CD36-negative, CD45R-negative, CD56-negative, CD57-negative, CD235a-negative, and GR1-negative. Transcription factors- GATA1-positive, PU.1-positive. basophil CL:0000771 Any of the immature or mature forms of a granular leukocyte with a nucleus that usually has two lobes connected by one or more slender threads of chromatin, and cytoplasm containing coarse, round granules that are uniform in size and which can be stained by the dye eosin. Eosinophils are CD9-positive, CD191-positive, and CD193-positive. polymorphonuclear leucocyte polymorphonuclear leukocyte BTO:0000399 CALOHA:TS-0279 FMA:62861 eosinocyte eosinophilic granulocyte eosinophilic leucocyte eosinophilic leukocyte cell Eosinophils are also CD14-negative, CD32-positive, CD44-positive, CD48-positive, CD69-positive, CD192-negative, MBP1-positive, MBP2-positive, TLR2-negative, TLR4-negative, and lineage-negative (B220, CD2, CD14, CD19, CD56, CD71, CD117, CD123, CD235a (glycophorin A), and TER119). The cytokines IL-3, IL-5, and GM-CSF are involved in their development and differentiation. Usually considered CD16-negative, CD16 is observed on eosinophilic metamyelocyte. eosinophil CL:0000775 Any of the immature or mature forms of a granular leukocyte that in its mature form has a nucleus with three to five lobes connected by slender threads of chromatin, and cytoplasm containing fine inconspicuous granules and stainable by neutral dyes. PMN poly polymorphonuclear leucocyte polymorphonuclear leukocyte polymorphonuclear neutrophil polynuclear neutrophilic leucocyte polynuclear neutrophilic leukocyte BTO:0000130 CALOHA:TS-0688 FMA:62860 neutrocyte neutrophil leucocyte neutrophil leukocyte neutrophilic leucocyte neutrophilic leukocyte cell neutrophil CL:0000825 A lymphoid progenitor cell that is committed to the natural killer cell lineage, expressing CD122 (IL-15) receptor, but lacking many of the phenotypic characteristics of later stages of natural killer cell development such as expression of NK activating and inhibitory molecules. In human this cell has the phenotype CD34-positive, CD45RA-positive, CD10-positive, CD117-negative, and CD161 negative. NKP natural killer cell progenitor pro-natural killer cell cell null cell preNK cell Most markers only described for human pro NK cells. pro-NK cell CL:0000826 A progenitor cell of the B cell lineage, with some lineage specific activity such as early stages of recombination of B cell receptor genes, but not yet fully committed to the B cell lineage until the expression of PAX5 occurs. pre-pro B cell BTO:0003104 pro-B lymphocyte pro-B-cell pro-B-lymphocyte progenitor B cell progenitor B lymphocyte progenitor B-cell progenitor B-lymphocyte cell pre-B cell (Philadelphia nomenclature) Human pro-B cells are reportedly CD10-positive, CD22-positive, CD34-positive, CD38-positive, CD45-low, CD48-positive, CD79a-positive, CD127-positive, CD184-positive, RAG-positive, TdT-positive, Vpre-B-positive, pre-BCR-negative, IgD-negative, and IgM-negative. Transcription factors expressed: Pax5-positive, EBF-positive, E2A-negative, Ikaros-negative, and PU.1-negative. pro-B cell CL:0000827 A lymphoid progenitor cell of the T cell lineage, with some lineage specific marker expression, but not yet fully committed to the T cell lineage. pro-T lymphocyte progenitor T cell DN1 cell DN1 thymocyte TN1 cell cell pro-T cell CL:0000835 The most primitive precursor in the granulocytic series, having fine, evenly distributed chromatin, several nucleoli, a high nuclear-to-cytoplasmic ration (5:1-7:1), and a nongranular basophilic cytoplasm. They reside in the bone marrow. BTO:0000187 FMA:83524 cell myeloblast CL:0000836 A precursor in the granulocytic series, being a cell intermediate in development between a myeloblast and myelocyte, that has distinct nucleoli, a nuclear-to-cytoplasmic ratio of 5:1 to 3:1, and containing a few primary cytoplasmic granules. Markers for this cell are fucosyltransferase FUT4-positive, CD33-positive, integrin alpha-M-negative, low affinity immunoglobulin gamma Fc region receptor III-negative, and CD24-negative. CALOHA:TS-0825 FMA:83530 cell promyelocyte CL:0000837 A hematopoietic multipotent progenitor cell is multipotent, but not capable of long-term self-renewal. These cells are characterized as lacking lineage cell surface markers and being CD34-positive in both mice and humans. BTO:0000725 CALOHA:TS-0448 MPP hemopoietic progenitor cell cell Markers differ between mouse and human. hematopoietic multipotent progenitor cell CL:0000838 A progenitor cell restricted to the lymphoid lineage. lymphoid progenitor cell BTO:0004731 CALOHA:TS-2025 FMA:70338 cell Note that this is a class of cell types, not an identified single cell type. lymphoid lineage restricted progenitor cell CL:0000839 A progenitor cell restricted to the myeloid lineage. myeloid progenitor cell BTO:0004730 CALOHA:TS-2099 FMA:70339 cell Note that this is a class of cell types, not an identified single cell type. myeloid lineage restricted progenitor cell CL:0000842 A leukocyte with a single non-segmented nucleus in the mature form. BTO:0000878 CALOHA:TS-0768 FMA:86713 peripheral blood mononuclear cell cell mononuclear cell CL:0000945 A lymphocyte of B lineage is a lymphocyte that expresses CD19 on the cell surface. An additional defining characteristic is the commitment to express an immunoglobulin complex. cell Types of B lineage lymphocytes include B cells and antibody secreting cells (plasmablasts and plasma cells). Lymphocytes of B cell lineage can be distinguished from those of T cell lineage by their lack of CD3e (as part of the T cell receptor complex). lymphocyte of B lineage CL:0000988 A cell of a hematopoietic lineage. BTO:0000574 CALOHA:TS-2017 FMA:70366 FMA:83598 haematopoietic cell haemopoietic cell hemopoietic cell cell hematopoietic cell CL:0000995 CD71-positive common myeloid precursor OR CD7-negative lymphoid precursor OR CD7-positive lymphoid cell Originally described in the dendritic cell ontology (DC_CL:1100000)(PMID:19243617). CD34-positive, CD38-positive common myeloid progenitor OR CD34-positive, CD38-positive common lymphoid progenitor CL:0001012 cell Originally described in the dendritic cell ontology (DC_CL:1110000)(PMID:19243617). CD7-negative lymphoid progenitor OR granulocyte monocyte progenitor CL:0001021 A common lymphoid progenitor that is CD10-positive, CD45RA-positive, CD34-positive and CD38-positive. CD10-positive common lymphocyte precursor CD10-positive common lymphocyte progenitor CD10-positive common lymphoid precursor cell These markers are associated with human common lymphoid progenitors. Originally described in the dendritic cell ontology (DC_CL:0000032)(PMID:19243617). CD34-positive, CD38-positive common lymphoid progenitor CL:0001024 CD133-positive hematopoietic stem cell is a hematopoietic stem cell that is CD34-positive, CD90-positive, and CD133-positive. CALOHA:TS-0448 FMA:86475 CD133-positive hematopoietic stem cell cell Cell markers are associated with human hematopoietic stem cells. Originally described in the dendritic cell ontology (DC_CL:0000035)(PMID:19243617). CD34-positive, CD38-negative hematopoietic stem cell CL:0001026 A common myeloid progenitor that is CD34-positive, CD38-positive, IL3ra-low, CD10-negative, CD7-negative, CD45RA-negative, and IL-5Ralpha-negative. CD71-positive common myeloid precursor cell Markers are associated with human cell type. Originally described in the dendritic cell ontology (DC_CL:0000038)(PMID:19243617). CD34-positive, CD38-positive common myeloid progenitor CL:0001027 CD7-negative lymphoid progenitor cell is a lymphoid progenitor cell that is CD34-positive, CD7-negative and CD45RA-negative. CD7-negative lymphoid precursor cell These markers are associated with human cells. Originally described in the dendritic cell ontology (DC_CL:0000039)(PMID:19243617). CD7-negative lymphoid progenitor cell CL:0001034 A cell that is maintained or propagated in a controlled artificial environment for use in an investigation. haendel 2012-01-12T09:58:38Z cell 'In vitro', translating literally to 'in glass', typically refers to a controlled, often sterile, laboratory setting where cells or other specimens are placed by some agent for the purpose of studying or manipulating them as part of some research investigation. 'In vitro' is intended to contrast with 'native',which refers to cells or other biological entities that are found in a natural setting. It describes unicellular organisms removed from a natural environement and multicellular organism cells removed from an organism, or cells derived in culture from such displaced cells. cell in vitro CL:0001035 A connective tissue cell found in bone. adiehl 2011-11-16T04:28:16Z cell bone cell CL:0001059 A progenitor cell committed to myeloid lineage, including the megakaryocyte and erythroid lineages. These cells are CD34-positive, and express Gata1, Gata2, C/EBPa, and Pu.1. CMP common myeloid precursor, CD34-positive cell CFU-GEMM CFU-S colony forming unit granulocyte, erythrocyte, macrophage, and megakaryocyte multipotential myeloid stem cell myeloid stem cell pluripotent stem cell (bone marrow) CMP are reportedly CD16-positive, CD32-positive, CD38-positive, CD45RA-negative, CD110-negative, CD117-positive, CD123-positive, and SCA1-negative. common myeloid progenitor, CD34-positive CL:0001060 A hematopoietic oligopotent progenitor cell that has the ability to differentiate into limited cell types but lacks lineage cell markers and self renewal capabilities. Cell lacks hematopoeitic lineage markers. tmeehan 2010-01-06T03:43:27Z cell hematopoietic oligopotent progenitor cell, lineage-negative CL:0002009 A progenitor cell that can give rise to plasmacytoid and myeloid dendritic cells, and to monocytes and macrophages. tmeehan 2010-01-19T02:51:58Z MDP cell macrophage dendritic cell progenitor CL:0002031 A hematopoietic progenitor cell that is capable of developing into only one lineage of hematopoietic cells. tmeehan 2010-01-06T03:43:20Z cell hematopoietic lineage restricted progenitor cell CL:0002032 A hematopoietic oligopotent progenitor cell that has the ability to differentiate into limited cell types but lacks lineage cell markers and self renewal capabilities. Cell lacks hematopoeitic lineage markers. tmeehan 2010-01-06T03:43:27Z cell This cell type is intended to be compatible with any vertebrate hematopoietic oligopotent progenitor cell. For mammalian hematopoietic oligopotent progenitor cells known to be lineage-negative, please use the term 'hematopoietic oligopotent progenitor cell' (CL_0001060). hematopoietic oligopotent progenitor cell CL:0002043 A hematopoietic multipotent progenitor cell that is CD34-positive, CD38-negative, CD45RA-negative, and CD90-negative. tmeehan 2010-01-12T11:14:15Z cell Cell markers are associated with human hematopoietic multipotent progenitor cells. CD34-positive, CD38-negative multipotent progenitor cell CL:0002064 A secretory cell found in pancreatic acini that secretes digestive enzymes and mucins. This cell is a typical zymogenic cell, have a basal nucleus and basophilic cytoplasm consisting of regular arrays of granular endoplasmic reticulum with mitochondria and dense secretory granules. tmeehan 2010-06-24T03:16:29Z BTO:0000028 CALOHA:TS-0737 FMA:63032 acinar cell of pancreas cell pancreatic acinar cell CL:0002067 An enterocrine cell that produces glucagon. tmeehan 2010-09-10T10:48:54Z FMA:62939 cell type A enterocrine cell CL:0002076 An epithelial cell derived from endoderm. tmeehan 2010-06-29T03:38:14Z FMA:69075 cell endo-epithelial cell CL:0002078 Epithelial cell derived from mesoderm or mesenchyme. tmeehan 2010-06-29T03:49:14Z FMA:69076 epithelial mesenchymal cell cell meso-epithelial cell CL:0002079 Epithelial cell found in the ducts of the pancreas. This cell type contributes to the high luminal pH. tmeehan 2010-06-30T08:49:43Z FMA:63099 cell pancreatic ductal cell CL:0002087 A leukocyte that lacks granules. tmeehan 2010-07-22T11:30:33Z FMA:62855 agranular leukocyte cell nongranular leukocyte CL:0002092 A cell found in the bone marrow. This can include fibroblasts, macrophages, adipocytes, osteoblasts, osteoclasts, endothelial cells and hematopoietic cells. tmeehan 2010-07-22T04:48:15Z BTO:0004850 FMA:83621 cell MH consider whether bone marrow cells are bone cells in the structural sense vs. being part of bone organ sense. bone marrow cell CL:0002139 An endothelial cell of the vascular tree, which includes blood vessels and lymphatic vessels. tmeehan 2010-08-24T02:06:40Z BTO:0001854 CALOHA:TS-1106 FMA:67755 vascular endothelial cell cubodial endothelial cell of vascular tree cell These cells are reportedly CD31-positive, CD34-positive, CD144-positive, TAL1-positive. endothelial cell of vascular tree CL:0002191 A cell involved in the formation of a granulocyte. tmeehan 2010-08-30T12:54:27Z FMA:83519 cell granulocytopoietic cell CL:0002193 A cell type that is the first of the maturation stages of the granulocytic leukocytes normally found in the bone marrow. Granules are seen in the cytoplasm. The nuclear material of the myelocyte is denser than that of the myeloblast but lacks a definable membrane. The cell is flat and contains increasing numbers of granules as maturation progresses. tmeehan 2010-08-30T01:08:19Z BTO:0000734 FMA:83525 cell myelocyte CL:0002194 A cell involved in the formation of a monocyte (monopoiesis). tmeehan 2010-08-30T01:27:48Z FMA:83552 cell monopoietic cell CL:0002202 An epithelial cell of the tracheobronchial tree. tmeehan 2010-09-02T02:09:14Z CL:1000407 FMA:66816 cell epithelial cell of tracheobronchial tree CL:0002242 A cell containing at least one nucleus. tmeehan 2010-09-07T03:32:33Z FMA:67513 cell nucleate cell CL:0002275 A PP cell located in the islets of the pancreas. tmeehan 2010-09-10T03:30:31Z BTO:0000805 FMA:70588 PP cell of pancreatic islet PP-cell of pancreatic islet pancreatic polypeptide-secreting cell cell The term PP cell of pancreatic acinus was obsoleted due to a lack of evidence, making PP cell of pancreatic islets synonymous with pancreatic PP cell. pancreatic PP cell CL:0002293 An epithelial cell of the thymus. Epithelial reticular cells are pleomorphic, stellate, non-phagocytic cells which seem to be supportive in function and are held together by desmosomes. They replace the fibroblastoid reticular cells found in other lymphoid organs. Other epithelial cells in the medulla have the ultrastructure of secretory cells. Although different epithelial cells throughout the thymus appear alike by light microscopy their ultrastructure and function varies. tmeehan 2010-09-13T02:34:22Z CL:1000459 CALOHA:TS-1040 FMA:72208 epithelial cell of thymus gland epithelial reticular cell epithelial reticular cell of thymus thymic epithelial cell cell epithelial cell of thymus CL:0002320 A cell of the supporting or framework tissue of the body, arising chiefly from the embryonic mesoderm and including adipose tissue, cartilage, and bone. tmeehan 2010-09-15T03:01:54Z CL:1000406 CALOHA:TS-2096 FMA:63875 cell connective tissue cell CL:0002321 A cell of the embryo. tmeehan 2010-09-15T03:39:21Z CALOHA:TS-0263 FMA:82840 FMA:82841 WBbt:0007028 cell embryonic cell CL:0002322 A stem cell of embryonic origin. tmeehan 2010-09-15T03:44:35Z BTO:0001086 CALOHA:TS-0263 FMA:82841 ESC cell This is an in vitro cell type and may be removed in future releases. These cells are reportedly SSEA-4-positive, CD73-negative, and CD324-positive. embryonic stem cell CL:0002328 An epithelial cell of the bronchus. tmeehan 2010-09-20T02:00:00Z BTO:0002922 cell bronchial epithelial cell CL:0002334 An undifferentiated fibroblast that can be stimulated to form a fat cell. tmeehan 2010-09-20T02:31:53Z BTO:0001107 cell preadipocyte CL:0002351 A multi-fate stem cell that is able to differentiate into the pancreas alpha, beta and delta endocrine cells. This cell type expresses neurogenin-3 and Isl-1. tmeehan 2010-09-21T04:41:06Z pancreatic endocrine progenitor pancreatic islet progenitor cell cell progenitor cell of endocrine pancreas CL:0002365 An epithelial cell of the medullary thymus. This cell type expresses a diverse range of tissue-specific antigens. This promiscuous gene expression is a cell-autonomous property of medullary epithelial cells and is maintained during the entire period of thymic T cell output. tmeehan 2010-09-23T03:17:14Z BTO:0004563 mTEC cell medullary thymic epithelial cell CL:0002368 An endo-epithelial cell of the respiratory tract. tmeehan 2010-09-23T04:38:49Z BTO:0004533 airway epithelial cell cell respiratory epithelial cell CL:0002371 A cell of an organism that does not pass on its genetic material to the organism's offspring (i.e. a non-germ line cell). tmeehan 2010-09-24T09:44:42Z BTO:0001268 FMA:72300 WBbt:0008378 cell somatic cell CL:0002494 A cell located in the heart, including both muscle and non muscle cells. tmeehan 2010-12-07T09:37:22Z BTO:0001539 CALOHA:TS-0115 FMA:83808 FMA:84791 heart cell cell From Onard of the FMA: Cardiac muscle cell or cardiac myocyte is a striated muscle cell. Cardiocyte on the other hand is any cell in the heart which includes cells other than muscle cells (e.g. endothelial cell of endocardium). Unless there is a consensus among anatomists that cardiocytes refer only to muscle cells, we will treat them as a general class of cells in the heart. cardiocyte CL:0002544 An arterial endothelial cell that is part of the aorta endothelium. tmeehan 2011-02-28T03:54:42Z BTO:0003245 CALOHA:TS-0047 cell aortic endothelial cell CL:0002546 An endothelial progenitor cell that participates in angiogenesis during development. tmeehan 2011-02-28T04:20:39Z cell See CL:0002619. embryonic blood vessel endothelial progenitor cell CL:0002632 tmeehan 2011-06-21T12:29:31Z cell epithelial cell of lower respiratory tract CL:0005018 A cell that secretes ghrelin, the peptide hormone that stimulates hunger. cell ghrelin secreting cell CL:0005019 Ghrelin secreting cells found in the found in the exocrine pancreas. pancreatic E cell cell In mammals the endocrine pancreas is called the Islets of Langerhans. pancreatic epsilon cell CL:0005026 Multi fate stem cell that gives rise to to both hepatocytes and cholangiocytes as descendants. hepatoblast CL:0007004 Cell that is part of the neural crest region of the neuroepithelium, prior to migration. Note that not all premigratory neural crest cells may become migratory neural crest cells. haendel 2012-06-27T08:27:35Z cell premigratory neural crest cell CL:0008001 Any hematopoietic cell that is a precursor of some other hematopoietic cell type. hematopoietic precursor cell CL:0008024 An endocrine cell that is part of the pancreas. cell pancreatic endocrine cell CL:0010021 cardiac myoblast CL:0011115 A cell that, by division or terminal differentiation, can give rise to other cell types. Work is needed on GO 'cell differentiation' before it is clear whether the equivalent class definition 'native cell' that capable_of some 'cell differentiation' works. Also, may want to consider merging this with non-terminally differentiated cell. precursor cell CL:1000413 A blood vessel endothelial cell that is part of an arterial endothelium. CL:0002542 BTO:0004758 FMA:67761 KUPO:0001095 arterial endothelial cell cell endothelial cell of artery CL:1000415 An epithelial cell that is part of the gallbladder. FMA:67780 cell epithelial cell of gall bladder CL:1000488 An epithelial cell that is part of the bile duct. Cholangiocytes contribute to bile secretion via net release of bicarbonate and water. They are cuboidal epithelium in the small interlobular bile ducts, but become columnar and mucus secreting in larger bile ducts approaching the porta hepatis and the extrahepatic ducts. FMA:86481 epithelial cell of bile duct cell cholangiocyte CL:1001433 An epithelial cell of the exocrine pancreas. FMA:70986 exocrine pancreas cell cell epithelial cell of exocrine pancreas CL:1001599 Glandular cell of exocrine pancreas epithelium. Example: pancreatic acinar cell, glandular cells in pancreatic canaliculi, glandular cells in pancreatic ducts. BTO:0000028 CALOHA:TS-1242 exocrine pancreas glandular cell pancreas exocrine glandular cells pancreas exocrine glandular cell CL:1001610 Hematopoietic cells resident in the bone marrow. Include: hematopoietic stem cells (lymphoid stem cells and myeloid stem cells) and the precursor cells for thrombocytes, erythrocytes, basophils, neutrophils, eosinophils, monocytes and lymphocytes. CALOHA:TS-2109 bone marrow hematopoietic cells bone marrow poietic cells bone marrow hematopoietic cell CP:0000000 Cytoplasm that exhibits molecular interaction for acidic dyes under specific pH conditions. tmeehan 2010-05-25T01:36:34Z cell neutrophillic cytoplasm CP:0000027 Cytoplasm that exhibits molecular interaction for acidic dyes under specific pH conditions. tmeehan 2009-12-22T04:23:25Z eosinophilic cell acidophilic cytoplasm CP:0000028 Cytoplasm that exhibits molecular interaction for basic dyes under specific pH conditions. tmeehan 2009-12-22T04:24:54Z cell basophilic cytoplasm CP:0000035 Cytoplasm that exhibits affinity for both basic and acid stains under specific pH conditions. tmeehan 2009-12-28T04:25:23Z cell polychromatophilic cytoplasm CP:0000037 A nucleus size quality which is relatively high compared to the amount of cytoplasm present in the same cell. tmeehan 2009-12-23T10:53:24Z cell increased nucleus size ENVO:00001998 Any material within 2 m from the Earth's surface that is in contact with the atmosphere, with the exclusion of living organisms, areas with continuous ice not covered by other material, and water bodies deeper than 2 m. soil ENVO:00010483 A portion of environmental material is a fiat object which forms the medium or part of the medium of an environmental system. environmental material ERO:0000378 A material processing technique that uses operative manual and instrumental techniques on a patient to investigate and/or treat a pathological condition such as disease or injury or to help improve bodily function or appearance. surgery ERO:0001211 A DNA sequencing by ligation technique that involves a bead-based method that uses a complex approach of adapter ligation followed by adapter decoding, reading the sequence in increments of four nucleotides; this method made it susceptible to sequence-specific bias or loss of specific sequences. massively parallel signature sequencing ERO:0001334 Specimen creation of a sample of tissue from a living body for diagnostic purposes. biopsy ERO:0001400 A cell line that is derived from a stem cell. stem cell derived cell line ERO:0001716 A database is an organized collection of data, today typically in digital form. database FMA:63919 Fetal structure, which is a developmental form of a vertebrate animal at any given time point from 8 weeks of gestation to birth (or hatching). Examples: There is only one fetus. Fetus GAZ:00000448 A reference to a place on the Earth, by its name or by its geographical location. geographical location GO:0000785 The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome. chromatin GO:0000791 A dispersed and relatively uncompacted form of chromatin. euchromatin GO:0000792 A compact and highly condensed form of chromatin. heterochromatin GO:0001649 The process whereby a relatively unspecialized cell acquires the specialized features of an osteoblast, a mesodermal or neural crest cell that gives rise to bone. osteoblast differentiation GO:0001667 Cell migration that is accomplished by extension and retraction of a pseudopodium. ameboidal-type cell migration GO:0001816 The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. cytokine production GO:0001820 The regulated release of serotonin by a cell. Serotonin (5-hydroxytryptamine, or 5-HT) is a monoamine synthesised in serotonergic neurons in the central nervous system, enterochromaffin cells in the gastrointestinal tract and some immune system cells. serotonin secretion GO:0002200 The somatic process allowing for the production of immune receptors whose specificity is not encoded in the germline genomic sequences. somatic diversification of immune receptors GO:0002228 The promotion of an immune response by natural killer cells through direct recognition of target cells or through the release of cytokines. natural killer cell mediated immunity GO:0002244 The process in which precursor cell type acquires the specialized features of a hematopoietic progenitor cell, a class of cell types including myeloid progenitor cells and lymphoid progenitor cells. hematopoietic progenitor cell differentiation GO:0002376 Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats. immune system process GO:0002449 Any process involved in the carrying out of an immune response by a lymphocyte. lymphocyte mediated immunity GO:0002456 Any process involved in the carrying out of an immune response by a T cell. T cell mediated immunity GO:0002460 An immune response based on directed amplification of specific receptors for antigen produced through a somatic diversification process that includes somatic recombination of germline gene segments encoding immunoglobulin superfamily domains, and allowing for enhanced responses upon subsequent exposures to the same antigen (immunological memory). Recombined receptors for antigen encoded by immunoglobulin superfamily domains include T cell receptors and immunoglobulins (antibodies). An example of this is the adaptive immune response found in Mus musculus. adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains GO:0002521 The process in which a relatively unspecialized hemopoietic precursor cell acquires the specialized features of a leukocyte. A leukocyte is an achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue. leukocyte differentiation GO:0002562 The process in which immune receptor genes are diversified through recombination of the germline genetic elements within a single genetic locus. somatic diversification of immune receptors via germline recombination within a single locus GO:0002573 The process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of any cell of the myeloid leukocyte lineage. myeloid leukocyte differentiation GO:0002682 Any process that modulates the frequency, rate, or extent of an immune system process. regulation of immune system process GO:0002694 Any process that modulates the frequency, rate, or extent of leukocyte activation. regulation of leukocyte activation GO:0002790 The controlled release of a peptide from a cell or a tissue. peptide secretion GO:0003006 A developmental process in which a progressive change in the state of some part of an organism specifically contributes to its ability to form offspring. developmental process involved in reproduction GO:0003013 A organ system process carried out by any of the organs or tissues of the circulatory system. The circulatory system is an organ system that moves extracellular fluids to and from tissue within a multicellular organism. circulatory system process GO:0003674 Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions. molecular_function GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. catalytic activity GO:0003964 Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). Catalyzes RNA-template-directed extension of the 3'- end of a DNA strand by one deoxynucleotide at a time. RNA-directed DNA polymerase activity GO:0005575 The part of a cell or its extracellular environment in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together. cellular_component GO:0005634 A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. nucleus GO:0005730 A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome. nucleolus GO:0005737 All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. cytoplasm GO:0005773 A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol. vacuole GO:0005840 An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins. ribosome GO:0006139 Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids. nucleobase-containing compound metabolic process GO:0006259 Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides. DNA metabolic process GO:0006260 The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA. DNA replication GO:0006304 The covalent alteration of one or more nucleotide sites in DNA, resulting in a change in its properties. DNA modification GO:0006306 The covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine. DNA methylation GO:0006323 Any process in which DNA and associated proteins are formed into a compact, orderly structure. DNA packaging GO:0006338 Dynamic structural changes to eukaryotic chromatin occurring throughout the cell division cycle. These changes range from the local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation. chromatin remodeling GO:0006464 The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications) occurring at the level of an individual cell. Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification). cellular protein modification process GO:0006725 The chemical reactions and pathways involving aromatic compounds, any organic compound characterized by one or more planar rings, each of which contains conjugated double bonds and delocalized pi electrons, as carried out by individual cells. cellular aromatic compound metabolic process GO:0006810 The directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore. transport GO:0006811 The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. ion transport GO:0006812 The directed movement of cations, atoms or small molecules with a net positive charge, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. cation transport GO:0006837 The directed movement of serotonin into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Serotonin (5-hydroxytryptamine) is a monoamine neurotransmitter occurring in the peripheral and central nervous systems. serotonin transport GO:0006915 A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died. apoptotic process GO:0006950 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation). response to stress GO:0006955 Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat. immune response GO:0006996 A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an organelle within a cell. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. organelle organization GO:0007049 The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division. cell cycle GO:0007113 A mitotic cell cycle in which chromosomes are replicated and sister chromatids separate, but spindle formation, nuclear membrane breakdown and nuclear division do not occur, resulting in an increased number of chromosomes in the cell. endomitotic cell cycle GO:0007143 A cell cycle process by which the cell nucleus divides as part of a meiotic cell cycle in the female germline. female meiotic division GO:0007159 The attachment of a leukocyte to another cell via adhesion molecules. leukocyte cell-cell adhesion GO:0007276 The generation and maintenance of gametes in a multicellular organism. A gamete is a haploid reproductive cell. gamete generation GO:0007281 The process whose specific outcome is the progression of an immature germ cell over time, from its formation to the mature structure (gamete). A germ cell is any reproductive cell in a multicellular organism. germ cell development GO:0007565 The set of physiological processes that allow an embryo or foetus to develop within the body of a female animal. It covers the time from fertilization of a female ovum by a male spermatozoon until birth. female pregnancy GO:0007596 The sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers. blood coagulation GO:0008015 The flow of blood through the body of an animal, enabling the transport of nutrients to the tissues and the removal of waste products. blood circulation GO:0008150 Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end. biological_process GO:0008152 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. metabolic process GO:0008219 Any biological process that results in permanent cessation of all vital functions of a cell. A cell should be considered dead when any one of the following molecular or morphological criteria is met: (1) the cell has lost the integrity of its plasma membrane; (2) the cell, including its nucleus, has undergone complete fragmentation into discrete bodies (frequently referred to as "apoptotic bodies"); and/or (3) its corpse (or its fragments) have been engulfed by an adjacent cell in vivo. cell death GO:0009058 The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones. biosynthetic process GO:0009059 The chemical reactions and pathways resulting in the formation of a macromolecule, any 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. macromolecule biosynthetic process GO:0009306 The controlled release of proteins from a cell. protein secretion GO:0009730 The series of events in which a carbohydrate stimulus is received by a cell and converted into a molecular signal. detection of carbohydrate stimulus GO:0009732 The series of events in which a stimulus from a hexose is received and converted into a molecular signal. detection of hexose stimulus GO:0009743 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a carbohydrate stimulus. response to carbohydrate GO:0009746 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a hexose stimulus. response to hexose GO:0009914 The directed movement of hormones into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. hormone transport GO:0009987 Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. cellular process GO:0010467 The process in which a gene's sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form. gene expression GO:0010817 Any process that modulates the levels of hormone within an organism or a tissue. A hormone is any substance formed in very small amounts in one specialized organ or group of cells and carried (sometimes in the bloodstream) to another organ or group of cells in the same organism, upon which it has a specific regulatory action. regulation of hormone levels GO:0015031 The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. protein transport GO:0015106 Catalysis of the transfer of bicarbonate from one side of a membrane to the other. Bicarbonate is the hydrogencarbonate ion, HCO3-. bicarbonate transmembrane transporter activity GO:0015671 The directed movement of oxygen (O2) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. oxygen transport GO:0015696 The directed movement of ammonium into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Ammonium is the cation NH4+ which is formed from N2 by root-nodule bacteria in leguminous plants and is an excretory product in ammonotelic animals. ammonium transport GO:0015833 The directed movement of peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. peptide transport GO:0015844 The directed movement of monoamines, organic compounds that contain one amino group that is connected to an aromatic ring by an ethylene group (-CH2-CH2-), into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. monoamine transport GO:0015850 The directed movement of an organic hydroxy compound (organic alcohol) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. An organic hydroxy compound is an organic compound having at least one hydroxy group attached to a carbon atom. organic hydroxy compound transport GO:0016023 A membrane-bounded vesicle found in the cytoplasm of the cell. cytoplasmic membrane-bounded vesicle GO:0016043 A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component. cellular component organization GO:0016337 The attachment of one cell to another cell via adhesion molecules, where both cells are part of the same organism. single organismal cell-cell adhesion GO:0016447 The process in which immunoglobulin genes are formed through recombination of the germline genetic elements, as known as immunoglobulin gene segments, within a single locus. somatic recombination of immunoglobulin gene segments GO:0016477 The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues. Cell migration is a central process in the development and maintenance of multicellular organisms. cell migration GO:0016568 The alteration of DNA, protein, or sometimes RNA, in chromatin, which may result in changing the chromatin structure. chromatin modification GO:0016570 The covalent alteration of one or more amino acid residues within a histone protein. histone modification GO:0017145 The self-renewing division of a stem cell. A stem cell is an undifferentiated cell, in the embryo or adult, that can undergo unlimited division and give rise to one or several different cell types. stem cell division GO:0019219 Any cellular process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids. regulation of nucleobase-containing compound metabolic process GO:0019222 Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. regulation of metabolic process GO:0019538 The chemical reactions and pathways involving a specific protein, rather than of proteins in general. Includes protein modification. protein metabolic process GO:0019724 Any process involved with the carrying out of an immune response by a B cell, through, for instance, the production of antibodies or cytokines, or antigen presentation to T cells. B cell mediated immunity GO:0019814 A protein complex that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains, held together by disulfide bonds and sometimes complexed with additional proteins. An immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph. immunoglobulin complex GO:0019815 An immunoglobulin complex that is present in the plasma membrane of B cells and that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains and a signaling subunit, a heterodimer of the Ig-alpha and Ig-beta proteins. B cell receptor complex GO:0019882 The process in which an antigen-presenting cell expresses antigen (peptide or lipid) on its cell surface in association with an MHC protein complex. antigen processing and presentation GO:0022407 Any process that modulates the frequency, rate or extent of attachment of a cell to another cell. regulation of cell-cell adhesion GO:0022414 A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents. reproductive process GO:0022610 The attachment of a cell or organism to a substrate or other organism. biological adhesion GO:0023061 The process in which a signal is secreted or discharged into the extracellular medium from a cellular source. signal release GO:0030017 The repeating unit of a myofibril in a muscle cell, composed of an array of overlapping thick and thin filaments between two adjacent Z discs. sarcomere GO:0030072 The regulated release of a peptide hormone from a cell. peptide hormone secretion GO:0030073 The regulated release of proinsulin from secretory granules (B granules) in the B cells of the pancreas; accompanied by cleavage of proinsulin to form mature insulin. insulin secretion GO:0030098 The process in which a relatively unspecialized precursor cell acquires specialized features of a lymphocyte. A lymphocyte is a leukocyte commonly found in the blood and lymph that has the characteristics of a large nucleus, a neutral staining cytoplasm, and prominent heterochromatin. lymphocyte differentiation GO:0030099 The process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of any cell of the myeloid leukocyte, megakaryocyte, thrombocyte, or erythrocyte lineages. myeloid cell differentiation GO:0030141 A small subcellular vesicle, surrounded by a membrane, that is formed from the Golgi apparatus and contains a highly concentrated protein destined for secretion. Secretory granules move towards the periphery of the cell and upon stimulation, their membranes fuse with the cell membrane, and their protein load is exteriorized. Processing of the contained protein may take place in secretory granules. secretory granule GO:0030154 The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state. cell differentiation GO:0030182 The process in which a relatively unspecialized cell acquires specialized features of a neuron. neuron differentiation GO:0030217 The process in which a precursor cell type acquires characteristics of a more mature T-cell. A T cell is a type of lymphocyte whose definin characteristic is the expression of a T cell receptor complex. T cell differentiation GO:0030218 The process in which a myeloid precursor cell acquires specializes features of an erythrocyte. erythrocyte differentiation GO:0030219 The process in which a myeloid precursor cell acquires specializes features of a megakaryocyte. megakaryocyte differentiation GO:0030224 The process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of a monocyte. monocyte differentiation GO:0030225 The process in which a relatively unspecialized monocyte acquires the specialized features of a macrophage. macrophage differentiation GO:0030261 The progressive compaction of dispersed interphase chromatin into threadlike chromosomes prior to mitotic or meiotic nuclear division, or during apoptosis, in eukaryotic cells. chromosome condensation GO:0030263 The compaction of chromatin during apoptosis. apoptotic chromosome condensation GO:0030316 The process in which a relatively unspecialized monocyte acquires the specialized features of an osteoclast. An osteoclast is a specialized phagocytic cell associated with the absorption and removal of the mineralized matrix of bone tissue. osteoclast differentiation GO:0030529 A macromolecular complex containing both protein and RNA molecules. ribonucleoprotein complex GO:0030659 The lipid bilayer surrounding a cytoplasmic vesicle. cytoplasmic vesicle membrane GO:0030667 The lipid bilayer surrounding a secretory granule. secretory granule membrane GO:0030851 The process in which a myeloid precursor cell acquires the specialized features of a granulocyte. Granulocytes are a class of leukocytes characterized by the presence of granules in their cytoplasm. These cells are active in allergic immune reactions such as arthritic inflammation and rashes. This class includes basophils, eosinophils and neutrophils. granulocyte differentiation GO:0030855 The process in which a relatively unspecialized cell acquires specialized features of an epithelial cell, any of the cells making up an epithelium. epithelial cell differentiation GO:0031016 The process whose specific outcome is the progression of the pancreas over time, from its formation to the mature structure. The pancreas is an endoderm derived structure that produces precursors of digestive enzymes and blood glucose regulating enzymes. pancreas development GO:0031018 The process whose specific outcome is the progression of the endocrine pancreas over time, from its formation to the mature structure. The endocrine pancreas is made up of islet cells that produce insulin, glucagon and somatostatin. endocrine pancreas development GO:0031090 A membrane that is one of the two lipid bilayers of an organelle envelope or the outermost membrane of single membrane bound organelle. organelle membrane GO:0031323 Any process that modulates the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances. regulation of cellular metabolic process GO:0031410 A vesicle formed of membrane or protein, found in the cytoplasm of a cell. cytoplasmic vesicle GO:0031982 Any small, fluid-filled, spherical organelle enclosed by membrane or protein. vesicle GO:0031988 Any small, fluid-filled, spherical organelle enclosed by a lipid bilayer. membrane-bounded vesicle GO:0032501 Any biological process, occurring at the level of a multicellular organism, pertinent to its function. multicellular organismal process GO:0032502 A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition. developmental process GO:0032940 The controlled release of a substance by a cell. secretion by cell GO:0032991 A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which the constituent parts function together. macromolecular complex GO:0033152 The process in which immunoglobulin gene segments are recombined within a single locus utilizing the conserved heptamer and nonomer recombination signal sequences (RSS). For immunoglobulin heavy chains V, D, and J gene segments are joined, and for immunoglobulin light chains V and J gene segments are joined. immunoglobulin V(D)J recombination GO:0034109 The attachment of a cell to a second cell of the identical type via adhesion molecules. homotypic cell-cell adhesion GO:0034284 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a monosaccharide stimulus. response to monosaccharide GO:0034287 The series of events in which a stimulus from a monosaccharide is received and converted into a molecular signal. detection of monosaccharide stimulus GO:0034641 The chemical reactions and pathways involving various organic and inorganic nitrogenous compounds, as carried out by individual cells. cellular nitrogen compound metabolic process GO:0034645 The chemical reactions and pathways resulting in the formation of a macromolecule, any 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, carried out by individual cells. cellular macromolecule biosynthetic process GO:0036211 The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications). Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification). protein modification process GO:0036321 The regulated release of ghrelin from a cell. Ghrelin is a 28 amino acid hunger-stimulating peptide hormone. ghrelin secretion GO:0040030 Any heritable epigenetic process that modulates the frequency, rate or extent of protein function by self-perpetuating conformational conversions of normal proteins in healthy cells. This is distinct from, though mechanistically analogous to, disease states associated with prion propagation and amyloidogenesis. A single protein, if it carries a glutamine/asparagine-rich ('prion') domain, can sometimes stably exist in at least two distinct physical states, each associated with a different phenotype; propagation of one of these traits is achieved by a self-perpetuating change in the protein from one form to the other, mediated by conformational changes in the glutamine/asparagine-rich domain. Prion domains are both modular and transferable to other proteins, on which they can confer a heritable epigenetic alteration of function; existing bioinformatics data indicate that they are rare in non-eukarya, but common in eukarya. regulation of molecular function, epigenetic GO:0042101 A protein complex that contains a disulfide-linked heterodimer of T cell receptor (TCR) chains, which are members of the immunoglobulin superfamily, and mediates antigen recognition, ultimately resulting in T cell activation. The TCR heterodimer is associated with the CD3 complex, which consists of the nonpolymorphic polypeptides gamma, delta, epsilon, zeta, and, in some cases, eta (an RNA splice variant of zeta) or Fc epsilon chains. T cell receptor complex GO:0042110 The change in morphology and behavior of a mature or immature T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific. T cell activation GO:0042470 A tissue-specific, membrane-bounded cytoplasmic organelle within which melanin pigments are synthesized and stored. Melanosomes are synthesized in melanocyte cells. melanosome GO:0042571 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. immunoglobulin complex, circulating GO:0042575 A protein complex that possesses DNA polymerase activity and is involved in template directed synthesis of DNA. DNA polymerase complex GO:0042582 Primary lysosomal granule found in neutrophil granulocytes. Contains a wide range of hydrolytic enzymes and is released into the extracellular fluid. azurophil granule GO:0042589 The lipid bilayer surrounding a zymogen granule. zymogen granule membrane GO:0042611 A transmembrane protein complex composed of an MHC alpha chain and, in most cases, either an MHC class II beta chain or an invariant beta2-microglobin chain, and with or without a bound peptide, lipid, or polysaccharide antigen. MHC protein complex GO:0042613 A transmembrane protein complex composed of an MHC class II alpha and MHC class II beta chain, and with or without a bound peptide or polysaccharide antigen. MHC class II protein complex GO:0042886 The directed movement of an amide, any compound containing one, two, or three acyl groups attached to a nitrogen atom, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. amide transport GO:0043011 The process in which a monocyte acquires the specialized features of a dendritic cell, an immunocompetent cell of the lymphoid and hemopoietic systems and skin. myeloid dendritic cell differentiation GO:0043170 The chemical reactions and pathways involving macromolecules, any 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. macromolecule metabolic process GO:0043226 Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, and prokaryotic structures such as anammoxosomes and pirellulosomes. Excludes the plasma membrane. organelle GO:0043227 Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. membrane-bounded organelle GO:0043229 Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. intracellular organelle GO:0043231 Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. intracellular membrane-bounded organelle GO:0043232 Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane and occurring within the cell. Includes ribosomes, the cytoskeleton and chromosomes. intracellular non-membrane-bounded organelle GO:0043234 Any macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical. protein complex GO:0043235 Any protein complex that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function. receptor complex GO:0043412 The covalent alteration of one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological macromolecule, resulting in a change in its properties. macromolecule modification GO:0043414 The covalent attachment of a methyl residue to one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological macromolecule. macromolecule methylation GO:0043565 Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding. sequence-specific DNA binding GO:0044030 Any process that modulates the frequency, rate or extent of the covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine. regulation of DNA methylation GO:0044237 The chemical reactions and pathways by which individual cells transform chemical substances. cellular metabolic process GO:0044238 The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism. primary metabolic process GO:0044249 The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells. cellular biosynthetic process GO:0044260 The chemical reactions and pathways involving macromolecules, any 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, as carried out by individual cells. cellular macromolecule metabolic process GO:0044267 The chemical reactions and pathways involving a specific protein, rather than of proteins in general, occurring at the level of an individual cell. Includes cellular protein modification. cellular protein metabolic process GO:0044342 The multiplication or reproduction of pancreatic B cells, resulting in the expansion of an pancreatic B cell population. Pancreatic B cell are cells of the pancreas that secrete insulin. type B pancreatic cell proliferation GO:0044422 Any constituent part of an organelle, an organized structure of distinctive morphology and function. Includes constituent parts of the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, but excludes the plasma membrane. organelle part GO:0044424 Any constituent part of the living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm. intracellular part GO:0044425 Any constituent part of a membrane, a double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. membrane part GO:0044433 Any constituent part of cytoplasmic vesicle, a vesicle formed of membrane or protein, found in the cytoplasm of a cell. cytoplasmic vesicle part GO:0044444 Any constituent part of the cytoplasm, all of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. cytoplasmic part GO:0044446 A constituent part of an intracellular organelle, an organized structure of distinctive morphology and function, occurring within the cell. Includes constituent parts of the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton but excludes the plasma membrane. intracellular organelle part GO:0044449 Any constituent part of a contractile fiber, a fiber composed of actin, myosin, and associated proteins, found in cells of smooth or striated muscle. contractile fiber part GO:0044459 Any constituent part of the plasma membrane, the membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. plasma membrane part GO:0044464 Any constituent part of a cell, the basic structural and functional unit of all organisms. cell part GO:0044699 A biological process that involves only one organism. single-organism process GO:0044702 A biological process that directly contributes to the process of producing new individuals, involving a single organism. single organism reproductive process GO:0044703 A biological process that directly contributes to the process of producing new individuals, involving another organism. multi-organism reproductive process GO:0044706 A multicellular organism process which involves another multicellular organism of the same or different species. multi-multicellular organism process GO:0044707 A biological process occurring within a single, multicellular organism. single-multicellular organism process GO:0044710 A metabolic process - chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances - which involves a single organism. single-organism metabolic process GO:0044763 Any process that is carried out at the cellular level, occurring within a single organism. single-organism cellular process GO:0044765 The directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore, involving a single organism. single-organism transport GO:0044767 A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition, involving only one organism. single-organism developmental process GO:0045087 Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens. innate immune response GO:0045321 A change in morphology and behavior of a leukocyte resulting from exposure to a specific antigen, mitogen, cytokine, cellular ligand, or soluble factor. leukocyte activation GO:0045444 The process in which a relatively unspecialized cell acquires specialized features of an adipocyte, an animal connective tissue cell specialized for the synthesis and storage of fat. fat cell differentiation GO:0045580 Any process that modulates the frequency, rate or extent of T cell differentiation. regulation of T cell differentiation GO:0045595 Any process that modulates the frequency, rate or extent of cell differentiation, the process in which relatively unspecialized cells acquire specialized structural and functional features. regulation of cell differentiation GO:0045619 Any process that modulates the frequency, rate or extent of lymphocyte differentiation. regulation of lymphocyte differentiation GO:0046483 The chemical reactions and pathways involving heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings). heterocycle metabolic process GO:0046649 A change in morphology and behavior of a lymphocyte resulting from exposure to a specific antigen, mitogen, cytokine, chemokine, cellular ligand, or soluble factor. lymphocyte activation GO:0046879 The regulated release of hormones, substances with a specific regulatory effect on a particular organ or group of cells. hormone secretion GO:0046903 The controlled release of a substance by a cell or a tissue. secretion GO:0048103 The self-renewing division of a somatic stem cell, a stem cell that can give rise to cell types of the body other than those of the germ-line. somatic stem cell division GO:0048468 The process whose specific outcome is the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate. cell development GO:0048477 The complete process of formation and maturation of an ovum or female gamete from a primordial female germ cell. Examples of this process are found in Mus musculus and Drosophila melanogaster. oogenesis GO:0048609 The process, occurring above the cellular level, that is pertinent to the reproductive function of a multicellular organism. This includes the integrated processes at the level of tissues and organs. multicellular organismal reproductive process GO:0048856 The biological process whose specific outcome is the progression of an anatomical structure from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure, whatever form that may be including its natural destruction. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome. anatomical structure development GO:0048863 The process in which a relatively unspecialized cell acquires specialized features of a stem cell. A stem cell is a cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells. stem cell differentiation GO:0048869 A biological process whose specific outcome is the progression of a cell over time from an initial condition to a later condition. cellular developmental process GO:0048870 Any process involved in the controlled self-propelled movement of a cell that results in translocation of the cell from one place to another. cell motility GO:0050432 The regulated release of catecholamines by a cell. The catecholamines are a group of physiologically important biogenic amines that possess a catechol (3,4-dihydroxyphenyl) nucleus and are derivatives of 3,4-dihydroxyphenylethylamine. catecholamine secretion GO:0050776 Any process that modulates the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus. regulation of immune response GO:0050789 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. regulation of biological process GO:0050793 Any process that modulates the frequency, rate or extent of development, the biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult). regulation of developmental process GO:0050794 Any process that modulates the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. regulation of cellular process GO:0050863 Any process that modulates the frequency, rate or extent of T cell activation. regulation of T cell activation GO:0050878 Any process that modulates the levels of body fluids. regulation of body fluid levels GO:0050879 Any physiological process involved in changing the position of a multicellular organism or an anatomical part of a multicellular organism. multicellular organismal movement GO:0050896 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism. response to stimulus GO:0051052 Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving DNA. regulation of DNA metabolic process GO:0051171 Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds. regulation of nitrogen compound metabolic process GO:0051179 Any process in which a cell, a substance, or a cellular entity, such as a protein complex or organelle, is transported to or maintained in a specific location. localization GO:0051234 The directed movement of a cell, substance or cellular entity, such as a protein complex or organelle, to a specific location. establishment of localization GO:0051249 Any process that modulates the frequency, rate or extent of lymphocyte activation. regulation of lymphocyte activation GO:0051276 A process that is carried out at the cellular level that results in the assembly, arrangement of constituent parts, or disassembly of chromosomes, structures composed of a very long molecule of DNA and associated proteins that carries hereditary information. This term covers covalent modifications at the molecular level as well as spatial relationships among the major components of a chromosome. chromosome organization GO:0051594 The series of events in which a glucose stimulus is received by a cell and converted into a molecular signal. detection of glucose GO:0051704 A biological process which involves another organism of the same or different species. multi-organism process GO:0051937 The directed movement of catecholamines, a group of physiologically important biogenic amines that possess a catechol (3,4-dihydroxyphenyl) nucleus and are derivatives of 3,4-dihydroxyphenylethylamine. catecholamine transport GO:0055007 The process in which a cardiac muscle precursor cell acquires specialized features of a cardiac muscle cell. Cardiac muscle cells are striated muscle cells that are responsible for heart contraction. cardiac muscle cell differentiation GO:0060047 The multicellular organismal process in which the heart decreases in volume in a characteristic way to propel blood through the body. heart contraction GO:0060255 Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any 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. regulation of macromolecule metabolic process GO:0060290 The conversion of a differentiated cell of one fate into a differentiated cell of another fate without first undergoing cell division or reversion to a more primitive or stem cell-like fate. transdifferentiation GO:0060591 The process in which a mesenchymal cell, acquires specialized structural and/or functional features of a chondroblast. Differentiation includes the processes involved in commitment of a cell to a chondroblast fate. A chondroblast is a precursor cell to chondrocytes. chondroblast differentiation GO:0060986 The regulated release of a hormone into the circulatory system. endocrine hormone secretion GO:0065007 Any process that modulates a measurable attribute of any biological process, quality or function. biological regulation GO:0065008 Any process that modulates a qualitative or quantitative trait of a biological quality. A biological quality is a measurable attribute of an organism or part of an organism, such as size, mass, shape, color, etc. regulation of biological quality GO:0070091 The regulated release of glucagon from secretory granules in the A (alpha) cells of the pancreas (islets of Langerhans). glucagon secretion GO:0070253 The regulated release of somatostatin from secretory granules in the D cells of the pancreas. somatostatin secretion GO:0070486 The adhesion of one leukocyte to one or more other leukocytes via adhesion molecules. leukocyte aggregation GO:0070925 The aggregation, arrangement and bonding together of a set of components to form an organelle. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. organelle assembly GO:0071702 The directed movement of organic substances into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore. An organic substance is a molecular entity that contains carbon. organic substance transport GO:0071704 The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon. organic substance metabolic process GO:0071705 The directed movement of nitrogen-containing compounds into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. nitrogen compound transport GO:0071971 The aggregation, arrangement and bonding together of a set of components to form an extracellular vesicular exosome, a membrane-bounded vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. extracellular exosome assembly GO:0080090 Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism involving those compounds formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism. regulation of primary metabolic process GO:0090304 Any cellular metabolic process involving nucleic acids. nucleic acid metabolic process GO:0098602 The attachment, via cell adhesion molecules, of a cell to either another cell of the same organism, or to an underlying substrate of the same organism such as the extracellular matrix. single organism cell adhesion GO:1901360 The chemical reactions and pathways involving organic cyclic compound. organic cyclic compound metabolic process GO:1901576 The chemical reactions and pathways resulting in the formation of an organic substance, any molecular entity containing carbon. organic substance biosynthetic process GO:1902105 Any process that modulates the frequency, rate or extent of leukocyte differentiation. regulation of leukocyte differentiation GO:1902494 A protein complex which is capable of catalytic activity. catalytic complex GO:1902578 A localization which involves only one organism. single-organism localization GO:1902589 An organelle organization which involves only one organism. single-organism organelle organization GO:1903706 Any process that modulates the frequency, rate or extent of hemopoiesis. regulation of hemopoiesis GO:2000026 Any process that modulates the frequency, rate or extent of multicellular organismal development. regulation of multicellular organismal development 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:0000007 action specification Pour the contents of flask 1 into flask 2 a directive information entity that describes an action the bearer will take Alan Ruttenberg OBI Plan and Planned Process branch action specification IAO: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:0000027 data item Data items include counts of things, analyte concentrations, and statistical summaries. a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers. 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum. 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym. 2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/ JAR: datum -- well, this will be very tricky to define, but maybe some information-like stuff that might be put into a computer and that is meant, by someone, to denote and/or to be interpreted by some process... I would include lists, tables, sentences... I think I might defer to Barry, or to Brian Cantwell Smith JAR: A data item is an approximately justified approximately true approximate belief PERSON: Alan Ruttenberg PERSON: Chris Stoeckert PERSON: Jonathan Rees data data item IAO:0000028 symbol a serial number such as "12324X" a stop sign a written proper name such as "OBI" An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity. 20091104, MC: this needs work and will most probably change 2014-03-31: We would like to have a deeper analysis of 'mark' and 'sign' in the future (see https://code.google.com/p/information-artifact-ontology/issues/detail?id=154). PERSON: James A. Overton PERSON: Jonathan Rees based on Oxford English Dictionary symbol IAO: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 1 1 IAO:0000032 scalar measurement datum 10 feet. 3 ml. a scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label. 2009-03-16: we decided to keep datum singular in scalar measurement datum, as in this case we explicitly refer to the singular form Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them. PERSON: Alan Ruttenberg PERSON: Melanie Courtot scalar measurement datum IAO:0000033 directive information entity An information content entity whose concretizations indicate to their bearer how to realize them in a process. 2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. 2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it. 8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan PERSON: Alan Ruttenberg PERSON: Bjoern Peters directive information entity IAO: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: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:0000100 data set Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves). A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets. 2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type 2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction. person:Allyson Lister person:Chris Stoeckert OBI_0000042 group:OBI data set IAO:0000101 image An image is an affine projection to a two dimensional surface, of measurements of some quality of an entity or entities repeated at regular intervals across a spatial range, where the measurements are represented as color and luminosity on the projected on surface. person:Alan Ruttenberg person:Allyson person:Chris Stoeckert OBI_0000030 group:OBI image IAO:0000102 data about an ontology part data about an ontology part is a data item about a part of an ontology, for example a term Person:Alan Ruttenberg data about an ontology part IAO:0000104 plan specification PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice. A directive information entity with action specifications and objective specifications as parts that, when concretized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified. 2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. 2014-03-31: A plan specification can have other parts, such as conditional specifications. Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved Alan Ruttenberg OBI Plan and Planned Process branch OBI_0000344 2/3/2009 Comment from OBI review. Action specification not well enough specified. Conditional specification not well enough specified. Question whether all plan specifications have objective specifications. Request that IAO either clarify these or change definitions not to use them plan specification IAO: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: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: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: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:0000416 time measurement datum A scalar measurement datum that is the result of measuring a temporal interval 2009/09/28 Alan Ruttenberg. Fucoidan-use-case Person:Alan Ruttenberg time measurement datum IAO:0000429 email address Alan Ruttenberg 1/3/2012 - Provisional id, see issue at http://code.google.com/p/information-artifact-ontology/issues/detail?id=130&thanks=130&ts=1325636583 Person:Alan Ruttenberg Person:Chris Stoeckart email address IAO:0000572 documenting Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database. a planned process in which a document is created or added to by including the specified input in it. 6/11/9: Edited at OBI workshop. We need to be able identify a child form of information artifact which corresponds to something enduring (not brain like). This used to be restricted to physical document or digital entity as the output, but that excludes e.g. an audio cassette tape Bjoern Peters wikipedia http://en.wikipedia.org/wiki/Documenting documenting IAO:0000577 centrally registered identifier symbol The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed. A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry. PERSON: Alan Ruttenberg PERSON: Bill Hogan PERSON: Bjoern Peters PERSON: Melanie Courtot CRID symbol Original proposal from Bjoern, discussions at IAO calls centrally registered identifier symbol IAO:0000578 centrally registered identifier The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed. An information content entity that consists of a CRID symbol and additional information about the CRID registry to which it belongs. 2014-05-05: In defining this term we take no position on what the CRID denotes. In particular do not assume it denotes a *record* in the CRID registry (since the registry might not have 'records'). Alan, IAO call 20101124: potentially the CRID denotes the instance it was associated with during creation. Note, IAO call 20101124: URIs are not always CRID, as not centrally registered. We acknowledge that CRID is a subset of a larger identifier class, but this subset fulfills our current needs. OBI PURLs are CRID as they are registered with OCLC. UPCs (Universal Product Codes from AC Nielsen)are not CRID as they are not centrally registered. PERSON: Alan Ruttenberg PERSON: Bill Hogan PERSON: Bjoern Peters PERSON: Melanie Courtot CRID Original proposal from Bjoern, discussions at IAO calls centrally registered identifier IAO:0000579 centrally registered identifier registry PubMed is a CRID registry. It has a dataset of PubMed identifiers associated with journal articles. A CRID registry is a dataset of CRID records, each consisting of a CRID symbol and additional information which was recorded in the dataset through a assigning a centrally registered identifier process. PERSON: Alan Ruttenberg PERSON: Bill Hogan PERSON: Bjoern Peters PERSON: Melanie Courtot CRID registry Original proposal from Bjoern, discussions at IAO calls centrally registered identifier registry IAO:0000590 written name "Bill Clinton" "The Eiffel Tower" "United States of America" A textual entity that denotes a particular in reality. PERSON: Bill Hogan http://code.google.com/p/information-artifact-ontology/issues/detail?id=114 The qualifier "written" is to set it apart from spoken names. Also, note the restrictions to particulars. We are not naming universals. We could however, be naming, attributive collections which are particulars, so "All people located in the boundaries of the city of Little Rock, AR on June 18, 2011 at 9:50a CDT" would be a name. written name MP:0001261 a status with body weight that is grossly above the average, acceptable or desirable weight, usually due to accumulation of excess fat tissue in the body obese NBO:0000073 "The process of biting and mashing food with the teeth prior to swallowing." [NBO:GVG] chewing NCBITaxon:10090 Mus musculus Mus musculus NCBITaxon:10114 Rattus Rattus NCBITaxon:10116 Rattus norvegicus Rattus norvegicus NCBITaxon:10239 Viruses Viruses NCBITaxon:117571 Euteleostomi Euteleostomi NCBITaxon:2 Bacteria Bacteria NCBITaxon:2157 Archaea Archaea NCBITaxon:2759 Eukaryota Eukaryota NCBITaxon:314146 Euarchontoglires Euarchontoglires NCBITaxon:32443 Teleostei Teleostei NCBITaxon:32524 Amniota Amniota NCBITaxon:32561 Sauria Sauria NCBITaxon:39107 Murinae Murinae NCBITaxon:7742 Vertebrata <Metazoa> Vertebrata <Metazoa> NCBITaxon:7776 Gnathostomata <vertebrate> Gnathostomata <vertebrate> NCBITaxon:7955 Danio rerio Danio rerio NCBITaxon:8570 Serpentes Serpentes NCBITaxon:8782 Aves Aves NCBITaxon:9606 Homo sapiens Homo sapiens OBCS:0000164 A software that is used for the differential gene expression significance analysis of DNA microarray experiments for both standard and time course experiments. The outputs consist of bothe p-values and q-values. Elisabetta Manduchi EDGE Storey J.D. (2007) The optimal discovery procedure: A new approach to simultaneous significance testing, Journal of the Royal Statistical Society, Series B, 69: 347-368. Storey J.D., Dai J.Y., and Leek J.T. (2007) The optimal discovery procedure for large-scale significance testing, with applications to comparative microarray experiments, Biostatistics, 8: 414-432. Leek J.T,. Monsen E.C., Dabney A.R., and Storey J.D. (2006) EDGE: Extraction and analysis of differential gene expression, Bioinformatics, 22: 507-508. Storey J.D., Xiao W., Leek J.T., Tompkins R.G., and Davis R.W. (2005) Significance analysis of time course microarray experiments, Proceedings of the National Academy of Sciences, 102: 12837-12842. Beta Cell Biology Consortium Extraction of Differential Gene Expression software OBCS:0000165 A software that can be used to produce lists of differentially expressed genes with confidence measures attached. These lists are generated via a False Discovery Rate (FDR) method of controlling the false positives. Patterns from Gene Expression (PaGE) is more than a differential expression analysis tool. PaGE is a tool to attach descriptive, dependable, and easily interpretable expression patterns to genes across multiple conditions, each represented by a set of replicated array experiments. The input consists of (replicated) intensities from a collection of array experiments from two or more conditions (or from a collection of direct comparisons on 2-channel arrays). The output consists of patterns, one for each row identifier in the data file. One condition is used as a reference to which the other types are compared. The length of a pattern equals the number of non-reference sample types. The symbols in the patterns are integers, where positive integers represent up-regulation as compared to the reference sample type and negative integers represent down-regulation. The patterns are based on the false discovery rates for each position in the pattern, so that the number of positive and negative symbols that appear in each position of the pattern is as descriptive as the data variability allows. The patterns generated are easily interpretable in that integers are used to represent different levels of up- or down-regulation as compared to the reference sample type. Elisabetta Manduchi PaGE PMID:15797908 Grant G.R., Liu J., Stoeckert C.J.Jr. (2005) A practical false discovery rate approach to identifying patterns of differential expression in microarray data, Bioinformatics, 21(11): 2684-2690. Beta Cell Biology Consortium Patterns from Gene Expression software OBCS:0000166 A software that is used to identify transcription factor binding sites in a genome that have been enriched with aligned reads generated from ChIP-Seq technology. Elisabetta Manduchi, Jie Zheng GLITR PMID:19553195 Tuteja G., White P., Schug J., Kaestner K.H. (2009) Extracting transcription factor targets from ChIP-Seq data. Nucleic Acids Res., 37(17): e113. doi: 10.1093/nar/gkp536. Beta Cell Biology Consortium GLobal Identifier of Target Regions software OBCS:0000167 A data transformation to identify protein-binding regions in a genome sequence from the data generated from a ChIP-sequencing or ChIP-chip experiment. When the protein is a transcription factor, the region is a transcription factor binding site (TFBS). Jie Zheng http://en.wikipedia.org/wiki/Peak_calling peak calling OBI:0000011 planned process Injecting mice with a vaccine in order to test its efficacy A processual entity that realizes a plan which is the concretization of a plan specification. 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.) We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some objectives is a planned process. Bjoern Peters branch derived 6/11/9: Edited at workshop. Used to include: is initiated by an agent This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call) planned process OBI:0000015 biological feature identification objective Biological_feature_identification_objective is an objective role carried out by the proposition defining the aim of a study designed to examine or characterize a particular biological feature. Jennifer Fostel biological feature identification objective OBI:0000018 material supplier role Jackson Labs is an organization which provide mice as experimental material a role realized through the process of supplying materials such as animal subjects, reagents or other materials used in an investigation. Supplier role is a special kind of service, e.g. biobank PERSON:Jennifer Fostel material provider role supplier material supplier role OBI:0000025 reference substance role Calibration standard, positive control substance, vehicle Good Laboratory Practices: Questions and Answers - Test Control and Reference Substance Characterization http://www.epa.gov/enforcement/monitoring/programs/fifra/glpqanda-character.html a role inhering in a material entity that is realized when characteristics or responses elicited by the substance are used for comparison or reference. Person:Jennifer Fostel reference substance OBI reference substance role OBI:0000045 waiting not actively doing anything to a material for a duration of time. PERSON:Alan Ruttenberg OBI branch derived BP: I have doubts about the utility of this. We need a better handling/modeling of time (January 2008) waiting OBI:0000047 processed material Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples Is a material entity that is created or changed during material processing. PERSON: Alan Ruttenberg processed material OBI:0000049 mass spectrometer LCQ Fleet Ion Trap MSn manufactured by thermo fisher scientific A mass spectrometer is an instrument which is used to measure the mass to charge ratio of ions. All mass spectrometers consist of three basic parts: an ion source, a mass analyzer, and a detector system. The stages within the mass spectrometer are: 1. Production of ions from the sample 2. Separation of ions with different masses 3. Detection of the number of ions of each mass produced 4.Collection of data to generate the mass spectrum Frank Gibson http://en.wikipedia.org/wiki/Mass_spectrometry mass spectrometer OBI:0000052 microarray platform A microarray platform is a platform that contains the instruments, software and reagents needed to perform a microarray protocol. definition_source: OBI. OBI Instrument branch OBI Instrument branch microarray platform OBI:0000055 software optimization objective Software_optimization is a software_testing_objective role describing a study designed to identify the best software or parameters of the software. Jennifer Fostel software optimization objective OBI:0000066 investigation Lung cancer investigation using expression profiling, a stem cell transplant investigation, biobanking is not an investigation, though it may be part of an investigation a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s). Bjoern Peters OBI branch derived Could add specific objective specification Following OBI call November 2012,26th: it was decided there was no need for adding "achieves objective of drawing conclusion" as existing relations were providing equivalent ability. this note closes the issue and validates the class definition to be part of the OBI core editor = PRS study investigation OBI:0000067 evaluant role When a specimen of blood is assayed for glucose concentration, the blood has the evaluant role. When measuring the mass of a mouse, the evaluant is the mouse. When measuring the time of DNA replication, the evaluant is the DNA. When measuring the intensity of light on a surface, the evaluant is the light source. a role that inheres in a material entity that is realized in an assay in which data is generated about the bearer of the evaluant role Role call - 17nov-08: JF and MC think an evaluant role is always specified input of a process. Even in the case where we have an assay taking blood as evaluant and outputting blood, the blood is not the specified output at the end of the assay (the concentration of glucose in the blood is) examples of features that could be described in an evaluant: quality.... e.g. "contains 10 pg/ml IL2", or "no glucose detected") GROUP: Role Branch OBI Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. evaluant role OBI:0000068 reporting party role Person who prepares microarray data in MAGE-TAB format and submits to a database, such as ArrayExpress. The first section has been pre-designated as the 'Reporting Party' section and should be filled with the Reporting Party's personal information. http://www.mercedsheriff.com/SelfReporting.htm a study personnel role played by a party who reports the outcome of a study component MO:submitter mapped to this term. So, alternative term 'submitter' was added. Jennifer Fostel reporting party submitter OBI reporting party role OBI:0000070 assay Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house. A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies. 12/3/12: BP: the reference to the 'physical examination' is included to point out that a prediction is not an assay, as that does not require physical examiniation. PlanAndPlannedProcess Branch measuring scientific observation OBI branch derived study assay any method assay OBI:0000075 diagnosis textual entity diagnosis is an assessment of a disease or injury, its likely prognosis and treatment. Jennifer Fostel diagnosis textual entity OBI:0000079 culture medium A growth medium or culture medium is a substance in which microorganisms or cells can grow. Wikipedia, growth medium, Feb 29, 2008 a processed material that provides the needed nourishment for microorganisms or cells grown in vitro. changed from a role to a processed material based on on Aug 22, 2011 dev call. Details see the tracker item: http://sourceforge.net/tracker/?func=detail&aid=3325270&group_id=177891&atid=886178 Modification made by JZ. Person: Jennifer Fostel, Jie Zheng OBI culture medium OBI:0000086 reagent role Buffer, dye, a catalyst, a solvating agent. A role inhering in a biological or chemical entity that is intended to be applied in a scientific technique to participate (or have molecular components that participate) in a chemical reaction that facilitates the generation of data about some entity distinct from the bearer, or the generation of some specified material output distinct from the bearer. PERSON:Matthew Brush reagent PERSON:Matthew Brush Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. May 28 2013. Updated definition taken from ReO based on discussions initiated in Philly 2011 workshop. Former defnition described a narrower view of reagents in chemistry that restricts bearers of the role to be chemical entities ("a role played by a molecular entity used to produce a chemical reaction to detect, measure, or produce other substances"). Updated definition allows for broader view of reagents in the domain of biomedical research to include larger materials that have parts that participate chemically in a molecular reaction or interaction. (copied from ReO) Reagents are distinguished from instruments or devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in or have parts that participate in some chemical interaction or reaction during their intended participation in some technique. By contrast, instruments do not participate in a chemical reaction/interaction during the technique. Reagents are distinguished from study subjects/evaluants in that study subjects and evaluants are that about which conclusions are drawn and knowledge is sought in an investigation - while reagents, by definition, are not. It should be noted, however, that reagent and study subject/evaluant roles can be borne by instances of the same type of material entity - but a given instance will realize only one of these roles in the execution of a given assay or technique. For example, taq polymerase can bear a reagent role or an evaluant role. In a DNA sequencing assay aimed at generating sequence data about some plasmid, the reagent role of the taq polymerase is realized. In an assay to evaluate the quality of the taq polymerase itself, the evaluant/study subject role of the taq is realized, but not the reagent role since the taq is the subject about which data is generated. In regard to the statement that reagents are 'distinct' from the specified outputs of a technique, note that a reagent may be incorporated into a material output of a technique, as long as the IDENTITY of this output is distinct from that of the bearer of the reagent role. For example, dNTPs input into a PCR are reagents that become part of the material output of this technique, but this output has a new identity (ie that of a 'nucleic acid molecule') that is distinct from the identity of the dNTPs that comprise it. Similarly, a biotin molecule input into a cell labeling technique are reagents that become part of the specified output, but the identity of the output is that of some modified cell specimen which shares identity with the input unmodified cell specimen, and not with the biotin label. Thus, we see that an important criteria of 'reagent-ness' is that it is a facilitator, and not the primary focus of an investigation or material processing technique (ie not the specified subject/evaluant about which knowledge is sought, or the specified output material of the technique). reagent role OBI:0000094 material processing A cell lysis, production of a cloning vector, creating a buffer. A planned process which results in physical changes in a specified input material PERSON: Bjoern Peters PERSON: Frank Gibson PERSON: Jennifer Fostel PERSON: Melanie Courtot PERSON: Philippe Rocca Serra material transformation OBI branch derived material processing OBI:0000096 protocol testing objective Protocol_testing_objective is a methodology_testing_objective role describing a study designed to examine the effects of using different protocols. Jennifer Fostel protocol testing objective OBI:0000097 participant under investigation role Human subjects in a clinical trial, rats in a toxicogenomics study, tissue cutlures subjected to drug tests, fish observed in an ecotoxicology study. Parasite example: people are infected with a parasite which is then extracted; the particpant under investigation could be the parasite, the people, or a population of which the people are members, depending on the nature of the study. Lake example: a lake could realize this role in an investigation that assays pollution levels in samples of water taken from the lake. A role that is realized through the execution of a study design in which the bearer of the role participates and in which data about that bearer is collected. A participant can realize both "specimen role" and "participant under investigation role" at the same time. However "participant under investigation role" is distinct from "specimen role", since a specimen could somehow be involved in an investigation without being the thing that is under investigation. GROUP: Role Branch OBI Following OBI call November 2012,26th: 1. it was decided there was no need for moving the children class and making them siblings of study subject role. 2. it also settles the disambiguation about 'study subject'. This is about the individual participating in the investigation/study, Not the 'topic' (as in 'toxicity study') of the investigation/study This note closes the issue and validates the class definition to be part of the OBI core editor = PRS participant under investigation role OBI:0000101 measured expression level Examples are quantified data from an expression microarray experiment, PCR measurements, etc. A measurement datum that is the outcome of the quantification of an assay for the activity of a gene, or the number of RNA transcripts. person:Chris Stoeckert OBI Data Transformation branch measured expression level OBI:0000109 biological vector role 1983 Sci. Amer. Jan. 58/2 Plasmids are routinely used as vectors for introducing foreign DNA into bacteria. Some epidemiological aspects and vector role of tick infestation on layers in the Faisalabad district (Pakistan). http://journals.cambridge.org/action/displayAbstract;jsessionid=0373164489D00868AEEF2C556EB4FD29.tomcat1?fromPage=online&aid=624280 a biological vector role is a material to be added role that is realized by the process of transmitting material to the organism that is the target of the transmission. Feb 20, 2009. The material transmitted can be genetic information (as in cloning vector) or a pathogen (as in a disease vector) GROUP: Role Branch OBI and Wikipedia 6/12/2009 Alan made this a material to be added role, because it was, and because this speeded up reasoning biological vector role OBI:0000112 specimen role liver section; a portion of a culture of cells; a nemotode or other animal once no longer a subject (generally killed); portion of blood from a patient. a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation 22Jun09. The definition includes whole organisms, and can include a human. The link between specimen role and study subject role has been removed. A specimen taken as part of a case study is not considered to be a population representative, while a specimen taken as representing a population, e.g. person taken from a cohort, blood specimen taken from an animal) would be considered a population representative and would also bear material sample role. Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. blood taken from animal: animal continues in study, whereas blood has role specimen. something taken from study subject, leaves the study and becomes the specimen. parasite example - when parasite in people we study people, people are subjects and parasites are specimen - when parasite extracted, they become subject in the following study specimen can later be subject. GROUP: Role Branch OBI specimen role OBI:0000113 sequence feature identification objective Sequence_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize molecular features exhibited at the level of a macromolecular sequence, e.g. nucleic acid, protein, polysaccharide. Jennifer Fostel sequence feature identification objective OBI:0000115 intervention design PMID: 18208636.Br J Nutr. 2008 Jan 22;:1-11.Effect of vitamin D supplementation on bone and vitamin D status among Pakistani immigrants in Denmark: a randomised double-blinded placebo-controlled intervention study. An intervention design is a study design in which a controlled process applied to the subjects (the intervention) serves as the independent variable manipulated by the experimentalist. The treatment (perturbation or intervention) defined can be defined as a combination of values taken by independent variable manipulated by the experimentalists are applied to the recruited subjects assigned (possibly by applying specific methods) to treatment groups. The specificity of intervention design is the fact that independent variables are being manipulated and a response of the biological system is evaluated via response variables as monitored by possibly a series of assays. Philppe Rocca-Serra OBI branch derived intervention design OBI:0000116 worker role Public sector workers in states that run their own OSHA programs are covered by those states. http://www.osha.gov/as/opa/worker/index.html a personnel role played by a party who executes a component of the study plan; this can occur before, during, after or outside the study timeline "executes the study plan" includes the suppliers and manufacturers of reagents and other materials used in the study Person:Jennifer Fostel worker OBI worker role OBI:0000118 gene list Gene lists may arise from analysis to determine differentially expressed genes, may be collected from the literature for involvement in a particular process or pathway (e.g., inflammation), or may be the input for gene set enrichment analysis. A data set of the names or identifiers of genes that are the outcome of an analysis or have been put together for the purpose of an analysis. person:Chris Stoeckert group:OBI kind of report. (alan) need to be careful to distinguish from output of a data transformation or calculation. A gene list is a report when it is published as such? Relates to question of whether report is a whole, or whether it can be a part of some other narrative object. gene list OBI:0000131 molecular feature identification objective Molecular_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize molecular features of a biological system, e.g. expression profiling, copy number of molecular components, epigenetic modifications. Jennifer Fostel molecular feature identification objective OBI:0000134 hardware testing objective Hardware_testing_objective is a methodology_testing_objective role describing a study designed to examine the effects of using different hardware, e.g. scanner. Jennifer Fostel hardware testing objective OBI:0000162 complete nutrient role Rat chow; RPMI medium + serum; use example: CNS17 (Complete Nutrient System) Grow 3-2-4, http://www.kalyx.com/store/proddetail.cfm/ItemID/552307/CategoryID/12000/SubCatID/2755/file.htm A nutrient role that inheres in a material entity and is realized in the use of that material entity by an organism to provide all needed nourishment. Person: Jennifer Fostel complete nutrient complete nutrient role OBI:0000164 cDNA library PMID:6110205. collection of cDNA derived from mouse splenocytes. Mixed population of cDNAs (complementaryDNA) made from mRNA from a defined source, usually a specific cell type. This term should be associated only to nucleic acid interactors not to their proteins product. For instance in 2h screening use living cells (MI:0349) as sample process. ALT DEF (PRS):: a cDNA library is a collection of host cells, typically E.Coli cells but not exclusively. modified by transfer of plasmid DNA molecule used as vector containing a fragment or totality of cDNA molecule (the insert) . cDNA library may have an array of role and applications. PERSON: Luisa Montecchi PERSON: Philippe Rocca-Serra GROUP: PSI PRS: 22022008. class moved under population, modification of definition and replacement of biomaterials in previous definition with 'material' addition of has_role restriction cDNA library OBI:0000181 population PMID12564891. Environ Sci Technol. 2003 Jan 15;37(2):223-8. Effects of historic PCB exposures on the reproductive success of the Hudson River striped bass population. a population is a collection of individuals from the same taxonomic class living, counted or sampled at a particular site or in a particular area 1/28/2013, BP, on the call it was raised that we may want to switch to an external ontology for all populatin terms: http://code.google.com/p/popcomm-ontology/ PERSON: Philippe Rocca-Serra adapted from Oxford English Dictionnary rem1: collection somehow always involve a selection process population OBI:0000185 imaging assay An imaging assay is an assay to produce a picture of an entity. definition_source: OBI. PlanAndPlannedProcess Branch OBI branch derived imaging assay OBI:0000186 protocol optimization objective Protocol_optimization is a protocol_testing_objective role describing a study designed to identify the best protocol. This may be carried out by comparing different protocols or by modifying the parameters used within a single protocol. Jennifer Fostel protocol optimization objective OBI:0000198 biological replicate role A member of a dose-time group; a patient in a given arm of a trial a reference participant role realized by equivalent treatment of participants Person:Jennifer Fostel biological replicate OBI biological replicate role OBI:0000202 investigation agent role The person perform microarray experiments and submit microarray results (including raw data, processed data) with experiment description to ArrayExpress. A role borne by an entity and that is realized in a process that is part of an investigation in which an objective is achieved. These processes include, among others: planning, overseeing, funding, reviewing. Implementing a study means carrying out or performing the study and providing reagents or other materials used in the study and other tasks without which the study would not happen. Philly2013: Historically, this role would have been borne only by humans or organizations. However, we now also want to enable representing investigations run by robot scientists such as ADAM (King et al, Science, 2009) GROUP: Role Branch investigator OBI Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. study person role Philly2013: Historically, this role would have been borne only by humans or organizations. However, we now also want to enable investigations run by robot scientists such as ADAM (King et al, Science, 2009) investigation agent role OBI:0000204 nutrient role Luria broth; vitamin A; A nutrient is a substance used in an organism's metabolism which must be taken in from the environment. Wikipedia. a role that inheres in a material entity and is realized in the use of that material entity by an organism when it is used in that organism's metabolism and provides nourishment. GROUP: Role branch nutrient Wikipedia, feb 29, 2008 19 Feb 2009; old def: A nutrient role is a role played by a substance used in an organism's metabolism which is taken in from the environment and provides nourishment. nutrient role OBI:0000208 methodology testing objective Methodology_testing_objective is an objective role carried out by a proposition defining the aim of the study is to examine the effect of using different methodologies. Jennifer Fostel methodology testing objective OBI:0000219 cellular feature identification objective Cellular_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize a biological feature monitored at the cellular level, e.g. stage of cell cycle, stage of differentiation. Jennifer Fostel cellular feature identification objective OBI:0000220 reference subject role Saline treated rat; one of three identically-treated subjects a reference subject role which inheres in an organism or entity of organismal origin so that the characteristics or responses of the participant playing the reference participant role are used for comparison or reference Jennifer Fostel reference participant OBI reference subject role OBI:0000231 enzymatic cleavage Polymorphism R62W results in resistance of CD23 to enzymatic cleavage in cultured cells. Genes Immun. 2007 Apr;8(3):215-23. Epub 2007 Feb 15. PMID: 17301828 enzymatic cleavage is a protocol application to digest the fraction of input material that is susceptible to that enzyme PlanAndPlannedProcess Branch OBI branch derived enzymatic cleavage OBI:0000232 hardware optimization objective Hardware_optimization is a hardware_testing_objective describing a study designed to identify the best hardware. Jennifer Fostel hardware optimization objective OBI:0000242 software testing objective Software_testing_objective is a hardware_optimization role describing a study designed to examine the effects of using different software or software parameters, e.g. data processing software. Jennifer Fostel software testing objective OBI:0000245 organization PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods. An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members. BP: The definition summarizes long email discussions on the OBI developer, roles, biomaterial and denrie branches. It leaves open if an organization is a material entity or a dependent continuant, as no consensus was reached on that. The current placement as material is therefore temporary, in order to move forward with development. Here is the entire email summary, on which the definition is based: 1) there are organization_member_roles (president, treasurer, branch editor), with individual persons as bearers 2) there are organization_roles (employer, owner, vendor, patent holder) 3) an organization has a charter / rules / bylaws, which specify what roles there are, how they should be realized, and how to modify the charter/rules/bylaws themselves. It is debatable what the organization itself is (some kind of dependent continuant or an aggregate of people). This also determines who/what the bearer of organization_roles' are. My personal favorite is still to define organization as a kind of 'legal entity', but thinking it through leads to all kinds of questions that are clearly outside the scope of OBI. Interestingly enough, it does not seem to matter much where we place organization itself, as long as we can subclass it (University, Corporation, Government Agency, Hospital), instantiate it (Affymetrix, NCBI, NIH, ISO, W3C, University of Oklahoma), and have it play roles. This leads to my proposal: We define organization through the statements 1 - 3 above, but without an 'is a' statement for now. We can leave it in its current place in the is_a hierarchy (material entity) or move it up to 'continuant'. We leave further clarifications to BFO, and close this issue for now. PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Philippe Rocca-Serra PERSON: Susanna Sansone GROUP: OBI organization OBI:0000248 feed role Purina rat chow; cited use: Control; F = feed (rat chow); W = water; F. g. = feed-ginger concentrate. www.academicjournals.org/AJB/PDF/pdf2007/19Sep/Egwurugwu%20et%20al.pdf - Feb 29, 2008 a role that inheres in a material entity and is realized in the use of that material entity by lab animal to provide all needed nourishment. Person: Jennifer Fostel feed OBI feed role OBI:0000249 technical replicate role Aliquots of a tissue subjected to parallel assays technical replicate role is realized when two portions from one evaluant are used in replicate runs of an assay Person: Jennifer Fostel technical replicate technical replicate role OBI:0000257 DNA extraction A DNA extraction is a nucleic acid extraction where the desired output material is DNA. PlanAndPlannedProcess Branch OBI branch derived DNA extraction OBI:0000268 organism feature identification objective Organism_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize a biological feature monitored at the level of the organism, e.g. height, weight, stage of development, stage of life cycle. Jennifer Fostel organism feature identification objective OBI:0000272 protocol PCR protocol, has objective specification, amplify DNA fragment of interest, and has action specification describes the amounts of experimental reagents used (e..g. buffers, dNTPS, enzyme), and the temperature and cycle time settings for running the PCR. A plan specification which has sufficient level of detail and quantitative information to communicate it between investigation agents, so that different investigation agents will reliably be able to independently reproduce the process. PlanAndPlannedProcess Branch OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29) study protocol protocol OBI:0000274 adding a material entity into a target Injecting a drug into a mouse. Adding IL-2 to a cell culture. Adding NaCl into water. is a process with the objective to place a material entity bearing the 'material to be added role' into a material bearing the 'target of material addition role'. Class was renamed from 'administering substance', as this is commonly used only for additions into organisms. BP branch derived adding a material entity into a target OBI:0000275 analyte role Glucose in blood (measured in an assay to determine the concentration of glucose). A role borne by a molecular entity or an atom and realized in an analyte assay which achieves the objective to measure the magnitude/concentration/amount of the analyte in the entity bearing evaluant role interestingly, an analyte is still an analyte even if it is not detected. for this reason it does not bear a specified input role pH (technically the inverse log of [H+]) may be considered a quality; this remains to be tested. qualities such as weight, color are not assayed but measured, so they do not fall into this category. GROUP: Role Branch OBI Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. analyte role OBI:0000278 disease stage Stage II breast cancer, The timepoint of recovery from a disease a part of an occurrence of a disease process which is associated with position in the normal progression of the disease PERSON: Bjoern peters disease stage OBI:0000281 intraperitoneal injection is the injection of a material entity (bearing the administered substance role) into the peritoneum (bearing the target role) of an organism using a syringe BP intraperitoneal injection OBI:0000291 transcription factor binding site identification Transcription factor binding site identification in yeast: a comparison of high-density oligonucleotide and PCR-based microarray platforms. Funct Integr Genomics. 2007 Oct;7(4):335-45. Epub 2007 Jul 19. PMID: 17638031 a planned process with objective to find DNA region specifically recognized by proteins that function as transcription factors JZ: add equivalent axiom for classification add alternative term 'TF binding' which was used in BCBC database Philippe Rocca-Serra TF binding OBI transcription factor binding site identification OBI:0000319 material to be added role drug added to a buffer contained in a tube; substance injected into an animal; material to be added role is a protocol participant role realized by a material which is added into a material bearing the target of material addition role in a material addition process Role Branch OBI 9 March 09 from discussion with PA branch material to be added role OBI:0000338 drawing a conclusion based on data Concluding that a gene is upregulated in a tissue sample based on the band intensity in a western blot. Concluding that a patient has a infection based on measurement of an elevated body temperature and reported headache. Concluding that there were problems in an investigation because data from PCR and microarray are conflicting. Concluding that 'defects in gene XYZ cause cancer due to improper DNA repair' based on data from experiments in that study that gene XYZ is involved in DNA repair, and the conclusion of a previous study that cancer patients have an increased number of mutations in this gene. A planned process in which data gathered in an investigation is evaluated in the context of existing knowledge with the objective to generate more general conclusions or to conclude that the data does not allow one to draw general conclusion PERSON: Bjoern Peters PERSON: Jennifer Fostel Bjoern Peters drawing a conclusion based on data OBI:0000339 planning The process of a scientist thinking about and deciding what reagents to use as part of a protocol for an experiment. Note that the scientist could be human or a "robot scientist" executing software. a process of creating or modifying a plan specification 7/18/2011 BP: planning used to itself be a planned process. Barry Smith pointed out that this would lead to an infinite regression, as there would have to be a plan to conduct a planning process, which in itself would be the result of planning etc. Therefore, the restrictions on 'planning' were loosened to allow for informal processes that result in an 'ad hoc plan '. This required changing from 'has_specified_output some plan specifiction' to 'has_participant some plan specification'. Bjoern Peters Bjoern Peters Plans and Planned Processes Branch planning OBI:0000341 histological sample preparation histological sample preparation is the preparation of an input tissue via slicing and labeling to make tissue microstructure of interest visible in a future histology assay PERSON:Bjoern Peters OBI branch derived histological sample preparation OBI:0000345 mass analyzer The mass analyzer of the Voyager-DE(tm) STR Biospectrometry Workstation A Mass analyzer is a device that separates ions according to their mass-to-charge ratio. All mass spectrometers are based on dynamics of charged particles in electric and magnetic fields in vacuum where the two laws of Lorentz force law and Newton's second law of motion apply. Frank Gibson PERSON: Daniel Schober http://en.wikipedia.org/wiki/Mass_spectrometry#Mass_analyzer mass analyzer OBI:0000361 ion source The ion source of a Voyager-DE??? STR Biospectrometry Workstation An ion source is a device that is part of a mass spectrometer that ionizes the material under analysis. The ions are then transported by magnetic or electric fields to the mass analyzer. Techniques for ionization have been key to determining what types of samples can be analyzed by mass spectrometry. Electron ionization and chemical ionization are used for gases and vapors. In chemical ionization sources, the material is ionized by chemical ion-molecule reactions during collisions in the source. Two techniques often used with liquid and solid biological samples include electrospray ionization (due to John Fenn PMID 2675315.) and matrix-assisted laser desorption/ionization (MALDI, due to M. Karas and F. Hillenkamp (Measuring Mass: From Positive Rays to Proteins by Michael A. Grayson (Editor) (ISBN 0-941901-31-9))). Frank Gibson http://en.wikipedia.org/wiki/Mass_spectrometry#Ion_source ion source OBI:0000364 ion detector The ion detector of the Voyager-DE(tm) STR Biospectrometry Workstation An ion detector is a device that measures and records the charge induced or current produced when an ion passes by or hits a surface. In a scanning instrument the signal produced in the detector during the course of the scan versus where the instrument is in the scan (at what m/Q) will produce a mass spectrum, a record of ions as a function of m/Q. Frank Gibson http://en.wikipedia.org/wiki/Mass_spectrometry#Detector ion detector OBI:0000367 light emission function A light emission function is an excitation function to excite a material to a specific excitation state that it emits light. Bill Bug Daniel Schober Frank Gibson Melanie Courtot light emission function OBI:0000370 contain function A syringe, a beaker A contain function is a function to constrain a material entities location in space Bill Bug Daniel Schober Frank Gibson Melanie Courtot contain function OBI:0000371 heat function A heat function is a function that increases the internal kinetic energy of a material Bill Bug Daniel Schober Frank Gibson Melanie Courtot heat function OBI:0000372 material separation function A material separation function is a function that increases the resolution between two or more material entities. The to distinction between the entities is usually based on some associated physical quality. Bill Bug Daniel Schober Frank Gibson Melanie Courtot material separation function OBI:0000374 excitation function A excitation function is a function to inject energy by bombarding a material with energetic particles (e.g., photons) thereby imbuing internal material components such as electrons with additional energy. These internal, 'excited' particles may lead to the rupturing of covalent chemical bonds or may quickly relax back to there unexcited state with an exponential time course thereby locally emitting energy in the form of photons. Bill Bug Daniel Schober Frank Gibson Melanie Courtot excitation function OBI:0000376 synthesizing function A synthesizing function is a function to assemble new output materials from distinct input materials. The output materials typically consist of chemically distinct monomeric objects or object aggregate polymers. Bill Bug Daniel Schober Frank Gibson Melanie Courtot synthesizing function OBI:0000377 perturb function A perturb function is a function that disrupts the normal function of a system induced through either internal or external means. External means of perturbation include: (1) displacement fields in the physical sense - e.g., temperature change, osmotic shock, pressure change; (2) application of small molecules such as drugs or toxins to perturb the function of specific pathways or application of surfactants to perturb the normal function of plasma membrane. Internal means of perturbation include: (1) manipulation of gene function via gene knockout or transcript knockdown via RNAi; (2) directed genetic mutation leading to minimal aa alterations that interfere with peptide function. Bill Bug Daniel Schober Frank Gibson Melanie Courtot http://en.wikipedia.org/wiki/Perturbation_biology perturb function OBI:0000378 filter function A filter function is a function to prevent the flow of certain entities based on a quality or qualities of the entity while allowing entities which have different qualities to pass through Frank Gibson filter function OBI:0000379 mechanical function A mechanical function is a function that is realised via mechanical work (through an certain amount of energy transferred by some force). Bill Bug Daniel Schober Frank Gibson Melanie Courtot http://en.wikipedia.org/wiki/Mechanical_work mechanical function OBI:0000383 transfer function A transfer function is a function to displace a material from one location to another. Bill Bug Daniel Schober Frank Gibson Melanie Courtot transfer function OBI:0000385 ionization function The ion source in amass spectrometer An ionization function is a function to physically convert an atom or molecule into an ion by adding or removing charged particles such as electrons or other ions. Bill Bug Daniel Schober Frank Gibson Melanie Courtot http://en.wikipedia.org/wiki/Ionization ionization function OBI:0000387 cool function A cool function is a function to decrease the internal kinetic energy of a material below the initial kinetic energy of that type of material. Daniel Schober Frank Gibson Melanie Courtot cool function OBI:0000392 information processor function An information processor function is a function that converts information from one form to another, by a lossless process or an extraction process. Frank Gibson data processor function information processor function OBI:0000397 image acquisition function An image acquisition function is a function to acquire an image of a material Frank Gibson image acquisition function OBI:0000398 image creation device An image creation device is a device which captures a digitized image of an object Frank Gibson image acquisition device sep:00096 image creation device OBI:0000399 solid support function Taped, glued, pinned, dried or molecularly bonded to a solid support A solid support function is a function of a device on which an entity is kept in a defined position and prevented in its movement Daniel Schober Frank Gibson Melanie Courtot solid support function OBI:0000401 environment control function An environmental control function is a function that regulates a contained environment within specified parameter ranges. For example the control of light exposure, humidity and temperature. Bill Bug Daniel Schober Frank Gibson Melanie Courtot environment control function OBI:0000403 sort function A sort function is a function to distinguish material components based on some associated physical quality or entity and to partition the separate components into distinct fractions according to a defined order. Daniel Schober Frank Gibson Melanie Courtot sort function OBI:0000406 PCR product PCR products are the results of amplifcation process. Detection of a PCR products is used to detect DNA and RNA. is double stranded DNA that is the specified output of a polymerase chain reaction We are using PCR and not the written out words, as this is the most common used. GROUP: OBI BIomaterial Branch GROUP: OBI BIomaterial Branch PCR product OBI:0000409 nucleic acid template role a model or standard for making comparisons; wordnet.princeton.edu/perl/webwn 19 feb 2009 a reference substance role which inheres in nucleic acid material entity and is realized in the process of using the nucleic acid bearing the template role as a reference during synthesis of a reverse copy. nucleic acid template role OBI:0000411 cloning vector role pBluescript plays the role of a cloning vector a vector role played by a small, self-replicating DNA or RNA molecule - usually a plasmid or chromosome - and realized in a process whereby foreign DNA or RNA is inserted into the vector during the process of cloning. PERSON: Helen Parkinson cloning vector role OBI:0000415 polymerase chain reaction Opisthorchis viverrini: Detection by polymerase chain reaction (PCR) in human stool samples. Exp Parasitol. 2008 Sep 9. PMID: 18805413 PCR is the process in which a DNA polymerase is used to amplify a piece of DNA by in vitro enzymatic replication. As PCR progresses, the DNA thus generated is itself used as a template for replication. This sets in motion a chain reaction in which the DNA template is exponentially amplified. OBI Plan PCR adapted from wikipedai polymerase chain reaction OBI:0000416 cloning insert role cloning insert role is a role which inheres in DNA or RNA and is realized by the process of being inserted into a cloning vector in a cloning process. Feb 20, 2009. from Wikipedia: cloning of any DNA fragment essentially involves four steps: DNA fragmentation with restriction endonucleases, ligation of DNA fragments to a vector, transfection, and screening/selection. There are multiple processes involved, it is not just "cloning process" GROUP: Role branch OBII and Wikipedia cloning insert role OBI:0000419 reverse transcriptase enzyme and has_function some GO:0003964 (RNA-directed DNA polymerase activity) person:Melanie Courtot group:OBI reverse transcriptase OBI:0000422 syringe Accuracy of oral liquid measuring devices: comparison of dosing cup and oral dosing syringe.Ann Pharmacother. 2008 Jan;42(1):46-52. Epub 2007 Dec 4. PMID: 18056832 a processed material which is used to introduce or draw fluids from a material entity. A syringe is made of a piston and body. the movement of the piston in the body determines the amount/volume of fluid to inject or draw Philippe Rocca-Serra OBI Instrument adapted from Wikipedia syringe OBI:0000423 extract Up-regulation of inflammatory signalings by areca nut extract and role of cyclooxygenase-2 -1195G>a polymorphism reveal risk of oral cancer. Cancer Res. 2008 Oct 15;68(20):8489-98. PMID: 18922923 an extract is a material entity which results from an extraction process PERSON: Philippe Rocca-Serra extracted material GROUP: OBI Biomatrial Branch extract OBI:0000424 transcription profiling assay Whole genome transcription profiling of Anaplasma phagocytophilum in human and tick host cells by tiling array analysis. BMC Genomics. 2008 Jul 31;9:364. PMID: 18671858 An assay which aims to provide information about gene expression and transcription activity using ribonucleic acids collected from a material entity using a range of techniques and instrument such as DNA sequencers, DNA microarrays, Northern Blot Philippe Rocca-Serra gene expression profiling OBI transcription profiling transcription profiling assay OBI:0000425 averaging objective A mean calculation which has averaging objective is a descriptive statistics calculation in which the mean is calculated by taking the sum of all of the observations in a data set divided by the total number of observations. It gives a measure of the 'center of gravity' for the data set. It is also known as the first moment. An averaging objective is a data transformation objective where the aim is to perform mean calculations on the input of the data transformation. Elisabetta Manduchi James Malone PERSON: Elisabetta Manduchi averaging objective OBI:0000426 injection Multiple Small-Dose Injections Can Reduce the Passage of Sclerosant Foam into Deep Veins During Foam Sclerotherapy for Varicose Veins. Eur J Vasc Endovasc Surg. 2008 Oct 13. PMID: 18922712 injection is process which aims at introducing a compound or a mixture into a material entity (either biological entity or instrument) by relying on devices such as syringe or injector connection, attached or forced into a vascular system (veins of an organism or tubes of a machine) or in a tissue. Philippe Rocca-Serra OBI Biomaterial injection OBI:0000427 enzyme (protein or rna) or has_part (protein or rna) and has_function some GO:0003824 (catalytic activity) MC: known issue: enzyme doesn't classify under material entity for now as it isn't stated that anything that has_part some material entity is a material entity. If we add as equivalent classes to material entity has_part some material entity and part_of some material entity (each one in his own necessary and sufficient block) Pellet in P3 doesn't classify any more. person: Melanie Courtot GROUP:OBI enzyme OBI:0000429 intraperitoneal administration Rats were injected intraperitoneally with either rrIL-6 (250 ng/0.5 ml) or equal-volume sterile saline twice within an interval of 24 h The administration of a substance into the peritoneum of an organism Person:Bjoern Peters intraperitoneal administration OBI:0000430 plasmid plasmid = DNA and has_quality circular and has_function (is_realized_as some gene expression) GO:0010467 person:Melanie Courtot group:OBI plasmid OBI:0000434 adding material objective creating a mouse infected with LCM virus is the specification of an objective to add a material into a target material. The adding is asymmetric in the sense that the target material largely retains its identity BP adding material objective OBI:0000435 genotyping assay High-throughput genotyping of oncogenic human papilloma viruses with MALDI-TOF mass spectrometry. Clin Chem. 2008 Jan;54(1):86-92. Epub 2007 Nov 2.PMID: 17981923 an assay which generates data about a genotype from a specimen of genomic DNA. A variety of techniques and instruments can be used to produce information about sequence variation at particular genomic positions. Philippe Rocca-Serra genotype profiling, SNP genotyping OBI Biomaterial SNP analysis genotyping assay OBI:0000437 analyte measurement objective The objective to measure the concentration of glucose in a blood sample an assay objective to determine the presence or concentration of an analyte in the evaluant PERSON: Bjoern Peters PPPB branch analyte measurement objective OBI:0000441 assay objective the objective to determine the weight of a mouse. an objective specification to determine a specified type of information about an evaluated entity (the material entity bearing evaluant role) PPPB branch PPPB branch assay objective OBI:0000443 analyte assay example of usage: In lab test for blood glucose, the test is the assay, the blood bears evaluant_role and glucose bears the analyte role. The evaluant is considered an input to the assay and the information entity that records the measurement of glucose concentration the output An assay with the objective to capture information about the presence, concentration, or amount of an analyte in an evaluant. 2013-09-23: simplify equivalent axiom Note: is_realization of some analyte role isn't always true, for example when there is none of the analyte in the evaluant. For the moment we are writing it this way, but when the information ontology is further worked out this will be replaced with a condition discussing the measurement. logical def modified to remove expression below, as some analyte assays report below the level of detection, and therefore not a scalar measurement datum, replaced by measurement datum and ('has measurement unit label' some 'measurement unit label') and ('is quality measurement of' some 'molecular concentration')) PERSON:Bjoern Peters, Helen Parkinson, Philippe Rocca-Serra, Alan Ruttenberg PERSON:Bjoern Peters PERSON:Helen Parkinson PERSON:Philippe Rocca-Serra PERSON:Alan Ruttenberg GROUP:OBI Planned process branch analyte assay OBI:0000444 target of material addition role peritoneum of an animal receiving an interperitoneal injection; solution in a tube receiving additional material; location of absorbed material following a dermal application. target of material addition role is a role realized by an entity into which a material is added in a material addition process From Branch discussion with BP, AR, MC -- there is a need for the recipient to interact with the administered material. for example, a tooth receiving a filling was not considered to be a target role. GROUP: Role Branch OBI target of material addition role OBI:0000451 normalized data set A data set that is produced as the output of a normalization data transformation. PERSON: James Malone PERSON: Melanie Courtot normalized data set OBI:0000453 measure function A glucometer measures blood glucose concentration, the glucometer has a measure function. Measure function is a function that is borne by a processed material and realized in a process in which information about some entity is expressed relative to some reference. PERSON: Daniel Schober PERSON: Helen Parkinson PERSON: Melanie Courtot PERSON:Frank Gibson measure function OBI:0000455 consume data function Process data function is a function that is borne by in a material entity by virtue of its structure. When realized the material entity consumes data. PERSON: Daniel Schober PERSON: Frank Gibson PERSON: Melanie Courtot consume data function OBI:0000456 material transformation objective The objective to create a mouse infected with LCM virus. The objective to create a defined solution of PBS. an objective specifiction that creates an specific output object from input materials. PERSON: Bjoern Peters PERSON: Frank Gibson PERSON: Jennifer Fostel PERSON: Melanie Courtot PERSON: Philippe Rocca-Serra artifact creation objective GROUP: OBI PlanAndPlannedProcess Branch material transformation objective OBI:0000457 manufacturing Manufacturing is a process with the intent to produce a processed material which will have a function for future use. A person or organization (having manufacturer role) is a participant in this process Manufacturing implies reproducibility and responsibility AR This includes a single scientist making a processed material for personal use. PERSON: Bjoern Peters PERSON: Frank Gibson PERSON: Jennifer Fostel PERSON: Melanie Courtot PERSON: Philippe Rocca-Serra GROUP: OBI PlanAndPlannedProcess Branch manufacturing OBI:0000458 manufacturing objective is the objective to manufacture a material of a certain function (device) PERSON: Bjoern Peters PERSON: Frank Gibson PERSON: Jennifer Fostel PERSON: Melanie Courtot PERSON: Philippe Rocca-Serra GROUP: OBI PlanAndPlannedProcess Branch manufacturing objective OBI:0000471 study design execution injecting a mouse with PBS solution, weighing it, and recording the weight according to a study design. a planned process that realizes the concretization of a study design removed axiom has_part some (assay or 'data transformation') per discussion on protocol application mailing list to improve reasoner performance. The axiom is still desired. branch derived 6/11/9: edited at workshop. Used to be: study design execution is a process with the objective to generate data according to a concretized study design. The execution of a study design is part of an investigation, and minimally consists of an assay or data transformation. study design execution OBI:0000552 reverse transcribed polymerase chain reaction Harmonisation of multi-centre real-time reverse-transcribed PCR results of a candidate prognostic marker in breast cancer: an EU-FP6 supported study of members of the EORTC - PathoBiology Group. Span PN, Sieuwerts AM, Heuvel JJ, Spyratos F, Duffy MJ, Eppenberger-Castori S, Vacher S, O'Brien K, McKiernan E, Pierce A, Vuaroqueaux V, Foekens JA, Sweep FC, Martens JW. Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 reverse transcribe pcr is a process which allow amplification of cDNA during a pcr reaction while the cDNA results from a retrotranscription of messenger RNA isolated from a material entity. 3/21/10, BP:Modified definition to clarify that this is not the assay, but the material transformation Philippe Rocca-Serra RT-PCR reverse transcription polymerase chain reaction reverse transcribed polymerase chain reaction OBI:0000571 manufacturer role With respect to The Accuri C6 Flow Cytometer System, the organization Accuri bears the role manufacturer role. With respect to a transformed line of tissue culture cells derived by a specific lab, the lab whose personnel isolated the cll line bears the role manufacturer role. With respect to a specific antibody produced by an individual scientist, the scientist who purifies, characterizes and distributes the anitbody bears the role manufacturer role. Manufacturer role is a role which inheres in a person or organization and which is realized by a manufacturing process. GROUP: Role Branch OBI manufacturer role OBI:0000626 DNA sequencing Genomic deletions of OFD1 account for 23% of oral-facial-digital type 1 syndrome after negative DNA sequencing. Thauvin-Robinet C, Franco B, Saugier-Veber P, Aral B, Gigot N, Donzel A, Van Maldergem L, Bieth E, Layet V, Mathieu M, Teebi A, Lespinasse J, Callier P, Mugneret F, Masurel-Paulet A, Gautier E, Huet F, Teyssier JR, Tosi M, Frébourg T, Faivre L. Hum Mutat. 2008 Nov 19. PMID: 19023858 DNA sequencing is a sequencing process which uses deoxyribonucleic acid as input and results in a the creation of DNA sequence information artifact using a DNA sequencer instrument. Philippe Rocca-Serra OBI Branch derived nucleotide sequencing DNA sequencing OBI:0000634 DNA methylation profiling assay Genome-wide, high-resolution DNA methylation profiling using bisulfite-mediated cytosine conversion. Reinders J, Delucinge Vivier C, Theiler G, Chollet D, Descombes P, Paszkowski J. Genome Res. 2008 Mar;18(3):469-76. Epub 2008 Jan 24. PMID: 18218979 an assay which aims to provide information about state of methylation of DNA molecules using genomic DNA collected from a material entity using a range of techniques and instrument such as DNA sequencers and often relying on treatment with bisulfites to ensure cytosine conversion. Philippe Rocca-Serra OBI branch derived DNA methylation profiling DNA methylation profiling assay OBI:0000639 material separation objective The objective to obtain multiple aliquots of an enzyme preparation. The objective to obtain cells contained in a sample of blood. is an objective to transform a material entity into spatially separated components. PPPB branch PPPB branch material separation objective OBI:0000648 clustered data set A clustered data set is the output of a K means clustering data transformation A data set that is produced as the output of a class discovery data transformation and consists of a data set with assigned discovered class labels. PERSON: James Malone PERSON: Monnie McGee data set with assigned discovered class labels AR thinks could be a data item instead clustered data set OBI:0000650 differential expression analysis data transformation A differential expression analysis data transformation is a data transformation that has objective differential expression analysis and that consists of James Malone Melanie Courtot Monnie McGee WEB: differential expression analysis data transformation OBI:0000651 urine specimen a portion of urine collected from an organism 4/10/2011BP: It seems to me that the editor notes refer to a previous version, and are no longer relevant. This could be instead a kind of collection of secreted stuff. Among secreted stuff there is passive, and active. urine is secreted, passiv. lavage is secreted, active are we happy calling collection of urine a material separation? urine specimen OBI:0000652 material combination Mixing two fluids. Adding salt into water. Injecting a mouse with PBS. is a material processing with the objective to combine two or more material entities as input into a single material entity as output. created at workshop as parent class for 'adding material into target', which is asymmetric, while combination encompasses all addition processes. bp bp material combination OBI:0000654 device setting Examples, 300V for 4 hours, 200mvolts, 37degrees.A knob set a 300 V is the device setting, the protocol stating to set the instrument to 300V is a device setting specification a quality inheres_in some device and is concretization of some (device_setting_specification and is_about a quality of the device PERSON: Frank Gibson device setting OBI:0000659 specimen collection process drawing blood from a patient for analysis, collecting a piece of a plant for depositing in a herbarium, buying meat from a butcher in order to measure its protein content in an investigation A planned process with the objective of collecting a specimen. Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. Philly2013: A specimen collection can have as part a material entity acquisition, such as ordering from a bank. The distinction is that specimen collection necessarily involves the creation of a specimen role. However ordering cell lines cells from ATCC for use in an investigation is NOT a specimen collection, because the cell lines already have a specimen role. Philly2013: The specimen_role for the specimen is created during the specimen collection process. label changed to 'specimen collection process' on 10/27/2014, details see tracker: http://sourceforge.net/p/obi/obi-terms/716/ Bjoern Peters specimen collection 5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession 6/9/09: used at workshop specimen collection process OBI:0000668 error correction data transformation An error correction data transformation is a data transformation that has the objective of error correction, where the aim is to remove (correct for) erroneous contributions from the input to the data transformation. James Malone Monnie McGee EDITORS error correction data transformation OBI:0000671 sample from organism a material obtained from an organism in order to be a representative of the whole 5/29: This is a helper class for now we need to work on this: Is taking a urine sample a material separation process? If not, we will need to specify what 'taking a sample from organism' entails. We can argue that the objective to obtain a urine sample from a patient is enough to call it a material separation process, but it could dilute what material separation was supposed to be about. sample from organism OBI:0000674 center value A data item that is produced as the output of a center calculation data transformation and represents the center value of the input data. PERSON: James Malone PERSON: Monnie McGee median center value OBI:0000678 portioning objective The objective to obtain multiple aliquots of an enzyme preparation. A material separation objective aiming to separate material into multiple portions, each of which contains a similar composition of the input material. portioning objective OBI:0000679 average value A data item that is produced as the output of an averaging data transformation and represents the average value of the input data. PERSON: James Malone PERSON: Monnie McGee arithmetic mean average value OBI:0000680 whole organism preparation putting a mouse in the blender. Not: putting a mouse on a scale A material entity which is the output of a process in which one or more whole organisms are prepared in a way to make it easier to study them, and in which the great majority of organismal parts are maintained does this include injecting a dye to a patient to be able to visualize parts of his brain? If not, we should state that the components of the organism are substantially re-arranged. whole organism preparation OBI:0000681 separation into different composition objective The objective to obtain cells contained in a sample of blood. A material separation objective aiming to separate a material entity that has parts of different types, and end with at least one output that is a material with parts of fewer types (modulo impurities). We should be using has the grain relations or concentrations to distinguish the portioning and other sub-objectives separation into different composition objective OBI:0000684 specimen collection objective The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient. A objective specification to obtain a material entity for potential use as an input during an investigation. Bjoern Peters Bjoern Peters specimen collection objective OBI:0000686 material combination objective is an objective to obtain an output material that contains several input materials. PPPB branch bp material combination objective OBI:0000689 454 Genome Sequence 20 PMID: 18946007.Pyrosequencing analysis of the oral microflora of healthy adults. Keijser BJ, Zaura E, Huse SM, van der Vossen JM, Schuren FH, Montijn RC, ten Cate JM, Crielaard W. J Dent Res. 2008 Nov;87(11):1016-20. is a DNA sequencer which is manufactured by 454 Life Science Corporation and enables pyrosequencing to be performed. It comprises both optics and fluidics subsystems, which are controlled by a computer subsystem. The fluidics subsystem ensures accurate reagent dispensing. It consists of a reagents cassette (which holds the reagent containers), a sipper manifold, pumps, valves, and debubblers. The fluidics subsystem flows the sequencing reagents across the wells of the PicoTiterPlate device, and moves the spent reagents from the PicoTiterPlate device to the waste receptacle. The optics subsystem consists of a CCD camera and a camera controller. The camera captures the light emitted in the wells of the PicoTiterPlate device during each step of the sequencing cycle, and sends the digital images to the computer subsystem for processing. The computer controls the other Sequencer subsystems, and processes the digital images sent by the camera to extract the DNA sequence information. Philippe Rocca-Serra GS 20 454 Genome Sequence 20 OBI:0000690 immunoprecipitation PMID: 19419533. Arabidopsis RNA immunoprecipitation. Terzi LC, Simpson GG. Plant J. 2009 Jul;59(1):163-8. is a process which realizes a material separation objective by relying on antibodies to specifically binding to material entity Philippe Rocca-Serra OBI plan and planned process branch immunoprecipitation OBI:0000691 ABI 377 automated sequencer is a DNA sequencer which is manufactured by Applied Biosystems corporation (formerly Perkin-Elmer). It allows automated chain termination DNA sequencing. It has part polyacrylamide gel electrophoresis system and a laser -based detection system to detect fluorescence intensity emitted by the dyes attached to the dideoxyterminator nucleotides or to the primers. Philippe Rocca-Serra Applied Biosystems ABI 377 automated sequencer OBI:0000693 MeDIP-seq assay PMID: 18612301. A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Down TA, Rakyan VK, Turner DJ, Flicek P, Li H, Kulesha E, Gräf S, Johnson N, Herrero J, Tomazou EM, Thorne NP, Bäckdahl L, Herberth M, Howe KL, Jackson DK, Miretti MM, Marioni JC, Birney E, Hubbard TJ, Durbin R, Tavaré S, Beck S. Nat Biotechnol. 2008 Jul;26(7):779-85. is an assay which aims at identifying methylated sites in genomic DNA and determining methylation pattern that affect gene transcription by relying on immunoprecipitation of methylated genomic DNA, creation of a library of corresponding DNA fragments (either single or paired-end fragments) and subsequent sequencing using parallelized sequencing methods. Philippe Rocca-Serra Methylated DNA immunoprecipitation sequencing assay adapted from wikipedia MeDIP-seq assay OBI:0000694 animal feeding giving crickets to a snake. animal feeding is a process in which animals are provided with food In an investigation, this will typically be part of an animal care process Bjoern Peters branch derived animal feeding OBI:0000695 chain termination sequencing PMID: 271968. DNA sequencing with chain-terminating inhibitors. Sanger F, Nicklen S, Coulson AR. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463-7. is a DNA sequencing which rely on the use of dideoxynucleotides used in 4 distinct sequencing reaction on the same DNA sample. The dideoxynucleotides, once incorporated in the complementary DNA strand being synthesized by the DNA polymerase prevent any further chain elongation. The newly generated sequences are resolved on a polyacrylamide gel using electrophoresis and labels (either fluorochrome or radioactivity) are used to determine the nucleotide present at a given position Philippe Rocca-Serra Sanger sequencing dye terminator sequencing adapted from wikipedia chain termination sequencing OBI:0000696 AB SOLiD System PMID: 19336255. RNA-Seq-quantitative measurement of expression through massively parallel RNA-sequencing. Wilhelm BT, Landry JR. Methods. 2009 Jul;48(3):249-57. is a DNA sequencer which is manufactured by Applied Biosystems and which enable DNA sequencing by ligation Philippe Rocca-Serra Applied Biosystems AB SOLiD System OBI:0000697 Helicos sequencing PMID: 18388294. Single-molecule DNA sequencing of a viral genome. Harris TD, Buzby PR, Babcock H, Beer E, Bowers J, Braslavsky I, Causey M, Colonell J, Dimeo J, Efcavitch JW, Giladi E, Gill J, Healy J, Jarosz M, Lapen D, Moulton K, Quake SR, Steinmann K, Thayer E, Tyurina A, Ward R, Weiss H, Xie Z. Science. 2008 Apr 4;320(5872):106-9. is a DNA sequencing which allows sequence identification of billions of DNA molecules immobilized to a surface by using DNA polymerase and fluorescently labeled nucleotides added one at a time. The sequencing process does not requires amplification step and is typically able to produce reads of 25 base pair length. Philippe Rocca-Serra true single molecule sequencing adapted from wikipedia Helicos sequencing OBI:0000702 454 Genome Sequencer FLX PMID: 18616967. The Genome Sequencer FLX System--longer reads, more applications, straight forward bioinformatics and more complete data sets. Droege M, Hill B. J Biotechnol. 2008 Aug 31;136(1-2):3-10. is a DNA sequencer which is manufactured by 454 Life Science Corporation and enables pyrosequencing to be performed. It comprises both optics and fluidics subsystems, which are controlled by a computer subsystem. The fluidics subsystem ensures accurate reagent dispensing. It consists of a reagents cassette (which holds the reagent containers), a sipper manifold, pumps, valves, and debubblers. The fluidics subsystem flows the sequencing reagents across the wells of the PicoTiterPlate device, and moves the spent reagents from the PicoTiterPlate device to the waste receptacle. The optics subsystem consists of a CCD camera and a camera controller. The camera captures the light emitted in the wells of the PicoTiterPlate device during each step of the sequencing cycle, and sends the digital images to the computer subsystem for processing. The computer controls the other Sequencer subsystems, and processes the digital images sent by the camera to extract the DNA sequence information. Philippe Rocca-Serra 454 GS FLX GS-FLX adapted from https://www.roche-applied-science.com/servlet/RCProductDisplay?langId=-1&storeId=10202&productId=3.8.8.1.1.3&catalogId=10202&krypto=mgV8a0Sdps6%2BCXU8IoddmzNEyGgjde9j8MOFCiMzRsduELeenAlVZ%2FE1QR%2BxLpzNlqMZPLRHqaI%3D&ddkey=https:RCProductDisplay 454 Genome Sequencer FLX OBI:0000703 Illumina Genome Analyzer II PMID: 19336255. RNA-Seq-quantitative measurement of expression through massively parallel RNA-sequencing. Wilhelm BT, Landry JR.Methods. 2009 Jul;48(3):249-57. is a DNA sequence which is manufactured by Illumina (Solexa) corporation. it support sequencing of single or paired end clone libraries relying on sequencing by synthesis technology Philippe Rocca-Serra Illumina Corporation Illumina Genome Analyzer II OBI:0000705 Edman degradation PMID 4773306. Niall HD (1973). "Automated Edman degradation: the protein sequenator". Meth. Enzymol. 27: 942-1010 is a process which produces a sequence from an input peptide or protein. In this process, the amino-terminal (N-terminal) residue is labeled and cleaved from the peptide without disrupting the peptide bonds between other amino acid residues. adapted from Wikipedia (http://en.wikipedia.org/wiki/Edman_degradation) Edman degradation OBI:0000706 SOLiD sequencing PMID: 19119315. High-resolution analysis of the 5'-end transcriptome using a next generation DNA sequencer. Hashimoto S, Qu W, Ahsan B, Ogoshi K, Sasaki A, Nakatani Y, Lee Y, Ogawa M, Ametani A, Suzuki Y, Sugano S, Lee CC, Nutter RC, Morishita S, Matsushima K. PLoS One. 2009;4(1):e4108. is a DNA sequencing which allows sequence identification by relying on the following steps: 1. Primers hybridize to the P1 adapter sequence within the library template. 2. A set of four fluorescently labeled di-base probes compete for ligation to the sequencing primer. Specificity of the di-base probe is achieved by interrogating every 1st and 2nd base in each ligation reaction. 3. Multiple cycles of ligation, detection and cleavage are performed with the number of cycles determining the eventual read length. 4. Following a series of ligation cycles, the extension product is removed and the template is reset with a primer complementary to the n-1 position for a second round of ligation cycles Philippe Rocca-Serra adapted from Wikipedia and Applied Biosystems web site SOLiD sequencing OBI:0000710 Li-Cor 4300 DNA Analysis System is a DNA sequencer which is manufactured by Li-Cor corporation and enable automated chain termination based DNA sequencing Philippe Rocca-Serra OBI and Li-Cor Li-Cor 4300 DNA Analysis System OBI:0000711 library preparation PMID: 19570239. Construction and analysis of cotton (Gossypium arboreum L.) drought-related cDNA library. Zhang L, Li FG, Liu CL, Zhang CJ, Zhang XY. BMC Res Notes. 2009 Jul 2;2:120. is a process which results in the creation of a library from fragments of DNA using cloning vectors or oligonucleotides with the role of adaptors. Philippe Rocca-Serra library construction library preparation OBI:0000716 ChIP-seq assay PMID: 19275939 ChIP-seq: using high-throughput sequencing to discover protein-DNA interactions. Schmidt D, Wilson MD, Spyrou C, Brown GD, Hadfield J, Odom DT. Methods. 2009 Jul;48(3):240-8. Epub 2009 Mar 9. an assay which aims at identifying protein binding sites in genomic DNA and determining how protein may regulate gene transcription by relying on immunoprecipitation of DNA bound protein, creation of a library of corresponding DNA fragments (either single or paired-end fragments) and subsequent sequencing using parallelized sequencing methods. Philippe Rocca-Serra chromatin immunoprecipitation sequencing assay adapted from Wikipedia made some modification based on the discussion on 2011/4/4 obi dev call, using DNA sequencing instead of union of some specific DNA sequencing processes ChIP-seq assay OBI:0000717 HeliScope Single Molecule Sequencer is a DNA sequencer manufacturer by Helicos Corporation to carry out Single Molecule sequencing using reversible termination chemistry Philippe Rocca-Serra HeliScope Single Molecule Sequencer OBI:0000722 paired-end library PMID: 19339662. Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses. Genome Res. 2009 Apr;19(4):521-32. Fullwood MJ, Wei CL, Liu ET, Ruan Y. is a collection of short paired tags from the two ends of DNA fragments are extracted and covalently linked as ditag constructs Philippe Rocca-Serra mate-paired library paired-end tag (PET) library adapted from information provided by Solid web site paired-end library OBI:0000723 DNA sequencing by ligation PMID: 19546169. Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two base encoding. McKernan KJ, Peckham HE, Costa G, McLaughlin S, Tsung E, Fu Y, Clouser C, Dunkan C, Ichikawa J, Lee C, Zhang Z, Sheridan A, Fu H, Ranade S, Dimilanta E, Sokolsky T, Zhang L, Hendrickson C, Li B, Kotler L, Stuart J, Malek J, Manning J, Antipova A, Perez D, Moore M, Hayashibara K, Lyons M, Beaudoin R, Coleman B, Laptewicz M, Sanicandro A, Rhodes M, De La Vega F, Gottimukkala RK, Hyland F, Reese M, Yang S, Bafna V, Bashir A, Macbride A, Aklan C, Kidd JM, Eichler EE, Blanchard AP. Genome Res. 2009 Jun 22. is a DNA sequencing which relies on DNA ligase activity to perform chain extension during the sequencing reaction step. PERSON: Philippe Rocca-Serra DNA sequencing by ligation OBI:0000724 Solexa sequencing PMID: 18987734 Accurate whole human genome sequencing using reversible terminator chemistry. Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, Brown CG, Hall KP, Evers DJ, Barnes CL, Bignell HR, Boutell JM, Bryant J, Carter RJ, Keira Cheetham R, Cox AJ, Ellis DJ, Flatbush MR, Gormley NA, Humphray SJ, Irving LJ, Karbelashvili MS, Kirk SM, Li H, Liu X, Maisinger KS, Murray LJ, Obradovic B, Ost T, Parkinson ML, Pratt MR, Rasolonjatovo IM, Reed MT, Rigatti R, Rodighiero C, Ross MT, Sabot A, Sankar SV, Scally A, Schroth GP, Smith ME, Smith VP, Spiridou A, Torrance PE, Tzonev SS, Vermaas EH, Walter K, Wu X, Zhang L, Alam MD, Anastasi C, Aniebo IC, Bailey DM, Bancarz IR, Banerjee S, Barbour SG, Baybayan PA, Benoit VA, Benson KF, Bevis C, Black PJ, Boodhun A, Brennan JS, Bridgham JA, Brown RC, Brown AA, Buermann DH, Bundu AA, Burrows JC, Carter NP, Castillo N, Chiara E Catenazzi M, Chang S, Neil Cooley R, Crake NR, Dada OO, Diakoumakos KD, Dominguez-Fernandez B, Earnshaw DJ, Egbujor UC, Elmore DW, Etchin SS, Ewan MR, Fedurco M, Fraser LJ, Fuentes Fajardo KV, Scott Furey W, George D, Gietzen KJ, Goddard CP, Golda GS, Granieri PA, Green DE, Gustafson DL, Hansen NF, Harnish K, Haudenschild CD, Heyer NI, Hims MM, Ho JT, Horgan AM, Hoschler K, Hurwitz S, Ivanov DV, Johnson MQ, James T, Huw Jones TA, Kang GD, Kerelska TH, Kersey AD, Khrebtukova I, Kindwall AP, Kingsbury Z, Kokko-Gonzales PI, Kumar A, Laurent MA, Lawley CT, Lee SE, Lee X, Liao AK, Loch JA, Lok M, Luo S, Mammen RM, Martin JW, McCauley PG, McNitt P, Mehta P, Moon KW, Mullens JW, Newington T, Ning Z, Ling Ng B, Novo SM, O'Neill MJ, Osborne MA, Osnowski A, Ostadan O, Paraschos LL, Pickering L, Pike AC, Pike AC, Chris Pinkard D, Pliskin DP, Podhasky J, Quijano VJ, Raczy C, Rae VH, Rawlings SR, Chiva Rodriguez A, Roe PM, Rogers J, Rogert Bacigalupo MC, Romanov N, Romieu A, Roth RK, Rourke NJ, Ruediger ST, Rusman E, Sanches-Kuiper RM, Schenker MR, Seoane JM, Shaw RJ, Shiver MK, Short SW, Sizto NL, Sluis JP, Smith MA, Ernest Sohna Sohna J, Spence EJ, Stevens K, Sutton N, Szajkowski L, Tregidgo CL, Turcatti G, Vandevondele S, Verhovsky Y, Virk SM, Wakelin S, Walcott GC, Wang J, Worsley GJ, Yan J, Yau L, Zuerlein M, Rogers J, Mullikin JC, Hurles ME, McCooke NJ, West JS, Oaks FL, Lundberg PL, Klenerman D, Durbin R, Smith AJ. Nature. 2008 Nov 6;456(7218):53-9. is a DNA sequencing which allows sequence identification by relying on use of DNA polymerase and reversible terminator. The methods requires immobilization of genomic DNA fragment onto a surface and a specific clonal amplification step known as bridge PCR. Reliance on reversible terminator allow cycles of DNA chain extension by DNA polymerase and imaging without the need of electrophoretic separation of newly synthesized DNA fragment as with Sanger sequencing. Philippe Rocca-Serra reversible terminator sequencing adapted from Wikipedia and Illumina / Solexa web site (SS_DNAsequencing.pdf document available on july 2009) Solexa sequencing OBI:0000725 host role In biology, a host is an organism that harbors a virus or parasite, or a mutual or commensal symbiont, typically providing nourishment and shelter. http://en.wikipedia.org/wiki/Host_(biology) 30 March 09 host role is a role played by an organism and realized by providing nourishment, shelter or a means of reproduction to another organism within the organism playing the host role 30Mar09 virus reproducing inside a cell; bacteria causing a disease, host can be harmed or not. we want to avoid a cat sitting on my lap and an animal care technician; these are not examples or hosts; dental cares = on tooth, but part of outer layer of tooth, so covered by "within" in the definition GROUP: Role Branch 30 Mar09 submitted by vaccine community OBI http://en.wikipedia.org/wiki/Host_(biology) host role OBI:0000730 pyrosequencing Pyrosequencing sheds light on DNA sequencing. PMID: 1115661. Ronaghi M. Genome Res. 2001 Jan;11(1):3-11. Review. is a DNA sequencing which allows sequencing of a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step. The template DNA is immobilized, and solutions of A, C, G, and T nucleotides are added and removed after the reaction, sequentially. Light is produced only when the nucleotide solution complements the first unpaired base of the template. The sequence of solutions which produce chemiluminescent signals allows the determination of the sequence of the template. ssDNA template is hybridized to a sequencing primer and incubated with the enzymes DNA polymerase, ATP sulfurylase, luciferase and apyrase, and with the substrates adenosine 5-prime phosphosulfate (APS) and luciferin. Philippe Rocca-Serra Wikipedia (http://en.wikipedia.org/wiki/Pyrosequencing) and Roche 454 life science web site pyrosequencing OBI:0000731 recombinant vector A recombinant vector is created by a recombinant vector cloning process, and contains nucleic acids that can be amplified. It retains functions of the original cloning vector. recombinant vector OBI:0000734 DNA sequencing by synthesis PMID: 18263613. A new class of cleavable fluorescent nucleotides: synthesis and optimization as reversible terminators for DNA sequencing by synthesis. Turcatti G, Romieu A, Fedurco M, Tairi AP. Nucleic Acids Res. 2008 Mar;36(4):e25. is a DNA sequencing which relies on DNA polymerase activity to perform chain extension during the sequencing reaction step. PERSON: Philippe Rocca-Serra DNA sequencing by synthesis OBI:0000736 single fragment library is a collection of short tags from DNA fragments, are extracted and covalently linked as single tag constructs Philippe Rocca-Serra fragment library single fragment library OBI:0000737 cloning vector A cloning vector is an engineered material that is used as an input material for a recombinant vector cloning process to carry inserted nucleic acids. It contains an origin of replication for a specific destination host organism, encodes for a selectable gene product and contains a cloning site. cloning vector OBI:0000740 material sample role a role borne by a portion of blood taken to represent all the blood in an organism; the role borne by a population of humans with HIV enrolled in a study taken to represent patients with HIV in general. A material sample role is a specimen role borne by a material entity that is the output of a material sampling process. 7/13/09: Note that this is a relational role: between the sample taken and the 'sampled' material of which the sample is thought to be representative off. material sample role OBI:0000747 material sample blood drawn from patient to measure his systemic glucose level. A population of humans with HIV enrolled in a study taken to represent patients with HIV in general. A material entity that has the material sample role OBI: workshop sample population sample material sample OBI:0000748 bisulfite sequencing PMID: 19581485. High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing. Hodges E, Smith A, Kendall J, Xuan Z, Ravi K, Rooks M, Zhang M, Ye K, Battacharjee A, Brizuela L, McCombie WR, Wigler M, Hannon GJ, Hicks J. Genome Res. 2009 Jul 6. An assay which allows to determine the methylation status of genomic DNA using DNA sequencing techniques preceded by a bisulfite based chemical modification of genomic DNA at CpG island location. 8/19/09: Chris says that there may used to be a way of doing bisulfite sequencing comparing lengths of restriction fragments, which implies that it is possible to do without DNA sequencing. Philippe Rocca-Serra adapted from Wikipedia bisulfite sequencing OBI:0000750 study design independent variable In a study in which gene expression is measured in patients between 8 month to 4 years old that have mild or severe malaria and in which the hypothesis is that gene expression in that age group is a function of disease status, disease status is the independent variable. a directive information entity that is part of a study design. Independent variables are entities whose values are selected to determine its relationship to an observed phenomenon (the dependent variable). In such an experiment, an attempt is made to find evidence that the values of the independent variable determine the values of the dependent variable (that which is being measured). The independent variable can be changed as required, and its values do not represent a problem requiring explanation in an analysis, but are taken simply as given. The dependent variable on the other hand, usually cannot be directly controlled 2/2/2009 Original definition - In the design of experiments, independent variables are those whose values are controlled or selected by the person experimenting (experimenter) to determine its relationship to an observed phenomenon (the dependent variable). In such an experiment, an attempt is made to find evidence that the values of the independent variable determine the values of the dependent variable (that which is being measured). The independent variable can be changed as required, and its values do not represent a problem requiring explanation in an analysis, but are taken simply as given. The dependent variable on the other hand, usually cannot be directly controlled. In the Philly 2013 workshop the label was chosen to distinguish it from "dependent variable" as used in statistical modelling. See: http://en.wikipedia.org/wiki/Statistical_modeling PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Chris Stoeckert experimental factor independent variable Web: http://en.wikipedia.org/wiki/Dependent_and_independent_variables 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify thisdefinition please notify OBI. study factor study design independent variable OBI:0000751 study design dependent variable In a study in which gene expression is measured in patients between 8 month to 4 years old that have mild or severe malaria and in which the hypothesis is that gene expression in that age group is a function of disease status, the gene expression is the dependent variable. dependent variable specification is part of a study design. The dependent variable is the event studied and expected to change when the independent variable varies. 2/2/2009 In the design of experiments, independent variables are those whose values are controlled or selected by the person experimenting (experimenter) to determine its relationship to an observed phenomenon (the dependent variable). In such an experiment, an attempt is made to find evidence that the values of the independent variable determine the values of the dependent variable (that which is being measured). The independent variable can be changed as required, and its values do not represent a problem requiring explanation in an analysis, but are taken simply as given. The dependent variable on the other hand, usually cannot be directly controlled. In the Philly 2013 workshop the label was chosen to distinguish it from "dependent variable" as used in statistical modelling. See: http://en.wikipedia.org/wiki/Statistical_modeling PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Chris Stoeckert dependent variable WEB: http://en.wikipedia.org/wiki/Dependent_and_independent_variables 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify thisdefinition please notify OBI. study design dependent variable OBI:0000785 study design controlled variable In a study in which gene expression is measured in patients between 8 month to 4 years old that have mild or severe malaria and in which the hypothesis is that gene expression in that age group is a function of disease status, age is a controlled variable. Controlled variable specification is a part of a study design. They are the entities that could vary, but are kept constant to prevent their influence on the effect of the independent variable on the dependent. 2/2/2009 Original definition: Controlled variables are also important to identify in experiments. They are the variables that are kept constant to prevent their influence on the effect of the independent variable on the dependent. Every experiment has a controlling variable, and it is necessary to not change it, or the results of the experiment won't be valid In the Philly 2013 workshop the label was chosen to distinguish it from "controlled variable" as used in statistical modelling PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Chris Stoeckert controlled variable WEB: http://en.wikipedia.org/wiki/Control_variable 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify thisdefinition please notify OBI. study design controlled variable OBI:0000791 multiple testing correction objective Application of the Bonferroni correction A multiple testing correction objectives is a data transformation objective where the aim is to correct for a set of statistical inferences considered simultaneously multiple comparison correction objective http://en.wikipedia.org/wiki/Multiple_Testing_Correction multiple testing correction objective OBI:0000794 transcription factor binding site SO:0000235 PLace_holder for sequence ontology term transcription factor binding site OBI:0000796 purification objective the objective to obtain a pure fraction of a specific peptide when running an HPLC on a crude synthesis of peptides. The objective to separate a material entity into different compositions of which one or more have are purified fractions that contain higher concentration of a desired component, while others contain impurities and are not of interest PERSON:Bjoern Peters isolation objective BP 10/14/09, BP: This should be linked to the 'purified' 'currently conferred quality purification objective OBI:0000800 cross linking cross linking can be used as a probe to link proteins together, to check protein protein interactions A process in which bonds are created that link one polymer to another PERSON: Chris Stoeckert http://en.wikipedia.org/wiki/Cross-link cross linking OBI:0000806 material maintenance objective An objective specification maintains some or all of the qualities of a material over time. PERSON: Bjoern Peters PERSON: Bjoern Peters material maintenance objective OBI:0000809 amplified DNA Amplied DNA created by PCR DNA that has been produced in an enzymatic amplification process PERSON: Alan Ruttenberg Alan Ruttenberg amplified DNA OBI:0000811 primary structure of DNA macromolecule a quality of a DNA molecule that inheres in its bearer due to the order of its DNA nucleotide residues. placeholder for SO BP et al primary structure of DNA macromolecule OBI:0000831 DNA residue methylation a quality of a DNA residue that has a methyl group attached to it DNA residue methylation OBI:0000832 measurement device A ruler, a microarray scanner, a Geiger counter. A device in which a measure function inheres. GROUP:OBI Philly workshop OBI measurement device OBI:0000834 high molecular weight DNA extract Extraction of chromosomal DNA from mammalian cells by first isolating nucei The output of an extraction process in which DNA molecules above a molecular weight cutoff are purified in order to exclude DNA from organellas. PERSON:Chris Stoeckert OBI high molecular weight DNA extract OBI:0000838 material maintenance a process with that achieves the objective to maintain some or all of the characteristics of an input material over time material maintenance OBI:0000845 primary structure of RNA molecule The primary structure of an RNA molecule that is completely defined by the set of its nucleic residue parts and the linear order induced by the peptide bonds that hold them together Person:Bjoern Peters primary structure of RNA molecule OBI:0000848 polyA RNA extraction A RNA extraction process typically involving the use of poly dT oligomers in which the desired output material is polyA RNA. Person: Chris Stoeckert Person: Jie Zheng UPenn Group polyA RNA extraction OBI:0000849 organellar RNA extraction A RNA extraction process in which the desired output material is RNA in the organelle(s). Person: Chris Stoeckert Person: Jie Zheng UPenn Group organellar RNA extraction OBI:0000852 record of missing knowledge A statement in a journal article indicating that the age of a patient at the onset of disease is not known. A statement indicating that the weight of a mouse was not measured. a information content entity created to indicate that information about something is not available to the person recording it. This class should probably end up in IAO. It could be further breaken down to indicate different kinds of lack of knowledge, e.g. inability to determine something vs. no attempt made to determine something vs. no informatino available if it was even attempted to determine something. The design pattern should be generalizable. 'unknown sex' is the first example, and needed immediately. Bjoern Peters record of missing knowledge OBI:0000855 total RNA extraction A RNA extraction process in which total cellular and organelle RNA are extracted. Person: Chris Stoeckert Person: Jie Zheng UPenn Group total RNA extraction OBI:0000858 record of unknown sex A database record indicating that the tissue sample in a microarray experiment came from an organism for which the biological sex is not known to the person who created the record. a record indicating that the biological sex of an organism is not known. I think the statement is still about the instance of the biological sex quality of an organism. It is also about information available to the person making the statement. Bjoern Peters record of unknown sex OBI:0000859 cytoplasmic RNA extraction A RNA extraction process in which the desired output material is RNA in the cytoplasm. Person: Chris Stoeckert Person: Jie Zheng UPenn Group cytoplasmic RNA extraction OBI:0000862 nuclear RNA extract Isolation and purification of nuclear RNA from animal cells using Norgen Bioteck corp. cytoplasmic and nuclear RNA purification kit (http://www.norgenbiotek.com/display-product.php?ID=30) A RNA extract that is the output of an extraction process in which RNA molecules found in the nucleus, including mRNA precursors (pre-mRNA), are extracted. PERSON: Chris Stoeckert PERSON: Jie Zheng UPenn Group nuclear RNA extract OBI:0000869 polyA RNA extract Preparation of polyA RNA by cellulose-bound oligo-dT (Aviv, H., Leder, P. 1972. Purification of biologically active globin messenger RNA by chromatography on oligothymidylic acid-cellulose. Proc. Nat. Acad. Sci. USA 69, 1408-1412.) A RNA extract that is the output of an extraction process in which RNA molecules with poly A tail at its 3' end are purified. PERSON: Chris Stoeckert PERSON: Jie Zheng UPenn Group polyA RNA extract OBI:0000873 pre-mortem specimen material obtained through a liver biopsy from a human patient a specimen that was taken from a live organism Bjoern Peters MO_705 premortem pre-mortem specimen OBI:0000876 cytoplasmic RNA extract Cytoplasmic RNA extraction from mammalian tissues to create cDNA library (Carninci P, Nakamura M, Sato K, Hayashizaki Y, Brownstein MJ. Cytoplasmic RNA extraction from fresh and frozen mammalian tissues. Biotechniques. 2002;33:306–309.) A RNA extract that is the output of a RNA extraction process in which RNA molecules found in the cytoplasm are extracted. PERSON: Chris Stoeckert PERSON: Jie Zheng UPenn Group cytoplasmic RNA extract OBI:0000880 RNA extract an extract which is the output of an extraction process in which RNA molecules are isolated from a specimen. PERSON: Chris Stoeckert PERSON: Jie Zheng Group: UPenn Group RNA extract OBI:0000888 nuclear RNA extraction A RNA extraction process in which the desired output material is RNA in the nucleus. Person: Chris Stoeckert Person: Jie Zheng UPenn Group nuclear RNA extraction OBI:0000893 real time polymerase chain reaction assay A laboratory technique based on the PCR, which is used to amplify and simultaneously quantify a specific DNA molecule based on the use of complementary probes/primers. It enables both detection and quantification (as absolute number of copies or relative amount when normalized to DNA input or additional normalizing genes) of one or more specific sequences in a DNA sample. person: Bjoern Peters person: Melanie Courtot Q-PCR kinetic polymerase chain reaction qPCR quantitative real time polymerase chain reaction WEB: http://en.wikipedia.org/wiki/Real-time_polymerase_chain_reaction real time PCR real time polymerase chain reaction assay OBI:0000894 protein extract PMID: 20032479. A bovine whey protein extract stimulates human neutrophils to generate bioactive IL-1Ra through a NF-kappaB- and MAPK-dependent mechanism. Rusu D, Drouin R, Pouliot Y, Gauthier S, Poubelle PE. J Nutr. 2010 Feb;140(2):382-91. Epub 2009 Dec 23. a protein extract is the output of an extraction process from tissues or cell cultures resulting in a solution of cellular and/or organellar proteins in buffer solution used to prevent degradation, Person: Philippe Rocca-Serra OBI & wikipedia protein extract OBI:0000895 total RNA extract Extraction of total RNA from cells with Qiagen mini RNeasy kit. A RNA extract that is the output of an extraction process in which total celluar and organelle RNA molecules are isolated from a specimen. PERSON: Chris Stoeckert PERSON: Jie Zheng UPenn Group total RNA extract OBI:0000899 organellar RNA extract Extraction of organellar RNA from plant cells using organellar RNA binding protein. A RNA extract that is the output of an extraction process in which RNA molecules found in an organelle, e.g., mitochondrion, ER, or chloroplast, excluding the nucleus, are extracted. PERSON: Chris Stoeckert PERSON: Jie Zheng UPenn Group organellar RNA extract OBI:0000902 post mortem specimen the spleen taken from a dead mouse a specimen that was taken from a dead organism Bjoern Peters MO_416 postmortem post mortem specimen OBI:0000905 sequence feature annotation Information about a sequence region Bjoern Peters Bjoern Peters place holder for sequence ontology term sequence feature annotation OBI:0000908 labeled DNA extract a labeled specimen that is the output of a labeling process and has grain labeled DNA to be able to detect DNA in future experiments. Need to find out if we consider labeled nucleotides still nucleotides. It is after consulting with ChEBI group. Added duirng Mar 1, 2010 dev call Group: OBI group Group: OBI group labeled DNA extract OBI:0000915 freezing storage a fozen pellet used for later assay A storage process in temperature that maintenance the frozen status of the stored entities. 2010/3/3 Alan Ruttenberg: There is a question of whether we should have a separate objective to "prepare for maintenance" 2014/2/3 OBI dev call: "prepare for maintenance" is a separate process. For example, 'freezing' and 'flash freezing' are defined and can be used to produce frozen material for storage. Updated both textual and logical definition. Both input and output material of freezing storage have quality frozen. Person: Alan Ruttenberg, Mathias Brochhausen MO_481 frozen_storage OBI freezing storage OBI:0000919 animal euthanization Rats were euthanized with CO2 A process in which is the end of life of animal is brought about in accordance with local regulations on treatment of animal subjects and using a method which causes minimal pain and distress to the animal subject Helen Parkinson and Melissa Haendel animal sacrifice Melissa Haendel may later be refined with more specific list of organisms animal euthanization OBI:0000921 labeled RNA extract a labeled specimen that is the output of a labeling process and has grain labeled RNA to be able to detect RNA in future experiments. Need to find out if we consider labeled nucleotides still nucleotides. It is after consulting with ChEBI group. Added duirng Mar 1, 2010 dev call Group: OBI group Group: OBI group labeled RNA extract OBI:0000922 frozen specimen Frozen blood plasma A specimen that has been frozen in order to store it. Person:Alan Ruttenberg MO_610 frozen_sample frozen specimen OBI:0000924 labeled specimen A specimen that has been modified in order to be able to detect it in future experiments added during call 3/1/2010 OBI group labeled specimen OBI:0000927 lyophilization storage a storage process with input material entity and output freeze dried material for long time storage PERSON: Chris Stoeckert PERSON: Jie Zheng can link to freezing-dying equipment, such as freeze-dryer, rotary evaporator, if needed lyophilization storage OBI:0000931 study intervention the part of the execution of an intervention design study which is varied between two or more subjects in the study PERSON: Bjoern Peters GROUP: OBI study intervention OBI:0000932 material separation device flow cytometer A device with a separation function realized in a planed process material separation device OBI:0000934 intramuscular injection is the injection of a material entity (bearing the administered substance role) into the muscle (bearing the target role) of an organism using a syringe intramuscular injection OBI:0000947 service provider role Jackson Lab provides experimental animals, EBI provides training on databases, a core facility provides access to a DNA sequencer. is a role which inheres in a person or organization and is realized in in a planned process which provides access to training, materials or execution of protocols for an organization or person PERSON:Helen Parkinson service provider role OBI:0000950 paraffin specimen liver tissue embedded in paraffin a specimen that is output of a paraffin storage process in which specimen is embedded in paraffin PERSON: Chris Stoeckert PERSON: Jie Zheng MO_990 paraffin_sample paraffin specimen OBI:0000951 compound treatment design an intervention design in which the treatment is the administration of a compound This is meant to include all kinds of material administrations, including vaccinations, chemical compounds etc. PERSON: Bjoern Peters MO_555 compound_treatment_design compound treatment design OBI:0000953 processed specimen A tissue sample that has been sliced and stained for a histology study. A blood specimen that has been centrifuged to obtain the white blood cells. A specimen that has been intentionally physically modified. Bjoern Peters Bjoern Peters A tissue sample that has been sliced and stained for a histology study. processed specimen OBI:0000954 subcutaneous injection is the injection of a material entity (bearing the administered substance role) into the hypodermis (bearing the target role) of an organism using a syringe PERSON: Melanie Courtot subcutaneous injection OBI:0000965 lyophilized specimen freezing dried DNA a specimen that is output of a lyophilization storage process in which specimen is lyophilized for storage. PERSON: Chris Stoeckert PERSON: Jie Zheng MO_589 freeze_dried_sample lyophilized specimen OBI:0000967 container A device that can be used to restrict the location of material entities over time 03/21/2010: Added to allow classification of children (similar to what we want to do for 'measurement device'. Lookint at what classifies here, we may want to reconsider a contain function assigned to a part of an entity is necessarily also a function of the whole (e.g. is a centrifuge a container because it has test tubes as parts?) PERSON: Bjoern Peters container OBI:0000968 device A voltmeter is a measurement device which is intended to perform some measure function. An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure. A material entity that is designed to perform a function in a scientific investigation, but is not a reagent. 2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of "device", and are enumerating the types of roles that a reagent can perform. 2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example: (1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part. (2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay. (3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel. In the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent role is not transitive across the part_of relation). In this way, the asserted disjointness between a reagent and device holds, as both roles are never realized in the same bearer during execution of an assay. PERSON: Helen Parkinson instrument OBI development call 2012-12-17. device OBI:0000969 dose specification a protocol specifying to administer 1 ml of vaccine to a mouse a directive information entity that describes the dose that will be administered to a target dose specification OBI:0000971 fresh specimen a liver freshly removed from a rat a specimen that is output of a specimen creation process used for an investigation without storage. PERSON: Chris Stoeckert PERSON: Jie Zheng MO_730 fresh_sample fresh specimen OBI:0000973 sequence data example of usage: the representation of a nucleotide sequence in FASTA format used for a sequence similarity search. A measurement datum that representing the primary structure of a macromolecule(it's sequence) sometimes associated with an indicator of confidence of that measurement. Person:Chris Stoeckert GROUP: OBI sequence data OBI:0000977 paraffin storage a storage process with input organism or anatomical entity and paraffin and output material embedded in paraffin for long term storage PERSON: Chris Stoeckert PERSON: Jie Zheng UPenn Group need to specify paraffin or wax is one of specified input of the process paraffin storage OBI:0000981 agar stab specimen a specimen that is output of a process that cell culture inoculated into agar for long term storage. PERSON: Chris Stoeckert PERSON: Jie Zheng MO_971 agar_stab agar stab specimen OBI:0000985 growth condition intervention design A study design in which the independent variable is the environmental condition in which the specimen is growing PERSON: Bjoern Peters MO_588 growth_condition_design growth condition intervention design OBI:0000989 PCR instrument A device that is used to amplify a single or few copies of a piece of DNA across several orders of magnitude, generating thousands to millions of copies of a particular DNA sequence. 03/21/2010: Added because it is unclear if the thermal cycler definition is intentionally broader than PCR instrument. Contacted Melanie and Trish about this. Definitions and use of alternative terms need to be made consistent. PCR instrument OBI:0000994 intravenous injection is the injection of a material entity (bearing the administered substance role) into the vein (bearing the target role) of an organism using a syringe PERSON: Melanie Courtot intravenous injection OBI:0000995 administration of material to specimen Staining cells in a tissue slice with a dye. The directed combination of a material entity with a specimen. Bjoern Peters Bjoern Peters administration of material to specimen OBI:0000997 growth environment The collection of material entities and their qualities that are located near a live organism, tissue or cell and can influence its growth. Right now this may be incomplete. Should also cover e.g. sound, light as well. PERSON:Richard Scheuermann, Jie Zheng, Bjoern Peters OBI group growth environment OBI:0001003 agar stab storage a storage process with input cell culture and agar and output agar stab for long time storage PERSON: Chris Stoeckert PERSON: Jie Zheng UPenn Group need to specify that agar is one of input for this process agar stab storage OBI:0001007 image creation Taking a polaroid picture of a patients skin lesion; Using a digital camera to take a picture of a gel A planned process that captures an image of an object. PERSON: Jie Zheng image acquisition image creation OBI:0001010 nucleic acid extract An extract that is the output of an extraction process in which nucleic acid molecules are isolated from a specimen. PERSON: Jie Zheng UPenn Group nucleic acid extract OBI:0001028 feature extraction A planed process with objective of obtaining quantified values from an image. PERSON: Jie Zheng MO_928: feature_extraction feature extraction OBI:0001031 array image creation An image creation process that generate an image from the array. PERSON: Jie Zheng array image acquisition MO_929: image_acquisition array image creation OBI:0001032 light emission device A light source is an optical subsystem that provides light for use in a distant area using a delivery system (e.g., fiber optics) a device which has a function to emit light. Person:Helen Parkinson OBI light emission device OBI:0001033 perturbation device A homogenizer is a perturbation device. A perturbation device is a device which is designed to perform a perturb function Helen Parkinson OBI Vancouver workshop 2010 PERSON: Helen Parkinson perturbation device OBI:0001034 environmental control device A growth chamber is an environmental control device. An environmental control device is a device which has the function to control some aspect of the environment such as temperature, or humidity. Helen Parkinson OBI environmental control device OBI:0001051 DNA extract The output of an extraction process in which DNA molecules are purified in order to exclude DNA from organellas. Person: Jie Zheng Group: UPenn group DNA extract OBI:0001069 array manufacturer role a manufacturer role which is played by the person or organization that manufactured the array PERSON: Chris Stoeckert, Jie Zheng MO_695 array_manufacturer array manufacturer role OBI:0001088 tandem mass spectrometer A mass spectrometer in which ions are subjected to two or more sequential stages of analysis (which may be separated spatially or temporally) according to the quotient mass/charge. PERSON: Erik Segerdell http://goldbook.iupac.org/T06250.html tandem mass spectrometer OBI:0001140 spike-in quality control role a reference substance role that is borne by a material entity with a known amount which is mixed into the evaluant of assays for quality control or data normalization purposes PERSON: Chris Stoeckert, Jie Zheng, Bjoern Peter MO_937 spike_quality_control spike-in quality control role OBI:0001141 individual organism identifier a CRID symbol used to distinguish one individual organism from another. PERSON: Chris Stoeckert, Jie Zheng MO_169 Individual individual organism identifier OBI:0001142 dye swap quality control role a reference substance role that is borne by a material entity used in a dye swap design experiment for quality control or data normalization purposes PERSON: Chris Stoeckert, Jie Zheng MO_524 dye_swap_quality_control dye swap quality control role OBI:0001143 labeled nucleic acid extract a labeled specimen that is the output of a labeling process and has grain labeled nucleic acid for detection of the nucleic acid in future experiments. Person: Jie Zheng labeled extract MO_221 labeledExtract labeled extract labeled nucleic acid extract OBI:0001146 binding assay Determination of KD value for an antibody binding a protein using a BIACORE assay. Using plate bound antigen in an ELISA to determine if a mixture of serum antibodies bind the antigen. The following are NOT binding assays, as the desired output is not binding data: RNA microarray experiments to determine levels of gene expression. ChIP experiments to determine where in DNA a transcription factor binds. Using an IL-2 antibody on an ELISA plate to determine presence of IL-2 after stimulating a T cell culture. An assay with the objective to characterize the disposition of two or more material entities to form a complex. PERSON:Bjoern Peters, Randi Vita, Jason Greenbaum binding assay OBI:0001147 cell culture expansion a processual entity that results in the increase of cell numbers including grow of yeast and bacteria PERSON: Chris Stoeckert, Jie Zheng MO_758 grow BP: add it as subclass of 'cell culturing' JZ: No 'cell culturing' in OBI Has term 'cell co-culturing' and 'maintaining cell culture'. Don't think either of it fit. So leave the term under process. cell culture expansion OBI:0001148 gene knock out a genetic transformation that renders a gene non-functional, e.g. due to a point mutation, or the removal of all, or part of, the gene using recombinant methods. PERSON: Chris Stoeckert, Jie Zheng MO_771 gene_knock_out gene knock out OBI:0001149 gene knock in a genetic transformation that involves the insertion of a protein coding cDNA sequence at a particular locus in an organism's chromosome. Typically, this is done in mice since the technology for this process is more refined, and because mouse embryonic stem cells are easily manipulated. The difference between knock-in technology and transgenic technology is that a knock-in involves a gene inserted into a specific locus, and is a "targeted" insertion. PERSON: Chris Stoeckert, Jie Zheng MO_437 gene_knock_in WEB: http://en.wikipedia.org/wiki/Gene_Knock-in gene knock in OBI:0001150 chromosomal substitution A genetic transformation in which all, or part, of a chromosome from a donor replaces that of the recipient. It does not include chromosome recombination. For single gene insertion, use the term 'gene knock in'. PERSON: Chris Stoeckert, Jie Zheng MO_995 chromosomal_substitution chromosomal substitution OBI:0001151 genetically modified material a material entity, organism or cell, that is the output of a genetic transformation process. PERSON: Jie Zheng GROUP: OBI term is proposed by BP on Oct 25, 2010 dev call genetically modified material OBI:0001152 transfection a genetic transformation which relies on the use of physical, electrical and chemical phenomena to introduce DNA or RNA into a cell PERSON: Chris Stoeckert, Jie Zheng MO_366 transfection transfection OBI:0001153 genetic transformation objective a material transformation objective aims to create genetically modified organism or cell Person: Jie Zheng Person: Jie Zheng suggested to be added by BP and AR during Oct 25, 2010 dev call genetic transformation objective OBI:0001154 induced mutation a genetic transformation that the modification of the genetic material (either coding or non-coding) of an organism is caused by mutagenic compounds or irradiation. PERSON: Chris Stoeckert, Jie Zheng MO_564 induced_mutation induced mutation OBI:0001156 age since planting measurement datum An age measurement datum that is the result of the measurement of the age of an organism since planting, the process of placing a plant in media (e.g. soil) to allow it to grow, which excludes sowing. PERSON:Chris Stoeckert, Jie Zheng MO_495 planting Discussed by Jie and Chris, proposed to combine with different kinds of processes as initial time point. Proposed 'age measurement assay' is proceeded by some process. The process can be any kind of process defined in OBI. Think it is more flexible. However, it is hard to model due to lake of temporal predicates on Nov 15, 2010 dev call. Term proposed by Bjoern on Nov 8, 2010 dev call Supported by Alan on Nov 15, 2010 dev call age since planting measurement datum OBI:0001157 age since hatching measurement datum An age measurement datum that is the result of the measurement of the age of an organism since hatching, the process of emergence from an egg. PERSON:Chris Stoeckert, Jie Zheng MO_745 hatching age since hatching measurement datum OBI:0001158 age measurement assay An assay that measures the duration of temporal interval of a process that is part of the life of the bearer, where the initial time point of the measured process is the beginning of some transitional state of the bearer such as birth or when planted. This assay measures time not developmental stage. we recognize that development takes different time periods under different conditions such as media / temperature. For example, age measurement assay of fly age, the output likes 28 days but not mid-life of age at room temperature. PERSON: Alan Ruttenberg OBI group age measurement assay OBI:0001159 age since egg laying measurement datum An age measurement datum that is the result of the measurement of the age of an organism since egg laying, the process of the production of egg(s) by an organism. PERSON:Chris Stoeckert, Jie Zheng MO_767 egg laying age since egg laying measurement datum OBI:0001160 assay validation objective an objective specification to check the accuracy or the quality of the results of an assay by comparison with independent results PERSON: Chris Stoeckert, Jie Zheng GROUP: Penn Group assay validation objective OBI:0001161 age since germination measurement datum An age measurement datum that is the result of the measurement of the age of an organism since germination, the process consisting of physiological and developmental changes by a seed, spore, pollen grain (microspore), or zygote that occur after release from dormancy, and encompassing events prior to and including the first visible indications of growth. Definition of germination comes from GO. However, the term is deprecated from GO now because it is a grouping term without biological significance. PERSON:Chris Stoeckert, Jie Zheng MO_590 germination age since germination measurement datum OBI:0001162 validation by reverse transcription PCR design a study design in which checks the accuracy or the quality of the result of an assay by comparing with reverse transcription PCR results PERSON: Chris Stoeckert, Jie Zheng MO_986 reverse_transcription_PCR_quality_control validation by reverse transcription PCR design OBI:0001163 age since eclosion measurement datum An age measurement datum that is the result of the measurement of the age of an organism since eclosion, the process of emergence of an adult insect from its pupa or cocoon. PERSON:Chris Stoeckert, Jie Zheng MO_876 eclosion age since eclosion measurement datum OBI:0001164 age since sowing measurement datum An age measurement datum that is the result of the measurement of the age of an organism since sowing, the process of placing a seed or spore in some media with the intention to invoke germination. PERSON:Chris Stoeckert, Jie Zheng MO_748 sowing age since sowing measurement datum OBI:0001165 age since coitus measurement datum An age measurement datum that is the result of the measurement of the age of an organism since coitus, the process of copulation that occurs during the process of sexual reproduction. PERSON:Chris Stoeckert, Jie Zheng MO_783 coitus age since coitus measurement datum OBI:0001166 validation by real time PCR design a study design in which the accuracy or the quality of the result of an assay is checked by comparing with real time PCR results PERSON: Chris Stoeckert, Jie Zheng MO_434 real_time_PCR_quality_control validation by real time PCR design OBI:0001167 age measurement datum A time measurement datum that is the result of measurement of age of an organism note that we are currently defining subtypes of age measurement datum that specify when the age is relative to, e.g. planting, as we don't have adequate temporal predicates yet. life of bearer doesn't imply organism this assay measures time not developmental stage. we recognize that development can take different time periods under different conditions such as media / temperature age as a quality is dubious; we plan to revisit stages in development are currently handled with controlled vocabulary, such as 2-somite stage PERSON: Alan Ruttenberg, Chris Stoeckert, Jie Zheng MO_178 Age In MageTab file, we use initialTimePoint (a process) + age (a number expected) + TimeUnit (definied in UO, such as year, hour, day, etc.) Now we use the term label indicating the start time point of measuring the age, (number + TimeUnit) are expected instances of the class discussed on Nov 15, dev call All subtype will be defined by textual definition now. age measurement datum OBI:0001168 age since fertilization measurement datum An age measurement datum that is the result of the measurement of the age of an organism since fertilization, the process of the union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. Definition of fertilization comes from GO. PERSON:Chris Stoeckert, Jie Zheng MO_701 fertilization age since fertilization measurement datum OBI:0001169 age since birth measurement datum An age measurement datum that is the result of the measurement of the age of an organism since birth, the process of emergence and separation of offspring from the mother. PERSON:Chris Stoeckert, Jie Zheng MO_710 birth age since birth measurement datum OBI:0001170 reverse transcription polymerase chain reaction assay an assay that evaluates the concentration of RNA in a sample in which an RNA strand is first reverse transcribed into its DNA complement (complementary DNA, or cDNA) using the enzyme reverse transcriptase, and the resulting cDNA is amplified using traditional or real-time PCR. PERSON: Chris Stoeckert, Jie Zheng GROUP: Penn Group reverse transcription polymerase chain reaction assay OBI:0001175 selective organism creation objective an objective specification to generate a population or type of organism within species that have some uniform behavioral, morphological, physiological, or genetic characteristics with similarly bred organisms. PERSON: Chris Stoeckert, Jie Zheng WEB: wikipedia http://en.wikipedia.org/wiki/Cultivar http://en.wikipedia.org/wiki/Ecotype http://en.wikipedia.org/wiki/Strain_%28biology%29 selective organism creation objective OBI:0001177 RNA sequencing RNA sequencing is a sequencing process which uses ribonucleic acid as input and results in a the creation of RNA sequence information artifact BP 12/21:Created based on a request from Melanie Bjoern Peters Bjoern Peters RNA sequencing OBI:0001181 binding datum A data item that states if two or more material entities have the disposition to form a complex, and if so, how strong that disposition is. Bjoern Peters; Randi Vita binding datum OBI:0001185 selectively maintained organism An organism that is bred to have some uniform behavioral, morphological, physiological, or genetic characteristics with similarly bred organisms Bjoern Peters, Helen Parkinson, Philippe Rocca-Serra, Jie Zheng, Chris Stoeckert cultivar ecotype strain MO_9 StrainOrLine, MO_71 Ecotype, MO_124 Cultivar selectively maintained organism OBI:0001195 operator variation design A study design that assesses the operator performance and relation to data consistency and quality. Person: Chris Stoeckert, Jie Zheng MO_519 operator_variation_design operator variation design OBI:0001197 comparative genome hybridization by array design A study design that detects genomic copy number variations using microarray technology. Person: Chris Stoeckert, Jie Zheng MO_856 comparative_genome_hybridization_design comparative genome hybridization by array design OBI:0001199 in vivo design A study design that is conducted entirely in a living organism, e.g. a compound treatment in a mouse model. Person: Chris Stoeckert, Jie Zheng MO_454 in_vivo_design in vivo design OBI:0001200 genotyping by high throughput sequencing design A study design that classifies an individual or group of individuals on the basis of alleles, haplotypes, SNPs using high througput sequencing techniques. Person: Chris Stoeckert, Jie Zheng MO_560 genotyping_design genotyping by high throughput sequencing design OBI:0001202 innate behavior design A study design in which the innate behavior of the organism is examined, e.g. path finding in bees. Person: Chris Stoeckert, Jie Zheng MO_355 innate_behavior_design innate behavior design OBI:0001205 cell component comparison design A study design that compares samples from different cell components. Person: Chris Stoeckert, Jie Zheng MO_1019 cell_component_comparison_design cell component comparison design OBI:0001211 ex vivo design A study design where all or part of an organism is removed and studied in vitro, e.g. part of a mouse is removed and cultured in vitro. A cell culture with an established cell line is an in vitro experiment. Person: Chris Stoeckert, Jie Zheng MO_808 ex_vivo_design ex vivo design OBI:0001214 normalization testing design A study design that tests different normalization procedures. Person: Chris Stoeckert, Jie Zheng MO_729 normalization_testing_design normalization testing design OBI:0001225 genetic population background information genotype information 'C57BL/6J Hnf1a+/-' in this case, C57BL/6J is the genetic population background information a genetic characteristics information which is a part of genotype information that identifies the population of organisms proposed and discussed on San Diego OBI workshop, March 2011 Group: OBI group Group: OBI group genetic population background information OBI:0001226 environmental history design A study design in which some aspect of the organism's environmental history is studied, such as exposure to teratogen, radiation, climate etc. Person: Chris Stoeckert, Jie Zheng MO_698 environmental_history_design environmental history design OBI:0001234 epigenetic modification identification objective A molecular feature identification objective that aims to detect epigenetic modifications, such as DNA methylation, histone modifications. Chris Stoeckert, Jie Zheng Person: Chris Stoeckert epigenetic modification identification objective OBI:0001235 transcription profiling by tiling array assay An assay in which the transcriptome of a biological sample is analysed using a tiling path array. Person: James Malone EFO_0002769 transcription profiling by tiling array transcription profiling by tiling array assay OBI:0001239 transcription profiling by high throughput sequencing design A study design in which sequencing technology (e.g. Solexa/454) is used to generate RNA sequence, analyse the transcibed regions of the genome, and/or to quantitate transcript abundance Person: Chris Stoeckert, Jie Zheng Group: ArrayExpress production team transcription profiling by high throughput sequencing design OBI:0001247 genotyping by high throughput sequencing assay An assay in which high througput sequencer is used to detect polymorphisms in DNA samples Person: James Malone EFO_0002771: genotyping by high throughput sequencing genotyping by high throughput sequencing assay OBI:0001248 ChIP-chip assay an assay that aims to investigate the interactions between protein and DNA relying on chromatin immunoprecipitation ('ChIP') combined with microarray technology ('chip'). Specially, it allows the identification of protein binding sites on a genome-wide basis. Person: James Malone ChIP-on-chip assay WEB: http://en.wikipedia.org/wiki/ChIP-on-chip Philippe Rocca-Serra ChIP-chip assay OBI:0001252 array platform variation design A study design in which the array platform is compared, e.g. Agilent versus Affymetrix. Person: Chris Stoeckert, Jie Zheng MO_899 array_platform_variation_design array platform variation design OBI:0001258 ChIP-seq design A study design which aims to identify protein and DNA interactions using a combination of chromatin immunoprecipitation and high throughput sequencing. Massively parallel sequence analyses are used in conjunction with whole-genome sequence databases to analyze the interaction pattern of any protein with DNA, or the pattern of any epigenetic chromatin modifications. Person: Chris Stoeckert, Jie Zheng http://en.wikipedia.org/wiki/Chip-Sequencing ChIP-seq design OBI:0001259 translational bias design A study design that characterizes the association of transcripts and translation machinery. Person: Chris Stoeckert, Jie Zheng MO_939 translational_bias_design translational bias design OBI:0001266 DNA methylation profiling by high throughput sequencing assay An assay in which the methylation state of DNA is determined and is compared between samples using sequencing based technology Group: ArrayExpress production team, James Malone, Helen Parkinson EFO_0002761 methylation profiling by high throughput sequencing Philippe Rocca-Serra DNA methylation profiling by high throughput sequencing assay OBI:0001271 RNA-seq assay An assay in which sequencing technology (e.g. Solexa/454) is used to generate RNA sequence, analyse the transcibed regions of the genome, and or to quantitate transcript abundance PERSON: James Malone transcription profiling by high throughput sequencing EFO_0002770 transcription profiling by high throughput sequencing JZ: should be inferred as 'DNA sequencing'. Will check in the future. an assay that uses high-throughput sequencing technologies to sequence cDNA in order to get information about a sample's RNA content. RNA-Seq provides researchers with efficient ways to measure transcriptome data experimentally, allowing them to get information such as how different alleles of a gene are expressed, detect post-transcriptional mutations or identify gene fusions. WEB: http://en.wikipedia.org/wiki/RNA-Seq RNA-seq assay OBI:0001274 genotyping by array assay An assay in which an array is used to detect polymorphisms in DNA samples Group: ArrayExpress production team EFO_0002767: genotyping by array genotyping by array assay OBI:0001278 DNA methylation profiling by array design A study design in which the methylation state of DNA is determined and is compared between samples using array technology. Person: Chris Stoeckert, Jie Zheng GROUP: ArrayExpress production team DNA methylation profiling by array design OBI:0001282 translation profiling assay An assay in which surface-bound, translationally competent ribosome complexes are used to generate a translation profile for mRNA, which mRNA may be a single molecular species, or a combination of species, including complex mixtures such as those found in the set of mRNAs isolated from a cell or tissue. One or more components of the surface-bound ribosome complex may be labeled at specific positions to permit analysis of multiple or single molecules for determination of ribosomal conformational changes and translation kinetics. Translation profiles are used as the basis for comparison of an mRNA or set of mRNA species. The translation profile can be used to determine such characteristics as kinetics of initiation, kinetic of elongation, identity of the polypeptide product, and the like. Analysis of translation profiles may be used to determine differential gene expression, optimization of mRNA sequences for expression, screening drug candidates for an effect on translation. PERSON: James Malone EFO_0001033 translation profiling translation profiling assay OBI:0001285 in vitro design A study design that is done in a test tube or a culture dish, e.g. A bacterial invasion assay in an established cell culture. Person: Chris Stoeckert, Jie Zheng MO_347 in_vitro_design in vitro design OBI:0001286 RNAi profiling by array design A study design in which experiment double stranded RNA is synthesized with a sequence complementary to a gene(s) of interest and introduced into a cell or organism, where it is recognized as exogenous genetic material and activates the RNAi pathway resulting in knockdown of the transcripts and providing a means to study downstream changes in gene expression. Person: Chris Stoeckert, Jie Zheng Group: ArrayExpress production team RNAi profiling by array design OBI:0001290 transcription profiling by array design A study design that identifies forms and abundance of transcripts in the genome using microarray technology. Person: Chris Stoeckert, Jie Zheng MO_533 transcript_identification_design transcription profiling by array design OBI:0001293 disease state design A study design in which the pathological condition of a part, organ, or system of an organism is studied. The etiology may be from infection, genetic defect, or environmental stress. Person: Chris Stoeckert, Jie Zheng MO_902 disease_state_design disease state design OBI:0001294 wild type organism genotype information C57BL/6J wild type a genotype information about an organism and includes information that there are no known modifications to the genetic background. Generally it is the genotype information of a representative individual from a class of organisms. proposed and discussed on San Diego OBI workshop, March 2011 Group: OBI group Group: OBI group wild type organism genotype information OBI:0001304 RNAi profiling by array assay An assay in which double stranded RNA is synthesized with a sequence complementary to a gene(s) of interest and introduced into a cell or organism, where it is recognized as exogenous genetic material and activates the RNAi pathway resulting in knockdown of the transcripts and providing a means to study downstream changes in gene expression. PERSON: James Malone EFO_0001030 RNAi profiling by array RNAi profiling by array assay OBI:0001305 genotype information Genotype information can be: Mus musculus wild type (in this case the genetic population background information is Mus musculus), C57BL/6J Hnf1a+/- (in this case, C57BL/6J is the genetic population background information and Hnf1a+/- is the allele information a genetic characteristics information that is about the genetic material of an organism and minimally includes information about the genetic background and can in addition contain information about specific alleles, genetic modifications, etc. discussed on San Diego OBI workshop, March 2011 Group: OBI group Group: OBI group genotype information OBI:0001306 RNA stability design A study design that examines the stability and/or decay of RNA transcripts. Person: Chris Stoeckert, Jie Zheng MO_553 RNA_stability_design RNA stability design OBI:0001307 tiling microarray a DNA microarray which has short fragments of nucleic acid immobilized on a substrate. These are designed to cover the whole genome of the target species. Tiling arrays are used to determine genome binding in ChIP assays or to identify transcribed regions. Person: Helen Parkinson genome tiling array EFO_0002704: tiling array tiling microarray OBI:0001310 species comparison design A study design that assays differences between distinct species. Person: Chris Stoeckert, Jie Zheng MO_675 species_design species comparison design OBI:0001313 transcription profiling by RT-PCR design A study design which aims to examine the transcriptome of a biological sample by reverse transcription PCR (RT-PCR). Person: Chris Stoeckert, Jie Zheng Group: ArrayExpress production team transcription profiling by RT-PCR design OBI:0001318 proteomic profiling by array assay An assay that proteins in a sample are detected, quantified or otherwise analysed, e.g. antibody profiling using an array based technology Person: James Malone EFO_0002765 proteomic profiling by array proteomic profiling by array assay OBI:0001323 microRNA profiling by array design A study design in which a microRNA array is used to analyse the microRNA component of the transcriptome. Person: Chris Stoeckert, Jie Zheng Group: ArrayExpress production team microRNA profiling by array design OBI:0001328 organism development design A study design that assays events associated with development. Development applies to organism(s) acquiring a mature state. Person: Chris Stoeckert, Jie Zheng MO_892 development_or_differentiation_design organism development design OBI:0001329 family history design A study design in which the family history such as traits, characteristics, susceptibility to disease is studied. Person: Chris Stoeckert, Jie Zheng MO_544 family_history_design family history design OBI:0001331 transcription profiling identification objective A molecular feature identification objective that aims to characterize the abundance of transcripts Person: Chris Stoeckert, Jie Zheng Group: Penn Group transcription profiling identification objective OBI:0001332 DNA methylation profiling by array assay An assay in which the methylation state of DNA is determined and is compared between samples using array technology Person: James Malone EFO_0002759 methylation profiling by array Philippe Rocca-Serra DNA methylation profiling by array assay OBI:0001335 microRNA profiling by array assay An assay in which a microRNA array is used to analyse the microRNA component of the transcriptome. PERSON: James Malone EFO_0000753 microRNA profiling by array microRNA profiling by array assay OBI:0001336 quality control testing design A study design in which some aspects of the experiment is quality controlled for the purposes of quality assurance. Person: Chris Stoeckert, Jie Zheng MO_981 quality_control_testing_design quality control testing design OBI:0001337 clinical history design A study design that the organism's clinical history of diagnosis, treatments, e.g. vaccinations, surgery etc. is studied. Person: Chris Stoeckert, Jie Zheng MO_832 clinical_history_design clinical history design OBI:0001352 allele information genotype information 'C57BL/6J Hnf1a+/-' in this case, Hnf1a+/- is the allele information a genetic alteration information that about one of two or more alternative forms of a gene or marker sequence and differing from other alleles at one or more mutational sites based on sequence. Polymorphisms are included in this definition. discussed on San Diego OBI workshop, March 2011 Person: Chris Stoeckert, Jie Zheng MO_58 Allele allele information OBI:0001358 post-transcriptional modification design A study design in which a modification of the transcriptome, proteome (not genome) is made, for example RNAi, antibody targeting. Person: Chris Stoeckert, Jie Zheng MO_392 cellular_modification_design post transcription modification design? or more clear RNAi design / antibody targeting design? need to check the use cases post-transcriptional modification design OBI:0001361 transcription profiling by RT-PCR assay An assay in which the transcriptome of a biological sample is analysed by reverse transcription PCR (RT-PCR) Person: Anna Farne EFO_0002943: transcription profiling by RT-PCR transcription profiling by RT-PCR assay OBI:0001364 genetic alteration information a genetic characteristics information that is about known changes or the lack thereof from the genetic background, including allele information, duplication, insertion, deletion, etc. proposed and discussed on San Diego OBI workshop, March 2011 Group: OBI group Group: OBI group genetic alteration information OBI:0001365 cellular process design A study design that aims to study the processes that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. Person: Chris Stoeckert, Jie Zheng MO_810 cellular_process_design cellular process design OBI:0001369 wild type allele information an allele information that is about the allele found most frequently in natural populations, or in standard laboratory stocks for a given organism. discussed on San Diego OBI workshop, March 2011 Person: Chris Stoeckert, Jie Zheng MO_605 genotype wild type allele information OBI:0001374 injury design A study design in which the response of an organism(s) to injury or damage is studied. Person: Chris Stoeckert, Jie Zheng MO_726 injury_design injury design OBI:0001377 organism status comparison design A study design that compares samples from live and dead organisms. Person: Chris Stoeckert, Jie Zheng MO_841 organism_status_design organism status comparison design OBI:0001387 genotyping by array design A study design that classifies an individual or group of individuals on the basis of alleles, haplotypes, SNPs using microarray technology. Person: Chris Stoeckert, Jie Zheng MO_560 genotyping_design genotyping by array design OBI:0001393 comparative genomic hybridization by array assay An assay in which changes in DNA sequence copy number are analysed using a microarray. For example the analysis of LOH in tumor cells vs a non diseased sample or the comparison of clinical isolated of disease causing bacteria. Person: James Malone array CGH EFO_0000749: comparative genomic hybridization by array Philippe Rocca-Serra comparative genomic hybridization by array assay OBI:0001396 stimulus or stress design A study design in which the response of an organism(s) to the stress or stimulus is studied, e.g. osmotic stress, heat shock, radiation exposure, behavioral treatment etc. Person: Chris Stoeckert, Jie Zheng MO_568 stimulus_or_stress_design stimulus or stress design OBI:0001398 protein and DNA interaction identification objective A sequence feature identification objective that aims to characterize the interactions between protein and DNA which includes identification of transcription factor binding sites. Person: Chris Stoeckert, Jie Zheng MO_933 binding_site_identification_design protein and DNA interaction identification objective OBI:0001401 protocol optimization design A study design where different protocols or protocol parameters are compared aims to find an optimized protocol Person: Chris Stoeckert, Jie Zheng MO_934 optimization_design protocol optimization design OBI:0001403 ChIP-chip design A study design which aims to identify protein binding sites in genomic DNA by a combination of chromatin immunoprecipitation and DNA microarray (chip) assays. Person: Chris Stoeckert, Jie Zheng ChIP-on-chip design MO_933 binding_site_identification_design ChIP-chip design OBI:0001404 genetic characteristics information a data item that is about genetic material including polymorphisms, disease alleles, and haplotypes. Person: Chris Stoeckert, Jie Zheng MO_66 IndividualGeneticCharacteristics MO definition: The genotype of the individual organism from which the biomaterial was derived. Individual genetic characteristics include polymorphisms, disease alleles, and haplotypes. examples in ArrayExpress wild_type MutaMouse (CD2F1 mice with lambda-gt10LacZ integration) AlfpCre; SNF5 flox/knockout p53 knock out C57Bl/6 gp130lox/lox MLC2vCRE/+ fer-15; fem-1 df/df pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid) genetic characteristics information OBI:0001408 imprinting design A study design where differences in genetic imprinting of maternally- and paternally-inherited chromosomes (e.g., due to in vivo differences in chemical modification and/or chromatin structure) are compared. Person: Chris Stoeckert, Jie Zheng MO_914 imprinting_design imprinting design OBI:0001409 cell cycle design A study design that assays events that occur in relation to the cell cycle, which is the period between the formation of a cell, by division of its mother cell and the time when the cell itself divides to form two daughter cells. Person: Chris Stoeckert, Jie Zheng MO_822 cell_cycle_design cell cycle design OBI:0001410 translation profiling design A study design in which surface-bound, translationally competent ribosome complexes are used to generate a translation profile for mRNA, where mRNA may be a single molecular species, or a combination of species, including complex mixtures such as those found in the set of mRNAs isolated from a cell or tissue. One or more components of the surface-bound ribosome complex may be labeled at specific positions to permit analysis of multiple or single molecules for determination of ribosomal conformational changes and translation kinetics. Translation profiles are used as the basis for comparison of an mRNA or set of mRNA species. The translation profile can be used to determine such characteristics as kinetics of initiation, kinetic of elongation, identity of the polypeptide product, and the like. Analysis of translation profiles may be used to determine differential gene expression, optimization of mRNA sequences for expression, screening drug candidates for an effect on translation. Person: Chris Stoeckert, Jie Zheng Group: ArrayExpress production team translation profiling design OBI:0001411 cell type comparison design A study design that compares cells of different type, for example different cell lines. Person: Chris Stoeckert, Jie Zheng MO_764 cell_type_comparison_design cell type comparison design OBI:0001417 ChIP-chip by tiling array design A study design which aims to identify protein binding sites in genomic DNA by a combination of chromatin immunoprecipitation and tiling microarray (chip) assays. Person: Chris Stoeckert, Jie Zheng Group: ArrayExpress production team ChIP-chip by tiling array design OBI:0001418 dose response design A study design that examines the relationship between the size of the administered dose and the extent of the response. Person: Chris Stoeckert, Jie Zheng MO_485 dose_response_design dose response design OBI:0001419 ChIP-chip by tiling array assay An assay where chromatin immunoprecipitation (ChIP) is used in combination with tiling microarray technology Group: ArrayExpress production team EFO_0002762 ChIP-chip by tiling array ChIP-chip by tiling array assay OBI:0001422 organism part comparison design A study design that compares tissues, regions, organs within or between organisms Person: Chris Stoeckert, Jie Zheng MO_953 organism_part_comparison_design organism part comparison design OBI:0001425 protein binding site identification design A study design that investigates protein binding sites on nucleic acids. Person: Chris Stoeckert, Jie Zheng MO_933 binding_site_identification_design protein binding site identification design OBI:0001426 sex comparison design A study design that assays differences associated with an organism's sex, gender or mating type. Person: Chris Stoeckert, Jie Zheng MO_575 sex_design sex comparison design OBI:0001427 transcription profiling by tiling array design A study design in which gene expression on a genome-wide basis is evaluated, without bias toward coding or noncoding regions, using tiling arrays containing oligonucleotides that are either overlapping or spaced at regular intervals. Person: Chris Stoeckert, Jie Zheng MO_507 tiling_path_design transcription profiling by tiling array design OBI:0001429 cell differentiation design A study design that assays events associated with cell development or differentiation. Person: Chris Stoeckert, Jie Zheng MO_892 development_or_differentiation_design cell differentiation design OBI:0001430 transcription profiling design A study design that identifies forms and abundance of transcripts in the genome. Person: Chris Stoeckert, Jie Zheng MO_533 transcript_identification_design transcription profiling design OBI:0001432 operon identification design A study design that identifies locations and members of operons in a genome. Person: Chris Stoeckert, Jie Zheng MO_772 operon_identification_design operon identification design OBI:0001435 DNA methylation profiling by high throughput sequencing design A study design in which the methylation state of DNA is determined and is compared between samples using high throughput sequencing technology. Person: Chris Stoeckert, Jie Zheng GROUP: ArrayExpress production team DNA methylation profiling by high throughput sequencing design OBI:0001440 all pairs design A study design in which all specimens are compared to every other specimen. Person: Chris Stoeckert, Jie Zheng MO_565 all_pairs all pairs design OBI:0001441 proteomic profiling by array design A study design in which proteins in a sample are detected, quantified or otherwise analysed, e.g. antibody profiling using an array based technology Person: Chris Stoeckert, Jie Zheng Group: ArrayExpress production team proteomic profiling by array design OBI:0001444 genotyping design A study design that classifies an individual or group of individuals on the basis of alleles, haplotypes, SNPs. Person: Chris Stoeckert, Jie Zheng MO_560 genotyping_design genotyping design OBI:0001448 individual genetic characteristics comparison design A study design where genotype, haplotype, or other individual genetic characteristics are compared. Person: Chris Stoeckert, Jie Zheng MO_527 individual_genetic_characteristics_design individual genetic characteristics comparison design OBI:0001454 pathogenicity design A study design in which an infective agent such as a bacterium, virus, protozoan, fungus etc. infects a host organism(s) and the infective agent is assayed. Person: Chris Stoeckert, Jie Zheng MO_807 pathogenicity_design pathogenicity design OBI:0001460 genetic modification design A study design in which an organism(s) is studied that has had genetic material removed, rearranged, mutagenized or added, such as in a knock out. Person: Chris Stoeckert, Jie Zheng MO_447 genetic_modification_design genetic modification design OBI:0001463 transcription profiling by array assay An assay in which the transcriptome of a biological sample is analysed using array technology. Person: James Malone EFO_0002768: transcription profiling by array transcription profiling by array assay OBI:0001464 strain comparison design A study design that assays differences between multiple strains, cultivars, serovars, isolates, lines from organisms of a single species. Person: Chris Stoeckert, Jie Zheng MO_462 strain_or_line_design strain comparison design OBI:0001468 cell specimen A specimen primarily composed of cells collected from a multicellular organism or a cell culture PERSON: Chris Stoeckert, Jie Zheng MO_612 cell cell specimen OBI:0001472 specimen with known storage state A specimen for which it is known whether it has been subjected to storage of a specified type. PERSON: Chris Stoeckert, Jie Zheng MO_95 BiosourceType specimen with known storage state OBI:0001474 lowess group transformation A lowess transformation where a potentially different normalization curve is generated and used for two or more groups (delineated by some criteria); criteria could include blocks (e.g. print-tip groups) on an array, or the day on which mass spectrometry was performed. Person: Elisabetta Manduchi MO_861 lowess_group_normalization lowess group transformation OBI:0001477 lowess transformation A data transformation of normalizing ratio data by using a locally weighted polynomial regression (typically after a log transformation). The regression can be performed on log ratios resulting from the relation of two data sets versus the average log intensity data from the same two data sets or it can be performed on raw or log transformed values from one data set versus values from another. The goal could be to remove intensity-dependent dye-specific effects from the set of pair wise ratios. This method can be applied globally, or limited by one or more specified criteria. Person: Elisabetta Manduchi MO_720 lowess_normalization lowess transformation OBI:0001479 tissue specimen A specimen that derives from an anatomical part or substance arising from an organism. Examples of tissue specimen include tissue, organ, physiological system, blood, or body location (arm). PERSON: Chris Stoeckert, Jie Zheng MO_954 organism_part tissue specimen OBI:0001481 lowess global transformation A lowess transformation where the same normalization curve is used for all members of the data set; e.g. Features on an array, picked spots on a gel, or measured metabolites in a sample. Person: Elisabetta Manduchi MO_692 lowess_global_normalization lowess global transformation OBI:0001483 cell collecting A planned process that collects cells from culture. PERSON: Chris Stoeckert, Jie Zheng MO_982 harvest cell collecting OBI:0001494 linear amplification An example is the use of the T7 promoter for amplification by transcribing many RNA copies. An enzymatic amplification which amplifies nucleic acid sequence by making many copies off the same template. PERSON: Chris Stoeckert, Jie Zheng MO_997 linear_amplification linear amplification OBI:0001498 atmosphere A growth environment pertaining to the atmospheric conditions that is used to culture or grow an organism. PERSON: Chris Stoeckert, Jie Zheng MO_219 atmosphere atmosphere OBI:0001504 dissection A planned process that separates and isolates tissues for surgical purposes, or for the analysis or study of their structures. PERSON: Chris Stoeckert, Jie Zheng EFO_0003856 dissection MO_374 dissect dissection OBI:0001505 purification A planned process to separate a material entity into different compositions of which one or more have are purified fractions that contain higher concentration of a desired component, while others contain impurities and are not of interest PERSON: Chris Stoeckert, Jie Zheng MO_406 purify purification OBI:0001506 specimen with pre- or post-mortem status A specimen that has been established to be taken from a live (pre-mortem) or dead (post-mortem) organism. organizational term, used in description of specimen that is created from known pre- or post-mortem status PERSON: Chris Stoeckert, Jie Zheng MO_84 OrganismStatus specimen with pre- or post-mortem status OBI:0001508 sampling time measurement datum A time measurement datum when an observation is made or a sample is taken from a material as measured from some reference point. Person: Chris Stoeckert time point MO_738 timepoint sampling time measurement datum OBI:0001573 DNA sequence data The part of a FASTA file that contains the letters ACTGGGAA A sequence data item that is about the primary structure of DNA OBI call; Bjoern Peters OBI call; Melanie Courtout 8/29/11 call: This is added after a request from Melanie and Yu. They should review it further. This should be a child of 'sequence data', and as of the current definition will infer there. DNA sequence data OBI:0001588 binding A peptide binding to an MHC molecule to form a complex. The process of material entities forming complexes. 9/28/11 BP: The disposition referenced is the one of the ligand to bind the molecule. This along with binding as a function / process needs to be figured out with GO which is inconsistent at this point. PERSON: Bjoern Peters, Randi Vita IEDB binding OBI:0001617 PubMed ID A CRID symbol that is sufficient to look up a citation from the PubMed, a literature database of life sciences and biomedical information. Person: Chris Stoeckert, Jie Zheng PMID PubMed Identifier Website: http://en.wikipedia.org/wiki/Wikipedia:PMID Publication Citation NIAID GSCID-BRC PubMed ID OBI:0001674 cap analysis of gene expression 5' end-centered expression profiling using cap-analysis gene expression and next-generation sequencing. Takahashi H, Lassmann T, Murata M, Carninci P. Nat Protoc. 2012 Feb 23;7(3):542-61. doi: 10.1038/nprot.2012.005. PMID: 22362160 An assay which aims at monitoring RNA transcript abundances in biological samples by extracting 5' ends of capped transcripts, RTPCR and sequence those. Copy numbers of CAGE tags provide a way of quantification and provide a measure of expression of the transcriptome PERSON:Philippe Rocca-Serra; Marcus Chibucos CAGE PMID:14663149 cap analysis of gene expression OBI:0001700 immunoprecipitation assay Determining if a cell is producing a protein using a protein specific antibody to immunoprecipitate the cell lysate. Determining if the serum of a patient contains antibodies against HBV core protein by immunoprecipitating purified HBV core protein with the patients serum. An assay with the objective to determine presence of an analyte by mixing a solution of antigen and antibody and separating out bound antigen:antibody complexes using immunoprecipitation. Either the antibody has known specificy, and the antigen mixture is tested for the presence of a specific antigen, or the antigen solution is well defined and the antibody solution is tested for the presence of antigen specific antibodies. PERSON:Bjoern Peters, Randi Vita IEDB immunoprecipitation assay OBI:0001848 chromatin interaction analysis by paired-end tag sequencing Zhang, et al. ChIA-PET analysis of transcriptional chromatin interactions. Methods. 2012 Nov;58(3):289-99. [PMID:22926262] An assay that incorporates chromatin immunoprecipitation (ChIP)-based enrichment, chromatin proximity ligation, Paired-End Tags, and high-throughput sequencing to determine de novo long-range chromatin interactions genome-wide. Person: Venkat Malladi, Chris Stoeckert, Jie Zheng ChIA-PET ChIA-PET assay http://en.wikipedia.org/wiki/ChIA-PET ENCODE project chromatin interaction analysis by paired-end tag sequencing OBI:0001849 structural analysis by paired-end tag sequencing Yao, et al. Long Span DNA Paired-End-Tag (DNA-PET) Sequencing Strategy for the Interrogation of Genomic Structural Mutations and Fusion-Point-Guided Reconstruction of Amplicons. PLoS One. 2012;7(9):e46152 [PMID:23029419] An assay that incorporates Paired-End Tags and sequencing technology to determine structural variants. Person: Venkat Malladi, Chris Stoeckert, Jie Zheng DNA-PET DNA-PET assay Yao, et al. Long Span DNA Paired-End-Tag (DNA-PET) Sequencing Strategy for the Interrogation of Genomic Structural Mutations and Fusion-Point-Guided Reconstruction of Amplicons. PLoS One. 2012;7(9):e46152 [PMID:23029419] ENCODE project structural analysis by paired-end tag sequencing OBI:0001850 transcript analysis by paired-end tag sequencing Ruan, et al. Genome wide full-length transcript analysis using 5' and 3' paired-end-tag next generation sequencing (RNA-PET). Methods Mol Biol. 2012;809:535-62. [PMID:22113299] An assay that incorporates Paired-End Tags and sequencing technology to determine transcripts, gene structures, and gene expressions. Person: Venkat Malladi, Chris Stoeckert, Jie Zheng RNA-PET RNA-PET assay Ruan, et al. Genome wide full-length transcript analysis using 5' and 3' paired-end-tag next generation sequencing (RNA-PET). Methods Mol Biol. 2012;809:535-62. [PMID:22113299] ENCODE project transcript analysis by paired-end tag sequencing OBI:0001851 transcription start site identification objective A transcription profiling identification objective that aims to characterize the transcription start sites of genes. Person: Chris Stoeckert, Jie Zheng Penn Group transcription start site identification objective OBI:0001852 paired-end library preparation A library preparation that results in the creation of a library of the 5' and 3' ends of DNA or cDNA fragments using adaptors and endonucleases. The preparation may or may not include cloning process. Person: Venkat Malladi, Jie Zheng Venkat Malladi, Jie Zheng ENCODE project paired-end library preparation OBI:0001853 DNase I hypersensitive sites sequencing assay Sabo, et al. Discovery of functional noncoding elements by digital analysis of chromatin structure. Proc Natl Acad Sci U S A. 2004 Nov 30;101(48):16837-42. [PMID:15550541] An assay to identify the location of regulatory regions, based on the genome-wide sequencing of regions super sensitive to cleavage by DNase I. Person: Venkat Malladi, Chris Stoeckert, Jie Zheng DNase-seq DNase-seq assay http://en.wikipedia.org/wiki/DNase-Seq ENCODE project DNase I hypersensitive sites sequencing assay OBI:0001854 protein and RNA interaction identification objective A sequence feature identification objective that aims to characterize the interactions between protein and RNA. JZ: Term added for ENCODE project requested assays. Definition adapted from 'protein and DNA interaction identification objective'. Person: Jie Zheng Jie Zheng protein and RNA interaction identification objective OBI:0001857 RNP (ribonuclear particle) immunoprecipitation high- throughput sequencing assay Zhao et al. Genome-wide identification of polycomb-associated RNAs by RIP-seq. Molecular Cell (2010) vol. 40 (6) pp. 939-53 [PMID:21172659] An assay that combines immunoprecipitation of an RNA-binding protein and RNA-seq to identify mRNAs associated with selected RNA binding proteins (RBPs). Person: Venkat Malladi, Chris Stoeckert, Jie Zheng RIP-seq RIP-seq assay Zhao et al. Genome-wide identification of polycomb-associated RNAs by RIP-seq. Molecular Cell (2010) vol. 40 (6) pp. 939-53 [PMID:21172659] ENCODE project RNP (ribonuclear particle) immunoprecipitation high- throughput sequencing assay OBI:0001858 cross-linking immunoprecipitation high-throughput sequencing assay Heulga et al. Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins. Cell Rep. 2012 Feb 23;1(2):167-78. [PMID:22574288] An assay that employs UV-crosslinking between RNA and the protein, followed by immunoprecipitation with antibodies for the protein, fragmentation, and high-throughput used for screening for RNA sequences that interact with a particular RNA-binding protein. Person: Venkat Malladi, Chris Stoeckert, Jie Zheng CLIP-seq CLIP-seq assay HITS-CLIP Licatalosi et al. HITS-CLIP yields genome-wide insights into brain alternative RNA processing. Nature. 2008 Nov 27 456: 464-469 [PMID:18978773] ENCODE project cross-linking immunoprecipitation high-throughput sequencing assay OBI:0001859 formaldehyde-assisted isolation of regulatory elements assay Giresi, et al. FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin. Genome Research 17 (6): 877–85. [PMID:17179217] An assay to determine the sequences of those DNA regions in the genome associated with regulatory activity. Person: Venkat Malladi, Chris Stoeckert, Jie Zheng FAIRE-seq FAIRE-seq assay http://en.wikipedia.org/wiki/FAIRE-Seq ENCODE project formaldehyde-assisted isolation of regulatory elements assay OBI:0001861 methylation-sensitive restriction enzyme sequencing assay Maunakea et al. Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature. 2010 Jul 8;466(7303):253-7. [PMID:20613842] An assay that identifies unmethylated CpGs by use of methylation sensitive restriction enzymes to fragment DNA. Person: Venkat Malladi, Chris Stoeckert, Jie Zheng MRE-seq MRE-seq assay Maunakea et al. Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature. 2010 Jul 8;466(7303):253-7. [PMID:20613842] ENCODE project methylation-sensitive restriction enzyme sequencing assay OBI:0001862 reduced representation bisulfite sequencing assay Meissner et al. Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis. Nucleic Acids Res. 2005; 33(18): 5868–5877. [PMCID: PMC1258174] A bisulfite sequencing assay that identifies genomic methylation patterns by using a bisulfite based protocol that enriches CG-rich parts of the genome. Person: Venkat Malladi, Chris Stoeckert, Jie Zheng RRBS RRBS assay reduced representation bisulfite-seq Meissner et al. Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis. Nucleic Acids Res. 2005; 33(18): 5868–5877. [PMCID: PMC1258174] ENCODE project reduced representation bisulfite sequencing assay OBI:0001863 shotgun bisulfite-seq assay Cokus et al. Shotgun bisulfite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature. 2008 Mar 13;452(7184):215-9. [PMID:18278030]. A bisulfite sequencing assay that identifies methylated cytosines across the genome using high throughput sequencing. Person: Venkat Malladi, Chris Stoeckert, Jie Zheng Shotgun bisulfite sequencing WGBS WGSBS whole genome bisulfite sequencing whole-genome shotgun bisulfite sequencing Cokus et al. Shotgun bisulfite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature. 2008 Mar 13;452(7184):215-9. [PMID:18278030] ENCODE project shotgun bisulfite-seq assay OBI:0001864 RNA Annotation and Mapping of Promoters for the Analysis of Gene Expression assay Batut et al. High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression. Genome Research. 2013 Jan;23(1):169-80. [PMID:22936248] An assay that identifies transcription start sites (TSS), the quantification of their expression and the characterization of their transcripts using high throughput sequencing. Person: Venkat Malladi, Chris Stoeckert, Jie Zheng RAMPAGE Batut et al. High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression. Genome Research. 2013 Jan;23(1):169-80. [PMID:22936248] ENCODE project RNA Annotation and Mapping of Promoters for the Analysis of Gene Expression assay OBI:0001865 assay array A device made to be used in an analyte assay for immobilization of substances that bind the analyte at regular spatial positions on a surface. PERSON: Chris Stoeckert, Jie Zheng, Alan Ruttenberg Penn Group assay array OBI:0001866 secondary cultured cell A cultured cell that has been passaged or derives from a cell that has been passaged in culture. The term 'secondary cell culture' is generally used in biological texts/protocols to refer to any culture following an initial passage. We include it here because there are often a number of passages between a primary culture and the establishment of a stable, homogenous cell line. Such cultures are considered to be 'secondary cultures' but not 'cell lines' during this intermediate passaging/selection period between their derivation from a 'primary cell culture' and derivation into a 'cell line', which is a more specific type of secondary culture. Person: Matthew Brush PERSON: Matthew Brush A secondary cultured cell has been passaged in culture or is a descendant of such a cell that is derived through propagation in culture. secondary cultured cell OBI:0001867 establishing cell line a process whereby a new type of cell line is created, either through passaging of a primary cell culture to relative genetic stability and compositional homogeneity, or through some experimental modification of an existing cell line to produce a new line with novel characteristics (e.g. immortalization or some other stable genetic modification, or selection of some defined subset). 2013-4-20 MHB: For cases of initial establilshment of a line from a primary culture, successive passaging and/or selection processes can confer increasing degrees of genetic stability and compositional homogeneity as compared to the input primary culture. Historically, many texts consider the first passage as the clearest point to define the beginning of a line. However, in practice it is more often that case that more than one passage, and possibly additional selective techniques, may be required before a culture is deemed to have sufficient stability and homogeneity to be considered cell line. This is the view taken in OBI. Regardless, what is important is that some intentional, experimental step has been taken to establish a more homogenous and stable culture that can be characterized and progatated over time. Person: Matthew Brush PERSON:Matthew Brush establishing cell line OBI:0001905 secondary cultured cell population A cultured cell population that is derived through one or more passages in culture. The term 'secondary cell culture' is generally used in biological texts/protocols to refer to any culture of cells following an initial passage. We include it here because there are often a number of passages between a primary culture and the establishment of a stable, homogenous cell line. Such cultures are considered to be 'secondary cultures' but not 'cell lines' during this intermediate passaging/selection period between their derivation from a 'primary cell culture' and derivation into a 'cell line', which is a more specific type of secondary culture. PERSON:Matthew Brush secondary cell culture sample PERSON:Matthew Brush The concept of a 'secondary cultured cell population' covers cell lines as well as cultured cell populations more immediately derived from a primary culture which have yet to achieve adequate genetic stability and compositional homogeneity to be considered a cell line. The extent of the collection of cells in a 'secondary cultured cell population' is restricted only in that all cell members must share a propagation history (ie be derived through a common lineage of passages from an initial culture). Secondary cultured cell populations can be under active culture, stored in a quiescent state for future use, or applied experimentally. secondary cultured cell population OBI:0001909 conclusion based on data The conclusion that a gene is upregulated in a tissue sample based on the band intensity in a western blot. The conclusion that a patient has a infection based on measurement of an elevated body temperature and reported headache. The conclusion that there were problems in an investigation because data from PCR and microarray are conflicting. The following are NOT conclusions based on data: data themselves; results from pure mathematics, e.g. "13 is prime". An information content entity that is inferred from data. In the Philly 2013 workshop, we recognized the limitations of "conclusion textual entity", and we introduced this as more general. The need for the 'textual entity' term going forward is up for future debate. Group:2013 Philly Workshop group Group:2013 Philly Workshop group conclusion based on data OBI:0001912 cell freezing medium A processed material that serves as a liquid vehicle for freezing cells for long term quiescent stroage, which contains chemicls needed to sustain cell viability across freeze-thaw cycles. PERSON: Matthew Brush cell freezing medium OBI:0001914 multiplex ligation-mediated amplification A polymerase chain reaction that amplifies multiple targets with a single primer pair mediated by hybridization of a primer with its target sequence using ligation. Chris Stoeckert, Jie Zheng LMA MLPA Multiplex ligation-dependent probe amplification web: http://en.wikipedia.org/wiki/Multiplex_Ligation-dependent_Probe_Amplification Pubmed: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1867615/ multiplex ligation-mediated amplification OBI:0001916 DNA replication identification objective A molecular feature identification objective that aims to examine charateristics of DNA replication, such as replication time. Chris Stoeckert, Jie Zheng Group: Penn Group DNA replication identification objective OBI:0001917 chromosome conformation identification objective A molecular feature identification objective that aims to determine spatial organization of chromatin. Chris Stoeckert, Jie Zheng Group: Penn Group chromosome conformation identification objective OBI:0001919 Carbon-copy chromosome conformation capture assay van Berkum et al. Determining spatial chromatin organization of large genomic regions using 5C technology. Methods Mol Biol (2009) vol. 567 pp. 189-213 [PMID:19588094] An assay that is used to analyze the organization of chromosomes at the genome-wide scale. Venkat Malladi, Chris Stoeckert, Jie Zheng 5C 5C assay "Dostie et al. Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements. Genome Res. 2006 October; 16(10):1299-309.[PMID:16954542]" ENCODE project Carbon-copy chromosome conformation capture assay OBI:0001920 DNA replication timing by sequencing assay Hansen et al. Sequencing newly replicated DNA reveals widespread plasticity in human replication timing. Proc Natl Acad Sci U S A. 2010 January 5; 107(1): 139–144. [PMID:19966280] An assay in which timing of DNA replication is quantified as a function of genome position based on genome-wide sequencing. Venkat Malladi, Chris Stoeckert, Jie Zheng Repli-seq Repli-seq assay Hansen et al. Sequencing newly replicated DNA reveals widespread plasticity in human replication timing. Proc Natl Acad Sci U S A. 2010 January 5; 107(1): 139–144. [PMID:19966280] ENCODE project DNA replication timing by sequencing assay OBI:0001922 microRNA profiling by high throughput sequencing assay Juhlia et al. MicroRNA expression profiling reveals miRNA families regulating specific biological pathways in mouse frontal cortex and hippocampus. PLoS One. 2011;6(6). [PMID: 21731767] A RNA-seq assay in which high throughput sequencing technology is used to analyse the microRNA component of the transcriptome. Person: Venkat Malladi, Chris Stoeckert, Jie Zheng miRNA-seq microRNA-seq microRNA-seq assay http://www.ebi.ac.uk/efo/EFO_0002896 ENCODE project microRNA profiling by high throughput sequencing assay OBI:0001923 protein sequencing by tandem mass spectrometry assay Taylor et al.Implementation and uses of automated de novo peptide sequencing by tandem mass spectrometry. Anal Chem. 2001 Jun;73(11):2594-604. [PMID:11403305] A sequencing assay in which amino acid sequences of proteins is determined using multiple rounds of mass spectrometry and molecule fragmentation. Person: Venkat Malladi, Chris Stoeckert, Jie Zheng Hunt et al. Protein sequencing by tandem mass spectrometry. Proc Natl Acad Sci U S A. 1986;83(17): 6233–6237. [PMID:3462691] ENCODE project protein sequencing by tandem mass spectrometry assay OBI:0001924 micrococcal nuclease digestion followed by high throughput sequencing assay Cui et al.Genome-wide approaches to determining nucleosome occupancy in metazoans using MNase-Seq. Methods Mol Biol. 2012;833:413-9. [PMID:22183607] An assay to identify nucleosome positioning by genome wide sequencing of regions senstative to digestion by micrococal nuclease Person: Venkat Malladi, Chris Stoeckert, Jie Zheng MNase-seq MNase-seq assay Johnson et al. Flexibility and constraint in the nucleosome core landscape of Caenorhabditis elegans chromatin. Genome Res. 2006 Dec;16(12):1505-16. [PMID:17038564] JZ: should be inferred as 'DNA sequencing'. Will check in the future. ENCODE project micrococcal nuclease digestion followed by high throughput sequencing assay OBI:0001925 chromatin immunoprecipitation with exonuclease sequencing assay Rhee et al. Comprehensive Genome-wide Protein-DNA Interactions Detected at Single-Nucleotide Resolution. Cell. 2011 Dec;147(6):1408-19. [PMID:22153082] A ChIP-seq assay to identify protein binding sites using an exonuclease to provide greater binding resolution of immunoprecipitation assay by genome wide sequencing. Person: Venkat Malladi, Chris Stoeckert, Jie Zheng ChIP-exo assay Rhee et al. Comprehensive Genome-wide Protein-DNA Interactions Detected at Single-Nucleotide Resolution. Cell. 2011 Dec;147(6):1408-19. [PMID:22153082] ENCODE project chromatin immunoprecipitation with exonuclease sequencing assay OBI:0001926 microRNA profiling assay A transcription profiling assay in which aims to quantify the microRNA species within a biological sample. Person: Venkat Malladi, Chris Stoeckert, Jie Zheng miRNA expression assay microRNA expression assay Kolbert et al. Multi-Platform Analysis of MicroRNA Expression Measurements in RNA from Fresh Frozen and FFPE Tissues. PLoS One. 2013;8(1):e52517 [PMID: 23382819] ENCODE project microRNA profiling assay 1 1 OBI:0001931 scalar value specification A value specification that consists of two parts: a numeral and a unit label PERSON:Bjoern Peters scalar value specification OBI:0001933 value specification The value of 'positive' in a classification scheme of "positive or negative"; the value of '20g' on the quantitative scale of mass. An information content entity that specifies a value within a classification scheme or on a quantitative scale. This term is currently a descendant of 'information content entity', which requires that it 'is about' something. A value specification of '20g' for a measurement data item of the mass of a particular mouse 'is about' the mass of that mouse. However there are cases where a value specification is not clearly about any particular. In the future we may change 'value specification' to remove the 'is about' requirement. PERSON:Bjoern Peters value specification OBI:0001936 molecular-labeled material a material entity that is the specified output of an addition of molecular label process that aims to label some molecular target to allow for its detection in a detection of molecular label assay PERSON:Matthew Brush OBI developer call, 3-12-12 molecular-labeled material OBI:0001956 assay using chromatin immunoprecipitation http://www.lifetechnologies.com/uk/en/home/life-science/epigenetics-noncoding-rna-research/chromatin-remodeling/chromatin-immunoprecipitation-chip.html an assay which uses immunoprecipitation and which produces data about protein-DNA interaction or DNA epigenetic modification as per user (pployd) request and proposal by Alan Ruttenberg http://sourceforge.net/p/obi/obi-terms/707/ PERSON: Philippe Rocca-Serra assay using chromatin immunoprecipitation OBI:0001957 hardware testing design A study design that aims to compare different types of hardware for performance, reproducibility, accuracy and precision. Person: Jie Zheng MO_734 hardware_variation_design hardware testing design OBI:0001958 systematic review study design Red blood cell transfusion in patients with traumatic brain injury: a systematic review protocol. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4090399/ The effect of moderate gestational alcohol consumption during pregnancy on speech and language outcomes in children: a systematic review. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3892059/ A study design for identifying in the literature prior studies of a pre-determined phenomenon or set of related phenomena according to certain criteria, extracting findings from these studies, and summarizing these findings and/or attempting to draw new conclusions from them which were not justified by any of the individual, prior studies. Many systematic reviews also assess the quality of the studies so reviewed. PERSON: Bill Hogan systematic review study design OBI:0001960 taxonomic diversity assessment by targeted gene survey http://www.ncbi.nlm.nih.gov/pubmed/20679230 http://www.ncbi.nlm.nih.gov/pubmed/25367129 is an assay which aims to provide information about taxonomic information and community diversity by mean of sequencing specific genomic regions used as marker of identity or diversity. PERSON:Philippe Rocca-Serra targeted gene survey DNA barcoding OBI environmental gene survey targeted gene survey taxonomic diversity assessment by targeted gene survey OBI:0001964 decision-theoretic analysis objective An objective specification which what includes a description of two or more alternative actions to take in a particular situation and a metric that enables comparisons of the two actions. The objective specified is achieved in a planned process which includes a data transformation, the output of which is an identification of the 'best' choice according to the metric. The best action to take is typically defined as the one that maximizes expected utility. PERSON: Bill Hogan decision analysis objective PERSON: Bill Hogan decision-theoretic analysis objective OBI:0001965 decision analysis study design a study design that has a decision analysis objective specification as part PERSON: Bill Hogan PERSON: Bill Hogan decision analysis study design OBI:0001969 biodiversity assessment objective biodiversity assessment objective is an objective of a planned process aimed at producing data item whose interpretation should provide insight about variety of biological species found in a biological sample at macroscopic or microscopic level PERSON:Philippe Rocca-Serra PRS for OBI biodiversity assessment objective OBI:0002014 DNA methylation profiling by ChIP-chip assay A ChIP-chip assay that identifies sites of DNA methylation. Person: Chris Stoeckert, Jie Zheng DNA methylation ChIP-chip Penn group Beta Cell Biology Consoritum DNA methylation profiling by ChIP-chip assay OBI:0002015 transcription profiling by MPSS assay An assay in which the transcriptome of a biological sample is analysed using Massive Parallel Signature Sequencing (MPSS). Person: Chris Stoeckert, Jie Zheng expression MPSS http://en.wikipedia.org/wiki/Massively_parallel_signature_sequencing Beta Cell Biology Consoritum transcription profiling by MPSS assay OBI:0002016 histone modification identification by ChIP-chip assay A ChIP-chip assay to identify regions containing specific histones and their modifications. Person: Chris Stoeckert, Jie Zheng histone modification ChIP-chip Penn group Beta Cell Biology Consoritum histone modification identification by ChIP-chip assay OBI:0002017 histone modification identification by ChIP-Seq assay A ChIP-seq assay to identify regions containing specific histones and their modifications. Person: Chris Stoeckert, Jie Zheng histone modification ChIP-Seq Penn group Beta Cell Biology Consoritum histone modification identification by ChIP-Seq assay OBI:0002018 transcription factor binding site identification by ChIP-chip assay A ChIP-chip assay to identify binding sites for transcription factors. Person: Chris Stoeckert, Jie Zheng TF Binding ChIP-chip Penn group Beta Cell Biology Consoritum transcription factor binding site identification by ChIP-chip assay OBI:0002019 transcription factor binding site identification by ChIP-Seq assay A ChIP-seq assay to identify binding sites for transcription factors. Person: Chris Stoeckert, Jie Zheng TF Binding ChIP-Seq Penn group Beta Cell Biology Consoritum transcription factor binding site identification by ChIP-Seq assay OBI:0002020 epigenetic modification assay An assay that identifies epigenetic modification including histone modifications, open chromatin, and DNA methylation. Person: Chris Stoeckert, Jie Zheng Penn group Beta Cell Biology Consoritum epigenetic modification assay OBI:0002021 NextSeq 500 A DNA sequencer which is a desktop sequencer ideal for smaller-scale studies manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. Person: Venkat Malladi, Chris Stoeckert, Jie Zheng Illumina NextSeq 500 http://systems.illumina.com/systems/nextseq-sequencer.html ENCODE project NextSeq 500 OBI:0002033 translation-associated transcript leader sequencing pmid:23580730 An RNA-seq assay that combines TL-seq with polysome fractionation Details see tracker: https://sourceforge.net/p/obi/obi-terms/725/ Janos Demeter, Chris Stoeckert TATL-seq pmid:23580730 Saccharomyces Genome Database (SGD) translation-associated transcript leader sequencing OBI:0002034 transcript leader sequencing pmid:23580730 An RNA-seq assay combining enzymatic capture of m(7)G-capped mRNA 5' ends with high-throughput sequencing. Details see tracker: https://sourceforge.net/p/obi/obi-terms/725/ Janos Demeter, Chris Stoeckert TL-seq pmid:23580730 Saccharomyces Genome Database (SGD) transcript leader sequencing OBI:0002038 ribosomal profiling by sequencing assay Aspden et al., (August 2014). "Extensive translation of small open reading frames revealed by poly-ribo-seq." eLIFE 2014;3:e03528 A RNA-seq assay to sequence only mRNA protected by the ribosome during translation. Person: Venkat Malladi, Chris Stoeckert, Jie Zheng Ribo-seq Ribo-seq assay ribosomal profiling Ingolia, Nicholas T. (28 January 2014). "Ribosome profiling: new views of translation, from single codons to genome scale". Nature Reviews Genetics 15 (3): 205-213. doi:10.1038/nrg3645. PMID 24468696. ENCODE project ribosomal profiling by sequencing assay OBI:0002041 self-transcribing active regulatory region sequencing assay Bohla et al., (September 2014). "A functional insulator screen identifies NURF and dREAM components to be required for enhancer-blocking." PLoS One 9(9):e107765. doi: 10.1371/journal.pone.0107765. A RNA-seq assay to identify the sequences that act as transcriptional enhancers in a direct, quantitative, and genome-wide manner from sheared genomic DNA. Person: Venkat Malladi, Chris Stoeckert, Jie Zheng STARR-seq STARR-seq assay self-transcribing active regulatory region sequencing Arnold et al. (January 2013). "Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq". Science 339 (6123): 1074-7. ENCODE project self-transcribing active regulatory region sequencing assay OBI:0002042 carbon-copy chromosome conformation capture assay followed by sequencing assay Fudenberg et al., (November 2014). "High order chromatin architecture shapes the landscape of chromosomal alterations in cancer." Nat Biotechol 29(12):1109-13. doi: 10.1038/nbt.2049. A carbon-copy chromosome conformation capture assay to analyze the organization of chromosomes in an unbiased, genome-wide manner using high throughput sequening following carbon-copy chromosome conformation capture. Person: Venkat Malladi, Chris Stoeckert, Jie Zheng Carbon-copy chromosome conformation capture assay followed by sequencing HiC HiC assay Lieberman-Aiden E, et al. (2009). Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326: 289-293. ENCODE project carbon-copy chromosome conformation capture assay followed by sequencing assay OBI:0002043 individual-nucleotide resolution cross-linking and immunoprecipitation sequencing assay König et al., (18 January 2012). "Protein-RNA interactions: new genomic technologies and perspectives". Nature Reviews Genetics 13 (2): 77-83. doi:10.1038/nrg3141 A cross-linking immunoprecipitation high-throughput sequencing assay to identify protein-RNA interactions by using UV light to covalently bind proteins and RNA molecules, allowing for a very stringent purification of the linked protein-RNA complexes. Person: Venkat Malladi, Chris Stoeckert, Jie Zheng iCLIP iCLIP assay individual-nucleotide resolution cross-linking and immunoprecipitation Huppertz et al., (February 2014). "iCLIP: protein-RNA interactions at nucleotide resolution.". Methods (San Diego, Calif.) 65 (3): 274-87. doi:10.1016/j.ymeth.2013.10.011 ENCODE project individual-nucleotide resolution cross-linking and immunoprecipitation sequencing assay OBI:0002044 RNA Bind-n-Seq assay A RNA-seq assay that comprehensively characterizes sequence and structural specificity of RNA binding proteins (RBPs) Person: Venkat Malladi, Chris Stoeckert, Jie Zheng RBNS RNA Bind-n-Seq RNBS assay Lambert et al., (June 2014). "RNA Bind-n-Seq: quantitative assessment of the sequence and structural binding specificity of RNA binding proteins." Mol Cell. 2014 Jun 5;54(5):887-900. doi: 10.1016/j.molcel.2014.04.016 ENCODE project RNA Bind-n-Seq assay OBI:0002045 poly(A)-site sequencing assay Wu et al., (July 2014). "Genome-wide determination of poly(A) sites in Medicago truncatula: evolutionary conservation of alternative poly(A) site choice. BMC Genomics. 2014 Jul 21;15:615. doi: 10.1186/1471-2164-15-615. A RNA-seq assay for quantitatively profiling RNA polyadenylation at the transcriptome level. Person: Venkat Malladi, Chris Stoeckert, Jie Zheng PAS-seq PAS-seq assay Poly(A)-site sequencing Shepard et al., (April 2011). "Complex and dynamic landscape of RNA polyadenylation revealed by PAS-Seq." RNA. 2011 Apr;17(4):761-72. doi: 10.1261/rna.2581711 ENCODE project poly(A)-site sequencing assay OBI:0100026 organism Drosophila melanogaster 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 James Malone Jie Zheng Tomasz Adamusiak MO_508 NIFSTD:birnlex_376 WEB: http://en.wikipedia.org/wiki/Organism 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. 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. E.g Drosophila melanogaster organism organism EFO_URI: http://www.ebi.ac.uk/efo/EFO_0000634 OBI:0100051 specimen Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen. A material entity that has the specimen role. Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. PERSON: James Malone PERSON: Philippe Rocca-Serra GROUP: OBI Biomaterial Branch specimen OBI:0100060 cultured cell population A cultured cell population applied in an experiment: "293 cells expressing TrkA were serum-starved for 18 hours and then neurotrophins were added for 10 min before cell harvest." (Lee, Ramee, et al. "Regulation of cell survival by secreted proneurotrophins." Science 294.5548 (2001): 1945-1948). A cultured cell population maintained in vitro: "Rat cortical neurons from 15 day embryos are grown in dissociated cell culture and maintained in vitro for 8–12 weeks" (Dichter, Marc A. "Rat cortical neurons in cell culture: culture methods, cell morphology, electrophysiology, and synapse formation." Brain Research 149.2 (1978): 279-293). A processed material comprised of a collection of cultured cells that has been continuously maintained together in culture and shares a common propagation history. 2013-6-5 MHB: This OBI class was formerly called 'cell culture', but label changed and definition updated following CLO alignment efforts in spring 2013, during which the intent of this class was clarified to refer to portions of a culture or line rather than a complete cell culture or line. PERSON:Matthew Brush cell culture sample PERSON:Matthew Brush The extent of a 'cultured cell population' is restricted only in that all cell members must share a propagation history (ie be derived through a common lineage of passages from an initial culture). In being defined in this way, this class can be used to refer to the populations that researchers actually use in the practice of science - ie are the inputs to culturing, experimentation, and sharing. The cells in such populations will be a relatively uniform population as they have experienced similar selective pressures due to their continuous co-propagation. And this population will also have a single passage number, again owing to their common passaging history. Cultured cell populations represent only a collection of cells (ie do not include media, culture dishes, etc), and include populations of cultured unicellular organisms or cultured multicellular organism cells. They can exist under active culture, stored in a quiescent state for future use, or applied experimentally. cultured cell population OBI:0100066 organ section A liver slice used in a perfusion experiment. Thyroidectomy during laryngectomy for advanced laryngeal carcinoma--whole organ section study with long-term functional evaluation. Clin Otolaryngol Allied Sci. 1995 Apr;20(2):145-9. PMID: 7634521 A processed material which derives from an organ and results from a process of dissection or histological sample preparation a portion(formerly an organ section is portion of an organ removed from the context of the organ) PERSON: Helen Parkinson PERSON: Philippe Rocca-Serra GROUP: CEBS GROUP: OBI Biomaterial Branch organ section OBI:0200000 data transformation The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value. A planned process that produces output data from input data. Elisabetta Manduchi Helen Parkinson James Malone Melanie Courtot Philippe Rocca-Serra Richard Scheuermann Ryan Brinkman Tina Hernandez-Boussard data analysis data processing Branch editors data transformation OBI:0200005 feature extraction objective A feature extraction objective is a data transformation objective where the aim of the data transformation is to generate quantified values from a scanned image. Elisabetta Manduchi James Malone TERM: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#feature_extraction feature extraction objective OBI:0200021 linlog transformation This can be used for microarray normalization, e.g. to normalize the data from a two-channel expression microarray assay, as described in PMID 16646782. A linlog transformation is a data transformation, described in PMID 16646782, whose input is a matrix [y_ik] and whose output is a matrix obtained by applying formula (9) of this paper, where values below an appropriately determined threshold (dependent on the row i) are transformed via a polynomial of degree 1, and values above this threshold are transformed via a logarithm. Elisabetta Manduchi Philippe Rocca-Serra PMID: 16646782 linlog transformation OBI:0200023 loess global transformation A loess global transformation is a loess transformation where only one loess fitting is performed, utilizing one subset of (or possibly all of) the data points in the input so that there is only one resulting loess curve y=f(x) which is used for the transformation. Elisabetta Manduchi James Malone Melanie Courtot Philippe Rocca-Serra OTHER: Editor's generalization based on MGED Ontology term loess global transformation OBI:0200024 loess group transformation A loess group transformation is a loess transformation where the input is partitioned into groups and for each group a loess fitting is performed, utilizing a subset of (or possibly all of) the data points in that group. Thus, a collection of loess curves y=f_i(x) is generated, one per group. Each (x, y) in the input is transformed into (x, y-f_i(x)), where f_i(x) is the curve corresponding to the group to which that data point belongs. Elisabetta Manduchi James Malone Melanie Courtot Philippe Rocca-Serra OTHER: Editor's generalization based on MGED Ontology term loess group transformation OBI:0200025 loess scale group transformation A loess scale group transformation is a data transformation consisting in the application of a scale adjustment following a loess group transformation, to render the group variances for the second variable (y) similar. Has objective scaling. Elisabetta Manduchi James Malone Melanie Courtot OTHER: Editor's generalization based on MGED Ontology term loess scale group transformation OBI:0200026 total intensity transformation single This can be used as a simple normalization method for expression microarray assays. For example, each intensity from a one-channel microarray assay is multiplied by a constant so that the output mean intensity over the microarray equals a desired target T (the multiplicative constant in this case is the T/(mean intensity)). A total intensity transformation single is a data transformation that takes as input an n-dimensional (real) vector and multiplies each component of this vector by a coefficient, where the coefficient is obtained by taking the sum of the input components or of a subset of these, multiplied by a constant of choice. Elisabetta Manduchi Helen Parkinson James Malone Melanie Courtot Philippe Rocca-Serra OTHER: Adjusted from MGED Ontology Note that if the word "sum" is replaced by the word "mean" in the definition, the resulting definition is equivalent. total intensity transformation single OBI:0200027 total intensity transformation paired This can be used as a simple normalization method for the two channels from a two-channel expression microarray assay or from two related one-channel expression microarray assays. A total intensity transformation paired is a data transformation that takes as input two n-dimensional (real) vectors and multiplies each component of the first vector by a coefficient, where the coefficient is obtained by taking the ratio of the sum of the second input components or of a subset of these by the sum of the first input components or of a subset of these (the same subset is used for the two vectors). Elisabetta Manduchi Philippe Rocca-Serra OTHER: Adjusted from MGED Ontology Note that if the word "sum" is replaced by the word "mean" in the definition, the resulting definition is equivalent. total intensity transformation paired OBI:0200028 quantile transformation This can be used for expression microarray assay normalization and it is referred to as "quantile normalization", according to the procedure described e.g. in PMID 12538238. A quantile transformation is a data transformation that takes as input a collection of data sets, where each can be thought as an n-dimensional (real) vector, and which transforms each data set so that the resulting output data sets have equal quantiles. Elisabetta Manduchi PERSON: Elisabetta Manduchi quantile transformation OBI:0200031 differential expression analysis objective Analyses implemented by the SAM (http://www-stat.stanford.edu/~tibs/SAM), PaGE (www.cbil.upenn.edu/PaGE) or GSEA (www.broad.mit.edu/gsea/) algorithms and software A differential expression analysis objective is a data transformation objective whose input consists of expression levels of entities (such as transcripts or proteins), or of sets of such expression levels, under two or more conditions and whose output reflects which of these are likely to have different expression across such conditions. Elisabetta Manduchi PERSON: Elisabetta Manduchi differential expression analysis objective OBI:0200055 dye swap merge A dye swap merge is a replicate analysis which takes as input data from paired two-channel microarray assays where the sample labeled with one dye in the first assay is labeled with the other dye in the second assay and vice versa. The output for each reporter is obtained by combining its (raw or possibly pre-processed) M values in the two assays, where the M value in an assay is defined as the difference of the log intensities in the two channels. This can be used as a normalization step, when appropriate assumptions are met. Elisabetta Manduchi James Malone PERSON: Elisabetta Manduchi PERSON: James Malone dye swap merge OBI:0200056 moving average The moving average is often used to handle data from tiling arrays. A moving average is a data transformation in which center calculations, usually mean calculations, are performed on values within a sliding window across the input data set. Elisabetta Manduchi Helen Parkinson Philippe Rocca-Serra PERSON: Elisabetta Manduchi PERSON: Helen Parkinson moving average OBI:0200057 replicate analysis Replicate analysis can be used in microarray analysis to identify and potentially exclude low quality data. A replicate analysis is a data transformation in which data from replicates are combined, e.g. through descriptive statistics calculations, and the results might be utilized for a variety of purposes, like assessing reproducibility, identifying outliers, normalizing, etc. Elisabetta Manduchi Helen Parkinson PERSON: Helen Parkinson PERSON:Elisabetta Manduchi replicate analysis OBI:0200071 loess transformation A loess transformation is a data transformation that takes as input a collection of real number pairs (x, y) and, after performing (one or more) loess fittings, utilizes the resulting curves to transform each (x, y) in the input into (x, y-f(x)) where f(x) is one of the fitted curves. Elisabetta Manduchi James Malone Melanie Courtot Philippe Rocca-Serra OTHER: Editor's generalization based on MGED Ontology term loess transformation OBI:0200089 multiple testing correction method A multiple testing correction method is a hypothesis test performed simultaneously on M > 1 hypotheses. Multiple testing procedures produce a set of rejected hypotheses that is an estimate for the set of false null hypotheses while controlling for a suitably define Type I error rate Monnie McGee multiple testing procedure PAPER: Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 9-10. multiple testing correction method OBI:0200166 data transformation objective normalize objective An objective specification to transformation input data into output data Modified definition in 2013 Philly OBI workshop James Malone PERSON: James Malone data transformation objective OBI:0200167 data normalization objective Quantile transformation which has normalization objective can be used for expression microarray assay normalization and it is referred to as "quantile normalization", according to the procedure described e.g. in PMID 12538238. A normalization objective is a data transformation objective where the aim is to remove systematic sources of variation to put the data on equal footing in order to create a common base for comparisons. Elisabetta Manduchi Helen Parkinson James Malone PERSON: Elisabetta Manduchi PERSON: Helen Parkinson PERSON: James Malone data normalization objective OBI:0200168 correction objective Type I error correction A correction objective is a data transformation objective where the aim is to correct for error, noise or other impairments to the input of the data transformation or derived from the data transformation itself James Malone PERSON: James Malone PERSON: Melanie Courtot correction objective OBI:0200169 normalization data transformation A normalization data transformation is a data transformation that has objective normalization. James Malone PERSON: James Malone normalization data transformation OBI:0200170 averaging data transformation An averaging data transformation is a data transformation that has objective averaging. James Malone PERSON: James Malone averaging data transformation OBI:0200175 class discovery data transformation A class discovery data transformation (sometimes called unsupervised classification) is a data transformation that has objective class discovery. James Malone clustering data transformation unsupervised classification data transformation PERSON: James Malone class discovery data transformation OBI:0200177 center calculation objective A mean calculation which has center calculation objective is a data transformation in which the center of the input data is discovered through the calculation of a mean average. A center calculation objective is a data transformation objective where the aim is to calculate the center of an input data set. James Malone PERSON: James Malone center calculation objective OBI:0200178 class discovery objective A class discovery objective (sometimes called unsupervised classification) is a data transformation objective where the aim is to organize input data (typically vectors of attributes) into classes, where the number of classes and their specifications are not known a priori. Depending on usage, the class assignment can be definite or probabilistic. James Malone clustering objective discriminant analysis objective unsupervised classification objective PERSON: Elisabetta Manduchi PERSON: James Malone class discovery objective OBI:0200181 center calculation data transformation A center calculation data transformation is a data transformation that has objective of center calculation. James Malone PERSON: James Malone center calculation data transformation OBI:0200183 scaling objective Scaling gene expression data for cross platform analysis http://www.springerprotocols.com/Abstract/doi/10.1007/978-1-59745-454-4_13 is a data transformation objective where all, or some of a data set is adjusted by some data transformation according to some scale, for example a user defined minimum or maximum Awaiting English definition from Monnie McGee James Malone Person:Helen Parkinson scaling objective OBI:0200185 scaling data transformation A scaling data transformation is a data transformation that has objective scaling. James Malone PERSON: James Malone scaling data transformation OBI:0200186 error correction objective Application of a multiple testing correction method An error correction objective is a data transformation objective where the aim is to remove (correct for) erroneous contributions arising from the input data, or the transformation itself. James Malone, Helen Parkinson PERSON: James Malone error correction objective OBI:0300310 sequential design PMID: 17710740.Pharm Stat. 2007 Aug 20.Sequential design approaches for bioequivalence studies with crossover designs. Any design in which the decision as to whether to enroll the next patient, pair of patients, or block of patients is determined by whether the cumulative treatment difference for all previous patients is within specified limits. Enrollment is continued if the difference does not exceed the limits. It is terminated if it does Philippe Rocca-Serra MUSC Provenance: OCI sequential design OBI:0300311 observation design PMID: 12387964.Lancet. 2002 Oct 12;360(9340):1144-9.Deficiency of antibacterial peptides in patients with morbus Kostmann: an observation study. observation design is a study design in which subjects are monitored in the absence of any active intervention by experimentalists. Philippe Rocca-Serra OBI branch derived observation design OBI:0302716 pool of specimens A pool of specimens is a mixture of a population of samples which have been gathered from one or more sample populations, obtained by the physical process of mixing individual specimens, e.g. mixing the DNA collected from the individual fish. check with advisors as to how to represent multiple instances of any class? a set of specimens which have been gathered from one or more sample_populations, obtained by the physical process of mixing individual specimens, e.g. mixing the DNA collected from the individual fish PERSON: Jennifer Fostel GROUP: CEBS pool of specimens OBI:0302859 genetically modified organism A protocol for removal of antibiotic resistance cassettes from human embryonic stem cells genetically modified by homologous recombination or transgenesis. Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 an organism that is the output of a genetic transformation process PERSON: Philippe Rocca-Serra OBI Biomaterial genetically modified organism OBI:0302884 extraction nucleic acid extraction using phenol chloroform A material separation in which a desired component of an input material is separated from the remainder Current the output of material processing defined as the molecular entity, main component in the output material entity, rather than the material entity that have grain molecular entity. 'nucleic acid extract' is the output of 'nucleic acid extraction' and has grain 'nucleic acid'. However, the output of 'nucleic acid extraction' is 'nucleic acid' rather than 'nucleic acid extract'. We are aware of this issue and will work it out in the future. Person:Bjoern Peters Philippe Rocca-Serra extraction OBI:0302886 centrifugation PMID: 18428461.Purification of oligodendrocytes and their progenitors using immunomagnetic separation and Percoll gradient centrifugation. Curr Protoc Neurosci. 2001 May;Chapter 3:Unit 3.12. centrifugation is a process separating molecules by size or density using centrifugal forces generated by a spinning rotor. G-forces of several hundred thousand times gravity are generated in ultracentrifugation Philippe Rocca-Serra adapted from http://www.fao.org/DOCREP/003/X3910E/X3910E06.htm centrifugation OBI:0302887 staining PMID: 18540298. Role of modified bleach method in staining of acid-fast bacilli in lymph node aspirates. Acta Cytol. 2008 May-Jun;52(3):325-8. Staining is a process which results in the addition a class-specific (DNA, proteins, lipids, carbohydrates) dye to a substrate to qualify or quantify the presence of a specific compound. Philippe Rocca-Serra adapted from Wikipedia: http://en.wikipedia.org/wiki/Staining staining OBI:0302888 washing PMID: 6874122. Dialysis leucopenia--no correction after prolonged washing of the membrane. Int J Artif Organs. 1983 May;6(3):113-4. washing is a process by which a material entity acting as contaminant (e.g. excess staining reagent) is removed by application of one or more cycles of solution in flow. Philippe Rocca-Serra OBI-Branch washing OBI:0302889 irradiation PMID: 18563778.Histological and modeling study of skin thermal injury to 2.0 mum laser irradiation.Lasers Surg Med. 2008 Jun 18;40(5):358-370. irradiation is a process by which a material entity is exposed to radiative energy, which could be ionizing radiation (such as gamma rays or X-rays) or not such as UV light or microwaves Philippe Rocca-Serra adapted from wikipedia (http://en.wikipedia.org/wiki/Irradiation) irradiation OBI:0302892 enzymatic ligation PMID: 17853876. Enzymatic ligation assisted by nucleases: simultaneous ligation and digestion promote the ordered assembly of DNA. Nat Protoc. 2007;2(9):2198-202. An enzymatic ligation is a planned process in which molecules are joined by covalent bonds through the action of an material entity with a ligase activity Philippe Rocca-Serra OBI-Branch enzymatic ligation OBI:0302893 storage PMID: 18550121.Total Prostate Specific Antigen Stability Confirmed After Long-Term Storage of Serum at -80C. J Urol. 2008 Jun 10. A maintenance process by which material entities that are not actively metabolizing are placed in well identified location and possibly under controlled environment in ad-hoc devices/structures in order to preserve and protect them from decay/alteration and maintain availability Philippe Rocca-Serra OBI-Branch storage OBI:0302894 cell lysis PMID: 18484276.Cell lysis with dimethyl sulphoxide produces stable homogeneous solutions in the dichlorofluorescein oxidative stress assay. Free Radic Res. 2008 May;42(5):435-41. cell lysis is a process by which cell membrane integrity of live cells is compromised and leads to cell death. Cell lysis may be achieved by means of viral action or osmotic shock. BP, JG, RV: There is also a need for the unplanned cell lysis, which is probably not in the scope of OBI, but should be linked to from this process. Philippe Rocca-Serra adapted from wikipedia [http://en.wikipedia.org/wiki/Lysis] cell lysis OBI:0302902 immobilization PMID: 18562258. The immobilization of proteins on biodegradable fibers via biotin-streptavidin bridges.Acta Biomater. 2008 May 23. immbolization is a process by which material entity become (possibly covalently but not necessarily) attached to the surface of another material entity used a substratum. Philippe Rocca-Serra OBI-Branch immobilization OBI:0302903 nucleic acid hybridization PMID: 18555787.Quantitative analysis of DNA hybridization in a flowthrough microarray for molecular testing. Anal Biochem. 2008 May 27. a planned process by which totally or partially complementary, single-stranded nucleic acids are combined into a single molecule called heteroduplex or homoduplex to an extent depending on the amount of complementarity. Philippe Rocca-Serra adapted from wikipedia [http://en.wikipedia.org/wiki/Nucleic_acid_hybridization] hybridization assay nucleic acid hybridization OBI:0400043 flow cell Biofilm Flow Cell Aparatus in the fluidic subsystem where the sheath and sample meet. Can be one of several types; jet-in-air, quartz cuvette, or a hybrid of the two. The sample flows through the center of a fluid column of sheath fluid in the flow cell. Person:John Quinn flow_cell http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm flow cell OBI:0400044 flow cytometer FACS Calibur A flow_cytometer is an instrument for counting, examining and sorting microscopic particles in suspension. It allows simultaneous multiparametric analysis of the physical and/or chemical characteristics of single cells flowing through an optical and/or electronic detection apparatus. A flow cytometer is an instrument that can be used to quantitatively measure the properties of individual cells in a flowing medium. John Quinn http://en.wikipedia.org/wiki/Flow_cytometer flow cytometer OBI:0400065 light source A light source is an optical subsystem that provides light for use in a distant area using a delivery system (e.g., fiber optics). Light sources may include one of a variety of lamps (e.g., xenon, halogen, mercury). Most light sources are operated from line power, but some may be powered from batteries. They are mostly used in endoscopic, microscopic, and other examination and/or in surgical procedures. The light source is part of the optical subsystem. In a flow cytometer the light source directs high intensity light at particles at the interrogation point. The light source in a flow cytometer is usually a laser. Elizabeth M. Goralczyk John Quinn Olga Tchuvatkina Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 light source OBI:0400078 obscuration bar obscuration bar in a flow cytometer An obscuration bar is a an optical subsystem which is a strip of metal or other material that serves to block out direct light from the illuminating beam. The obscuration bar prevents the bright light scattered in the forward directions from burning out the collection device. Daniel Schober Flow Cytometry: First Principles, by Alice Longobardi Givan, ISBN-10: 0471382248, ISBN-13: 978-0471382249 John Quinn obscuration bar OBI:0400079 optical filter 720 LP filter, 580/30 BP filter An optical filter is an optical subsystem that selectively transmits light having certain properties (often, a particular range of wavelengths, that is, range of colours of light), while blocking the remainder. They are commonly used in photography, in many optical instruments, and to colour stage lighting Optical filters can be arranged to segregate and collect light by wave length. John Quinn http://en.wikipedia.org/wiki/Optical_filter optical filter OBI:0400082 photodetector A photomultiplier tube, a photo diode A photodetector is a device used to detect and measure the intensity of radiant energy through photoelectric action. In a cytometer, photodetectors measure either the number of photons of laser light scattered on impact with a cell (for example), or the flourescence emitted by excitation of a fluorescent dye. John Quinn http://einstein.stanford.edu/content/glossary/glossary.html photodetector OBI:0400099 flow cytometer sorter BioSorter2000, LSR2 A flow_cytometer_sorter is a flow_cytometer that analyzes and separates or sorts particles passing through (based on properties measured during analysis) to collect cells of interest. John Quinn Melanie Courtot http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm flow cytometer sorter OBI:0400103 DNA sequencer ABI 377 DNA Sequencer, ABI 310 DNA Sequencer A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences. Trish Whetzel MO DNA sequencer OBI:0400104 array scanner GenePix 4200A, GenePix4000B An processed material which acquires images of fluorescence (induced with lasers) from labeled molecules on the surface of the microarray chip Trish Whetzel GROUP: MGED Ontology array scanner OBI:0400105 arrayer BioRobotics Microgrid II TAS, Affymetrix GMS 417 a device which deposits biological material onto a substrate in a defined pattern. Trish Whetzel MO_697 arrayer arrayer OBI:0400106 centrifuge A device with a rapidly rotating container that applies centrifugal force to its contents Melanie Courtot Person: Jennifer Fostel Trish Whetzel http://en.wikipedia.org/wiki/Centrifuge centrifuge OBI:0400107 computer Apple PowerBook, Dell OptiPlex A computer is an instrument which manipulates (stores, retrieves, and processes) data according to a list of instructions. Melanie Courtot Trish Whetzel http://en.wikipedia.org/wiki/Computer computer OBI:0400108 heating block An instrument used to heat and/or maintain material at a set temperature. A heating block is an instrument or part of an instrument which raises or maintains the temperature of a sample to a defined constant temperature during certain parts of an assay Daniel Schober MO heating block OBI:0400109 homogenizer mortar, blender A homogenizer is an instrument for the homogenization of various types of material, such as tissue, plant, food, soil, and many others. Melanie Courtot Trish Whetzel http://en.wikipedia.org/wiki/Homogenizer homogenizer OBI:0400110 hybridization chamber Glass Array Hybridization Cassette A device which is used to maintain constant contact of a liquid on an array. This can be either a glass vial or slide. Trish Whetzel MO_563 hybridization_chamber hybridization chamber OBI:0400111 hybridization station Labnet Problot12 A device which is used to maintain the temperature of one or more hybridization_chamber(s) at a defined, constant temperature. Trish Whetzel MO_497 hybridization station hybridization station OBI:0400112 liquid handler Beckman BioMek 2000 a device that is used for automated liquid transfer and handling. liquid_handling_instrument MO_868 liquid_handler DS: Is this class justified? Its a unnamed class. If so, put a fluidic_system and the fluidic_subsystem as subclasses. TW: This is required by MO. FG & DS: Capture as function. All: Needs to be reviewed, according to query use case. If we keep it its kept as unnamed owl class. The liquid handling class remains but as an undefined class with are unlikely to have children. It is expected that the reasoner would classifiy appropriate classes under this class that meet the have the liquid_handling function relation. DS: Is this class justified? Its a unnamed class. If so, put a fluidic_system and the fluidic_subsystem as subclasses. TW: This is required by MO. FG: Or as function. liquid handler OBI:0400113 oligonucleotide synthesizer Automated Multiplex Oligonucleotide Synthesizer An instrument used to chemically synthesize oligonucleotides. Trish Whetzel MO oligonucleotide synthesizer OBI:0400114 sonicator Sonicator 3000 A device that converts a variable electrical current to mechanical vibration of a metallic probe. The device is used for the lysis of cells, the mixing of compounds or solutions, to framgent molecules of DNA, or to create emulsions. Trish Whetzel MO sonicator OBI:0400115 spectrophotometer Helios Gamma Spectrophotometer A spectrophotometer is an instrument that measures the intensity of light as a function of the color, or more specifically, the wavelength of light, transmitted by a substance. Melanie Courtot Trish Whetzel MO spectrophotometer OBI:0400116 thermal cycler Piko(tm) 96-well Thermal Cycler An instrument that is capable of repeatedly altering and maintaining specific temperatures for defined periods of time. Melanie Courtot Trish Whetzel DNA_amplifier PCR_machine Polymerase_Chain_Reaction_ machine thermocycler MO thermal cycler OBI:0400118 vortexer VWR Genie 2 A vortexer is an instrument that mixes small vials of liquid by creating a rotation of the liquid around its own center. It consists of an electric motor with the drive shaft oriented vertically and attached to a cupped rubber piece mounted slightly off-center. As the motor runs the rubber piece oscillates rapidly in a circular motion. When a test tube or other appropriate container is pressed into the rubber cup (or touched to its edge) the motion is transmitted to the liquid inside and a vortex is created. Melanie Courtot Trish Whetzel vortex_mixer http://en.wikipedia.org/wiki/Vortex_mixer vortexer OBI:0400119 microarray wash station ArrayIt(r) Microarray Wash Station a device that is used to wash Affymetrix-type arrays. Trish Whetzel MO_626 wash_station microarray wash station OBI:0400120 temperature control bath VWR Signature Deep-Chamber Heated Water Bath. A water bath is used for temperatures up to 100 degrees C. An oil bath is employed for temperatures over 100 degrees C. A temperature_control_bath is a device that has the function to regulate the temperature of a material, the function to contain fluid and the function to vary and maintain the temperature of the contained fluid. Heat exchange (energy transfer) between the material and the heating element is facilitated via the contained fluid. A temperature_control_bath is composed of a container, a heating element and/or a cooling element and a means to adjust the needed temperature. In most cases also a timer and a means to stir the fluid is provided as well. Alan Ruttenburg Daniel Schober Frank Gibson OBI Instrument branch DS: This was heated_bath. It was renamed to reflect the possability that the same bath can be used for cooling. We can now define the temperature variables and based on that infer if it is a cooling device or a heating device (also quite relative to surrounding temperature). temperature control bath OBI:0400137 cytometer A cytometer is an instrument for counting and measuring cells. Melanie Courtot http://medical.merriam-webster.com/medical/cytometer cytometer OBI:0400147 microarray An affymetrix U133 array is a microarray. Microarrays include 1 and 2-color arrays, custom and commercial arrays (e.g, Affymetrix, Agilent, Nimblegen, Illumina, etc.) for expression profiling, DNA variant detection, protein binding, and other genomic and functional genomic assays. A processed material that is made to be used in an analyte assay. It consists of a physical immobilisation matrix in which substances that bind the analyte are placed in regular spatial position. Daniel Schober PERSON: Chris Stoeckert microarray OBI:0400148 DNA microarray Moran G, Stokes C, Thewes S, Hube B, Coleman DC, Sullivan D (2004). "Comparative genomics using Candida albicans DNA microarrays reveals absence and divergence of virulence-associated genes in Candida dubliniensis". Microbiology 150: 3363-3382. doi:10.1099/mic.0.27221-0. PMID 15470115 A DNA-microarray is a microarray that is used as a physical 2D immobilisation matrix for DNA sequences. DNA microarray-bound DNA fragments are used as targets for a hybridising probed sample. PERSON: Daniel Schober PERSON: Frank Gibson DNA Chip DNA-array Web:<http://en.wikipedia.org/wiki/DNA_microarray>@2008/03/03 DNA microarray OBI:0400149 protein microarray The most common protein microarray is the antibody microarray, where antibodies are spotted onto the protein chip and are used as capture molecules to detect proteins from cell lysate solutions. A protein-microarray is a microarray, ususlly a piece of glass, on which different molecules of protein have been affixed at separate locations in an ordered manner. These are used to identify protein-protein or protein-small molecule interactions. Daniel Schober PERSON: Daniel Schober protein microarray OBI:0400153 droplet sorter A droplet sorter is part_of a flow cytometer sorter that converts the carrier fluid stream into individual droplets, and these droplets are directed into separate locations for recovery (enriching the original sample for particles of interest based on qualities determined by gating) or disposal. OBI Instrument branch OBI Instrument branch droplet sorter OBI:0400155 water bath A water bath was used to allow for cell incubation at 38 degree centigrade for 8 hours. A water bath is a temperature control bath in which a water acts as contact medium enabling temperature transfer from the heating element or cooling element to the sample. The temperature can be controlled in the 0 to 100 degree centigrade range (under normal pressure). Daniel Schober PERSON: Daniel Schober water bath OBI:0400168 microtome PMID: 9974145.Serial sectioning of thick tissue with a novel vibrating blade microtome. Brain Res Brain Res Protoc. 1999 Jan;3(3):302-7. A microtome is a mechanical instrument used to cut biological specimens into very thin segments for further treatment (e.g. ISH) and ultimately microscopic or histologic examination. Most microtomes provide cooling facilities (cryo-microtome) and use a steel blade to cut a slice of defined thickness. Some are automatic, and some are driven by hand. PERSON: Phillippe Rocca-Serra PERSON: Daniel Schober microtome OBI:0500000 study design a matched pairs study design describes criteria by which subjects are identified as pairs which then undergo the same protocols, and the data generated is analyzed by comparing the differences between the paired subjects, which constitute the results of the executed study design. A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution. Editor note: there is at least an implicit restriction on the kind of data transformations that can be done based on the measured data available. PERSON: Chris Stoeckert experimental design rediscussed at length (MC/JF/BP). 12/9/08). The definition was clarified to differentiate it from protocol. study design OBI:0500001 clinical study design PMID: 17655677.J Cardiovasc Electrophysiol. 2007 Aug;18(9):965-71.Biventricular versus right ventricular pacing in patients with AV block (BLOCK HF): clinical study design and rationale. Plan for the precise procedure to be followed in a clinical trial, including planned and actual timing of events, choice of control group, method of allocating treatments, blinding methods; assigns a subject to pass through one or more epochs in the course of a trial. Specific design elements, e.g., crossover, parallel; dose-escalation [Modified from Pocock, Clinical Trials: A Practical Approach] The definition needs to be extended to other things than simply patients PlanAndPlannedProcess Branch Clinical Research Glossary Version 4.0 CDICS glossary group clinical study design OBI:0500002 repeated measure design PMID: 10959922.J Biopharm Stat. 2000 Aug;10(3):433-45.Equivalence in test assay method comparisons for the repeated-measure, matched-pair design in medical device studies: statistical considerations. a study design which use the same individuals and exposure them to a set of conditions. The effect of order and practice can be confounding factor in such designs PlanAndPlannedProcess Branch http://www.holah.karoo.net/experimentaldesigns.htm repeated measure design OBI:0500003 cross over design PMID: 17601993-Objective: HIV-infected patients with lipodystrophy (HIV-lipodystrophy) are insulin resistant and have elevated plasma free fatty acid (FFA) concentrations. We aimed to explore the mechanisms underlying FFA-induced insulin resistance in patients with HIV-lipodystrophy. Research Design and Methods: Using a randomized placebo-controlled cross-over design, we studied the effects of an overnight acipimox-induced suppression of FFA on glucose and FFA metabolism by using stable isotope labelled tracer techniques during basal conditions and a two-stage euglycemic, hyperinsulinemic clamp (20 mU insulin/m(2)/min; 50 mU insulin/m(2)/min) in nine patients with nondiabetic HIV-lipodystrophy. All patients received antiretroviral therapy. Biopsies from the vastus lateralis muscle were obtained during each stage of the clamp. Results: Acipimox treatment reduced basal FFA rate of appearance by 68.9% (52.6%-79.5%) and decreased plasma FFA concentration by 51.6 % (42.0%-58.9%), (both, P < 0.0001). Endogenous glucose production was not influenced by acipimox. During the clamp the increase in glucose-uptake was significantly greater after acipimox treatment compared to placebo (acipimox: 26.85 (18.09-39.86) vs placebo: 20.30 (13.67-30.13) mumol/kg/min; P < 0.01). Insulin increased phosphorylation of Akt (Thr(308)) and GSK-3beta (Ser(9)), decreased phosphorylation of glycogen synthase (GS) site 3a+b and increased GS-activity (I-form) in skeletal muscle (P < 0.01). Acipimox decreased phosphorylation of GS (site 3a+b) (P < 0.02) and increased GS-activity (P < 0.01) in muscle. Conclusion: The present study provides direct evidence that suppression of lipolysis in patients with HIV-lipodystrophy improves insulin-stimulated peripheral glucose-uptake. The increased glucose-uptake may in part be explained by increased dephosphorylation of GS (site 3a+b) resulting in increased GS activity. a repeated measure design which ensures that experimental units receive, in sequence, the treatment (or the control), and then, after a specified time interval (aka *wash-out periods*), switch to the control (or treatment). In this design, subjects (patients in human context) serve as their own controls, and randomization may be used to determine the ordering which a subject receives the treatment and control Philippe Rocca-Serra (source: http://www.sbu.se/Filer/Content0/publikationer/1/literaturesearching_1993/glossary.html) cross over design OBI:0500004 n-to-1 design N-of-1 design is a cross-over design in which the same patient is repeatedly randomised to receive either the experimental treatment or its control (Senn, 1993). Philippe Rocca-Serra Adapted from http://www.childrens-mercy.org/stats/definitions/crossover.htm and source:http://symptomresearch.nih.gov/chapter_6/sec1/csss1pg1.htm) n-to-1 design OBI:0500005 matched pairs design PMID: 17288613-BSTRACT: BACKGROUND: Physicians in Canadian emergency departments (EDs) annually treat 185,000 alert and stable trauma victims who are at risk for cervical spine (C-spine) injury. However, only 0.9% of these patients have suffered a cervical spine fracture. Current use of radiography is not efficient. The Canadian C-Spine Rule is designed to allow physicians to be more selective and accurate in ordering C-spine radiography, and to rapidly clear the C-spine without the need for radiography in many patients. The goal of this phase III study is to evaluate the effectiveness of an active strategy to implement the Canadian C-Spine Rule into physician practice. Specific objectives are to: 1) determine clinical impact, 2) determine sustainability, 3) evaluate performance, and 4) conduct an economic evaluation. METHODS: We propose a matched-pair cluster design study that compares outcomes during three consecutive 12-months before, after, and decay periods at six pairs of intervention and control sites. These 12 hospital ED sites will be stratified as teaching or community hospitals, matched according to baseline C-spine radiography ordering rates, and then allocated within each pair to either intervention or control groups. During the after period at the intervention sites, simple and inexpensive strategies will be employed to actively implement the Canadian C-Spine Rule. The following outcomes will be assessed: 1) measures of clinical impact, 2) performance of the Canadian C-Spine Rule, and 3) economic measures. During the 12-month decay period, implementation strategies will continue, allowing us to evaluate the sustainability of the effect. We estimate a sample size of 4,800 patients in each period in order to have adequate power to evaluate the main outcomes. DISCUSSION: Phase I successfully derived the Canadian C-Spine Rule and phase II confirmed the accuracy and safety of the rule, hence, the potential for physicians to improve care. What remains unknown is the actual change in clinical behaviors that can be affected by implementation of the Canadian C-Spine Rule, and whether implementation can be achieved with simple and inexpensive measures. We believe that the Canadian C-Spine Rule has the potential to significantly reduce health care costs and improve the efficiency of patient flow in busy Canadian EDs. A matched pair design is a study design which use groups of individuals associated (hence matched) to each other based on a set of criteria, one member going to one treatment, the other member receiving the other treatment. Philippe Rocca-Serra http://www.holah.karoo.net/experimentaldesigns.htm matched pairs design OBI:0500006 parallel group design PMID: 17408389-Purpose: Proliferative vitreoretinopathy (PVR) is the most important reason for blindness following retinal detachment. Presently, vitreous tamponades such as gas or silicone oil cannot contact the lower part of the retina. A heavier-than-water tamponade displaces the inflammatory and PVR-stimulating environment from the inferior area of the retina. The Heavy Silicone Oil versus Standard Silicone Oil Study (HSO Study) is designed to answer the question of whether a heavier-than-water tamponade improves the prognosis of eyes with PVR of the lower retina. Methods: The HSO Study is a multicentre, randomized, prospective controlled clinical trial comparing two endotamponades within a two-arm parallel group design. Patients with inferiorly and posteriorly located PVR are randomized to either heavy silicone oil or standard silicone oil as a tamponading agent. Three hundred and fifty consecutive patients are recruited per group. After intraoperative re-attachment, patients are randomized to either standard silicone oil (1000 cSt or 5000 cSt) or Densiron((R)) as a tamponading agent. The main endpoint criteria are complete retinal attachment at 12 months and change of visual acuity (VA) 12 months postoperatively compared with the preoperative VA. Secondary endpoints include complete retinal attachment before endotamponade removal, quality of life analysis and the number of retina affecting re-operation within 1 year of follow-up. Results: The design and early recruitment phase of the study are described. Conclusions: The results of this study will uncover whether or not heavy silicone oil improves the prognosis of eyes with PVR. A parallel group design or independent measure design is a study design which uses unique experimental unit each experimental group, in other word no two individuals are shared between experimental groups, hence also known as parallel group design. Subjects of a treatment group receive a unique combination of independent variable values making up a treatment Philippe Rocca-Serra independent measure design http://www.holah.karoo.net/experimentaldesigns.htm parallel group design OBI:0500007 randomized complete block design http://www.stats.gla.ac.uk/steps/glossary/anova.html,(A researcher is carrying out a study of the effectiveness of four different skin creams for the treatment of a certain skin disease. He has eighty subjects and plans to divide them into 4 treatment groups of twenty subjects each. Using a randomised blocks& design, the subjects are assessed and put in blocks of four according to how severe their skin condition is; the four most severe cases are the first block, the next four most severe cases are the second block, and so on to the twentieth block. The four &members of each block are then randomly assigned, one to each of the four treatment groups. http://www.stats.gla.ac.uk/steps/glossary/anova.html#rbd)) A randomized complete block design is_a study design which assigns randomly treatments to block. The number of units per block equals the number of treatment so each block receives each treatment exactly once (hence the qualifier 'complete'). The design was originally devised from field trials used in agronomy and agriculture. The analysis assumes that there is no interaction between block and treatment. The method was then used in other settings So The randomised complete block design is a design in which the subjects are matched according to a variable which the experimenter wishes to control. The subjects are put into groups (blocks) of the same size as the number of treatments. The members of each block are then randomly assigned to different treatment groups. Philippe Rocca-Serra http://www.tufts.edu/~gdallal/ranblock.htm randomized complete block design OBI:0500008 balanced incomplete block design PMID: 7622388.Health Educ Q. 1995 May;22(2):201-10.Balanced incomplete block design: description, case study, and implications for practice. balanced incomplete block design is a kind of factorial design where all treatment pairs occur together within a block an equal number ?? times. ??ii' is the number of times treatment i occurs with i' Philippe Rocca-Serra http://en.wikipedia.org/wiki/Block_design and http://www.stat.psu.edu/~jglenn/stat503/05_factorial/02_factorial_IBD.html balanced incomplete block design OBI:0500009 loop design PMID: 12933549 A loop experiment design is where labeled extracts are compared in consecutive pairs. synonym: circular design Philippe Rocca-Serra on behalf of MO MO_912 loop design OBI:0500010 reference design PMID: 12933549 A reference experiment design type is where all samples are compared to a common reference. Philippe Rocca-Serra on behalf of MO MO_699 reference design OBI:0500011 latin square design PMID: 17582121-Our objective was to examine the effects of dietary cation-anion difference (DCAD) with different concentrations of dietary crude protein (CP) on performance and acid-base status in early lactation cows. Six lactating Holstein cows averaging 44 d in milk were used in a 6 x 6 Latin square design with a 2 x 3 factorial arrangement of treatments: DCAD of -3, 22, or 47 milliequivalents (Na + K - Cl - S)/100 g of dry matter (DM), and 16 or 19% CP on a DM basis. Linear increases with DCAD occurred in DM intake, milk fat percentage, 4% fat-corrected milk production, milk true protein, milk lactose, and milk solids-not-fat. Milk production itself was unaffected by DCAD. Jugular venous blood pH, base excess and HCO3(-) concentration, and urine pH increased, but jugular venous blood Cl- concentration, urine titratable acidity, and net acid excretion decreased linearly with increasing DCAD. An elevated ratio of coccygeal venous plasma essential AA to nonessential AA with increasing DCAD indicated that N metabolism in the rumen was affected, probably resulting in more microbial protein flowing to the small intestine. Cows fed 16% CP had lower urea N in milk than cows fed 19% CP; the same was true for urea N in coccygeal venous plasma and urine. Dry matter intake, milk production, milk composition, and acid-base status did not differ between the 16 and 19% CP treatments. It was concluded that DCAD affected DM intake and performance of dairy cows in early lactation. Feeding 16% dietary CP to cows in early lactation, compared with 19% CP, maintained lactation performance while reducing urea N excretion in milk and urine. Latin square design is_a study design which allows in its simpler form controlling 2 levels of nuisance variables (also known as blocking variables).he 2 nuisance factors are divided into a tabular grid with the property that each row and each column receive each treatment exactly once. Philippe Rocca-Serra Adapted from: http://www.itl.nist.gov/div898/handbook/pri/section3/pri3321.htm and latin square design OBI:0500012 graeco latin square design PMID: 6846242-Beaton et al (Am J Clin Nutr 1979;32:2546-59) reported on the partitioning of variance in 1-day dietary data for the intake of energy, protein, total carbohydrate, total fat, classes of fatty acids, cholesterol, and alcohol. Using the same food intake data and the expanded National Heart, Lung and Blood Institute food composition data base, these analyses of sources of variance have been expanded to include classes of carbohydrate, vitamin A, vitamin C, thiamin, riboflavin, niacin, calcium, iron, total ash, caffeine, and crude fiber. The analyses relate to observed intakes (replicated six times) of 30 adult males and 30 adult females obtained under a paired Graeco-Latin square design with sequence of interview, interviewer, and day of the week as determinants. Neither sequence nor interviewer made consistent contribution to variance. In females, day of the week had a significant effect for several nutrients. The major partitioning of variance was between interindividual variation (between subjects) and intraindividual variation (within subjects) which included both true day-to-day variation in intake and methodological variation. For all except caffeine, the intraindividual variability of 1-day data was larger than the interindividual variability. For vitamin A, almost all of the variance was associated with day-to-day variability. One day data provide a very inadequate estimate of usual intake of individuals. In the design of nutrition studies it is critical that the intended use of dietary data be a major consideration in deciding on methodology. There is no ideal dietary method. There may be preferred methods for particular purposes. Greco-Latin square design is a study design which relates to Latin square design Philippe Rocca-Serra Adapted from: http://www.itl.nist.gov/div898/handbook/pri/section3/pri3321.htm and only 2 articles in pubmed ->probably irrelevant graeco latin square design OBI:0500013 hyper graeco latin square design PRS to do Philippe Rocca-Serra Adapted from: http://www.itl.nist.gov/div898/handbook/pri/section3/pri3321.htm and no example found in pubmed->not in use in the community hyper graeco latin square design OBI:0500014 factorial design PMID: 17582121-Our objective was to examine the effects of dietary cation-anion difference (DCAD) with different concentrations of dietary crude protein (CP) on performance and acid-base status in early lactation cows. Six lactating Holstein cows averaging 44 d in milk were used in a 6 x 6 Latin square design with a 2 x 3 factorial arrangement of treatments: DCAD of -3, 22, or 47 milliequivalents (Na + K - Cl - S)/100 g of dry matter (DM), and 16 or 19% CP on a DM basis. Linear increases with DCAD occurred in DM intake, milk fat percentage, 4% fat-corrected milk production, milk true protein, milk lactose, and milk solids-not-fat. Milk production itself was unaffected by DCAD. Jugular venous blood pH, base excess and HCO3(-) concentration, and urine pH increased, but jugular venous blood Cl- concentration, urine titratable acidity, and net acid excretion decreased linearly with increasing DCAD. An elevated ratio of coccygeal venous plasma essential AA to nonessential AA with increasing DCAD indicated that N metabolism in the rumen was affected, probably resulting in more microbial protein flowing to the small intestine. Cows fed 16% CP had lower urea N in milk than cows fed 19% CP; the same was true for urea N in coccygeal venous plasma and urine. Dry matter intake, milk production, milk composition, and acid-base status did not differ between the 16 and 19% CP treatments. It was concluded that DCAD affected DM intake and performance of dairy cows in early lactation. Feeding 16% dietary CP to cows in early lactation, compared with 19% CP, maintained lactation performance while reducing urea N excretion in milk and urine. factorial design is_a study design which is used to evaluate two or more factors simultaneously. The treatments are combinations of levels of the factors. The advantages of factorial designs over one-factor-at-a-time experiments is that they are more efficient and they allow interactions to be detected. In statistics, a factorial design experiment is an experiment whose design consists of two or more factors, each with discrete possible values or levels, and whose experimental units take on all possible combinations of these levels across all such factors. Such an experiment allows studying the effect of each factor on the response variable, as well as the effects of interactions between factors on the response variable. Philippe Rocca-Serra http://www.stats.gla.ac.uk/steps/glossary/anova.html#facdes And from wikipedia (01/03/2007): http://en.wikipedia.org/wiki/Factorial_experiment) factorial design OBI:0500015 2x2 factorial design PMID: 17561240-The present experiment evaluates the effects of intermittent exposure to a social stimulus on ethanol and water drinking in rats. Four groups of rats were arranged in a 2x2 factorial design with 2 levels of Social procedure (Intermittent Social vs Continuous Social) and 2 levels of sipper Liquid (Ethanol vs Water). Intermittent Social groups received 35 trials per session. Each trial consisted of the insertion of the sipper tube for 10 s followed by lifting of the guillotine door for 15 s. The guillotine door separated the experimental rat from the conspecific rat in the wire mesh cage during the 60 s inter-trial interval. The Continuous Social groups received similar procedures except that the guillotine door was raised during the entire duration of the session. For the Ethanol groups, the concentrations of ethanol in the sipper [3, 4, 6, 8, 10, 12, 14, and 16% (vol/vol)] increased across sessions, while the Water groups received 0% ethanol (water) in the sipper throughout the experiment. Both Social procedures induced more intake of ethanol than water. The Intermittent Social procedure induced more ethanol intake at the two highest ethanol concentration blocks (10-12% and 14-16%) than the Continuous Social procedure, but this effect was not observed with water. Effects of social stimulation on ethanol drinking are discussed. a factorial design which has 2 experimental factors (aka independent variables) and 2 factor levels per experimental factors Philippe Rocca-Serra PMID: 17561240 2x2 factorial design OBI:0500016 fractional factorial design A fractional factorial design is_a study design in which only an adequately chosen fraction of the treatment combinations required for the complete factorial experiment is selected to be run Philippe Rocca-Serra http://www.itl.nist.gov/div898/handbook/pri/section3/pri334.htm From ASQC (1983) Glossary & Tables for Statistical Quality Control fractional factorial design OBI:0500017 dye swap design PMID: 17411393-Dye-specific bias effects, commonly observed in the two-color microarray platform, are normally corrected using the dye swap design. This design, however, is relatively expensive and labor-intensive. We propose a self-self hybridization design as an alternative to the dye swap design. In this design, the treated and control samples are labeled with Cy5 and Cy3 (or Cy3 and Cy5), respectively, without dye swap, along with a set of self-self hybridizations on the control sample. We compare this design with the dye swap design through investigation of mouse primary hepatocytes treated with three peroxisome proliferator-activated receptor-alpha (PPARalpha) agonists at three dose levels. Using Agilent's Whole Mouse Genome microarray, differentially expressed genes (DEG) were determined for both the self-self hybridization and dye swap designs. The DEG concordance between the two designs was over 80% across each dose treatment and chemical. Furthermore, 90% of DEG-associated biological pathways were in common between the designs, indicating that biological interpretations would be consistent. The reduced labor and expense for the self-self hybridization design make it an efficient substitute for the dye swap design. For example, in larger toxicogenomic studies, only about half the chips are required for the self-self hybridization design compared to that needed in the dye swap design. An experiment design type where the label orientations are reversed. exact synonym: flip dye, dye flip Philippe Rocca-Serra on behalf of MO MO_858 dye swap design OBI:0500018 replicate design A replicate experimental design type is where a series of replicates are performed to evaluate reproducibility or as a pilot study to determine the appropriate number of replicates for a subsequent experiments. Philippe Rocca-Serra on behalf of MO MO_885 replicate design OBI:0500019 self vs self design PMID: 17411393-Dye-specific bias effects, commonly observed in the two-color microarray platform, are normally corrected using the dye swap design. This design, however, is relatively expensive and labor-intensive. We propose a self-self hybridization design as an alternative to the dye swap design. In this design, the treated and control samples are labeled with Cy5 and Cy3 (or Cy3 and Cy5), respectively, without dye swap, along with a set of self-self hybridizations on the control sample. We compare this design with the dye swap design through investigation of mouse primary hepatocytes treated with three peroxisome proliferator-activated receptor-alpha (PPARalpha) agonists at three dose levels. Using Agilent's Whole Mouse Genome microarray, differentially expressed genes (DEG) were determined for both the self-self hybridization and dye swap designs. The DEG concordance between the two designs was over 80% across each dose treatment and chemical. Furthermore, 90% of DEG-associated biological pathways were in common between the designs, indicating that biological interpretations would be consistent. The reduced labor and expense for the self-self hybridization design make it an efficient substitute for the dye swap design. For example, in larger toxicogenomic studies, only about half the chips are required for the self-self hybridization design compared to that needed in the dye swap design. A study design that investigates variance and error estimates in the experimental system, and is where the same extract is compared. Philippe Rocca-Serra on behalf of MO MO_490 self vs self design OBI:0500020 time series design PMID: 14744830-Microarrays are powerful tools for surveying the expression levels of many thousands of genes simultaneously. They belong to the new genomics technologies which have important applications in the biological, agricultural and pharmaceutical sciences. There are myriad sources of uncertainty in microarray experiments, and rigorous experimental design is essential for fully realizing the potential of these valuable resources. Two questions frequently asked by biologists on the brink of conducting cDNA or two-colour, spotted microarray experiments are 'Which mRNA samples should be competitively hybridized together on the same slide?' and 'How many times should each slide be replicated?' Early experience has shown that whilst the field of classical experimental design has much to offer this emerging multi-disciplinary area, new approaches which accommodate features specific to the microarray context are needed. In this paper, we propose optimal designs for factorial and time course experiments, which are special designs arising quite frequently in microarray experimentation. Our criterion for optimality is statistical efficiency based on a new notion of admissible designs; our approach enables efficient designs to be selected subject to the information available on the effects of most interest to biologists, the number of arrays available for the experiment, and other resource or practical constraints, including limitations on the amount of mRNA probe. We show that our designs are superior to both the popular reference designs, which are highly inefficient, and to designs incorporating all possible direct pairwise comparisons. Moreover, our proposed designs represent a substantial practical improvement over classical experimental designs which work in terms of standard interactions and main effects. The latter do not provide a basis for meaningful inference on the effects of most interest to biologists, nor make the most efficient use of valuable and limited resources. Groups of assays that are related as part of a time series. Philippe Rocca-Serra on behalf of MO MO_887 time series design OBI:0600002 tumor grading Determination of the grade (severity/stage) of a tumor sample, used in cancer biology to describe abnormalities/qualities of tumor cells or tissues. Values can be described by terms from NCI Thesaurus. Compiled by Helen Parkinson for Transcriptomics thanks to Adam Witney grading of tumor OBI branch derived; submitted by MO tumor grading OBI:0600005 collecting specimen from organism taking a sputum sample from a cancer patient, taking the spleen from a killed mouse, collecting a urine sample from a patient a process with the objective to obtain a material entity that was part of an organism for potential future use in an investigation PERSON:Bjoern Peters IEDB collecting specimen from organism OBI:0600006 killing Terminal sacrifice of animals by cervical dislocation at the end of an investigation. A protocol application in which an organism is intentionally put to death difficult to place this properly - JG. Death process (e.g. unscheduled death) is out of scope but should be added somewhere. All killings have death process as a part, but not all death processes are part of a killing. Jennifer Fostel Philippe Rocca-Serra death status type euthanisia life termination sacrifice CEBS, Biomaterial_branch killing 1 OBI:0600007 administering substance in vivo Balb/c mice received an intracameral or subconjunctival injection of trinitrophenylated spleen cells injecting mice with 10 ug morphine intranasally, a patient taking two pills of 1 mg aspirin orally A process by which a substance is intentionally given to an organism resulting in exposure of the organism to that substance. 2009-11-10. Tracker: https://sourceforge.net/tracker/?func=detail&aid=2893050&group_id=177891&atid=886178 Different routes and means of administration should go as children underneath this Update the definition based on the discussion. Details see the tracker: https://sourceforge.net/p/obi/obi-terms/738/ needs roles such as perturber and perturbee (children of input role). Perturb is too strong. Host might be the name for one role. Others considered: Doner, Donated, Acceptor. Bjoern Peters Person:Bjoern Peters IEDB administering substance in vivo OBI:0600009 exposure of material to environment Putting cells in a freezer at -80C. Cy5-labeled DNA is irradiated with a laser to excite the fluorophore. Inducing a phase transition in a material by putting it in an environment with a specific temperature. Oxygen deprivation in a chamber. a planned process in which an input material is exposed to a defined set of conditions in a controlled environment. The environment is a specified input. Bjoern Peters IEDB Alan says there will be problmes, e.g. with selection by survival exposure of material to environment OBI:0600011 acclimatization placing mice in animal facility for 2 weeks prior to an experiment to accustom them to their environment, reducing stress A protocol application in which an object is left in an environment for some period of time, until some qualities of interest are in equilibrium with that environment. Jennifer Fostel CEBS, Biomaterial_branch acclimatization OBI:0600014 material component separation Using a cell sorter to separate a mixture of T cells into two fractions; one with surface receptor CD8 and the other lacking the receptor, or purification a material processing in which components of an input material become segregated in space Bjoern Peters IEDB material component separation 2 OBI:0600016 pooling specimens http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=104564; Combining spleens of 20 mice, Combining supernatant from a cell culture obtained at different time points physical combination of several instances of like material PlanAndPlannedProcess Branch sample pooling OBI branch derived like' is one of the things that you should be controling for in a well-designed experiment. The instances of material need to have the same class. pooling specimens OBI:0600018 material portioning pouring 50 mL aliquots of fetal calf serum into conical tubes from a 500 mL stock a material processing in which the input substance is partitioned into a number of portions that are similar in composition. PERSON:Bjoern Peters aliquoting apportioning OBI branch derived material portioning OBI:0600020 histology the counting of the number of cells with fluorescent label at their surface to determine the percentage of the population which was activated the visual examination of cells or tissue (or images of them) with an assessment regarding a quality of the cells or tissue. Parts are: staining, imaging, judgement PERSON:Compiled by Helen Parkinson for Transcriptomics thanks to Adam Witney histopathology OBI branch derived PRS:20090901: addition of alternative term = histopathology need to incorporate parts\n---\nThis is a very vague term, it should be in the same place as transcriptomics, proteomics metaboloimcs. It is the 'study' of tissues, not the process of studying tissues\n histology OBI:0600022 excision Cutting out the portion of a gel which contains a DNA fragment the use physical means to remove a portion of a substance from the rest Alan Ruttenberg, Kevin Clancy www.crohnsresource.com/glossary.jsp (via google define:resection) excision OBI:0600023 non specific enzymatic cleavage The use of agarase to digest an agar gel a protocol application to digest the fraction of input material that is susceptible to that enzyme PERSON:Kevin Clancy OBI branch derived non specific enzymatic cleavage OBI:0600024 maintaining cell culture When harvesting blood from a human, isolating T cells, and then limited dilution cloning of the cells, the maintaining_cell_culture step comprises all steps after the initial dilution and plating of the cells into culture, e.g. placing the culture into an incubator, changing or adding media, and splitting a cell culture a protocol application in which cells are kept alive in a defined environment outside of an organism. part of cell_culturing PlanAndPlannedProcess Branch OBI branch derived maintaining cell culture OBI:0600028 artificially induced reverse transcription The use of M-MLV reverse transcriptase from the Moloney murine leukemia virus to transcribe an RNA sample into cDNA a protocol with the objective to transcribe single-stranded RNA into complementary DNA (cDNA) It could also be added that the reverse transcriptase is bearer of a GO:0003964 RNA-directed DNA polymerase activity, which is realized in this process. We need to indicate the relationship between the cDNA generated and the RNA that was used as a template. This may be outside of the OBI scope PERSON:Kevin Clancy OBI branch derived artificially induced reverse transcription OBI:0600033 cell permeabilization Electroporation of HeLa cells to allow transfection with pUC19. A protocol application to permeabilize cell membranes, allowing molecules to more easily pass through the membrane than was possible prior to the protocol application need to add output cell has_quality permeable PERSON:Bjoern Peters OBI branch derived definition blessed by Jay, Alan, Randi cell permeabilization OBI:0600036 establishing cell culture a process through which a new type of cell culture or cell line is created, either through the isolation and culture of one or more cells from a fresh source, or the deliberate experimental modification of an existing cell culture (e.g passaging a primary culture to become a secondary culture or line, or the immortalization or stable genetic modification of an existing culture or line). PERSON:Matthew Brush PERSON:Matthew Brush A 'cell culture' as used here referes to a new lineage of cells in culture deriving from a single biological source.. New cultures are established through the initial isolation and culturing of cells from an organismal source, or through changes in an existing cell culture or line that result in a new culture with unique characteristics. This can occur through the passaging/selection of a primary culture into a secondary culture or line, or experimental modifications of an existing cell culture or line such as an immortalization process or other stable genetic modification. This class covers establishment of cultures of either multicellular organism cells or unicellular organisms. establishing cell culture OBI:0600037 cell culture splitting The act of taking a cell culture of high density, counting the cells, removing part of the cells, and re-seeding a select number of the cells into new flasks with fresh tissue culture media. The act of taking part of a homogeneous cell culture and creating one or more additional separate cultures of similar qualities. input: cell_culture, output cell_culture min cardinality 2. part of cell culturing PlanAndPlannedProcess Branch cell culture passaging OBI branch derived An active cell culture is typically split when it has grown to confluence in its culture dish. Cell culture splitting of a cell culture sample results in an increase in its passage number, which measures how long a sample has been propagated in vitro, and therefore how many selective or genetic changes it is likely to have undergone. cell culture splitting OBI:0600038 addition of molecular label The addition of phycoerytherin label to an anti-CD8 antibody, to label all antibodies. The addition of anti-CD8-PE to a population of cells, to label the subpopulation cells that are CD8+. a material processing technique intended to add a molecular label to some input material entity, to allow detection of the molecular target of this label in a detection of molecular label assay PERSON:Matthew Brush labeling OBI developer call, 3-12-12 addition of molecular label OBI:0600041 concentrate Evaporation of the solution containing DNA to increase the concentration of the DNA molecules a protocol application to create an output material with an increased density of a material of interest that is part of the input material by separating other parts of the input material PERSON:Kevin Clancy OBI branch derived concentrate OBI:0600043 genetic transformation The transduction of E. coli through the introduction of a plasmid encoding for M. avium p35 the introduction. alteration or integration of genetic material into a cell or organism PERSON:Kevin Clancy genetic modification OBI branch derived genetic transformation OBI:0600047 sequencing assay The use of the Sanger method of DNA sequencing to determine the order of the nucleotides in a DNA template the use of a chemical or biochemical means to infer the sequence of a biomaterial has_output should be sequence of input; we don't have sequence well defined yet PlanAndPlannedProcess Branch OBI branch derived sequencing assay OBI:0600048 vector mediated amplification E coli expressing the gene for M avium p35 were cultured in order to produce p35. The process of creating a copy of some biological entity in cell culture PERSON:Kevin Clancy OBI branch derived vector mediated amplification OBI:0600050 specific enzymatic cleavage The use of a protease to digest a protein into peptides a protocol application to digest the fraction of input material that is susceptible to that enzyme PERSON:Kevin Clancy OBI branch derived specific enzymatic cleavage OBI:0600056 protease cleavage the use of trypsin to cleave pepsin into peptide fragments protease cleavage is an enzymatic cleavage which relies on enzyme with protease activity to act on proteins and produce polypeptides (protein fragments). enzymatic digestion PlanAndPlannedProcess Branch OBI branch derived protease cleavage OBI:0600058 enzymatic amplification the use of a polymerase chain reaction to amplify a fragment of DNA the use of enzymes to increase the number of molecules of a biomaterial PERSON:Kevin Clancy OBI branch derived enzymatic amplification OBI:0600064 recombinant vector cloning a planned process with the objective to insert genetic material into a cloning vector for future replication of the inserted material pa_branch (Alan, Randi, Kevin, Jay, Bjoern) molecular cloning OBI branch derived recombinant vector cloning OBI:0666666 RNA extraction A RNA extraction is a nucleic acid extraction where the desired output material is RNA PlanAndPlannedProcess Branch OBI branch derived requested by Helen Parkinson for MO RNA extraction OBI:0666667 nucleic acid extraction Phenol / chlorophorm extraction disolvation of protein content folllowed by ethanol precipitation of the nucleic acid fraction over night in the fridge followed by centrifugation to obtain a nucleic acid pellet. a material separation to recover the nucleic acid fraction of an input material PlanAndPlannedProcess Branch OBI branch derived requested by Helen Parkinson for MO. Could be defined class nucleic acid extraction OBI:1000029 phage display library PMID: 15905471.Nucleic Acids Res. 2005 May 19;33(9):e81.Oligonucleotide-assisted cleavage and ligation: a novel directional DNA cloning technology to capture cDNAs. Application in the construction of a human immune antibody phage-display library. [Phage display library encoding fragments of human antibodies. m-rna library encoding for 9-mer peptides] a phage display library is a collection of materials in which a mixture of genes or gene fragments is expressed and can be individually selected and amplified. PERSON: Bjoern Peters PERSON: Philippe Rocca-Serra display library WEB: http://www.immuneepitope.org/home.do PRS: 22022008. class moved under population, modification of definition and replacement of biomaterials in previous definition with 'material' addition of has_role restriction phage display library OBI:1000036 cell lysate The effect of vaccination with the lysate of heat-shocked tumor cells on nitric oxide production in BALB/c mice with fibrosarcoma tumor. Cell Biol Int. 2008 Jul;32(7):835-40. PMID: 18455932 a cell lysate is a material entity which is output of a cell lysis process PRS:22-02-2008: is a material which has output_role during lysis protocol-application. old defintion: A mixture (collection) of cell components created by rupturing of the cell wall resulting from a lysis process PERSON: Susanna Sansone lysate lysed material GROUP: PSI cell lysate OBI:1000207 assay bead Dynabeads are commercially available magnetic beads which are precoated with antibodies specific for select cellular receptors and are used to separate cell populations. A globular or round particle of defined physicochemical properties and size which can be exploited as either the primary substance for detection or as a secondary solid platform for the attachment of bioactive molecules. DS: Probably better modeled as a role. OBI bead assay bead OBI:1110021 infection the detrimental process in which an infectious agent colonizes or replicates in a host environment IEDB IEDB infection OBI:1110022 adaptive immune receptor is a receptor produced by cells of the adaptive immune system with the purpose of binding epitopes. IEDB IEDB adaptive immune receptor OBI:1110055 obsolete_disease placeholder to be imported from disease ontology IEDB IEDB http://purl.obolibrary.org/obo/OGMS_0000031 obsolete_disease 1 OBI:1110093 disposition to infect an organism Is a role borne by an agent, and realized when in contact with or inside another organism in which it is capable of replicating and causing disease IEDB IEDB disposition to infect an organism OBI:1110108 material to be added A mixture of peptides that is being added into a cell culture. a material that is added to another one in a material combination process 10/26/09: This defined class is used as a 'macro expression' to reduce the size of the IEDB export 2010/02/24 Alan Ruttenberg: I think this might generate confusion as the common use of the term would consider something to be a specimen during the realization of the role, not only if it bears it. However having this class as a probe, or for display, or as a macro might be useful. Ideally we would mark or segregate such classes IEDB material to be added OBI:1110109 target of material addition A cell culture into which a mixture of peptides is being added. A material entity into which another is being added in a material combinatino process 10/26/09: This defined class is used as a 'macro' to reduce the size of the IEDB export. IEDB target of material addition OBI:1110122 pathologic process abnormal, harmful processes caused by or associated with a disease IEDB IEDB pathologic process OGMS:0000015 A series of statements representing health-relevant qualities of a patient and of a patient's family. clinical history OGMS:0000023 A (combination of) quality(ies) of an organism determined by the interaction of its genetic make-up and environment that differentiates specific instances of a species from other instances of the same species. phenotype OGMS:0000031 A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism. disease OGMS:0000063 The totality of all processes through which a given disease instance is realized. disease course OGMS:0000090 A processual entity whose completion is hypothesized (by a healthcare provider) to alleviate the signs and symptoms associated with a disorder treatment A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities. PATO:0000072 trait quality PATO:0000001 quality PATO:0000001 A time quality inhering in a bearer by virtue of how long the bearer has existed. quality PATO:0000011 age PATO:0000011 A single physical entity inhering in an bearer by virtue of the bearer's quantities or relative ratios of subparts. PATO:0002015 compositionality content structure, composition quality PATO:0000025 For example calcium composition (which may inhere in bone), haemoglobin composition (which may inhere in blood). composition PATO:0000025 A quality inhering in a substance by virtue of the amount of the bearer's there is mixed with another substance. concentration quality PATO:0000033 concentration of PATO:0000033 An organismal quality inhering in a bearer by virtue of the bearer's ability to undergo sexual reproduction in order to differentiate the individuals or types involved. quality PATO:0000047 biological sex PATO:0000047 A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure. quality PATO:0000051 morphology PATO:0000051 A morphological quality inhering in a bearer by virtue of the bearer's ratios of distances between its features (points, edges, surfaces and also holes etc). PATO:0001647 relational shape quality quality PATO:0000052 Shapes are invariant on size transformations. Shapes can be subdivided into 2D and 3D shapes, We can also make a distinction between shapes of complete self-connected objects, and shapes of parts of objects. shape PATO:0000052 quality PATO:0000068 TODO: define this or obsolete it and move children somewhere else. qualitative PATO:0000068 A quality inhering in a bearer by virtue of the whether the bearer differs from normal or average. quality PATO:0000069 deviation(from_normal) PATO:0000069 A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude. quality PATO:0000117 size PATO:0000117 A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form. PATO:0001452 relational structural quality quality PATO:0000141 structure PATO:0000141 A physical quality of the thermal energy of a system. quality PATO:0000146 temperature PATO:0000146 A quality in which events occur in sequence. quality PATO:0000165 time PATO:0000165 An organismal quality inhering in a bearer or a population by virtue of the bearer's disposition to survive and develop normally or the number of surviving individuals in a given population. quality PATO:0000169 viability PATO:0000169 A quality of a single physical entity which is held by a bearer when the latter exhibits complete growth, differentiation, or development. quality PATO:0000261 maturity PATO:0000261 A biological sex quality inhering in an individual or a population that only produces gametes that can be fertilised by male gametes. quality PATO:0000383 female PATO:0000383 A biological sex quality inhering in an individual or a population whose sex organs contain only male gametes. quality PATO:0000384 male PATO:0000384 A shape quality inhering in a bearer by virtue of the bearer's being such that every part of the surface or the circumference is equidistant from the center. quality round rounded PATO:0000411 circular PATO:0000411 A quality inhering in a bearer by virtue of the bearer's exhibiting no deviation from normal or average. quality average PATO:0000461 normal PATO:0000461 A size quality which is relatively high. PATO:0001202 quality big enlarged expanded great large PATO:0000586 increased size PATO:0000586 A spheroid quality inhering in a bearer by virtue of the bearer's being oval with two axes of symmetry, as produced by a conical section. ellipse-shaped ellipsoid elliptical quality oval ovoid PATO:0000947 elliptic PATO:0000947 A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities. PATO:0002079 Wikipedia:Physical_property relational physical quality quality PATO:0001018 physical quality PATO:0001018 A quality which inheres in a continuant. PATO:0001237 PATO:0001238 snap:Quality monadic quality of a continuant multiply inhering quality of a physical entity quality of a continuant quality of a single physical entity quality of an object quality of continuant monadic quality of an object monadic quality of continuant quality PATO:0001241 Relational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles. physical object quality PATO:0001241 A mating type that indicates whether the F plasmid has integrated into the chromosome. quality PATO:0001335 bacterial mating type PATO:0001335 A yeast mating type. quality PATO:0001337 yeast mating type PATO:0001337 A biological sex quality inhering in a population of multiple sexes. quality PATO:0001338 For example a mixture of females and male or males and hermaphrodites. mixed sex PATO:0001338 A composition quality inhering in an bearer by virtue of the bearer's homogeneity of a biomaterial. quality PATO:0001339 biomaterial purity PATO:0001339 A biological sex quality inhering in an organism or a population with both male and female sexual organs in one individual. intersex quality PATO:0001340 hermaphrodite PATO:0001340 A S. cerevisiae mating type cells that secrete a pheromone that in alpha haploids stimulates processes that lead to mating. a quality PATO:0001341 a mating type (yeast) PATO:0001341 A S. cerevisiae mating type. quality PATO:0001342 Saccharomyces cerevisiae mating type PATO:0001342 A S. pombe mating type determined by the gene configuration on the mat1 locus. quality PATO:0001343 Schizosaccharomyces pombe mating type PATO:0001343 A S. cerevisiae mating type cells that secrete a pheromone that stimulates a haploids. alpha quality PATO:0001344 alpha mating type (yeast) PATO:0001344 A S. pombe mating type determined by the mat1-Mc and mat1-Mi on the mat1 locus. M h - quality PATO:0001345 h minus PATO:0001345 A S. pombe mating type determined by the mat1-Pc and mat1-Pi on the mat1 locus. P h+ quality PATO:0001346 h plus PATO:0001346 A bacterial mating type indicating the presence of F plasmid in a bacterial cell. quality PATO:0001347 F mating type PATO:0001347 A bacterial mating type indicating the absence of F plasmid in a bacterial cell. F- quality PATO:0001348 F minus mating type PATO:0001348 A cellular quality inhering in a bearer by virtue of the bearer's number of homologous sets of chromosomes in the nucleus or primary chromosome-containing compartment of the cell, each set essentially coding for all the biological traits of the organism. quality PATO:0001374 ploidy PATO:0001374 A ploidy quality inhering in a bearer by virtue of the bearer's containing a single set of homologous chromosomes. quality PATO:0001375 haploid PATO:0001375 A ploidy quality inhering in a bearer by virtue of the bearer's containing more than two homologous sets of chromosomes. quality PATO:0001377 polyploid PATO:0001377 A ploidy quality inhering in a bearer by virtue of the bearer's containing a non-integral multiple of the monoploid number, due to extra or missing chromosomes. quality PATO:0001385 aneuploid PATO:0001385 A ploidy quality inhering in a bearer by virtue of the bearer's containing an integral multiple of the monoploid number, possibly excluding the sex-determining chromosomes. quality PATO:0001393 euploid PATO:0001393 A ploidy quality inhering in a bearer by virtue of the bearer's having two copies (homologs) of each chromosome, usually one from the mother and one from the father. quality PATO:0001394 The exact number may be one or two different from the 2n number and still be classified as diploidy (although with aneuploidy). Nearly all mammals are diploid organisms, although all individuals have some small fracton of cells that are polyploidy. diploid PATO:0001394 A monadic quality of continuant that exists at the cellular level of organisation. quality PATO:0001396 cellular quality PATO:0001396 A cellular quality that arises by virtue of whether the bearer's disposition to differentiate into one or more mature cell types. quality PATO:0001397 cellular potency PATO:0001397 A cellular potency that is the capacity to produce only one differentiated cell type. quality PATO:0001400 Unipotent cells have the quality of self-renewal which distinguishes them from non-stem cells. unipotent PATO:0001400 A cellular potency that is the capacity to form multiple differentiated cell types of a specific lineage and lack self renewing capacity. quality PATO:0001401 Less potent than multipotent, often thought of as precursor or progenitor cell status. oligopotent PATO:0001401 A cellular potency that is the capacity to form multiple differentiated cell types. quality PATO:0001402 multipotent PATO:0001402 A cellular quality inhering in a bearer by virtue of bearer's number of nuclei. quality PATO:0001404 nucleate quality PATO:0001404 A nucleate quality inhering in a bearer by virtue of the bearer's having no nucleus. quality PATO:0001405 anucleate PATO:0001405 A nucleate quality inhering in a bearer by virtue of the bearer's having one nucleus. quality PATO:0001407 mononucleate PATO:0001407 A shape quality inhering in a bearer by virtue of the bearer's being marked by narrow lines or grooves, usually parallel. quality PATO:0001410 striated PATO:0001410 A viability quality inhering in a bearer by virtue of the bearer's condition before death. quality PATO:0001421 alive PATO:0001421 A viability quality inhering in a bearer by virtue of the cessation of the bearer's life. quality PATO:0001422 dead PATO:0001422 A quality inhering in a bearer by virtue of the bearer's lacking complete growth, differentiation, or development. quality underdeveloped PATO:0001501 immature PATO:0001501 A quality inhering in a bearer by virtue of the bearer's exhibiting complete growth, differentiation, or development. quality PATO:0001701 mature PATO:0001701 A shape quality in a bearer by virtue of the bearer's curving inward. quality PATO:0001857 concave PATO:0001857 A convex 3-D shape quality inhering in a bearer by virtue of the bearer's exhibiting a consistently-sized round cross section. PATO:0001203 rod-like rod-shaped tubulate quality PATO:0001873 cylindrical PATO:0001873 A shape quality inhering in a bearer by virtue of the bearer's being cylindrical, in which the height is less than the diameter. disc-shaped disk-shaped quality PATO:0001874 discoid PATO:0001874 quality PATO:0001894 phenotypic sex PATO:0001894 A biological sex quality inhering in an individual or a population that undergo sexual reproduction. quality PATO:0001895 mating type PATO:0001895 A quality inhering in a bearer by virtue of the bearer's being kept below its freezing point. quality PATO:0001985 frozen PATO:0001985 A quality that inheres in an entire organism or part of an organism. quality PATO:0001995 organismal quality PATO:0001995 A quality that inheres in an entire population or part of a population. quality PATO:0002003 population quality PATO:0002003 Surface shape that refers to the inward or outward curvature of the surface. quality PATO:0002005 concavity PATO:0002005 A shape that inheres in a 2 dimensional entity, such as a cross section or projection of a 3 dimensional entity. quality 2-D projection cross-sectional PATO:0002006 2-D shape PATO:0002006 A complete three dimensional shape in which for every line connecting pair of points on the object is within the object. Or: a shape lacking cavities. Contrast: concave. Image:http://upload.wikimedia.org/wikipedia/commons/0/06/Convex_polygon_illustration1.png quality PATO:0002007 Use this term or an is_a child of this term when the entire shape of the object is known. convex 3-D shape PATO:0002007 A concave quality inhering in a bearer by virtue of the bearer's curving inward on both sides or surfaces. quality PATO:0002039 biconcave PATO:0002039 A molecular quality that arises from the molecular attraction exerted between two atoms or compounds. George Gkoutos 2009-09-18T01:16:16Z quality PATO:0002070 affinity PATO:0002070 An affinity inhering in a tissue constituent by virtue of the bearer exhibiting a molecular interaction for basic dyes under specific ph conditions. george 2009-10-05T12:05:23Z quality PATO:0002094 basophilic PATO:0002094 A quality which inheres in a molecular entity, a single molecule, atom, ion, radical etc. George Gkoutos 2010-03-10T03:18:15Z PATO:0002061 relational molecular quality quality PATO:0002182 molecular quality PATO:0002182 A shape that inheres in a 3 dimensional entity. george 2010-10-05T12:31:16Z quality PATO:0002266 3-D shape PATO:0002266 A quality that has a value that is increased compared to normal or average. George Gkoutos 2011-06-16T06:39:43Z quality PATO:0002300 increased quality PATO:0002300 A quality of an object that has a value that is increased compared to normal or average. George Gkoutos 2011-06-16T06:54:01Z quality PATO:0002305 increased object quality PATO:0002305 A shape constituting a transition between a rectangle and a circle; a closed curve, of which the circle and ellipse are special cases, whose parametric equation is x = a.cos2/rt, y = b.cos2/rt George Gkoutos 2011-10-12T12:45:16Z Lamé curve quality PATO:0002318 superelliptic PATO:0002318 A shape quality inhering in a bearer by virtue of the bearer's being marked by narrow lines or grooves, usually parallel, that are oriented transversely relative to the long axis of the bearer. gkoutos 2013-09-15T12:29:15Z quality PATO:0002478 transversely striated PATO:0002478 PR:000000001 An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA. protein PR:000001002 A protein that is a translation product of the human CD19 gene or a 1:1 ortholog thereof. It is composed of an N-terminal extracellular domain containing two Ig-like C2-type (immunoglobulin-like) domains, followed by a single-pass transmembrane segment and a cytoplasmic C-terminal tail. CD19 expression is restricted to members of the B cell lineage. It functions as a co-receptor for B-cell antigen receptor (BCR), regulating signal transduction. CD19 molecule PR:000001003 A protein that is a translation product of the human CD34 gene or a 1:1 ortholog thereof. It is a leukocyte membrane protein expressed specifically by lymphohematopoietic progenitor cells. It contains a single-pass transmembrane domain and that show distinct expression on early hematopoietic precursors and vascular-associated tissue. Acts as a scaffold that presents selectin carbohydrate ligands in a clustered, tissue specific manner to allow for higher avidity interactions between leukocytes and endothelial cells during the inflammatory process. In common with related sialomucins (endoglycan and podocalyxin), the extracellular region is dominated by an N-terminal mucin-like domain, which is densely substituted with sialylated O-linked carbohydrates. The mucin-like region is followed by a cysteine-containing and presumably globular domain. This domain may fold into an immunoglobulin-like structure as the positions of 2 of the cysteines are conserved in the C2 set of the immunoglobulin superfamily. The cytoplasmic domain is around 73-76 residues long and highly conserved. CD34 molecule PR:000001004 A protein that is a translation product of the human CD4 gene or a 1:1 ortholog thereof. CD4 is an accessory protein for MHC class-II antigen/T-cell receptor interaction. It is the primary receptor for HIV-1. CD4 has four immunoglobulin-like domains in its extracellular region that share the same structure, but can differ in sequence. CD4 molecule PR:000001006 A protein that is a translation product of the human PTPRC gene or a 1:1 ortholog thereof. It is composed of an extracellular domain, a single transmembrane segment and two tandem intracytoplasmic protein-tyrosine phosphatase domains. Contains 1 to 3 copies of the Fibronectin type III domain (Pfam:PF00041) followed by two copies of the Protein-tyrosine phosphatase (Pfam:PF00102) domain. Receptor-type tyrosine-protein phosphatase C (CD45) regulates signal transduction and lymphocyte activation by specific association with receptor molecules on T and B cells. Multiple isoforms of CD45 (180-235 kDa) can be generated asa result of alternative splicing of three variable exons 4(A), 5(B) and 6(C), encoding sequences at the N-terminal extracellular domain of the molecule. receptor-type tyrosine-protein phosphatase C PR:000001012 An integrin alpha with A domain that is a translation product of the human ITGAM gene or a 1:1 ortholog thereof. They constitute subunits of the integrin alpha-M/beta-2 receptor. This receptor is implicated in various adhesive interactions of monocytes, macrophages and granulocytes as well as in mediating the uptake of complement-coated particles. It is also a receptor for fibrinogen, factor X and ICAM1. integrin alpha-M PR:000001015 A receptor-type tyrosine-protein phosphatase C that is a translation product of a mature transcript of the PTPRC gene, that includes the region encoded by the variable exon 4(A), and lacks the region encoded by exons 5(B) and 6(C). receptor-type tyrosine-protein phosphatase C isoform CD45RA PR:000001020 A CD3 subunit that is a translation product of the human CD3E gene or a 1:1 ortholog thereof. CD3 epsilon PR:000001024 A neural cell adhesion molecule NCAM that is a translation product of the human NCAM1 gene or a 1:1 ortholog thereof. neural cell adhesion molecule 1 PR:000001083 A protein that is a translation product of the human CD2 gene or a 1:1 ortholog thereof. CD2 molecule PR:000001084 A protein that is a translation product of the human CD8A gene or a 1:1 ortholog thereof. CD8 is a transmembrane that is a co-receptor for MHC class-I antigen/T-cell receptor interaction. The most common form of CD8 is composed of a CD8 alpha and a CD8 beta chain. T-cell surface glycoprotein CD8 alpha chain PR:000001197 A rhodopsin-like G-protein coupled receptor that is a translation product of the CCR1, CCR3, or CCR1L1 genes (the last found so far only in mouse). chemokine receptor CCR1/3/1L PR:000001254 A chemokine receptor CCR1/3/1L that is a translation product of the human CCR1 gene or a 1:1 ortholog thereof. C-C chemokine receptor type 1 PR:000001255 A chemokine receptor CCR1/3/1L that is a translation product of the human CCR3 gene or a 1:1 ortholog thereof. C-C chemokine receptor type 3 PR:000001289 A protein that is a translation product of the human MS4A1 gene or a 1:1 ortholog thereof. membrane-spanning 4-domains subfamily A member 1 PR:000001307 A protein that is a translation product of the human CD44 gene or a 1:1 ortholog thereof. CD44 molecule PR:000001332 A protein that is a translation product of the human CEACAM8 gene or a 1:1 ortholog thereof. carcinoembryonic antigen-related cell adhesion molecule 8 PR:000001343 A protein that is a translation product of the human CD69 gene or a 1:1 ortholog thereof. A type II transmembrane protein with a C-type lectin binding domain in the extracellular portion of the molecule. Involved in lymphocyte proliferation and functions as a signal transmitting receptor in lymphocytes, natural killer (NK) cells, and platelets. CD69 molecule PR:000001344 A protein that is a translation product of the human ENPP3 gene or a 1:1 ortholog thereof. ectonucleotide pyrophosphatase/phosphodiesterase family member 3 PR:000001345 A protein that is a translation product of the human ENG gene or a 1:1 ortholog thereof. endoglin PR:000001355 A protein with a core domain architecture consisting of an extracellular domain containing two copies of the Immunoglobulin domain (Pfam:PF00047), followed by a single-pass transmembrane region and a small intracellular domain. The active protein is a low affinity receptor for immunoglobulin gamma chain Fc region. Human II-a, II-b, and II-c represent a recent gene expansion and are equally related to mouse II, III, and IV. Human III-A and III-B are closely related and closer to mouse IV than to mouse III. immunoglobulin gamma Fc receptor II/III/IV PR:000001381 A protein that is a translation product of the human IL2RB gene or a 1:1 ortholog thereof. interleukin-2 receptor subunit beta PR:000001408 An ADP-ribosyl cyclase that is a translation product of the human CD38 gene or a 1:1 ortholog thereof. ADP-ribosyl cyclase 1 PR:000001444 A cadherin that is a translation product of the human CDH5 gene or a 1:1 ortholog thereof. cadherin-5 PR:000001456 A fucosyltransferase that is a translation product of the human FUT4 gene or a 1:1 ortholog thereof. alpha-(1,3)-fucosyltransferase FUT4 PR:000001479 An immunoglobulin gamma Fc receptor II/III/IV that is a translation product of the mouse Fcgr2 gene or a 1:1 ortholog thereof. low affinity immunoglobulin gamma Fc region receptor II PR:000001483 An immunoglobulin gamma Fc receptor II/III/IV that is a translation product of the mouse Fcgr3 gene or a 1:1 ortholog thereof. low affinity immunoglobulin gamma Fc region receptor III PR:000001559 A tumor-associated calcium signal transducer that is a translation product of the human EPCAM gene or a 1:1 ortholog thereof. epithelial cell adhesion molecule PR:000001786 A prominin that is a translation product of the human PROM1 gene or a 1:1 ortholog thereof. prominin-1 PR:000001800 A protein that is a translation product of the human NT5E gene or a 1:1 ortholog thereof. 5'-nucleotidase PR:000001809 A protein that is a translation product of the CD59 or closely related gene. This gene is present as a single copy in human and has undergone a lineage-specific duplication in mouse. CD59 antigen has a core architecture consisting of one UPAR/Ly-6 domain (Pfam:PF00021), a small domain of about 70 amino acids and containing 5 conserved disulfide bonds. It is both N- and O-glycosylated and is a GPI-anchored protein that releases soluble forms in some tissues. CD59-like glycoprotein PR:000001836 A protein that is a translation product of the human CD7 gene or a 1:1 ortholog thereof. CD7 molecule PR:000001839 A protein that is a translation product of the human CD5 gene or a 1:1 ortholog thereof. T-cell surface glycoprotein CD5 PR:000001843 A protein that is a translation product of the human THY1 gene or a 1:1 ortholog thereof. Thy-1 membrane glycoprotein PR:000001865 A protein that is a translation product of the human IL3RA gene or a 1:1 ortholog thereof. interleukin-3 receptor class 2 alpha chain PR:000001867 A protein that is a translation product of the human IL5RA gene or a 1:1 ortholog thereof. interleukin-5 receptor subunit alpha PR:000001869 A protein that is a translation product of the human IL7R gene or a 1:1 ortholog thereof. interleukin-7 receptor subunit alpha PR:000001874 A protein that is a translation product of the KLRB1 gene or its closely related paralogs (KLRB1A-F). There are lineage-specific expansions in mouse and rat. KLRB1-like protein PR:000001879 A protein that is a translation product of the human SPN gene or a 1:1 ortholog thereof. leukosialin PR:000001889 A protein that is a translation product of the human CD14 gene or a 1:1 ortholog thereof. CD14 molecule PR:000001892 A protein that is a translation product of the human CD33 gene or a 1:1 ortholog thereof. CD33 molecule PR:000001898 A protein that is a translation product of the human MME gene or a 1:1 ortholog thereof. neprilysin PR:000001903 A protein that is a translation product of the human PAX5 gene or a 1:1 ortholog thereof. paired box protein PAX-5 PR:000001932 A protein that is a translation product of the human CD24 gene or a 1:1 ortholog thereof. signal transducer CD24 PR:000001944 A protein that is a translation product of the human SPI1 gene or a 1:1 ortholog thereof. transcription factor PU.1 PR:000001945 A protein that is a translation product of the human TFRC gene or a 1:1 ortholog thereof. transferrin receptor protein 1 PR:000001950 A protein that is a translation product of the human CD40LG gene or a 1:1 ortholog thereof. tumor necrosis factor ligand superfamily member 5 PR:000001969 A protein that is a translation product of the human PLAUR gene or a 1:1 ortholog thereof. urokinase plasminogen activator surface receptor PR:000002065 A CSF-1/PDGF receptor-type tyrosine-protein kinase that is a translation product of the human KIT gene or a 1:1 ortholog thereof. mast/stem cell growth factor receptor PR:000002112 A vascular endothelial growth factor receptor that is a translation product of the human KDR gene or a 1:1 ortholog thereof. vascular endothelial growth factor receptor 2 PR:000002978 A ly-6-like protein that is a translation product of the mouse Ly6g gene or a 1:1 ortholog thereof. lymphocyte antigen 6G PR:000002981 A protein that is a translation product of the mouse Ly76 gene or a 1:1 ortholog thereof. lymphocyte antigen 76 PR:000005178 A tetraspanin that is a translation product of the human CD9 gene or a 1:1 ortholog thereof. CD9 molecule PR:000005307 A protein that is a translation product of the human CEBPA gene or a 1:1 ortholog thereof. CCAAT/enhancer-binding protein alpha PR:000006611 A protein that is a translation product of the human DNTT gene or a 1:1 ortholog thereof. DNA nucleotidylexotransferase PR:000007431 An immunoglobulin gamma Fc receptor II/III/IV that is a translation product of the human FCER1A gene or a 1:1 ortholog thereof. high affinity immunoglobulin epsilon receptor subunit alpha PR:000007602 A protein that is a translation product of the human FOXA1 gene or a 1:1 ortholog thereof. hepatocyte nuclear factor 3-alpha PR:000007603 A protein that is a translation product of the human FOXA2 gene or a 1:1 ortholog thereof. hepatocyte nuclear factor 3-beta PR:000007857 A protein that is a translation product of the human GATA1 gene or a 1:1 ortholog thereof. erythroid transcription factor PR:000007858 A protein that is a translation product of the human GATA2 gene or a 1:1 ortholog thereof. endothelial transcription factor GATA-2 PR:000007891 A protein that is a translation product of the human GCG gene or a 1:1 ortholog thereof. glucagon PR:000008652 A protein that is a translation product of the human HNF1A gene or a 1:1 ortholog thereof. hepatocyte nuclear factor 1-alpha PR:000008654 A protein that is a translation product of the human HNF4A gene or a 1:1 ortholog thereof. hepatocyte nuclear factor 4-alpha PR:000009054 A protein that is a translation product of the human INS gene or a 1:1 ortholog thereof. insulin PR:000009062 A protein that is a translation product of the human INSM1 gene or a 1:1 ortholog thereof. insulinoma-associated protein 1 PR:000009116 A protein that is a translation product of the human ISL1 gene or a 1:1 ortholog thereof. insulin gene enhancer protein ISL-1 PR:000010047 A protein that is a translation product of the human MAFA gene or a 1:1 ortholog thereof. transcription factor MafA PR:000011152 A protein that is a translation product of the human NEUROD1 gene or a 1:1 ortholog thereof. neurogenic differentiation factor 1 PR:000011158 A protein that is a translation product of the human NEUROG3 gene or a 1:1 ortholog thereof. neurogenin-3 PR:000011242 A protein that is a translation product of the human NKX2-2 gene or a 1:1 ortholog thereof. homeobox protein Nkx-2.2 PR:000011250 A protein that is a translation product of the human NKX6-1 gene or a 1:1 ortholog thereof. homeobox protein Nkx-6.1 PR:000011639 A protein that is a translation product of the human ONECUT1 gene or a 1:1 ortholog thereof. hepatocyte nuclear factor 6 PR:000012523 A protein that is a translation product of the human PDX1 gene or a 1:1 ortholog thereof. pancreas/duodenum homeobox protein 1 PR:000013418 A protein that is a translation product of the human PTF1A gene or a 1:1 ortholog thereof. pancreas transcription factor 1 subunit alpha PR:000013824 A protein that is a translation product of the human RBPJ gene or a 1:1 ortholog thereof. recombining binding protein suppressor of hairless PR:000013825 A protein that is a translation product of the human RBPJL gene or a 1:1 ortholog thereof. recombining binding protein suppressor of hairless-like protein PR:000015424 A protein that is a translation product of the human SOX17 gene or a 1:1 ortholog thereof. transcription factor SOX-17 PR:000016043 A protein that is a translation product of the human TAL1 gene or a 1:1 ortholog thereof. T-cell acute lymphocytic leukemia protein 1 PR:000023089 A protein that is a translation product of the Escherichia coli K-12 ligA gene or a 1:1 ortholog thereof. DNA ligase REO:0000002 antibody reagent REO:0000171 a reagent role inhering in a molecular entity intended to associate with some molecular target to serve as a proxy for the presence, abundance, or location of this target in a detection of molecular label assay. molecular label role REO:0000280 a molecular reagent intended to associate with some molecular target to serve as a proxy for the presence, abundance, or location of this target in a detection of molecular label assay molecular label REO:0000383 a cell that is the output of some malignant cell transformation process whereby a cell in vivo becomes capable of causing cancer in an organism. Such cells are typically able to proliferate indefinitely if cultured in vitro. cancer cell REO:0000501 An antibody reagent produced by clonal hybridoma cells deriving from the fusion of a single activasted B-cell with a neoplastic cell, such that antibodies isolated from such cells are monospecific for a single epitope. A collection of such antibodies has specificity for a single epitopes on its target antigen - versus a collection of 'polyclonal antibodies', which recognize various different epitopes. But at the structural level of the individual molecular reagent, there is of course no distinction between mono- and poly-clonal antibodies. monoclonal antibody REO:0000502 an antibody reagent that is output from an antibody production process that yields a heterogenous collection of antibodies that are not mono-specific (ie individual antibodies in the collection may recognize different epitopes becasue they arise from more than one clone of B-lymphocyte cells). Polyclonal antibodies are typically manufactured through an antibody production technique in which a host organism is immunized with a specific immunogen and antibodies purified from serum collected following the induced immune response. A collection of such antibodies has specificity for various different epitopes on its target antigen - versus a collection of 'monoclonal antibodies', which all recognize a single epitope. But at the structural level of the individual molecular reagent, there is of course no distinction between mono- and poly-clonal antibodies. polyclonal antibody RS:0002307 ICR SO:0000001 A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. region SO:0000104 A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation. polypeptide SO:0000110 Any extent of continuous biological sequence. sequence_feature SO:0000150 A sequence obtained from a single sequencing experiment. Typically a read is produced when a base calling program interprets information from a chromatogram trace file produced from a sequencing machine. read SO:0000165 A cis-acting sequence that increases the utilization of (some) eukaryotic promoters, and can function in either orientation and in any location (upstream or downstream) relative to the promoter. enhancer SO:0000276 Small, ~22-nt, RNA molecule that is the endogenous transcript of a miRNA gene (or the product of other non coding RNA genes. Micro RNAs are produced from precursor molecules (SO:0000647) that can form local hairpin structures, which ordinarily are processed (usually via the Dicer pathway) such that a single miRNA molecule accumulates from one arm of a hairpin precursor molecule. Micro RNAs may trigger the cleavage of their target molecules or act as translational repressors. miRNA SO:0000336 A sequence that closely resembles a known functional gene, at another locus within a genome, that is non-functional as a consequence of (usually several) mutations that prevent either its transcription or translation (or both). In general, pseudogenes result from either reverse transcription of a transcript of their "normal" paralog (SO:0000043) (in which case the pseudogene typically lacks introns and includes a poly(A) tail) or from recombination (SO:0000044) (in which case the pseudogene is typically a tandem duplication of its "normal" paralog). pseudogene SO:0000443 An attribute to describe the kind of biological sequence. polymer_attribute SO:0000462 A non-functional descendant of a functional entity. pseudogenic_region SO:0000590 The signal recognition particle (SRP) is a universally conserved ribonucleoprotein. It is involved in the co-translational targeting of proteins to membranes. The eukaryotic SRP consists of a 300-nucleotide 7S RNA and six proteins: SRPs 72, 68, 54, 19, 14, and 9. Archaeal SRP consists of a 7S RNA and homologues of the eukaryotic SRP19 and SRP54 proteins. In most eubacteria, the SRP consists of a 4.5S RNA and the Ffh protein (a homologue of the eukaryotic SRP54 protein). Eukaryotic and archaeal 7S RNAs have very similar secondary structures, with eight helical elements. These fold into the Alu and S domains, separated by a long linker region. Eubacterial SRP is generally a simpler structure, with the M domain of Ffh bound to a region of the 4.5S RNA that corresponds to helix 8 of the eukaryotic and archaeal SRP S domain. Some Gram-positive bacteria (e.g. Bacillus subtilis), however, have a larger SRP RNA that also has an Alu domain. The Alu domain is thought to mediate the peptide chain elongation retardation function of the SRP. The universally conserved helix which interacts with the SRP54/Ffh M domain mediates signal sequence recognition. In eukaryotes and archaea, the SRP19-helix 6 complex is thought to be involved in SRP assembly and stabilizes helix 8 for SRP54 binding. SRP_RNA SO:0000655 An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product. ncRNA SO:0000673 An RNA synthesized on a DNA or RNA template by an RNA polymerase. transcript SO:0000704 A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions. gene SO:0000771 A quantitative trait locus (QTL) is a polymorphic locus which contains alleles that differentially affect the expression of a continuously distributed phenotypic trait. Usually it is a marker described by statistical association to quantitative variation in the particular phenotypic trait that is thought to be controlled by the cumulative action of alleles at multiple loci. QTL SO:0000831 A region of a gene. gene_member_region SO:0000902 A transgene is a gene that has been transferred naturally or by any of a number of genetic engineering techniques from one organism to another. transgene SO:0000988 A quality of a nucleotide polymer that has no terminal nucleotide residues. circular SO:0000999 A region of sequence from the end of a BAC clone that may provide a highly specific marker. BAC_end SO:0001217 protein_coding_gene SO:0001263 ncRNA_gene SO:0001265 miRNA_gene SO:0001266 scRNA_gene SO:0001267 snoRNA_gene SO:0001268 snRNA_gene SO:0001272 tRNA_gene SO:0001411 A region defined by its disposition to be involved in a biological process. biological_region SO:0001498 A region of sequence from the end of a YAC clone that may provide a highly specific marker. YAC_end SO:0001500 A biological_region characterized as a single heritable trait in a phenotype screen. The heritable phenotype may be mapped to a chromosome but generally has not been characterized to a specific gene locus. heritable_phenotypic_marker SO:0001637 A gene that encodes for ribosomal RNA. rRNA_gene SO:0001639 A gene that encodes an RNase P RNA. RNase_P_RNA_gene SO:0001640 A gene that encodes a RNase_MRP_RNA. RNase_MRP_RNA_gene SO:0001641 A gene that encodes large intervening non-coding RNA. lincRNA_gene SO:0001643 A telomerase RNA gene is a non coding RNA gene the RNA product of which is a component of telomerase. telomerase_RNA_gene SO:0001741 A gene segment which when incorporated by somatic recombination in the final gene transcript results in a nonfunctional product. pseudogenic_gene_segment SO:3000000 A gene component region which acts as a recombinational unit of a gene whose functional form is generated through somatic recombination. gene_segment UBERON:0000002 uterine cervix Lower, narrow portion of the uterus where it joins with the top end of the vagina. uterine cervix UBERON:0000006 islet of Langerhans the clusters of hormone-producing cells that are scattered throughout the pancreas islet of Langerhans UBERON:0000007 pituitary gland The pituitary gland is an endocrine gland that secretes hormones that regulate many other glands [GO]. An endocrine gland located ventral to the diencephalon and derived from mixed neuroectodermal and non neuroectodermal origin [ZFIN]. pituitary gland UBERON:0000014 zone of skin Any portion of the organ that covers that body and consists of a layer of epidermis and a layer of dermis. zone of skin UBERON:0000016 endocrine pancreas The part of the pancreas that is part of the endocrine system and is made up of islet cells, which produce insulin, glucagon and somatostatin. endocrine pancreas UBERON:0000017 exocrine pancreas The part of the pancreas that is part of the exocrine system and which produces and store zymogens of digestive enzymes, such as chymotrypsinogen and trypsinogen in the acinar cells [GO]. exocrine pancreas UBERON:0000020 sense organ An organ that is capable of transducing sensory stimulus to the nervous system. sense organ UBERON:0000025 tube Any hollow cylindrical anatomical structure containing a lumen through which substances are transported. tube UBERON:0000029 lymph node Any of the rounded masses of lymphoid tissue that are surrounded by a capsule of connective tissue, are distributed along the lymphatic vessels, and contain numerous lymphocytes which filter the flow of lymph. lymph node UBERON:0000033 head The head is the anterior-most division of the body [GO]. head UBERON:0000042 serous membrane multi-tissue structure that is comprised of a secretory epithelial layer (mesothelium) and a connective tissue layer. serous membrane UBERON:0000044 dorsal root ganglion * Sensory ganglia located on the dorsal spinal roots within the vertebral column. The spinal ganglion cells are pseudounipolar. The single primary branch bifurcates sending a peripheral process to carry sensory information from the periphery and a central branch which relays that information to the spinal cord or brain. (MSH) * ganglion found on the posterior root of each spinal nerve, composed of the unipolar nerve cell bodies of the sensory neurons of the nerve. (CSP) dorsal root ganglion UBERON:0000045 ganglion A biological tissue mass, most commonly a mass of nerve cell bodies. ganglion UBERON:0000058 duct A tubular structure that transports or secretes substances. duct UBERON:0000059 large intestine A subdivision of the digestive tract that connects the small intestine to the cloaca or anus. Lacks or has few villi[Kardong]. large intestine UBERON:0000061 anatomical structure Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. anatomical structure UBERON:0000062 organ Anatomical structure that performs a specific function or group of functions [WP]. organ UBERON:0000063 organ segment Organ region with one or more fixed or anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyeball[FMA]. organ segment UBERON:0000064 organ part Anatomical structure which has as its direct parts two or more types of tissue and is continuous with one or more anatomical structures likewise constituted by two or more portions of tissues distinct from those of their complement. Examples: osteon, cortical bone, neck of femur, bronchopulmonary segment, left lobe of liver, anterior right side of heart, interventricular branch of left coronary artery, right atrium, mitral valve, head of pancreas[FMA]. organ part UBERON:0000065 respiratory tract Anatomical structure that is part of the respiratory system. In mammals consists of upper and lower tracts respiratory tract UBERON:0000068 embryo stage A life cycle stage that starts with fertilization and ends with the fully formed embryo. embryo stage UBERON:0000072 segment of respiratory tract An organ segment that is part of a respiratory tract [Automatically generated definition]. segment of respiratory tract UBERON:0000077 mixed endoderm/mesoderm-derived structure An anatomical structure that develops from the endoderm and the mesoderm. mixed endoderm/mesoderm-derived structure UBERON:0000078 mixed ectoderm/mesoderm/endoderm-derived structure An anatomical structure that develops from the ectoderm, mesoderm and endoderm. mixed ectoderm/mesoderm/endoderm-derived structure UBERON:0000092 post-embryonic stage stage succeeding embryo, including mature structure post-embryonic stage UBERON:0000105 life cycle stage A spatiotemporal region encompassing some part of the life cycle of an organism. life cycle stage UBERON:0000112 sexually immature stage sexually immature stage UBERON:0000113 post-juvenile adult stage The stage of being a sexually mature adult animal. post-juvenile adult stage UBERON:0000115 lung epithelium The epithelial layer of the lung. lung epithelium UBERON:0000117 respiratory tube A tube in the respiratory system. Examples: bronchus, bronchiole, trachea. respiratory tube UBERON:0000122 neuron projection bundle A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses. neuron projection bundle UBERON:0000160 intestine Segment of the alimentary canal extending from the stomach to the anus and, in humans and other mammals, consists of two segments, the small intestine and the large intestine. intestine UBERON:0000168 segment of colon An organ segment that is part of a colon [Automatically generated definition]. segment of colon UBERON:0000178 blood Circulating body substance which consists of blood plasma and hemoglobin-carrying red blood cells. Excludes blood analogues (see UBERON:0000179 haemolymphatic fluid). blood UBERON:0000200 gyrus A ridge on the cerebral cortex. It is generally surrounded by one or more sulci . gyrus UBERON:0000359 preputial gland A aired, lobulated, modified sebaceous glands located in the inguinal region adjacent to the penis and vagina, with pheromonal functions in male rodents; in males, the preputial gland empties into the preputial cavity and in females, the preputial (aka clitoral) gland duct empties into the clitoral fossa. preputial gland UBERON:0000451 prefrontal cortex The anterior part of the frontal lobes of the brain, lying in front of the motor and premotor areas.nnThis brain region has been implicated in planning complex cognitive behaviors, personality expression, decision making and moderating correct social behavior. The basic activity of this brain region is considered to be orchestration of thoughts and actions in accordance with internal goals.nnThe most typical psychological term for functions carried out by the pre-frontal cortex area is executive function. Executive function relates to abilities to differentiate among conflicting thoughts, determine good and bad, better and best, same and different, future consequences of current activities, working toward a defined goal, prediction of outcomes, expectation based on actions, and social 'control' (the ability to suppress urges that, if not suppressed, could lead to socially-unacceptable outcomes).nnMany authors have indicated an integral link between a person's personality and the functions of the prefrontal cortex. - definition adapted from Wikipedia prefrontal cortex UBERON:0000463 organism substance Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body. organism substance UBERON:0000465 material anatomical entity Anatomical entity that has mass. material anatomical entity UBERON:0000468 multicellular organism Anatomical structure that is an individual member of a species and consists of more than one cell. multicellular organism UBERON:0000471 compound organ component Multi-tissue structure that is part of a compound organ. compound organ component UBERON:0000473 testis A gonad of a male animal. A gonad produces and releases sperm. testis UBERON:0000475 organism subdivision Anatomical structure which is a subdivision of a whole organism, consisting of components of multiple anatomical systems, largely surrounded by a contiguous region of integument. organism subdivision UBERON:0000477 anatomical cluster Anatomical group that has its parts adjacent to one another. anatomical cluster UBERON:0000478 extraembryonic structure A multicellular anatomical structure that is associated with an embryo and derived from the zygote from which it develops, but which does not contribute to the embryo proper or to structures that are part of the same organism after embryogenesis. extraembryonic structure UBERON:0000479 tissue Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation. tissue UBERON:0000481 multi-tissue structure Anatomical structure that has as its parts two or more portions of tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types. multi-tissue structure UBERON:0000483 epithelium Portion of tissue, that consists of one or more layers of epithelial cells connected to each other by cell junctions and which is underlain by a basal lamina. Examples: simple squamous epithelium, glandular cuboidal epithelium, transitional epithelium, myoepithelium[CARO]. epithelium UBERON:0000485 simple columnar epithelium Unilaminar epithelium, which consists of a single layer of columnar cells. Examples: ciliated columnar epithelium, gastric epithelium, microvillus columnar epithelium.[FMA] simple columnar epithelium UBERON:0000487 simple squamous epithelium Unilaminar epithelium which consists of a single layer of squamous cells. Examples: pulmonary alveolar epithelium, endothelium.[FMA] simple squamous epithelium UBERON:0000489 cavitated compound organ Compound organ that contains one or more macroscopic anatomical spaces. cavitated compound organ UBERON:0000490 unilaminar epithelium Epithelium which consists of a single layer of epithelial cells. Examples: endothelium, mesothelium, glandular squamous epithelium.[FMA] unilaminar epithelium UBERON:0000922 embryo Anatomical entity that comprises the organism in the early stages of growth and differentiation that are characterized by cleavage, the laying down of fundamental tissues, and the formation of primitive organs and organ systems. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant. embryo UBERON:0000923 germ layer A layer of cells produced during the process of gastrulation during the early development of the animal embryo, which is distinct from other such layers of cells, as an early step of cell differentiation. The three types of germ layers are the endoderm, ectoderm, and mesoderm. germ layer UBERON:0000924 ectoderm Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue. ectoderm UBERON:0000925 endoderm Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut. endoderm UBERON:0000926 mesoderm The middle germ layer of the embryo, between the endoderm and ectoderm. mesoderm UBERON:0000945 stomach An expanded region of the vertebrate alimentary tract that serves as a food storage compartment and digestive organ. A stomach is lined, in whole or in part by a glandular epithelium. stomach UBERON:0000947 aorta The main trunk of the systemic arterial system that carries blood from the heart to all the organs and other structures of the body, bringing oxygenated blood to all parts of the body in the systemic circulation aorta UBERON:0000948 heart A myogenic muscular circulatory organ found in the vertebrate cardiovascular system composed of chambers of cardiac muscle. It is the primary circulatory organ. heart UBERON:0000955 brain The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell[WP]. brain UBERON:0000956 cerebral cortex The thin layer of gray matter on the surface of the cerebral hemisphere that develops from the telencephalon. It consists of the neocortex (6 layered cortex or isocortex), the hippocampal formation and the olfactory cortex. cerebral cortex UBERON:0000966 retina The retina is the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates. retina UBERON:0000970 eye An organ that detects light. eye UBERON:0000981 femur Endochondral longbone connecting the pelvic girdle with posterior zeugopodium skeleton.[VSAO, modified]. femur UBERON:0000982 skeletal joint Anatomical cluster that consists of two or more adjacent skeletal structures, which may be interconnected by various types of tissue[VSAO]. skeletal joint UBERON:0000988 pons Brainstrem structure that has as its parts the pontine tegmentum and basal part of pons[FMA]. pons UBERON:0000991 gonad Reproductive organ that produces and releases eggs (ovary) or sperm (testis). gonad UBERON:0000992 female gonad the gonad of a female organism which contains germ cells female gonad UBERON:0000995 uterus the female muscular organ of gestation in which the developing embryo or fetus is nourished until birth uterus UBERON:0000996 vagina A fibromuscular tubular tract leading from the uterus to the exterior of the body in female placental mammals and marsupials, or to the cloaca in female birds, monotremes, and some reptiles[WP]. vagina UBERON:0000998 seminal vesicle Either of a pair of glandular pouches that lie one on either side of the male reproductive tract and in the human male secrete a sugar- and protein-containing fluid into the ejaculatory duct. seminal vesicle UBERON:0001003 skin epidermis The outer layer of the skin[WP]. cellular, multilayered epithelium derived from the ectoderm[ZFA]. skin epidermis UBERON:0001013 adipose tissue Portion of connective tissue composed of adipocytes enmeshed in areolar tissue adipose tissue UBERON:0001018 axon tract A group of axons linking two or more neuropils and having a common origin, termination[FBbt]. axon tract UBERON:0001040 yolk sac A sac-like expansion of the ventral wall of the intestine, narrowed into a yolk stalk near the body[Hyman's]. Membranous sac attached to an embryo, providing early nourishment in the form of yolk in bony fishes, sharks, reptiles, birds, and primitive mammals. It functions as the developmental circulatory system of the human embryo, before internal circulation begins. In the mouse, the yolk sac is the first site of blood formation, generating primitive macrophages and erythrocytes[WP]. yolk sac UBERON:0001044 saliva-secreting gland saliva-secreting exocrine glands of the oral cavity[GO] saliva-secreting gland UBERON:0001062 anatomical entity Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. anatomical entity UBERON:0001064 ventral pancreatic duct A duct joining the pancreas to the common bile duct to supply pancreatic juices which aid in digestion provided by the exocrine pancreas. The pancreatic duct joins the common bile duct just prior to the ampulla of Vater, after which both ducts perforate the medial side of the second portion of the duodenum at the major duodenal papilla. ventral pancreatic duct UBERON:0001088 urine Excretion that is the output of a kidney urine UBERON:0001091 calcareous tooth Organ with a cavity which consist of dentine surrounded by enamel. Examples: incisor, molar. calcareous tooth UBERON:0001103 diaphragm A thin musculomebranous barrier that separates the abdominal and thoracic cavities. Often used for breathing control diaphragm UBERON:0001132 parathyroid gland The parathyroid gland is an endocrine gland for secretion of parathyroid hormone, usually found as a pair, embedded in the connective tissue capsule on the posterior surface of the thyroid gland. Parathyroid regulates calcium and phosphorous metabolism. parathyroid gland UBERON:0001133 cardiac muscle tissue Muscle composed of cardiac muscle cells that is part of the heart[ZFA]. involuntary striated muscle found in the walls of the heart, specifically the myocardium[Wikipedia]. Tissue which consists of cardiac myocytes surrounded by cardiac endomysium. Examples: Cardiac muscle tissue proper, conducting tissue of heart[FMA]. cardiac muscle tissue UBERON:0001134 skeletal muscle tissue Muscle tissue that consists primarily of skeletal muscle fibers. skeletal muscle tissue UBERON:0001135 smooth muscle tissue Muscle tissue which is unstriated, composed primarily of smooth muscle fibers surrounded by a reticulum of collagen and elastic fibers. Smooth muscle differs from striated muscle in the much higher actin/myosin ratio, the absence of conspicuous sarcomeres and the ability to contract to a much smaller fraction of its resting length[GO]. Tissue which consists of smooth muscle . Examples: Arrector muscle of hair, Muscularis mucosae. smooth muscle tissue UBERON:0001153 caecum A pouch in the digestive tract that connects the ileum with the ascending colon of the large intestine. It is separated from the ileum by the ileocecal valve, and is the beginning of the large intestine. It is also separated from the colon by the cecocolic junction. caecum UBERON:0001154 vermiform appendix A blind-ended tube connected to the cecum, from which it develops embryologically[WP]. vermiform appendix UBERON:0001155 colon Last portion of the large intestine before it becomes the rectum. colon UBERON:0001156 ascending colon Segment of the colon which is continuous with the cecum proximally and the transverse colon distally.[FMA,modified] ascending colon UBERON:0001159 sigmoid colon The part of the large intestine that is closest to the rectum and anus. It forms a loop that averages about 40 cm. in length, and normally lies within the pelvis, but on account of its freedom of movement it is liable to be displaced into the abdominal cavity. sigmoid colon UBERON:0001165 pyloric antrum the area at the bottom of the stomach on the caudal side of the pyloric canal that contains gastrin-producing G cells, which stimulate acid production, and the luminal pH-sensitive population of somatostatin-producing D cells pyloric antrum UBERON:0001235 adrenal cortex the thick outer layer of the adrenal gland that produces and secretes steroid hormones such as corticosterone, estrone and aldosterone adrenal cortex UBERON:0001255 urinary bladder distensible musculomembranous organ situated in the anterior part of the pelvic cavity in which urine collects before excretion[MP]. urinary bladder UBERON:0001263 pancreatic acinus The secretory units of the exocrine pancreas, where fluid containing digestive enzymes is produced; consists of a group of secretory cells surrounding a luminal space that connects to the pancreatic duct. pancreatic acinus UBERON:0001264 pancreas An endoderm derived structure that produces precursors of digestive enzymes and blood glucose regulating enzymes[GO]. pancreas UBERON:0001296 myometrium the smooth muscle coat of the uterus, which forms the main mass of the organ and surrounds and supports the endometrium myometrium UBERON:0001301 epididymis the elongated structure connected to the posterior surface of the testis that transports, stores, and matures spermatozoa between testis and vas deferens epididymis UBERON:0001343 seminiferous tubule of testis the tubules in the testes where spermatogenesis occurs seminiferous tubule of testis UBERON:0001347 white adipose tissue Connective tissue consisting of fat-storing cells and arranged in lobular groups or along minor blood vessels[MP,modified] white adipose tissue UBERON:0001348 brown adipose tissue A thermogenic form of adipose tissue that is composed of brown adipocytes[MP,modified] brown adipose tissue UBERON:0001388 gastrocnemius The most superficial muscle of the triceps surae group, in the posterior portion of the lower hindleg. gastrocnemius UBERON:0001389 soleus muscle A deep muscle of the triceps surae group, in the superficial posterior compartment of the leg. soleus muscle UBERON:0001474 bone element Skeletal element that is composed of bone tissue. bone element UBERON:0001485 knee joint The knee joint joins the thigh with the leg and consists of two articulations: one between the femur and tibia, and one between the femur and patella. It is the largest and most complicated joint in the human body. The knee is a mobile trocho-ginglymus (i.e. a pivotal hinge joint), which permits flexion and extension as well as a slight medial and lateral rotation[WP,unvetted]. knee joint UBERON:0001515 thoracic aorta the part of the aorta that extends from the origin at the heart to the diaphragm, and from which arises numerous branches that supply oxygenated blood to the chest cage and the organs within the chest thoracic aorta UBERON:0001516 abdominal aorta Abdominal part of aorta: the distal part of the descending aorta, which is the continuation of the thoracic part and gives rise to the inferior phrenic, lumbar, median sacral, superior and inferior mesenteric, middle suprarenal, renal, and testicular or ovarian arteries, and celiac trunk[BTO]. The abdominal aorta is the largest artery in the abdominal cavity. As part of the aorta, it is a direct continuation of descending aorta(of the thorax). [WP,unvetted]. abdominal aorta UBERON:0001558 lower respiratory tract The segment of respiratory tract from the trachea to the lungs[WP,modified] lower respiratory tract UBERON:0001630 muscle organ Organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work[GO]. Nonparenchymatous organ that primarily consists of skeletal muscle tissue aggregated into macroscopic fasciculi by connective tissue; together with other muscles, it constitutes the muscular system. Examples: biceps, diaphragm, masseter, right third external intercostal muscle, external oblique, levator ani, serratus anterior[FMA]. muscle organ UBERON:0001637 artery An epithelial tube or tree of tibes that transports blood away from the heart[modified from AEO definition]. artery UBERON:0001638 vein Any of the tubular branching vessels that carry blood from the capillaries toward the heart. vein UBERON:0001684 mandible A dentary bone that is the only bone in one of the lateral halves of the lower jaw skeleton. mandible UBERON:0001723 tongue A muscular organ in the floor of the mouth. tongue UBERON:0001736 submandibular gland Either of the paired compound tubuloalveolar (aka tubuloacinar) major salivary glands composed of both serous and mucous secretory cells and situated beneath the mandible. submandibular gland UBERON:0001805 autonomic ganglion ganglion that has dendrites that form a junction between autonomic nerves originating from the central nervous system and autonomic nerves innervating their target organs in the periphery. There are two subtypes, sympathetic ganglion and parasympathetic ganglion. autonomic ganglion UBERON:0001806 sympathetic ganglion A ganglion of the sympathetic nervous system. Examples: paravertebral and the prevertebral ganglia, which include the sympathetic chain ganglia, the superior, middle, and inferior cervical ganglia, and the aorticorenal, celiac, and stellate ganglia sympathetic ganglion UBERON:0001807 paravertebral ganglion Trunk ganglion which is part of a bilaterally paired set of sympathetic ganglia located anterior and lateral to the spinal cord. paravertebral ganglion UBERON:0001808 parasympathetic ganglion Ganglion containing neurons that receive innervation from parasympathetic neurons in the central nervous system and subserves parasympathetic functions through innervation of smooth muscle, cardiac muscle and glands. parasympathetic ganglion UBERON:0001817 lacrimal gland The lacrimal glands are paired almond-shaped glands, located in or near the orbital region, that secrete the aqueous layer of the tear film.[WP]. lacrimal gland UBERON:0001821 sebaceous gland A holocrine gland that secretes sebum into the hair follicles, or in hairless areas into ducts.[MP]. sebaceous gland UBERON:0001829 major salivary gland One of the three largest glands of the oral cavity that secrete most of the saliva, including the parotid, submandibular, and sublingual glands. major salivary gland UBERON:0001831 parotid gland The parotid gland is the largest of the salivary glands. It is found wrapped around the mandibular ramus, and it secretes saliva through Stensen's duct into the oral cavity, to facilitate mastication and swallowing. [WP,unvetted]. parotid gland UBERON:0001870 frontal cortex Anterior portion of the neocortex, lying anterior to the central sulcus in humans. It is bounded by the parietal cortex posteriorly and the temporal cortex laterally[NIFSTD,modified]. frontal cortex UBERON:0001872 parietal lobe Upper central part of the cerebral hemisphere. (MSH) parietal lobe UBERON:0001873 caudate nucleus Subcortical nucleus of telecephalic origin consisting of an elongated gray mass lying lateral to and bordering the lateral ventricle. It is divided into a head, body and tail in some species. caudate nucleus UBERON:0001875 globus pallidus Subcortical nucleus, functionally part of the basal ganglia, which consists of two segments the external (or lateral) and internal (or medial) separated by the medial medullary lamina in primates. In rodents, The globus pallidus lateral is separated from the medial segment by the fibers of the internal capsule/cerebral peduncle. globus pallidus UBERON:0001876 amygdala Subcortical brain region lying anterior to the hippocampal formation in the temporal lobe and anterior to the temporal horn of the lateral ventricle in some species. It is usually subdivided into several groups. Functionally, it is not considered a unitary structure (MM). amygdala UBERON:0001891 midbrain Organ component of neuraxis that has as its parts the tectum, cerebral peduncle, midbrain tegmentum and cerebral aqueduct[FMA]. The brain region between the forebrain anteriorly and the hindbrain posteriorly, including the tectum dorsally and the midbrain tegmentum ventrally[ZFA]. The midbrain is the middle division of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes a ventral part containing the cerebral peduncles and a dorsal tectum containing the corpora quadrigemina and that surrounds the aqueduct of Sylvius connecting the third and fourth ventricles)[GO]. midbrain UBERON:0001896 medulla oblongata Organ component of neuraxis that has as its parts the medullary reticular formation, inferior olivary complex and cochlear nuclear complex, among other structures[FMA]. The medulla oblongata lies directly above the spinal cord and controls vital autonomic functions such as digestion, breathing and the control of heart rate[GO]. medulla oblongata UBERON:0001897 dorsal plus ventral thalamus Subcortical brain region consisting of paired gray matter bodies in the dorsal diencephalon and forming part of the lateral wall of the third ventricle of the brain. The thalamus represents the major portion of the diencephalon and is commonly divided into cellular aggregates known as nuclear groups.(MeSH). The dorsal topographic division of the interbrain. The macrodissected adult human thalamus was clearly illustrated by Vesalius in 1543 and the term as defined here was introduced by His in 1893. It includes the traditional epithalamus, dorsal thalamus, and ventral thalamus of Herrick (1910, pp. 494, 498). Also see Kuhlenbeck (1927, Ch. 9) and Jones (1985, p. 87). dorsal plus ventral thalamus UBERON:0001898 hypothalamus A specialized brain region of the ventral diencephalon arising near the end of the segmentation period; the embryonic hypothalamic region will give rise to the posterior pituitary gland as well as a number of brain nuclei. [ZFA]. One of the most important functions of the hypothalamus is to link the nervous system to the endocrine system via the pituitary gland (hypophysis).[Wikipedia]. hypothalamus UBERON:0001906 subthalamic nucleus The subthalamic nucleus is the lens-shaped nucleus located in the ventral part of the subthalamus on the inner aspect of the internal capsule that is concerned with the integration of somatic motor function[GO]. subthalamic nucleus UBERON:0001911 mammary gland A specialized accessory gland of the skin of mammals that secretes milk. The gland is typically only developed in females, and regresses in males. mammary gland UBERON:0001917 endothelium of artery An endothelium that is part of an artery [Automatically generated definition]. endothelium of artery UBERON:0001928 preoptic area Area of the forebrain anterior to the posterior tuberculum and the hypothalamus and ventral to the ventral thalamus[ZFA]. preoptic area UBERON:0001954 Ammon's horn A part of the brain consisting of a three layered cortex located in the forebrain bordering the medial surface of the lateral ventricle. The term hippocampus is often used synonymously with hippocampal formation which consists of the hippocampus proper or Cornu Ammonis, the dentate gyrus and the subiculum. Ammon's horn UBERON:0001981 blood vessel A vessel through which blood circulates in the body. blood vessel UBERON:0001986 endothelium A layer of epithelium that lines the heart, blood vessels (endothelium, vascular), lymph vessels (endothelium, lymphatic), and the serous cavities of the body[MESH]. Simple squamous epithelium which lines blood and lymphatic vessels and the heart[FMA] endothelium UBERON:0001987 placenta organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin[GO]. The fetal portion of the placenta is known as the villous chorion. The maternal portion is known as the decidua basalis. The two portions are held together by anchoring villi that are anchored to the decidua basalis by the cytotrophoblastic shell. placenta UBERON:0001989 superior cervical ganglion Trunk ganglion which is bilaterally paired and located at the anterior end of the sympathetic ganglion chain. superior cervical ganglion UBERON:0001997 olfactory epithelium A sensory epithelium inside the nasal cavity that is responsible for detecting odors[WP]. olfactory epithelium UBERON:0002020 gray matter A nervous system structure composed primarily of nerve cell bodies (somas). May also include dendrites and the initial unmyelinated portion of axons. gray matter UBERON:0002028 hindbrain The most posterior of the three principal regions of the brain. In mammals and birds the hindbrain is divided into a rostral metencephalon and a caudal myelencephalon. In zebrafish, with the exception of the cerebellum, the ventral remainder of the metencephalon can be separated only arbitrarily from the more caudal myelencephalic portion of the medulla oblongata (From: Neuroanatomy of the Zebrafish Brain)[ZFA]. Organ component of neuraxis that has as its parts the pons, cerebellum and medulla oblongata[FMA]. hindbrain UBERON:0002031 epithelium of bronchus An epithelium that is part of a bronchus [Automatically generated definition]. epithelium of bronchus UBERON:0002036 striated muscle tissue Tissue which consists of striated muscle fibers surrounded by endomysium. Examples: Skeletal muscle tissue, Cardiac muscle tissue[FMA]. striated muscle tissue UBERON:0002037 cerebellum Part of the metencephalon that lies in the posterior cranial fossa behind the brain stem. It is concerned with the coordination of movement[MESH]. A large dorsally projecting part of the brain concerned especially with the coordination of muscles and the maintenance of bodily equilibrium, situated between the brain stem and the back of the cerebrum , and formed in humans of two lateral lobes and a median lobe[BTO]. Brain structure derived from the anterior hindbrain, and perhaps including posterior midbrain. The cerebellum plays a role in somatic motor function, the control of muscle tone, and balance[ZFA]. cerebellum UBERON:0002046 thyroid gland A two-lobed endocrine gland found in all vertebrates, located in front of and on either side of the trachea in humans, and producing various hormones, such as triiodothyronine and calcitonin[BTO]. thyroid gland UBERON:0002048 lung Respiration organ that develops as an oupocketing of the esophagus. lung UBERON:0002050 embryonic structure Anatomical structure that is part of an embryo. embryonic structure UBERON:0002058 ciliary ganglion The ciliary ganglion is a parasympathetic ganglion located in the posterior orbit. It measures 1P2 millimeters in diameter and contains approximately 2,500 neurons (adapted from Wikipedia) ciliary ganglion UBERON:0002066 umbilical vein The umbilical vein is a blood vessel present during fetal development that carries oxygenated blood from the placenta to the growing fetus. [WP,unvetted]. umbilical vein UBERON:0002072 hypodermis Lowermost layer of the integumentary system in vertebrates. Types of cells that are found in the hypodermis are fibroblasts, adipose cells, and macrophages. It is derived from the mesoderm, but unlike the dermis, it is not derived from the dermatome region of the mesoderm. The hypodermis is used mainly for fat storage[WP]. hypodermis UBERON:0002075 viscus An organ that is located within the body cavity (or in its extension, in the scrotum); it consists of organ parts that are embryologically derived from endoderm, splanchnic mesoderm or intermediate mesoderm; together with other organs, the viscus constitutes the respiratory, gastrointestinal, urinary, reproductive and immune systems, or is the central organ of the cardiovascular system. Examples: heart, lung, esophagus, kidney, ovary, spleen. viscus UBERON:0002106 spleen the organ that functions to filter blood and to store red corpuscles and platelets spleen UBERON:0002107 liver An exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes[GO]. liver UBERON:0002108 small intestine Subdivision of digestive tract that connects the stomach to the large intestine and is where much of the digestion and absorption of food takes place (with the exception of ruminants). The mammalian small intestine is long and coiled and can be differentiated histologically into: duodenum, jejunem, ileum[WP,cjm,Kardong]. small intestine UBERON:0002110 gall bladder An organ that aids digestion and stores bile produced by the liver[WP]. gall bladder UBERON:0002113 kidney A paired organ of the urinary tract which has the production of urine as its primary function. kidney UBERON:0002114 duodenum The first part of the small intestine. At the junction of the stomach and the duodenum the alimentary canal is inflected. The duodenum first goes anteriorly for a short distance, turns dorsally, and eventually caudally, thus it is a U-shaped structure with two horizontal sections (a ventral and a dorsal one). duodenum UBERON:0002116 ileum the portion of the small intestine that extends from the jejunum to the colon ileum UBERON:0002124 medulla of thymus Medullary portion of thymus. The reticulum is coarser than in the cortex, the lymphoid cells are relatively fewer in number, and there are found peculiar nest-like bodies, the concentric corpuscles of Hassall. These concentric corpuscles are composed of a central mass, consisting of one or more granular cells, and of a capsule formed of epithelioid cells. They are the remains of the epithelial tubes, which grow out from the third branchial pouches of the embryo to form the thymus. Each follicle is surrounded by a vascular plexus, from which vessels pass into the interior, and radiate from the periphery toward the center, forming a second zone just within the margin of the medullary portion. In the center of the medullary portion there are very few vessels, and they are of minute size. medulla of thymus UBERON:0002185 bronchus the upper conducting airways of the lung; these airways arise from the terminus of the trachea bronchus UBERON:0002240 spinal cord Part of the central nervous system located in the vertebral canal continuous with and caudal to the brain; demarcated from brain by plane of foramen magnum. It is composed of an inner core of gray matter in which nerve cells predominate, and an outer layer of white matter in which myelinated nerve fibers predominate, and surrounds the central canal. (CUMBO) spinal cord UBERON:0002255 vomeronasal organ An organ thought to supplement the olfactory system in receiving pheromonic communication. The sensory part of the organ is in two long, thin sacs, situated on either side of the nasal septum at its base. vomeronasal organ UBERON:0002264 olfactory bulb A bulbous anterior projection of the olfactory lobe that is the place of termination of the olfactory nerves and is especially well developed in lower vertebrates (as fishes)[BTO]. olfactory bulb UBERON:0002285 telencephalic ventricle A brain ventricle that is part of a telencephalon. In mammals and species with an evaginated telencephalon, this is one of a pair of lateral structures, one in each hemisphere telencephalic ventricle UBERON:0002308 nucleus of brain A neural nucleus that is part of the brain. nucleus of brain UBERON:0002331 umbilical cord The connecting cord from the developing embryo to the placenta. umbilical cord UBERON:0002336 corpus callosum White matter structure containing massive numbers of commissural fibers connecting cortical areas in the two cerebral hemispheres.it is subdivided into a genu, a rostrum, a body, and a splenium. (MM) corpus callosum UBERON:0002342 neural crest A specialized region of ectoderm found between the neural ectoderm (neural plate) and non-neural ectoderm and composed of highly migratory pluripotent cells that delaminate in early embryonic development from the dorsal neural tube and give rise to an astounding variety of differentiated cell types[MP]. neural crest UBERON:0002352 atrioventricular node Subdivision of conducting system of heart which is located in the muscular part of the interatrial septum that is continuous with the atrioventricular bundle.[FMA] atrioventricular node UBERON:0002358 peritoneum A serous membrane that lines the peritoneal cavity[VHOG,modified]. peritoneum UBERON:0002365 exocrine gland A gland that secretes products (excluding hormones and other chemical messengers) into ducts (duct glands) which lead directly into the external environment[WP]. Typical exocrine glands include sweat glands, salivary glands, mammary glands, stomach, liver, pancreas exocrine gland UBERON:0002367 prostate gland The prostate gland is a partly muscular, partly glandular body that is situated near the base of the mammalian male urethra and secretes an alkaline viscid fluid which is a major constituent of the ejaculatory fluid. prostate gland UBERON:0002368 endocrine gland Endocrine glands are glands of the endocrine system that secrete their products directly into the circulatory system rather than through a duct.[WP, modified]. endocrine gland UBERON:0002369 adrenal gland Either of a pair of complex endocrine organs near the anterior medial border of the kidney consisting of a mesodermal cortex that produces glucocorticoid, mineralocorticoid, and androgenic hormones and an ectodermal medulla that produces epinephrine and norepinephrine[BTO]. adrenal gland UBERON:0002370 thymus Anatomical structure of largely lymphoid tissue that functions in cell-mediated immunity by being the site where T cells develop. thymus UBERON:0002371 bone marrow the soft tissue that fills the cavities of bones bone marrow UBERON:0002372 tonsil either of the two small almond-shaped masses of lymph tissue found on either side of the oropharynx tonsil UBERON:0002384 connective tissue Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance. connective tissue UBERON:0002385 muscle tissue Muscle tissue is a contractile tissue made up of actin and myosin fibers[GO]. muscle tissue UBERON:0002394 bile duct Any of the ducts that form the biliary tree, carrying bile from the liver to the small intestine. bile duct UBERON:0002405 immune system Anatomical system that protects the body from foreign substances, cells, and tissues by producing the immune response and that includes especially the thymus, spleen, lymphoid tissue, lymphocytes including the B cells and T cells, and antibodies. immune system UBERON:0002407 pericardium The combination of pericardial sac (a double-walled sac containing the heart and the roots of the great vessels) plus fibrous pericardium. pericardium UBERON:0002419 skin gland A gland that is part of a skin of body [Automatically generated definition]. skin gland UBERON:0002420 basal ganglion An individual member of a collection of basal ganglia. Basal ganglia are subcortical masses of gray matter in the forebrain and midbrain that are richly interconnected and so viewed as a functional system. The nuclei usually included are the caudate nucleus (caudoputamen in rodents), putamen, globus pallidus, substantia nigra (pars compacta and pars reticulata) and the subthalamic nucleus. Some also include the nucleus accumbens and ventral pallidum[NIF,modified]. basal ganglion UBERON:0002428 limb bone A bone that is part of a limb [Automatically generated definition]. limb bone UBERON:0002435 striatum A region of the forebrain consisting of the caudate nucleus, putamen and fundus striati.[GO]. striatum UBERON:0002513 endochondral bone Replacement bone that forms within cartilage. endochondral bone UBERON:0002530 gland an organ that functions as a secretory or excretory organ gland UBERON:0002544 digit A subdivision of the autopod that has as part a series of phalanges together with associated vasculature, musculature, integument and nerves. It is continuous with the metapodial subdivision of the autopod, but does not include the metapodials. In species such as humans, fully formed digits are distinct, whereas in other species the digits may be connected by interdigital webbing, or may be completely unseparated (for example, in cetaceans). digit UBERON:0002616 regional part of brain Anatomical divisons of the brain according to one or more criteria, e.g. cytoarchitectural, gross anatomy. Parts may be contiguous in 3D or not, e.g., basal ganglia. Regions of brain across multiple species are contained within this category. regional part of brain UBERON:0002623 cerebral peduncle Synonym for macrodissected adult human tegmentum (Vicq d'Azyr, 1784; Swanson, 2000); pp. 555-556. Later used thus by for example His (1893b, p. 178), Herrick (1915, p. 160), Strong & Elwyn (1943, p. 17), Carpenter (1976, p. 367), Williams & Warwick (1980, p. 935). cerebral peduncle UBERON:0002691 ventral tegmental area Unpaired midbrain region situated in the ventromedial portion of the reticular formation. The VTA is medial to the substantia nigra and ventral to the red nucleus, and extends caudally from the posterior hypothalamus in the diencephalon. The VTA contains dopamine neurons that project to various limbic and cortical areas and is a critical component of the brain's reward circuitry. ventral tegmental area UBERON:0002967 cingulate gyrus One of the convolutions on the medial surface of the cerebral hemisphere. It surrounds the rostral part of the brain and interhemispheric commissure and forms part of the limbic system. (MSH) One of three essential structures comprising the limbic lobe, the other two being the hippocampus and parahippocampal gyrus. (CSP) cingulate gyrus UBERON:0003102 surface structure Anatomical structure that overlaps the outer epithelial layer and is adjacent to the space surrounding the organism. surface structure UBERON:0003103 compound organ Anatomical structure that has as its parts two or more multi-tissue structures of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona fide boundaries from other distinct anatomical structures of different types. compound organ UBERON:0003126 trachea The trachea is the portion of the airway that attaches to the bronchi as it branches [GO:dph]. trachea UBERON:0003129 skull Anatomical structure that is part of the head consisting entirely of cranium and mandible[WP]. skull UBERON:0003133 reproductive organ An organ involved in reproduction reproductive organ UBERON:0003258 endoderm of foregut An endoderm that is part of a foregut [Automatically generated definition]. endoderm of foregut UBERON:0003283 mesentery of oesophagus A mesentery that is part of a esophagus [Automatically generated definition]. mesentery of oesophagus UBERON:0003296 gland of diencephalon Any gland that is part of the diencephalon. Examples: pineal gland, neurohypophysis. gland of diencephalon UBERON:0003297 gland of integumental system A gland that is part of a integumental system [Automatically generated definition]. gland of integumental system UBERON:0003408 gland of gut A gland that is part of a digestive tract [Automatically generated definition]. gland of gut UBERON:0003457 head bone A bone that is part of a head [Automatically generated definition]. head bone UBERON:0003462 facial bone A bone that is part of a facial skeleton [Automatically generated definition]. facial bone UBERON:0003464 hindlimb bone A bone that is part of a hindlimb region. Examples: any pes phalanx, femur. Counter-examples: ischium, pubis (they are part of the pelvic girdle) hindlimb bone UBERON:0003469 respiratory system artery An artery that is part of a respiratory system [Automatically generated definition]. respiratory system artery UBERON:0003509 arterial blood vessel A blood vessel that is part of the arterial system. Includes artery, arteriole and aorta. arterial blood vessel UBERON:0003528 brain gray matter A gray matter that is part of a brain [Automatically generated definition]. brain gray matter UBERON:0003606 limb long bone A long bone that is part of a limb [Automatically generated definition]. limb long bone UBERON:0003608 hindlimb long bone A long bone that is part of a hindlimb [Automatically generated definition]. hindlimb long bone UBERON:0003643 respiratory system arterial blood vessel An arterial blood vessel that is part of a respiratory system [Automatically generated definition]. respiratory system arterial blood vessel UBERON:0003657 limb joint Any joint that is part of a (free) limb. limb joint UBERON:0003729 mouth mucosa A mucous membrane that lines the mouth. mouth mucosa UBERON:0003889 fallopian tube Initial section of the oviduct through which the ova pass from the ovary to the uterus fallopian tube UBERON:0003913 tooth-like structure hard bony, calcareous, or chitinous organ found in the mouth or pharynx of an animal and used in procuring or masticating food. tooth-like structure UBERON:0003914 epithelial tube Epithelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system. epithelial tube UBERON:0003915 endothelial tube Any endothelium that has the quality of being cylindrical [Automatically generated definition]. endothelial tube UBERON:0003922 pancreatic epithelial bud The embryonic pancreas develops from two separate anlagen in the foregut epithelium, one dorsal and two ventral pancreatic buds[PMID]. pancreatic epithelial bud UBERON:0003924 ventral pancreatic bud pancreatic bud that gives rise to the major pancreatic duct. ventral pancreatic bud UBERON:0003928 digestive system duct A duct that is part of a digestive system [Automatically generated definition]. digestive system duct UBERON:0003937 sex gland Any of the organized aggregations of cells that function as secretory or excretory organs and are associated with reproduction. sex gland UBERON:0003947 brain ventricle/choroid plexus The brain ventricles or their associated choroid plexuses brain ventricle/choroid plexus UBERON:0004086 brain ventricle one of the system of communicating cavities in the brain that are continuous with the central canal of the spinal cord, that like it are derived from the medullary canal of the embryo, that are lined with an epithelial ependyma, and that contain a serous fluid brain ventricle UBERON:0004111 anatomical conduit Any tube, opening or passage that connects two distinct anatomical spaces. anatomical conduit UBERON:0004119 endoderm-derived structure An anatomical structure that develops (entirely or partially) from the endoderm. endoderm-derived structure UBERON:0004120 mesoderm-derived structure An anatomical structure that develops (entirely or partially) from the mesoderm. mesoderm-derived structure UBERON:0004121 ectoderm-derived structure An anatomical structure that develops (entirely or partially) from the ectoderm. ectoderm-derived structure UBERON:0004177 hemopoietic organ Organ that is part of the hematopoietic system. hemopoietic organ UBERON:0004256 hindlimb zeugopod muscle A muscle organ that is part of a hindlimb zeugopod (lower leg) [Automatically generated definition]. hindlimb zeugopod muscle UBERON:0004363 pharyngeal arch artery One of a series of paired embryological vascular structures formed within a pharyngeal arch; in the adult, some of these vessels give rise to the great vessels[MP] pharyngeal arch artery UBERON:0004375 bone of free limb or fin A bone that is part of an appendage [Automatically generated definition]. bone of free limb or fin UBERON:0004457 cavity lining cavity lining UBERON:0004638 blood vessel endothelium An endothelium that lines the blood vasculature. Other endothelia may line lymph vessels, the heart blood vessel endothelium UBERON:0004700 arterial system endothelium An endothelium that is part of an arterial system [Automatically generated definition]. arterial system endothelium UBERON:0004742 dentary The dentary is a dermal bone that forms the antero-lateral part of the lower jaw in fishes and amphibians, extending to the whole lower jaw in mammals[VHOG,modified]. dentary UBERON:0004756 dermal skeletal element dermis-derived entity that is made of skeletal tissue. dermal skeletal element UBERON:0004765 skeletal element Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles. skeletal element UBERON:0004768 bone of lower jaw Any bone that is part of the lower jaw skeleton. This includes (when present): the dentary/mandible, the articular, the splenial, the suprangular bone of lower jaw UBERON:0004802 respiratory tract epithelium the pseudostratified ciliated epithelium that lines much of the conducting portion of the airway, including part of the nasal cavity and larynx, the trachea, and bronchi respiratory tract epithelium UBERON:0004807 respiratory system epithelium An epithelium that is part of a respiratory system [Automatically generated definition]. respiratory system epithelium UBERON:0004815 lower respiratory tract epithelium An epithelium that is part of a lower respiratory tract [Automatically generated definition]. lower respiratory tract epithelium UBERON:0004851 aorta endothelium the thin layer of flat cells that line the aorta and form a barrier between circulating blood in the lumen and the rest of the vessel wall aorta endothelium UBERON:0004852 cardiovascular system endothelium An endothelium that is part of the cardiovascular system. cardiovascular system endothelium UBERON:0004921 subdivision of digestive tract A proximal-distal subdivision of the digestive tract. subdivision of digestive tract UBERON:0004923 organ component layer A part of a wall of an organ that forms a layer. organ component layer UBERON:0005020 mucosa of tongue A mucosa that is part of a tongue [Automatically generated definition]. mucosa of tongue UBERON:0005057 immune organ An organ that is part of a immune system [Automatically generated definition]. immune organ UBERON:0005156 reproductive structure An anatomical structure that is part of the reproductive system. reproductive structure UBERON:0005162 multi cell part structure A structure consisting of multiple cell components but which is not itself a cell and does not have (complete) cells as a part. multi cell part structure UBERON:0005172 abdomen element An organ or element that is in the abdomen. Examples: spleen, intestine, kidney, abdominal mammary gland. abdomen element UBERON:0005177 trunk region element An organ or element that part of the trunk region. The trunk region can be further subdividied into thoracic (including chest and thoracic cavity) and abdominal (including abdomen and pelbis) regions. trunk region element UBERON:0005181 thoracic segment organ An organ that part of the thoracic segment region. This region can be further subdividied chest and thoracic cavity regions. thoracic segment organ UBERON:0005291 embryonic tissue A portion of tissue that is part of an embryo. embryonic tissue UBERON:0005301 male preputial gland One of the sebaceous glands of the corona and neck of the glans penis. male preputial gland UBERON:0005384 nasal cavity epithelium An epithelium that lines the nasal cavity. nasal cavity epithelium UBERON:0005399 male reproductive gland A sex gland that is part of a male reproductive system. male reproductive gland UBERON:0005401 cerebral hemisphere gray matter A gray matter that is part of a cerebral hemisphere. cerebral hemisphere gray matter UBERON:0005439 definitive endoderm definitive endoderm UBERON:0005631 extraembryonic membrane Intrinsic membrane that arises from embryonic germ layers and grow to surround the developing embryo. extraembryonic membrane UBERON:0005800 segment of aorta Any portion of the aorta including the ascending and descending aorta, and aortic arch or a portion of the aortic orifice of the left ventricle. segment of aorta UBERON:0005902 occipital region Anatomical cluster that is located in the posterior region of the cranium and forms the margin of the foramen magnum and occipital condyles. occipital region UBERON:0005904 duct of male reproductive system Any of the ducts that are part of a male reproductive system. duct of male reproductive system UBERON:0005911 endo-epithelium Epithelium that derives from the endoderm. Examples: urothelium, transitional epithelium of ureter, epithelium of prostatic gland.[FMA] endo-epithelium UBERON:0006003 integumentary adnexa Anatomical structure embedded in or located in the integument that is part of the integumental system. Examples: hair, follicles, skin glands, claws, nails, feathers. integumentary adnexa UBERON:0006799 glandular epithelium An epithelium that is composed primarily of secretory cells. glandular epithelium UBERON:0006858 adrenal/interrenal gland This gland can either be a discrete structure located bilaterally above each kidney, or a cluster of cells in the head kidney that perform the functions of the adrenal gland. In either case, this organ consists of two cells types, aminergic chromaffin cells and steroidogenic cortical cells[GO] adrenal/interrenal gland UBERON:0006914 squamous epithelium An epithelium characterised by its most superficial layer consisting of squamous epithelial cells. squamous epithelium UBERON:0006925 digestive gland A gland, such as the liver or pancreas, that secretes into the alimentary canal substances necessary for digestion. digestive gland UBERON:0007100 primary circulatory organ A hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood or analogs[GO,modified]. primary circulatory organ UBERON:0007196 tracheobronchial tree The structure from the trachea, bronchi, and bronchioles that forms the airways that supply air to the lungs. The lining of the tracheobronchial tree consists of ciliated columnar epithelial cells. tracheobronchial tree UBERON:0007329 pancreatic duct A duct that is part of the pancreas and connected to the duodenum. pancreatic duct UBERON:0007376 outer epithelium The epidermis is the entire outer epithelial layer of an animal, it may be a single layer that produces an extracellular material (e.g. the cuticle of arthropods) or a complex stratified squamous epithelium, as in the case of many vertebrate species[GO]. outer epithelium UBERON:0007499 epithelial sac An epithelial tube that is open at one end only. epithelial sac UBERON:0007592 ciliated columnar epithelium Simple columnar epithelium in which the luminal side of the cells bears cilia. Examples: epithelium of trachea, epithelium of uterine tube.[FMA] ciliated columnar epithelium UBERON:0007827 external nose External part of the olfactory apparatus. external nose UBERON:0008907 dermal bone Skeletal element that forms superficially in the organism, usually in association with the ectoderm[VSAO]. dermal bone UBERON:0009663 telencephalic nucleus A nucleus of brain that is part of a telencephalon. telencephalic nucleus UBERON:0009842 glandular acinus The many-lobed berry cluster of cells that is the terminous of a gland where the secretion is produced is acinar in form. glandular acinus UBERON:0009854 digestive tract diverticulum Branch or outpocketing of the digestive tract. digestive tract diverticulum UBERON:0009856 sac sac UBERON:0010000 multicellular anatomical structure An anatomical structure that has more than one cell as a part. multicellular anatomical structure UBERON:0010047 oral gland Gland of the epithelium lining the oral cavity. The most common are the salivary glands. oral gland UBERON:0010147 male accessory sex gland Any gland, other than the gonad, associated with the genital tract, such as the ampulla of the ductus deferens and the bulbourethral, prostate and vesicular glands of the male. male accessory sex gland UBERON:0010313 neural crest-derived structure An anatomical structure that develops from the neural crest. neural crest-derived structure UBERON:0010314 structure with developmental contribution from neural crest An anatomical structure that has some part that develops from the neural crest. structure with developmental contribution from neural crest UBERON:0010316 germ layer / neural crest germ layer / neural crest UBERON:0010363 endochondral element A skeletal element that has the potential to participate in endochondral ossification, and may participate in intramembranous ossification. endochondral element UBERON:0010371 ecto-epithelium Epithelium that derives from the ectoderm. Examples: epithelium of acinus of lactiferous duct, subscapular lens epithelium, epithelium of posterior surface of cornea. ecto-epithelium UBERON:0010499 pseudostratified ciliated columnar epithelium Epithelium composed of a single layer of cells, appearing as layered because the column-shaped cells vary in height so the nuclei are at different levels. The basal portions of all the cells are in contact with the basement membrane. It lines the respiratory system and the male reproductive tract. The cilia in the respiratory tract are motile, while the stereocilia in the male reproductive tract are immobile. pseudostratified ciliated columnar epithelium UBERON:0010740 bone of appendage girdle complex A bone that is part of an appendage girdle complex (i.e. any bone in a limb, fin or girdle). bone of appendage girdle complex UBERON:0011139 synovial limb joint Any synovial joint that is part of a (free) limb. synovial limb joint UBERON:0011215 central nervous system cell part cluster A multi cell part structure that is part of a central nervous system. central nervous system cell part cluster UBERON:0011300 gray matter of telencephalon A portion of gray matter that is part of a telencephalon. gray matter of telencephalon UBERON:0012275 meso-epithelium Epithelium that derives from the mesoderm. [Automatically generated definition]. meso-epithelium UBERON:0012360 bone of jaw A bone element that is part of a jaw region. bone of jaw UBERON:0012429 hemopoietic tissue Blood-forming tissue, consisting of reticular fibers and cells. Also known as hemopoietic tissue hemopoietic tissue UBERON:0013515 subdivision of uterine tube subdivision of uterine tube UBERON:0013522 subdivision of tube subdivision of tube UBERON:0013697 exocrine pancreas epithelium Epithelium lining the exocrine pancreas. exocrine pancreas epithelium UBERON:0013765 digestive system element Any of the organs or elements that are part of the digestive system. Examples: tongue, esophagus, spleen, crop, lunge feeding organ, tooth elements. digestive system element UBERON:0014374 embryoid body Embryoid bodies (EBs) are three-dimensional aggregates of pluripotent stem cells. embryoid body UBERON:0014892 skeletal muscle organ A muscle organ that consists of skeletal muscle tissue ensheathed in epimysium, that develops from myotome and that is innervated by some somatic motor neuron. Skeletal muscles are typically attached (via a tendon) to a bone but there are exceptions (e.g. intrinsic tongue muscles). skeletal muscle organ UBERON:0015022 hindlimb endochondral element A hindlimb bone or its cartilage or pre-cartilage precursor. hindlimb endochondral element UBERON:0015061 limb endochondral element A limb bone or its cartilage or pre-cartilage precursor. limb endochondral element UBERON:0015212 lateral structure Any structure that is placed on one side of the left-right axis of a bilaterian. lateral structure UBERON:0015787 upper respiratory conduit Any anatomical conduit which is part of the upper respiratory tract upper respiratory conduit UBERON:0016526 lobe of cerebral hemisphere Subdivision of telencephalon which is one of a number of subdivisions of each hemisphere separated by both real landmarks (sulci and fissures) and arbitrary boundaries[FMA,modified]. lobe of cerebral hemisphere UBERON:0017672 abdominal viscera A viscus that is part of a abdomen. abdominal viscera UBERON:0018707 bladder organ A membranous sac in animals that serves as the receptacle of a liquid or contains gas. bladder organ UBERON:0019306 nose epithelium nose epithelium UBERON:0019319 exocrine gland of integumental system An exocrine gland that is part of a integumental system. exocrine gland of integumental system UBERON:0034769 lymphomyeloid tissue lymphomyeloid tissue UBERON:0034921 multi organ part structure An multicellular anatomical structure that has subparts of multiple organs as a part. multi organ part structure UBERON:0034922 cell cluster A cluster of cells, largely surrounded by a morphological boundary. cell cluster UO:0000001 length unit A unit which is a standard measure of the distance between two points. length unit UO:0000002 mass unit A unit which is a standard measure of the amount of matter/energy of a physical object. mass unit UO:0000003 time unit A unit which is a standard measure of the dimension in which events occur in sequence. time unit UO:0000005 temperature unit A unit which is a standard measure of the average kinetic energy of the particles in a sample of matter. temperature unit UO:0000006 substance unit A unit which is a standardised quantity of an element or compound with uniform composition. substance unit UO:0000008 meter A length unit which is equal to the length of the path traveled by light in vacuum during a time interval of 1/299 792 458 of a second. meter UO:0000009 kilogram A mass unit which is equal to the mass of the International Prototype Kilogram kept by the BIPM at Svres, France. kilogram UO:0000010 second A time unit which is equal to the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the caesium 133 atom. second UO:0000012 kelvin A thermodynamic temperature unit which is equal to the fraction 1/273.16 of the thermodynamic temperature of the triple point of water. kelvin UO:0000013 mole A substance unit which is equal to the amount of substance of a molecular system which contains as many elementary entities as there are atoms in 0.012 kilogram of carbon 12. mole UO:0000015 centimeter A length unit which is equal to one hundredth of a meter or 10^[-2] m. centimeter UO:0000016 millimeter A length unit which is equal to one thousandth of a meter or 10^[-3] m. millimeter UO:0000017 micrometer A length unit which is equal to one millionth of a meter or 10^[-6] m. micrometer UO:0000018 nanometer A length unit which is equal to one thousandth of one millionth of a meter or 10^[-9] m. nanometer UO:0000021 gram A mass unit which is equal to one thousandth of a kilogram or 10^[-3] kg. gram UO:0000022 milligram A mass unit which is equal to one thousandth of a gram or 10^[-3] g. milligram UO:0000023 microgram A mass unit which is equal to one millionth of a gram or 10^[-6] g. microgram UO:0000024 nanogram A mass unit which is equal to one thousandth of one millionth of a gram or 10^[-9] g. nanogram UO:0000025 picogram A mass unit which is equal to 10^[-12] g. picogram UO:0000027 degree Celsius A temperature unit which is equal to one kelvin degree. However, they have their zeros at different points. The centigrade scale has its zero at 273.15 K. degree Celsius UO:0000028 millisecond A time unit which is equal to one thousandth of a second or 10^[-3] s. millisecond UO:0000029 microsecond A time unit which is equal to one millionth of a second or 10^[-6] s. microsecond UO:0000031 minute A time unit which is equal to 60 seconds. minute UO:0000032 hour A time unit which is equal to 3600 seconds or 60 minutes. hour UO:0000033 day A time unit which is equal to 24 hours. day UO:0000034 week A time unit which is equal to 7 days. week UO:0000035 month A time unit which is approximately equal to the length of time of one of cycle of the moon's phases which in science is taken to be equal to 30 days. month UO:0000036 year A time unit which is equal to 12 months which is science is taken to be equal to 365.25 days. year UO:0000039 micromole A substance unit equal to a millionth of a mol or 10^[-6] mol. micromole UO:0000041 nanomole A substance unit equal to one thousandth of one millionth of a mole or 10^[-9] mol. nanomole UO:0000042 picomole A substance unit equal to 10^[-12] mol. picomole UO:0000043 femtomole A substance unit equal to 10^[-15] mol. femtomole UO:0000044 attomole A substance unit equal to 10^[-18] mol. attomole UO:0000045 base unit A unit which is one of a particular measure to which all measures of that type can be related. base unit UO:0000051 concentration unit A unit which represents a standard measurement of how much of a given substance there is mixed with another substance. concentration unit UO:0000052 mass density unit A density unit which is a standard measure of the mass of a substance in a given volume. mass density unit UO:0000061 unit of molarity A concentration unit which is a standard measure of the number of moles of a given substance per liter of solution. unit of molarity UO:0000062 molar A unit of concentration which expresses a concentration of 1 mole of solute per liter of solution (mol/L). molar UO:0000063 millimolar A unit of molarity which is equal to one thousandth of a molar or 10^[-3] M. millimolar UO:0000064 micromolar A unit of molarity which is equal to one millionth of a molar or 10^[-6] M. micromolar UO:0000066 picomolar A unit of molarity which is equal to 10^[-12] M. picomolar UO:0000095 volume unit A unit which is a standard measure of the amount of space occupied by any substance, whether solid, liquid, or gas. volume unit UO:0000097 cubic centimeter A volume unit which is equal to one millionth of a cubic meter or 10^[-9] m^[3], or to 1 ml. cubic centimeter UO:0000098 milliliter A volume unit which is equal to one thousandth of a liter or 10^[-3] L, or to 1 cubic centimeter. milliliter UO:0000099 liter A volume unit which is equal to one thousandth of a cubic meter or 10^[-3] m^[3], or to 1 decimeter. liter UO:0000101 microliter A volume unit which is equal to one millionth of a liter or 10^[-6] L. microliter UO:0000102 nanoliter A volume unit which is equal to one thousandth of one millionth of a liter or 10^[-9] L. nanoliter UO:0000103 picoliter A volume unit which is equal to 10^[-12] L. picoliter UO:0000104 femtoliter A volume unit which is equal to 10^[-15] L. femtoliter UO:0000127 radiation unit A unit which is a standard measure of the amount of radiation emitted by a given radiation source as well as the amount of radiation absorbed or deposited in a specific material by a radiation source. radiation unit UO:0000128 activity (of a radionuclide) unit A unit which is a standard measure of the transformation (disintegration) rate of a radioactive substance. activity (of a radionuclide) unit UO:0000133 curie An activity (of a radionuclide) unit which is equal to the activity of a quantity of radioactive material in which there are 3.7 x 10^[10] atom disintegration per second (dps). curie UO:0000136 roentgen An exposure unit which is equal to the amount of radiation required to liberate positive and negative charges of one electrostatic unit of charge in 1 cm^[3] of air at standard temperature and pressure (STP). This corresponds to the generation of approximately 2.0810^[9] ion pairs. roentgen UO:0000140 Roentgen equivalent man A dose equivalent unit which when multiplied by hundred is equal to one sievert or 1 Sv. 1 Sv is equal to 100 rem. Roentgen equivalent man UO:0000147 disintegrations per minute An activity (of a radionuclide) unit which is equal to the activity of a quantity of radioactive material in which one nucleus decays per minute or there is one atom disintegration per minute. disintegrations per minute UO:0000148 counts per minute An activity (of a radionuclide) unit which is equal to the number of light emissions produced by ionizing radiation in one minute. counts per minute UO:0000157 light unit A unit which is a standard measure of the intensity of light. light unit UO:0000163 mass percentage A dimensionless concentration unit which denotes the mass of a substance in a mixture as a percentage of the mass of the entire mixture. mass percentage UO:0000164 mass volume percentage A dimensionless concentration unit which denotes the mass of the substance in a mixture as a percentage of the volume of the entire mixture. mass volume percentage UO:0000165 volume percentage A dimensionless concentration unit which denotes the volume of the solute in mL per 100 mL of the resulting solution. volume percentage UO:0000175 gram per liter A mass unit density which is equal to mass of an object in grams divided by the volume in liters. gram per liter UO:0000176 milligram per milliliter A mass unit density which is equal to mass of an object in milligrams divided by the volume in milliliters. milligram per milliliter UO:0000186 dimensionless unit A unit which is a standard measure of physical quantity consisting of only a numerical number without any units. dimensionless unit UO:0000187 percent A dimensionless ratio unit which denotes numbers as fractions of 100. percent UO:0000189 count unit A dimensionless unit which denotes a simple count of things. count unit UO:0000195 degree Fahrenheit A temperature unit which is equal to 5/9ths of a kelvin. Negative 40 degrees Fahrenheit is equal to negative 40 degrees Celsius. degree Fahrenheit UO:0000196 pH A dimensionless concentration notation which denotes the acidity of a solution in terms of activity of hydrogen ions (H+). pH UO:0000205 volume per unit volume A dimensionless concentration unit which denotes the given volume of the solute in the total volume of the resulting solution. volume per unit volume UO:0000207 milliliter per liter A volume per unit volume unit which is equal to one millionth of a liter of solute in one liter of solution. milliliter per liter UO:0000208 gram per deciliter A mass density unit which is equal to mass of an object in grams divided by the volume in deciliters. gram per deciliter UO:0000209 deciliter A volume unit which is equal to one tenth of a liter or 10^[-1] L. deciliter UO:0000213 colony forming unit per milliliter A colony forming unit which a measure of viable bacterial numbers in one milliliter. colony forming unit per milliliter UO:0000232 bit An information unit which refers to a digit in the binary numeral system, which consists of base 2 digits (ie there are only 2 possible values: 0 or 1). bit VT:0005215 Any measurable or observable characteristic related to the shape, structure, color or pattern of the cellular masses consisting of several to several hundred cells in the interstitial tissue of the pancreas; they are composed of five different cell types that make up the endocrine portion of the pancreas. islet of Langerhans morphology trait efo:EFO_0000220 A leukemia/lymphoma found predominately in children and adolescents and characterized by a high number of lymphoblasts and solid tumor lesions. Frequent sites involve LYMPH NODES, skin, and bones. It most commonly presents as leukemia. A neoplasm characterized by abnormalities of the lymphoid cell precursors leading to excessive lymphoblasts in the marrow and other organs. It is the most common cancer in children and accounts for the vast majority of all childhood leukemias. Leukemia with an acute onset, characterized by the presence of lymphoblasts in the bone marrow and the peripheral blood. It includes the acute B lymphoblastic leukemia and acute T lymphoblastic leukemia. Leukemia with an acute onset, characterized by the presence of lymphoblasts in the bone marrow and the peripheral blood. It includes the precursor B lymphoblastic leukemia and precursor T lymphoblastic leukemia. When the disease process is confined to a mass lesion with no or minimal evidence of blood and less than 25% marrow involvement, the diagnosis is lymphoblastic lymphoma; with blood and greater than 25% marrow involvement, ALL is the appropriate term. acute lymphoblastic leukemia efo:EFO_0000222 Clonal expansion of myeloid blasts in bone marrow, blood, and other tissue. Myeloid leukemias develop from changes in cells that normally produce NEUTROPHILS; BASOPHILS; EOSINOPHILS; and MONOCYTES. acute myeloid leukemia efo:EFO_0000224 An acute myeloid leukemia (AML) in which abnormal promyelocytes predominate. It is characterized by the t(15;17)(q22;q12) translocation. There are two variants: the typical and micro granular (hypo granular) variant. This AML is particularly sensitive to treatment with all trans-retinoic acid and has a favorable prognosis. (WHO, 2001) -- 2003 An acute myeloid leukemia (AML) in which abnormal promyelocytes predominate. It is characterized by the t(15;17)(q22;q12) translocation. There are two variants: the typical and microgranular variant. This AML is particularly sensitive to treatment with all trans-retinoic acid and has a favorable prognosis. (WHO, 2001) acute promyelocytic leukemia efo:EFO_0000270 A bronchial disease that is characterized by chronic inflammation and narrowing of the airways, which is caused by a combination of environmental and genetic factors resulting in recurring periods of wheezing (a whistling sound while breathing), chest tightness, shortness of breath, mucus production and coughing. The symptoms appear due to a variety of triggers such as allergens, irritants, respiratory infections, weather changes, excercise, stress, reflux disease, medications, foods and emotional anxiety. A chronic respiratory disease manifested as difficulty breathing due to the narrowing of bronchial passageways. A form of bronchial disorder with three distinct components: airway hyper-responsiveness (RESPIRATORY HYPERSENSITIVITY), airway INFLAMMATION, and intermittent AIRWAY OBSTRUCTION. It is characterized by spasmodic contraction of airway smooth muscle, WHEEZING, and dyspnea (DYSPNEA, PAROXYSMAL). Tendency of the smooth muscle of the tracheobronchial tree to contract more intensely in response to a given stimulus than it does in the response seen in normal individuals. This condition is present in virtually all symptomatic patients with asthma. The most prominent manifestation of this smooth muscle contraction is a decrease in airway caliber that can be readily measured in the pulmonary function laboratory. asthma efo:EFO_0000309 A form of undifferentiated malignant LYMPHOMA usually found in central Africa, but also reported in other parts of the world. It is commonly manifested as a large osteolytic lesion in the jaw or as an abdominal mass. B-cell antigens are expressed on the immature cells that make up the tumor in virtually all cases of Burkitt lymphoma. The Epstein-Barr virus (HERPESVIRUS 4, HUMAN) has been isolated from Burkitt lymphoma cases in Africa and it is implicated as the causative agent in these cases; however, most non-African cases are EBV-negative. Burkitts lymphoma efo:EFO_0000311 A malignant neoplasm in which new abnormal tissue grow by excessive cellular division and proliferation more rapidly than normal and continues to grow after the stimuli that initiated the new growth cease. cancer efo:EFO_0000339 Clonal hematopoetic disorder caused by an acquired genetic defect in PLURIPOTENT STEM CELLS. It starts in MYELOID CELLS of the bone marrow, invades the blood and then other organs. The condition progresses from a stable, more indolent, chronic phase (LEUKEMIA, MYELOID, CHRONIC PHASE) lasting up to 7 years, to an advanced phase composed of an accelerated phase (LEUKEMIA, MYELOID, ACCELERATED PHASE) and BLAST CRISIS. chronic myelogenous leukemia efo:EFO_0000365 A malignant tumor usually arising from the epithelium lining the large intestinal mucosa. Colon carcinoma is one of the most common malignancies in both males and females, and is especially common in North America and Europe. Grossly, most colon carcinomas are polypoid or ulcerating lesions. Microscopically, adenocarcinoma is the most frequently seen morphologic subtype. Prognosis depends on the stage of the disease (depth of invasion, metastasis to regional/distal lymph nodes or other anatomic sites). -- 2004 An adenocarcinoma arising from the colon. It is more frequently seen in populations with a Western type diet and in patients with a history of chronic inflammatory bowel disease. Signs and symptoms include intestinal bleeding, anemia, and change in bowel habits. According to the degree of cellular differentiation, colonic adenocarcinomas are divided into well differentiated, moderately, and poorly differentiated. Morphologic variants include the mucinous adenocarcinoma and signet-ring adenocarcinoma. Lymphatic or hematogenous spread can occur early in the process and lead to systemic disease. Tumors or cancer of the COLON or the RECTUM or both. Risk factors for colorectal cancer include chronic ULCERATIVE COLITIS; FAMILIAL POLYPOSIS COLI; exposure to ASBESTOS; and irradiation of the CERVIX UTERI. colorectal adenocarcinoma efo:EFO_0000369 A treatment process in which a chemical compound is administered to the subject under investigation. compound based treatment efo:EFO_0000400 A heterogeneous group of disorders characterized by HYPERGLYCEMIA and GLUCOSE INTOLERANCE. A metabolic disorder characterized by abnormally high blood sugar levels due to diminished production of insulin or insulin resistance/desensitization. diabetes mellitus efo:EFO_0000493 Family history is a form of clinicaly history specifically about relevant aspects of genetic preconditions or family member's clinical history. family history efo:EFO_0000549 A benign tumor of the PANCREATIC BETA CELLS. Insulinoma secretes excess INSULIN resulting in HYPOGLYCEMIA. A usually benign, well circumscribed neoplasm arising from the beta cells of the pancreas. Patients exhibit symptoms related to hypoglycemia due to inappropriate secretion of insulin. insulinoma efo:EFO_0000565 A cancer that affects the blood or bone marrow characterized by an abnormal proliferation of blood cells. A malignant (clonal) hematologic disorder, involving hematopoietic stem cells and characterized by the presence of primitive or atypical myeloid or lymphoid cells in the bone marrow and the blood. Leukemias are classified as acute or chronic based on the degree of cellular differentiation and the predominant cell type present. Leukemia is usually associated with anemia, fever, hemorrhagic episodes, and splenomegaly. Common leukemias include acute myeloid leukemia, chronic myelogenous leukemia, acute lymphoblastic or precursor lymphoblastic leukemia, and chronic lymphocytic leukemia. Treatment is vital to patient survival; untreated, the natural course of acute leukemias is normally measured in weeks or months, while that of chronic leukemias is more often measured in months or years. A progressive, malignant disease of the blood-forming organs, characterized by distorted proliferation and development of leukocytes and their precursors in the blood and bone marrow. Leukemias were originally termed acute or chronic based on life expectancy but now are classified according to cellular maturity. Acute leukemias consist of predominately immature cells; chronic leukemias are composed of more mature cells. (From The Merck Manual, 2006) leukemia efo:EFO_0000616 A benign or malignant tissue growth resulting from uncontrolled cell proliferation. Benign neoplastic cells resemble normal cells without exhibiting significant cytologic atypia, while malignant cells exhibit overt signs such as dysplastic features, atypical mitotic figures, necrosis, nuclear pleomorphism, and anaplasia. Representative examples of benign neoplasms include papillomas, cystadenomas, and lipomas; malignant neoplasms include carcinomas, sarcomas, lymphomas, and leukemias. neoplasm efo:EFO_0000647 An individual who does some experimental process. experiment performer efo:EFO_0001359 A subtype of DIABETES MELLITUS that is characterized by INSULIN deficiency. It is manifested by the sudden onset of severe HYPERGLYCEMIA, rapid progression to DIABETIC KETOACIDOSIS, and DEATH unless treated with insulin. The disease may occur at any age, but is most common in childhood or adolescence. An autoimmune disease of endocrine system and is_a diabetes mellitus that results from autoimmune destruction of insulin-producing beta cells of the pancreas. Diabetes mellitus characterized by insulin deficiency, sudden onset, severe hyperglycemia, rapid progression to ketoacidosis, and death unless treated with insulin. The disease may occur at any age, but is most common in childhood or adolescence. type I diabetes mellitus efo:EFO_0001360 A subclass of DIABETES MELLITUS that is not INSULIN-responsive or dependent (NIDDM). It is characterized initially by INSULIN RESISTANCE and HYPERINSULINEMIA; and eventually by GLUCOSE INTOLERANCE; HYPERGLYCEMIA; and overt diabetes. Type II diabetes mellitus is no longer considered a disease exclusively found in adults. Patients seldom develop KETOSIS but often exhibit OBESITY. A type of diabetes mellitus that is characterized by insulin resistance or desensitization and increased blood glucose levels. This is a chronic disease that can develop gradually over the life of a patient and can be linked to both environmental factors and heredity. type II diabetes mellitus efo:EFO_0001642 Malignant lymphoma composed of large B lymphoid cells whose nuclear size can exceed normal macrophage nuclei, or more than twice the size of a normal lymphocyte. The pattern is predominantly diffuse. Most of these lymphomas represent the malignant counterpart of B-lymphocytes at midstage in the process of differentiation. lymphoid neoplasm efo:EFO_0001734 data analyst efo:EFO_0001739 investigator efo:EFO_0001741 submitter efo:EFO_0001799 A group of people with a common cultural heritage that sets them apart from others in a variety of social relationships. (MSH); A social group characterized by a distinctive social and cultural tradition maintained from generation to generation, a common history and origin and a sense of identification with the group; members of the group have distinctive features in their way of life, shared experiences and often a common genetic heritage; these features may be reflected in their experience of health and disease. (NCI); Ethnicity - an arbitrary classification of the social group a person belongs to, and either identifies with or is identified with by others, as a result of a complex of cultural, biological, geographical and other factors such as linguistic, dietary and religion traditions; ancestry, background, allegiance, or association; and physical characteristics traditionally associated with race. Increasingly the concept is used synonymously with race but this use trend has a pragmatic basis rather than scientific. (NCI); The concept of ethnic origin is an attempt to classify people, not according to their current ethnicity, but according to where their ancestors came from. Ethnic origin has become a popular classification in statistics, where the concept of race has been largely discarded. (from Wikipedia) (NCI); a group of people with a common cultural heritage that sets them apart from others in a variety of social relationships. (CSP) An ethnic group is a population whose members have a common heritage that is real or presumed such as common culture, language, religion, behaviour or biological trait. ethnic group efo:EFO_0002427 myeloid neoplasm efo:EFO_0002529 Pancreatic beta -cell line of rat origin. INS-1 efo:EFO_0002543 mouse prenatal efo:EFO_0002547 NOD mouse efo:EFO_0002582 Theiler stage 11 efo:EFO_0002583 Theiler stage 17 efo:EFO_0002584 Theiler stage 21 efo:EFO_0002585 Theiler stage 22 efo:EFO_0002586 Theiler stage 24 efo:EFO_0002587 Theiler stage 26 efo:EFO_0002588 Theiler stage 28 is a mouse postnatal stage characterised by postnatal development after a mouse is newly born. Theiler stage 28 efo:EFO_0002756 Abstaining from food. fasting efo:EFO_0002829 The murine MIN6 cell line derived from in vivo immortalized insulin-secreting pancreatic beta cells. MIN6 efo:EFO_0002927 International Unit efo:EFO_0002966 pancreatic cell efo:EFO_0004390 mouse postnatal efo:EFO_0004391 Theiler stage 27 is a newborn mouse. Theiler stage 27 efo:EFO_0004393 Theiler stage 1 efo:EFO_0004394 Theiler stage 2 efo:EFO_0004395 Theiler stage 3 efo:EFO_0004396 Theiler stage 4 efo:EFO_0004397 Theiler stage 5 efo:EFO_0004398 Theiler stage 6 efo:EFO_0004399 Theiler stage 7 efo:EFO_0004400 Theiler stage 8 efo:EFO_0004401 Theiler stage 9 efo:EFO_0004402 Theiler stage 10 efo:EFO_0004403 Theiler stage 12 efo:EFO_0004404 Theiler stage 13 efo:EFO_0004405 Theiler stage 14 efo:EFO_0004406 Theiler stage 15 efo:EFO_0004407 Theiler stage 16 efo:EFO_0004408 Theiler stage 18 efo:EFO_0004409 Theiler stage 19 efo:EFO_0004410 Theiler stage 20 efo:EFO_0004411 Theiler stage 23 efo:EFO_0004412 Theiler stage 25 Feature Extraction Software oboInOwl:ObsoleteClass Obsolete Class owl:Thing 15.5 days after fertilization Person: Chris Stoeckert, Jie Zheng embryonic day 15.5 16.5 days after fertilization Person: Chris Stoeckert, Jie Zheng embryonic day 16.5 8.5 days after fertilization Person: Chris Stoeckert, Jie Zheng embryonic day 8.5 17.5 days after fertilization Person: Chris Stoeckert, Jie Zheng embryonic day 17.5 8.25 days after fertilization Person: Chris Stoeckert, Jie Zheng embryonic day 8.25 18.5 days after fertilization Person: Chris Stoeckert, Jie Zheng embryonic day 18.5 8 days after fertilization Person: Chris Stoeckert, Jie Zheng embryonic day 8 18 days after fertilization Person: Chris Stoeckert, Jie Zheng embryonic day 18 11.5 days after fertilization Person: Chris Stoeckert, Jie Zheng embryonic day 11.5 0 day after birth Person: Jie Zheng postnatal day 0 12.5 days after fertilization Person: Chris Stoeckert, Jie Zheng embryonic day 12.5 4 days after birth Person: Jie Zheng postnatal day 4 9.5 days after fertilization Person: Chris Stoeckert, Jie Zheng embryonic day 9.5 12 days after birth Person: Jie Zheng postnatal day 12 10.5 days after fertilization Person: Chris Stoeckert, Jie Zheng embryonic day 10.5 60 days after birth Person: Jie Zheng postnatal day 60 13.5 days after fertilization Person: Chris Stoeckert, Jie Zheng embryonic day 13.5 14.5 days after fertilization Person: Chris Stoeckert, Jie Zheng embryonic day 14.5 1 day after birth Person: Jie Zheng postnatal day 1 8 days after birth Person: Jie Zheng postnatal day 8 11.25 days after fertilization Person: Chris Stoeckert, Jie Zheng embryonic day 11.25 4 weeks after birth Person: Jie Zheng age 4 weeks age 8 weeks Person: Jie Zheng age 8 weeks age 10 weeks Person: Jie Zheng age 10 weeks age of an organism that fully grown or developed. Person: Jie Zheng adult example to be eventually removed example to be eventually removed failed exploratory term The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job Person:Alan Ruttenberg failed exploratory term metadata complete Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. metadata complete organizational term term created to ease viewing/sort terms for development purpose, and will not be included in a release PERSON:Alan Ruttenberg organizational term ready for release Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." ready for release metadata incomplete Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. metadata incomplete uncurated Nothing done yet beyond assigning a unique class ID and proposing a preferred term. uncurated pending final vetting All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. pending final vetting placeholder removed placeholder removed terms merged An editor note should explain what were the merged terms and the reason for the merge. terms merged term imported This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use. term imported term split This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created. term split to be replaced with external ontology term Terms with this status should eventually replaced with a term from another ontology. Alan Ruttenberg group:OBI to be replaced with external ontology term requires discussion A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. Alan Ruttenberg group:OBI requires discussion Helicos Philippe Rocca-Serra Helicos Roche Philippe Rocca-Serra Roche Illumina Philippe Rocca-Serra Illumina Li-Cor Philippe Rocca-Serra Li-Cor Applied Biosystems Philippe Rocca-Serra Applied Biosystems ## 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 Person:Alan Ruttenberg a produces b if some process that occurs_in a has_output b and amount of b is low relative to normal cases, where a and b are material entities. Examples: defective beta ccell line produces less amount of insulin Person: Jie Zheng produces_low_amount a produces b if some process that occurs_in a has_output b and amount of b is high relative to generally cases, where a and b are material entities. Person: Jie Zheng produces_high_amount has part my body has part my brain (continuant parthood, two material entities) my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) this year has part this day (occurrent parthood) a core relation that holds between a whole and its part Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. has_part has part realizes this disease course realizes this disease this investigation realizes this investigator role this shattering realizes this fragility to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process realizes preceded by An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. is preceded by preceded_by http://www.obofoundry.org/ro/#OBO_REL:preceded_by preceded by precedes precedes 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]) is about This document is about information artifacts and their representations is_about is a (currently) primitive relation that relates an information artifact to an entity. 7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. We will try to build it back up by elaborating the various subproperties that are more precisely defined. Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic. person:Alan Ruttenberg Smith, Ceusters, Ruttenberg, 2000 years of philosophy is about is quality measurement of m is a quality measurement of q at t when q is a quality there is a measurement process p that has specified output m, a measurement datum, that is about q 8/6/2009 Alan Ruttenberg: The strategy is to be rather specific with this relationship. There are other kinds of measurements that are not of qualities, such as those that measure time. We will add these as separate properties for the moment and see about generalizing later From the second IAO workshop [Alan Ruttenberg 8/6/2009: not completely current, though bringing in comparison is probably important] This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details. -- From the second IAO workshop, various comments, [commented on by Alan Ruttenberg 8/6/2009] unit of measure is a quality, e.g. the length of a ruler. [We decided to hedge on what units of measure are, instead talking about measurement unit labels, which are the information content entities that are about whatever measurement units are. For IAO we need that information entity in any case. See the term measurement unit label] [Some struggling with the various subflavors of is_about. We subsequently removed the relation represents, and describes until and only when we have a better theory] a represents b means either a denotes b or a describes describe: a describes b means a is about b and a allows an inference of at least one quality of b We have had a long discussion about denotes versus describes. From the second IAO workshop: An attempt at tieing the quality to the measurement datum more carefully. a is a magnitude means a is a determinate quality particular inhering in some bearer b existing at a time t that can be represented/denoted by an information content entity e that has parts denoting a unit of measure, a number, and b. The unit of measure is an instance of the determinable quality. From the second meeting on IAO: An attempt at defining assay using Barry's "reliability" wording assay: process and has_input some material entity and has_output some information content entity and which is such that instances of this process type reliably generate outputs that describes the input. This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details. Alan Ruttenberg is quality measurement of is_supported_by_data The relation between the conclusion "Gene tpbA is involved in EPS production" and the data items produced using two sets of organisms, one being a tpbA knockout, the other being tpbA wildtype tested in polysacharide production assays and analyzed using an ANOVA. The relation between a data item and a conclusion where the conclusion is the output of a data interpreting process and the data item is used as an input to that process OBI OBI Philly 2011 workshop is_supported_by_data has_specified_input see is_input_of example_of_usage A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. 8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works. PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Coutot has_specified_input has_specified_output A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Courtot has_specified_output is_specified_output_of A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. Alan Ruttenberg PERSON:Bjoern Peters is_specified_output_of achieves_planned_objective A cell sorting process achieves the objective specification 'material separation objective' This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process. BP, AR, PPPB branch PPPB branch derived modified according to email thread from 1/23/09 in accordince with DT and PPPB branch achieves_planned_objective has grain the relation of the cells in the finger of the skin to the finger, in which an indeterminate number of grains are parts of the whole by virtue of being grains in a collective that is part of the whole, and in which removing one granular part does not nec- essarily damage or diminish the whole. Ontological Whether there is a fixed, or nearly fixed number of parts - e.g. fingers of the hand, chambers of the heart, or wheels of a car - such that there can be a notion of a single one being missing, or whether, by contrast, the number of parts is indeterminate - e.g., cells in the skin of the hand, red cells in blood, or rubber molecules in the tread of the tire of the wheel of the car. Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. Definition take from the definition of granular parthood in the cited paper. Needs work to put into standard form PERSON: Alan Ruttenberg PAPER: Granularity, scale and collectivity: When size does and does not matter, Alan Rector, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349 has grain has value specification A relation between an information content entity and a value specification that specifies its value. PERSON: James A. Overton OBI has value specification inheres in this fragility inheres in this vase this red color inheres in this apple a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence A dependent inheres in its bearer at all times for which the dependent exists. inheres_in inheres in bearer of this apple is bearer of this red color this vase is bearer of this fragility a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. bearer_of is bearer of bearer of participates in this blood clot participates in this blood coagulation this input material (or this output material) participates in this process this investigator participates in this investigation a relation between a continuant and a process, in which the continuant is somehow involved in the process participates_in participates in has participant this blood coagulation has participant this blood clot this investigation has participant this investigator this process has participant this input material (or this output material) a relation between a process and a continuant, in which the continuant is somehow involved in the process Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. has_participant http://www.obofoundry.org/ro/#OBO_REL:has_participant has participant this catalysis function is a function of this enzyme a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. function_of is function of function of 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 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 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 This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations. derives from David Osumi-Sutherland starts_at_end_of X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) immediately preceded by Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814] Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part. Alexander Diehl Chris Mungall Lindsay Cowell PMID:19243617 <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0005886> and <http://purl.obolibrary.org/obo/BFO_0000051> some ?Y) has plasma membrane part Chris Mungall David Osumi-Sutherland Terry Meehan develops into 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 PMID:20123131 PMID:21208450 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)". RO_0000053 some (RO_0000054 only ?Y) capable of Elisabetta Manduchi Emily Greenfest-Allen Chris Stoeckert Jie Zheng The ontology is built based on OBI release 2015-04-13 This file is based on checkout of our SVN repository revision $Revision: 204$ https://github.com/obi-bcgo/bcgo A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface. For the formal definition, see Masci et al (PMID:19243617). has_high_plasma_membrane_amount A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface. For the formal definition, see Masci et al (PMID:19243617). has_low_plasma_membrane_amount http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 ?Y lacks_part http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 (http://purl.obolibrary.org/obo/GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y) lacks_plasma_membrane_part s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2. quality has_cross_section Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round. has_cross_section q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. quality increased_in_magnitude_relative_to This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'. increased_in_magnitude_relative_to