Vision Release: 1.0.02 Jens Hansen Yongqun Oliver He OSCI: Ontology of Stem Cell Investigation 05-25-2018 Alexander Diehl OSCI is a biomedical ontology in the area of stem cell investigation. OSCI imports existing ontologies such as CL, CLO, and OBI, and aims to support standardized stem cell representation, integration, and analysis. A biomedical ontology to support stem cell investigation OWL-DL William Duncan 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 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 BFO CLIF specification label An annotation property that represents an ID used in the NIH LINCS project. Oliver He, Jiangan Xie, Jie Zheng LINCS ID https://pubchem.ncbi.nlm.nih.gov/help.html An annotation property that represents a PubMed BioAssay Identifier accession number. Oliver He PubChem AID Oliver He An annotation property that describes known mutation(s) about a cell. Known mutation annotation Cell culture condition editor preferred label editor preferred label editor preferred term editor preferred term editor preferred term~editor preferred label The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> editor preferred label editor preferred label editor preferred term editor preferred term editor preferred term~editor preferred label 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 A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> example of usage example of usage has curation status PERSON:Alan Ruttenberg PERSON:Bill Bug PERSON:Melanie Courtot OBI_0000281 has curation status has curation status definition definition definition textual definition textual definition English language definitions of what NCI means by the concept. These are limited to 1024 characters. They may also include information about the definition's source and attribution in a form that can easily be interpreted by software. 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 definition definition textual 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 true editor_note 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. 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition editor definition editor definition editor term editor term editor alternative term An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent) PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> alternative term alternative term definition source formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 PERSON:Daniel Schober Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition source definition source definition source 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 true curator_notes curator note curator note curator notes curator notes term tracker item the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/ An IRI or similar locator for a request or discussion of an ontology term. Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg The 'tracker item' can associate a tracker with a specific ontology term. term tracker item The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition. Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg The 'term requester' can credit the person, organization or project who request the ontology term. ontology term requester 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 OBO foundry unique label An alternative name for a class or property which is unique across the OBO Foundry. The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools . PERSON:Alan Ruttenberg PERSON:Bjoern Peters PERSON:Chris Mungall PERSON:Melanie Courtot GROUP:OBO Foundry <http://obofoundry.org/> OBO foundry unique label elucidation person:Alan Ruttenberg Person:Barry Smith Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms elucidation elucidation has associated axiom(nl) Person:Alan Ruttenberg Person:Alan Ruttenberg An axiom associated with a term expressed using natural language has associated axiom(nl) has associated axiom(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 associated axiom(fol) true NHC0 code code code The semantic type describes the sort of thing or category to which a concept belongs in the context of the UMLS semantic network. P106 Conceptual Entity Semantic Type Semantic_Type In general, applying semantic types aids in allowing users (or computer programs) to draw conclusions about concepts by virtue of the categories to which they have been assigned. We use a set of semantic types developed for the UMLS Metathesaurus. There are currently 134 semantic types in the UMLS. Semantic_Type Semantic_Type Provides an alternative Preferred Name for use in some NCI systems. P107 Conceptual Entity Display Name Display_Name Display Name Display_Name Display_Name The word or phrase that NCI uses by preference to refer to the concept. P108 Conceptual Entity Preferred Name Preferred_Name Preferred Name Preferred Term Preferred_Name Preferred_Name Concept Unique Identifiers, or CUIs, are concept numbers assigned by the National Library of Medicine (NLM). If a concept in any NCI-maintained knowledgebase exists in the NLM Unified Medical Language System (UMLS), NCI includes the NLM CUI among the information we provide about the concept. P207 Conceptual Entity UMLS CUI UMLS_CUI UMLS_CUI UMLS_CUI This property is used to indicate when a non-EVS entity has contributed to, and has a stake in, a concept. This is used where such entities, within or outside NCI, have indicated the need to be able to track their own concepts. A single concept can have multiple instances of this property if multiple entities have such a defined stake. P322 Conceptual Entity Contributing Source Contributing_Source Contributing_Source Contributing_Source English language definitions of what a source other than NCI means by the concept. These are limited to 1024 characters. They include information about the definition's source in a form that can easily be interpreted by software. P325 Conceptual Entity [source] Definition ALT_DEFINITION ALT_DEFINITION ALT_DEFINITION true A retired unique concept identifier created and stored as Concept Name by legacy EVS software. Use of these values was long discouraged, but continued as late as 2009 when creation of new values ceased and Concept Name was retired. Legacy values are intended solely to help resolve and update earlier coding. P366 Conceptual Entity Legacy Concept Name Legacy Concept Name Legacy_Concept_Name Design notes are notations made by NCI vocabulary curators. They are intended to provide supplemental, unstructured information to the user or additional insight about the concept. P98 Conceptual Entity DesignNote DesignNote DesignNote DesignNote 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 the symbol assigned by the nomenclature authority Oliver He, Yue Liu symbol from nomenclature authority the full name assigned by the nomenclature authority Oliver He, Yue Liu full name from nomenclature authority A GeneID in the NCBI Gene database Oliver He, Yue Liu NCBI GeneID the NCBI LocusTag name of a gene Oliver He, Yue Liu NCBI LocusTag the map location of a gene Oliver He, Yue Liu gene map location a date of content modification Oliver He, Yue Liu modification date The NCBITaxon ontology ID of an organism. Oliver He, Yue Liu organism NCBITaxon ID A chromosome ID where a gene is located. Oliver He chromosome ID of gene an annotation property that specifies the type of a gene Oliver He type of gene an annotation property that specifies a nomenclature status Oliver He nomenclature status an annotation property that shows the GO information associated with a specific gene. Yongqun He YH: use the convention: GO_ID (EC: xx; Qualifier: xx; PMID: xxxxx;) where GO_ID is a GO ID, EC is the Evidence Code, Qualifier is a specific association type, and PMID is a PubMed ID of a paper that supports the gene-GO association. has GO association An annotation property that represents a gene's association with PubMed publication(s). Yongqun He YH: use the format: PMID: pmid1, pmid2, ... where pmid1 and pmid2 are specfic PubMed IDs (PMIDs). has PubMed association Bill Duncan <http://orcid.org/0000-0001-9625-1899> 2018-05-31T21:59:53Z stem cell ID Bill Duncan <http://orcid.org/0000-0001-9625-1899> 2018-05-31T22:00:25Z lot number Bill Duncan <http://orcid.org/0000-0001-9625-1899> 2018-05-31T22:00:39Z cell grade Bill Duncan <http://orcid.org/0000-0001-9625-1899> 2018-05-31T22:02:49Z contact information Bill Duncan <http://orcid.org/0000-0001-9625-1899> 2018-05-31T22:08:30Z reference publication Bill Duncan <http://orcid.org/0000-0001-9625-1899> 2018-05-31T22:31:59Z donor ID Bill Duncan <http://orcid.org/0000-0001-9625-1899> 2018-05-31T22:56:10Z donor testing method Bill Duncan <http://orcid.org/0000-0001-9625-1899> 2018-05-31T22:56:31Z donor screening method Bill Duncan <http://orcid.org/0000-0001-9625-1899> 2018-05-31T22:56:59Z source cell ID temporal interpretation An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context. temporal interpretation temporal interpretation https://code.google.com/p/obo-relations/wiki/ROAndTime https://github.com/oborel/obo-relations/wiki/ROAndTime UBPROP:0000001 uberon external_definition true external_definition This annotation property may be replaced with an annotation property from an external ontology such as IAO external_definition external_definition An alternate textual definition for a class taken unmodified from an external source. This definition may have been used to derive a generalized definition for the new class. UBPROP:0000007 uberon has_relational_adjective true has_relational_adjective has_relational_adjective has_relational_adjective Used to connect a class to an adjectival form of its label. For example, a class with label 'intestine' may have a relational adjective 'intestinal'. UBPROP:0000012 uberon external_ontology_notes true external_ontology_notes external_ontology_notes external_ontology_notes Notes on how similar or equivalent classes are represented in other ontologies. This annotation property may be replaced with an annotation property from an external ontology such as IAO A metadata relation between a class and its taxonomic rank (eg species, family) ncbi_taxonomy has_rank uberon dc-contributor true dc-contributor Examples of a Contributor include a person, an organisation, or a service. Typically, the name of a Contributor should be used to indicate the entity. An entity responsible for making contributions to the content of the resource. Contributor Contributor contributor Examples of a Creator include a person, an organisation, or a service. Typically, the name of a Creator should be used to indicate the entity. An entity primarily responsible for making the content of the resource. Creator Creator Typically, Date will be associated with the creation or availability of the resource. Recommended best practice for encoding the date value is defined in a profile of ISO 8601 [W3CDTF] and follows the YYYY-MM-DD format. A date associated with an event in the life cycle of the resource. Date Date Description may include but is not limited to: an abstract, table of contents, reference to a graphical representation of content or a free-text account of the content. An account of the content of the resource. Description Description Typically, Format may include the media-type or dimensions of the resource. Format may be used to determine the software, hardware or other equipment needed to display or operate the resource. Examples of dimensions include size and duration. Recommended best practice is to select a value from a controlled vocabulary (for example, the list of Internet Media Types [MIME] defining computer media formats). The physical or digital manifestation of the resource. Format Format The present resource may be derived from the Source resource in whole or in part. Recommended best practice is to reference the resource by means of a string or number conforming to a formal identification system. A reference to a resource from which the present resource is derived. Source Source Typically, a Subject will be expressed as keywords, key phrases or classification codes that describe a topic of the resource. Recommended best practice is to select a value from a controlled vocabulary or formal classification scheme. The topic of the content of the resource. Subject and Keywords Subject and Keywords Typically, a Title will be a name by which the resource is formally known. A name given to the resource. Title Title Mark Miller 2018-05-11T13:47:29Z has_alternative_id has_alternative_id has_broad_synonym has_broad_synonym database_cross_reference database_cross_reference Fully qualified synonym, contains the string, term type, source, and an optional source code if appropriate. Each subfield is deliniated to facilitate interpretation by software. FULL_SYN Synonym with Source Data has exact synonym has_exact_synonym has_exact_synonym has_narrow_synonym has_narrow_synonym has_obo_namespace has_obo_namespace has_related_synonym has_related_synonym Used to associate the concept defining a particular terminology subset with concepts that belong to this subset. Concept_In_Subset in subset in_subset in_subset label label 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 part_of http://www.obofoundry.org/ro/#OBO_REL:part_of 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 inheres-in_at inheresInAt b inheres_in c at t =Def. b is a dependent continuant & c is an independent continuant that is not a spatial region & b s-depends_on c at t. (axiom label in BFO2 Reference: [051-002]) Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'inheres in at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'inheres in@en(x,y,t)'. BFO 2 Reference: Inherence is a subrelation of s-depends_on which holds between a dependent continuant and an independent continuant that is not a spatial region. Since dependent continuants cannot migrate from one independent continuant bearer to another, it follows that if b s-depends_on independent continuant c at some time, then b s-depends_on c at all times at which a exists. Inherence is in this sense redundantly time-indexed.For example, consider the particular instance of openness inhering in my mouth at t as I prepare to take a bite out of a donut, followed by a closedness at t+1 when I bite the donut and start chewing. The openness instance is then shortlived, and to say that it s-depends_on my mouth at all times at which this openness exists, means: at all times during this short life. Every time you make a fist, you make a new (instance of the universal) fist. (Every time your hand has the fist-shaped quality, there is created a new instance of the universal fist-shaped quality.) BFO2 Reference: independent continuant that is not a spatial region BFO2 Reference: specifically dependent continuant (iff (inheresInAt a b t) (and (DependentContinuant a) (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))) // axiom label in BFO2 CLIF: [051-002] inheres in at all times realized in this disease is realized in this disease course this fragility is realized in this shattering this investigator role is realized in this investigation is realized by realized_in [copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process realized in realizes this disease course realizes this disease this investigation realizes this investigator role this shattering realizes this fragility to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process realizes concretized-by_st [copied from inverse property 'concretizes at some time'] You may concretize a piece of software by installing it in your computer [copied from inverse property 'concretizes at some time'] You may concretize a recipe that you find in a cookbook by turning it into a plan which exists as a realizable dependent continuant in your head. [copied from inverse property 'concretizes at some time'] you may concretize a poem as a pattern of memory traces in your head [copied from inverse property 'concretizes at some time'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'concretizes at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'concretizes@en'(x,y,t) [copied from inverse property 'concretizes at some time'] b concretizes c at t means: b is a specifically dependent continuant & c is a generically dependent continuant & for some independent continuant that is not a spatial region d, b s-depends_on d at t & c g-depends on d at t & if c migrates from bearer d to another bearer e than a copy of b will be created in e. (axiom label in BFO2 Reference: [075-002]) concretized by at some time concretizes_st concretizesAt You may concretize a piece of software by installing it in your computer You may concretize a recipe that you find in a cookbook by turning it into a plan which exists as a realizable dependent continuant in your head. you may concretize a poem as a pattern of memory traces in your head Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'concretizes at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'concretizes@en'(x,y,t) b concretizes c at t means: b is a specifically dependent continuant & c is a generically dependent continuant & for some independent continuant that is not a spatial region d, b s-depends_on d at t & c g-depends on d at t & if c migrates from bearer d to another bearer e than a copy of b will be created in e. (axiom label in BFO2 Reference: [075-002]) if b g-depends on c at some time t, then there is some d, such that d concretizes b at t and d s-depends_on c at t. (axiom label in BFO2 Reference: [076-001]) (forall (x y t) (if (concretizesAt x y t) (and (SpecificallyDependentContinuant x) (GenericallyDependentContinuant y) (exists (z) (and (IndependentContinuant z) (specificallyDependsOnAt x z t) (genericallyDependsOnAt y z t)))))) // axiom label in BFO2 CLIF: [075-002] (forall (x y t) (if (genericallyDependsOnAt x y t) (exists (z) (and (concretizesAt z x t) (specificallyDependsOnAt z y t))))) // axiom label in BFO2 CLIF: [076-001] concretizes at some time s-depends-on_at specificallyDependsOn A pain s-depends_on the organism that is experiencing the pain a gait s-depends_on the walking object. (All at some specific time.) a shape s-depends_on the shaped object one-sided s-dependence of a dependent continuant on an independent continuant: an instance of headache s-depends_on some head one-sided s-dependence of a dependent continuant on an independent continuant: an instance of temperature s-depends_on some organism one-sided s-dependence of a process on something: a process of cell death s-depends_on a cell one-sided s-dependence of a process on something: an instance of seeing (a relational process) s-depends_on some organism and on some seen entity, which may be an occurrent or a continuant one-sided s-dependence of one occurrent on another: a process of answering a question is dependent on a prior process of asking a question one-sided s-dependence of one occurrent on another: a process of obeying a command is dependent on a prior process of issuing a command one-sided s-dependence of one occurrent on multiple independent continuants: a relational process of hitting a ball with a cricket bat one-sided s-dependence of one occurrent on multiple independent continuants: a relational process of paying cash to a merchant in exchange for a bag of figs reciprocal s-dependence between occurrents: a process of buying and the associated process of selling reciprocal s-dependence between occurrents: a process of increasing the volume of a portion of gas while temperature remains constant and the associated process of decreasing the pressure exerted by the gas reciprocal s-dependence between occurrents: in a game of chess the process of playing with the white pieces is mutually dependent on the process of playing with the black pieces the one-sided dependence of an occurrent on an independent continuant: football match on the players, the ground, the ball the one-sided dependence of an occurrent on an independent continuant: handwave on a hand the three-sided reciprocal s-dependence of the hue, saturation and brightness of a color [45 the three-sided reciprocal s-dependence of the pitch, timbre and volume of a tone [45 the two-sided reciprocal s-dependence of the roles of husband and wife [20 Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'specifically depends on at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'specifically depends on@en(x,y,t)'. BFO 2 Reference: An entity – for example an act of communication or a game of football – can s-depends_on more than one entity. Complex phenomena for example in the psychological and social realms (such as inferring, commanding and requesting) or in the realm of multi-organismal biological processes (such as infection and resistance), will involve multiple families of dependence relations, involving both continuants and occurrents [1, 4, 28 BFO 2 Reference: S-dependence is just one type of dependence among many; it is what, in the literature, is referred to as ‘existential dependence’ [87, 46, 65, 20 BFO 2 Reference: the relation of s-depends_on does not in every case require simultaneous existence of its relata. Note the difference between such cases and the cases of continuant universals defined historically: the act of answering depends existentially on the prior act of questioning; the human being who was baptized or who answered a question does not himself depend existentially on the prior act of baptism or answering. He would still exist even if these acts had never taken place. BFO2 Reference: specifically dependent continuant\; process; process boundary To say that b s-depends_on a at t is to say that b and c do not share common parts & b is of its nature such that it cannot exist unless c exists & b is not a boundary of c and b is not a site of which c is the host [64 If b is s-depends_on something at some time, then b is not a material entity. (axiom label in BFO2 Reference: [052-001]) If b s-depends_on something at t, then there is some c, which is an independent continuant and not a spatial region, such that b s-depends_on c at t. (axiom label in BFO2 Reference: [136-001]) If occurrent b s-depends_on some independent continuant c at t, then b s-depends_on c at every time at which b exists. (axiom label in BFO2 Reference: [015-002]) an entity does not s-depend_on any of its (continuant or occurrent) parts or on anything it is part of. (axiom label in BFO2 Reference: [013-002]) if b s-depends_on c at t & c s-depends_on d at t then b s-depends_on d at t. (axiom label in BFO2 Reference: [054-002]) (forall (x y t) (if (and (Entity x) (or (continuantPartOfAt y x t) (continuantPartOfAt x y t) (occurrentPartOf x y) (occurrentPartOf y x))) (not (specificallyDependsOnAt x y t)))) // axiom label in BFO2 CLIF: [013-002] (forall (x y t) (if (and (Occurrent x) (IndependentContinuant y) (specificallyDependsOnAt x y t)) (forall (t_1) (if (existsAt x t_1) (specificallyDependsOnAt x y t_1))))) // axiom label in BFO2 CLIF: [015-002] (forall (x y t) (if (specificallyDependsOnAt x y t) (exists (z) (and (IndependentContinuant z) (not (SpatialRegion z)) (specificallyDependsOnAt x z t))))) // axiom label in BFO2 CLIF: [136-001] (forall (x y z t) (if (and (specificallyDependsOnAt x y t) (specificallyDependsOnAt y z t)) (specificallyDependsOnAt x z t))) // axiom label in BFO2 CLIF: [054-002] (forall (x) (if (exists (y t) (specificallyDependsOnAt x y t)) (not (MaterialEntity x)))) // axiom label in BFO2 CLIF: [052-001] specifically depends on at all times located-at-r_st occupiesSpatialRegionAt Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'occupies spatial region at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'occupies spatial region@en'(x,y,t) BFO2 Reference: independent continuant BFO2 Reference: spatial region b occupies_spatial_region r at t means that r is a spatial region in which independent continuant b is exactly located (axiom label in BFO2 Reference: [041-002]) every region r is occupies_spatial_region r at all times. (axiom label in BFO2 Reference: [042-002]) if b occupies_spatial_region r at t & b continuant_part_of b at t, then there is some r which is continuant_part_of r at t such that b occupies_spatial_region r at t. (axiom label in BFO2 Reference: [043-001]) (forall (r t) (if (Region r) (occupiesSpatialRegionAt r r t))) // axiom label in BFO2 CLIF: [042-002] (forall (x r t) (if (occupiesSpatialRegionAt x r t) (and (SpatialRegion r) (IndependentContinuant x)))) // axiom label in BFO2 CLIF: [041-002] (forall (x y r_1 t) (if (and (occupiesSpatialRegionAt x r_1 t) (continuantPartOfAt y x t)) (exists (r_2) (and (continuantPartOfAt r_2 r_1 t) (occupiesSpatialRegionAt y r_2 t))))) // axiom label in BFO2 CLIF: [043-001] occupies spatial region at some time http://www.ebi.ac.uk/efo/has_quality has_quality exists-at existsAt BFO2 Reference: entity BFO2 Reference: temporal region b exists_at t means: b is an entity which exists at some temporal region t. (axiom label in BFO2 Reference: [118-002]) exists at o-has-part hasOccurrentPart [copied from inverse property 'part of occurrent'] Mary’s 5th birthday occurrent_part_of Mary’s life [copied from inverse property 'part of occurrent'] The process of a footballer’s heart beating once is an occurrent part but not a temporal_part of a game of football. [copied from inverse property 'part of occurrent'] the first set of the tennis match occurrent_part_of the tennis match. b has_occurrent_part c = Def. c occurrent_part_of b. (axiom label in BFO2 Reference: [007-001]) [copied from inverse property 'part of occurrent'] BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion. [copied from inverse property 'part of occurrent'] BFO2 Reference: occurrent [copied from inverse property 'part of occurrent'] b occurrent_part_of c =Def. b is a part of c & b and c are occurrents. (axiom label in BFO2 Reference: [003-002]) (iff (hasOccurrentPart a b) (occurrentPartOf b a)) // axiom label in BFO2 CLIF: [007-001] has occurrent part o-has-ppart hasProperOccurrentPart [copied from inverse property 'proper part of occurrent'] b proper_occurrent_part_of c =Def. b occurrent_part_of c & b and c are not identical. (axiom label in BFO2 Reference: [005-001]) b has_proper_occurrent_part c = Def. c proper_occurrent_part_of b. [XXX-001 has proper occurrent part r-location-of_st [copied from inverse property 'occupies spatial region at some time'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'occupies spatial region at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'occupies spatial region@en'(x,y,t) [copied from inverse property 'occupies spatial region at some time'] BFO2 Reference: independent continuant [copied from inverse property 'occupies spatial region at some time'] BFO2 Reference: spatial region [copied from inverse property 'occupies spatial region at some time'] b occupies_spatial_region r at t means that r is a spatial region in which independent continuant b is exactly located (axiom label in BFO2 Reference: [041-002]) has spatial occupant at some time has-s-dep_st [copied from inverse property 'specifically depends on at some time'] A pain s-depends_on the organism that is experiencing the pain [copied from inverse property 'specifically depends on at some time'] a gait s-depends_on the walking object. (All at some specific time.) [copied from inverse property 'specifically depends on at some time'] a shape s-depends_on the shaped object [copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of a dependent continuant on an independent continuant: an instance of headache s-depends_on some head [copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of a dependent continuant on an independent continuant: an instance of temperature s-depends_on some organism [copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of a process on something: a process of cell death s-depends_on a cell [copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of a process on something: an instance of seeing (a relational process) s-depends_on some organism and on some seen entity, which may be an occurrent or a continuant [copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of one occurrent on another: a process of answering a question is dependent on a prior process of asking a question [copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of one occurrent on another: a process of obeying a command is dependent on a prior process of issuing a command [copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of one occurrent on multiple independent continuants: a relational process of hitting a ball with a cricket bat [copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of one occurrent on multiple independent continuants: a relational process of paying cash to a merchant in exchange for a bag of figs [copied from inverse property 'specifically depends on at some time'] reciprocal s-dependence between occurrents: a process of buying and the associated process of selling [copied from inverse property 'specifically depends on at some time'] reciprocal s-dependence between occurrents: a process of increasing the volume of a portion of gas while temperature remains constant and the associated process of decreasing the pressure exerted by the gas [copied from inverse property 'specifically depends on at some time'] reciprocal s-dependence between occurrents: in a game of chess the process of playing with the white pieces is mutually dependent on the process of playing with the black pieces [copied from inverse property 'specifically depends on at some time'] the one-sided dependence of an occurrent on an independent continuant: football match on the players, the ground, the ball [copied from inverse property 'specifically depends on at some time'] the one-sided dependence of an occurrent on an independent continuant: handwave on a hand [copied from inverse property 'specifically depends on at some time'] the three-sided reciprocal s-dependence of the hue, saturation and brightness of a color [45 [copied from inverse property 'specifically depends on at some time'] the three-sided reciprocal s-dependence of the pitch, timbre and volume of a tone [45 [copied from inverse property 'specifically depends on at some time'] the two-sided reciprocal s-dependence of the roles of husband and wife [20 [copied from inverse property 'specifically depends on at some time'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'specifically depends on at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'specifically depends on@en'(x,y,t) [copied from inverse property 'specifically depends on at some time'] BFO 2 Reference: An entity – for example an act of communication or a game of football – can s-depends_on more than one entity. Complex phenomena for example in the psychological and social realms (such as inferring, commanding and requesting) or in the realm of multi-organismal biological processes (such as infection and resistance), will involve multiple families of dependence relations, involving both continuants and occurrents [1, 4, 28 [copied from inverse property 'specifically depends on at some time'] BFO 2 Reference: S-dependence is just one type of dependence among many; it is what, in the literature, is referred to as ‘existential dependence’ [87, 46, 65, 20 [copied from inverse property 'specifically depends on at some time'] BFO 2 Reference: the relation of s-depends_on does not in every case require simultaneous existence of its relata. Note the difference between such cases and the cases of continuant universals defined historically: the act of answering depends existentially on the prior act of questioning; the human being who was baptized or who answered a question does not himself depend existentially on the prior act of baptism or answering. He would still exist even if these acts had never taken place. [copied from inverse property 'specifically depends on at some time'] BFO2 Reference: specifically dependent continuant\; process; process boundary [copied from inverse property 'specifically depends on at some time'] To say that b s-depends_on a at t is to say that b and c do not share common parts & b is of its nature such that it cannot exist unless c exists & b is not a boundary of c and b is not a site of which c is the host [64 has specific dependent at some time occupied-by [copied from inverse property 'occupies spatiotemporal region'] BFO 2 Reference: The occupies_spatiotemporal_region and occupies_temporal_region relations are the counterpart, on the occurrent side, of the relation occupies_spatial_region. [copied from inverse property 'occupies spatiotemporal region'] p occupies_spatiotemporal_region s. This is a primitive relation between an occurrent p and the spatiotemporal region s which is its spatiotemporal extent. (axiom label in BFO2 Reference: [082-003]) has spatiotemporal occupant occupies occupiesSpatiotemporalRegion BFO 2 Reference: The occupies_spatiotemporal_region and occupies_temporal_region relations are the counterpart, on the occurrent side, of the relation occupies_spatial_region. p occupies_spatiotemporal_region s. This is a primitive relation between an occurrent p and the spatiotemporal region s which is its spatiotemporal extent. (axiom label in BFO2 Reference: [082-003]) occupies spatiotemporal region o-part-of occurrentPartOf Mary’s 5th birthday occurrent_part_of Mary’s life The process of a footballer’s heart beating once is an occurrent part but not a temporal_part of a game of football. the first set of the tennis match occurrent_part_of the tennis match. [copied from inverse property 'has occurrent part'] b has_occurrent_part c = Def. c occurrent_part_of b. (axiom label in BFO2 Reference: [007-001]) BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion. BFO2 Reference: occurrent b occurrent_part_of c =Def. b is a part of c & b and c are occurrents. (axiom label in BFO2 Reference: [003-002]) occurrent_part_of is antisymmetric. (axiom label in BFO2 Reference: [123-001]) occurrent_part_of is reflexive (every occurrent entity is an occurrent_part_of itself). (axiom label in BFO2 Reference: [113-002]) occurrent_part_of is transitive. (axiom label in BFO2 Reference: [112-001]) occurrent_part_of satisfies unique product. (axiom label in BFO2 Reference: [125-001]) occurrent_part_of satisfies weak supplementation. (axiom label in BFO2 Reference: [124-001]) (forall (x y t) (if (and (occurrentPartOf x y t) (not (= x y))) (exists (z) (and (occurrentPartOf z y t) (not (exists (w) (and (occurrentPartOf w x t) (occurrentPartOf w z t)))))))) // axiom label in BFO2 CLIF: [124-001] (forall (x y t) (if (and (occurrentPartOf x y t) (occurrentPartOf y x t)) (= x y))) // axiom label in BFO2 CLIF: [123-001] (forall (x y t) (if (exists (v) (and (occurrentPartOf v x t) (occurrentPartOf v y t))) (exists (z) (forall (u w) (iff (iff (occurrentPartOf w u t) (and (occurrentPartOf w x t) (occurrentPartOf w y t))) (= z u)))))) // axiom label in BFO2 CLIF: [125-001] (forall (x y z) (if (and (occurrentPartOf x y) (occurrentPartOf y z)) (occurrentPartOf x z))) // axiom label in BFO2 CLIF: [112-001] (forall (x) (if (Occurrent x) (occurrentPartOf x x))) // axiom label in BFO2 CLIF: [113-002] part of occurrent o-ppart-of properOccurrentPartOf [copied from inverse property 'has proper occurrent part'] b has_proper_occurrent_part c = Def. c proper_occurrent_part_of b. [XXX-001 b proper_occurrent_part_of c =Def. b occurrent_part_of c & b and c are not identical. (axiom label in BFO2 Reference: [005-001]) (iff (properOccurrentPartOf a b) (and (occurrentPartOf a b) (not (= a b)))) // axiom label in BFO2 CLIF: [005-001] proper part of occurrent t-part-of temporalPartOf the 4th year of your life is a temporal part of your life\. The first quarter of a game of football is a temporal part of the whole game\. The process of your heart beating from 4pm to 5pm today is a temporal part of the entire process of your heart beating.\ The 4th year of your life is a temporal part of your life the process boundary which separates the 3rd and 4th years of your life. your heart beating from 4pm to 5pm today is a temporal part of the process of your heart beating b proper_temporal_part_of c =Def. b temporal_part_of c & not (b = c). (axiom label in BFO2 Reference: [116-001]) b temporal_part_of c =Def.b occurrent_part_of c & & for some temporal region t, b occupies_temporal_region t & for all occurrents d, t (if d occupies_temporal_region t & t? occurrent_part_of t then (d occurrent_part_of a iff d occurrent_part_of b)). (axiom label in BFO2 Reference: [078-003]) if b proper_temporal_part_of c, then there is some d which is a proper_temporal_part_of c and which shares no parts with b. (axiom label in BFO2 Reference: [117-002]) (forall (x y) (if (properTemporalPartOf x y) (exists (z) (and (properTemporalPartOf z y) (not (exists (w) (and (temporalPartOf w x) (temporalPartOf w z)))))))) // axiom label in BFO2 CLIF: [117-002] (iff (properTemporalPartOf a b) (and (temporalPartOf a b) (not (= a b)))) // axiom label in BFO2 CLIF: [116-001] (iff (temporalPartOf a b) (and (occurrentPartOf a b) (exists (t) (and (TemporalRegion t) (occupiesSpatioTemporalRegion a t))) (forall (c t_1) (if (and (Occurrent c) (occupiesSpatioTemporalRegion c t_1) (occurrentPartOf t_1 r)) (iff (occurrentPartOf c a) (occurrentPartOf c b)))))) // axiom label in BFO2 CLIF: [078-003] temporal part of st-projects-onto-s_st projects onto spatial region at some time s-projection-of-st_st spatial projection of spatiotemporal at some time st-projects-onto-t projects onto temporal region t-projection-of-st temporal projection of spatiotemporal spans occupiesTemporalRegion p occupies_temporal_region t. This is a primitive relation between an occurrent p and the temporal region t upon which the spatiotemporal region p occupies_spatiotemporal_region projects. (axiom label in BFO2 Reference: [132-001]) occupies temporal region span-of spanOf [copied from inverse property 'occupies temporal region'] p occupies_temporal_region t. This is a primitive relation between an occurrent p and the temporal region t upon which the spatiotemporal region p occupies_spatiotemporal_region projects. (axiom label in BFO2 Reference: [132-001]) has temporal occupant during-which-exists [copied from inverse property 'exists at'] BFO2 Reference: entity [copied from inverse property 'exists at'] BFO2 Reference: temporal region [copied from inverse property 'exists at'] b exists_at t means: b is an entity which exists at some temporal region t. (axiom label in BFO2 Reference: [118-002]) during which exists bearer-of_at bearerOfAt b bearer_of c at t =Def. c s-depends_on b at t & b is an independent continuant that is not a spatial region. (axiom label in BFO2 Reference: [053-004]) Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'bearer of at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'bearer of@en(x,y,t)'. BFO2 Reference: independent continuant that is not a spatial region BFO2 Reference: specifically dependent continuant (iff (bearerOfAt a b t) (and (specificallyDependsOnAt b a t) (IndependentContinuant a) (not (SpatialRegion a)) (existsAt b t))) // axiom label in BFO2 CLIF: [053-004] bearer of at all times has-d_at hasDispositionAt a has_disposition b at t =Def. b disposition_of a at t. (axiom label in BFO2 Reference: [069-001]) Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'has disposition at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'has disposition@en(x,y,t)'. (iff (hasDispositionAt a b t) (dispositionOf b a t)) // axiom label in BFO2 CLIF: [069-001] has disposition at all times has-s-dep_at has specific dependent at all times s-depends-on_st specificallyDependsOn A pain s-depends_on the organism that is experiencing the pain a gait s-depends_on the walking object. (All at some specific time.) a shape s-depends_on the shaped object one-sided s-dependence of a dependent continuant on an independent continuant: an instance of headache s-depends_on some head one-sided s-dependence of a dependent continuant on an independent continuant: an instance of temperature s-depends_on some organism one-sided s-dependence of a process on something: a process of cell death s-depends_on a cell one-sided s-dependence of a process on something: an instance of seeing (a relational process) s-depends_on some organism and on some seen entity, which may be an occurrent or a continuant one-sided s-dependence of one occurrent on another: a process of answering a question is dependent on a prior process of asking a question one-sided s-dependence of one occurrent on another: a process of obeying a command is dependent on a prior process of issuing a command one-sided s-dependence of one occurrent on multiple independent continuants: a relational process of hitting a ball with a cricket bat one-sided s-dependence of one occurrent on multiple independent continuants: a relational process of paying cash to a merchant in exchange for a bag of figs reciprocal s-dependence between occurrents: a process of buying and the associated process of selling reciprocal s-dependence between occurrents: a process of increasing the volume of a portion of gas while temperature remains constant and the associated process of decreasing the pressure exerted by the gas reciprocal s-dependence between occurrents: in a game of chess the process of playing with the white pieces is mutually dependent on the process of playing with the black pieces the one-sided dependence of an occurrent on an independent continuant: football match on the players, the ground, the ball the one-sided dependence of an occurrent on an independent continuant: handwave on a hand the three-sided reciprocal s-dependence of the hue, saturation and brightness of a color [45 the three-sided reciprocal s-dependence of the pitch, timbre and volume of a tone [45 the two-sided reciprocal s-dependence of the roles of husband and wife [20 Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'specifically depends on at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'specifically depends on@en'(x,y,t) BFO 2 Reference: An entity – for example an act of communication or a game of football – can s-depends_on more than one entity. Complex phenomena for example in the psychological and social realms (such as inferring, commanding and requesting) or in the realm of multi-organismal biological processes (such as infection and resistance), will involve multiple families of dependence relations, involving both continuants and occurrents [1, 4, 28 BFO 2 Reference: S-dependence is just one type of dependence among many; it is what, in the literature, is referred to as ‘existential dependence’ [87, 46, 65, 20 BFO 2 Reference: the relation of s-depends_on does not in every case require simultaneous existence of its relata. Note the difference between such cases and the cases of continuant universals defined historically: the act of answering depends existentially on the prior act of questioning; the human being who was baptized or who answered a question does not himself depend existentially on the prior act of baptism or answering. He would still exist even if these acts had never taken place. BFO2 Reference: specifically dependent continuant\; process; process boundary To say that b s-depends_on a at t is to say that b and c do not share common parts & b is of its nature such that it cannot exist unless c exists & b is not a boundary of c and b is not a site of which c is the host [64 If b is s-depends_on something at some time, then b is not a material entity. (axiom label in BFO2 Reference: [052-001]) If b s-depends_on something at t, then there is some c, which is an independent continuant and not a spatial region, such that b s-depends_on c at t. (axiom label in BFO2 Reference: [136-001]) If occurrent b s-depends_on some independent continuant c at t, then b s-depends_on c at every time at which b exists. (axiom label in BFO2 Reference: [015-002]) an entity does not s-depend_on any of its (continuant or occurrent) parts or on anything it is part of. (axiom label in BFO2 Reference: [013-002]) if b s-depends_on c at t & c s-depends_on d at t then b s-depends_on d at t. (axiom label in BFO2 Reference: [054-002]) (forall (x y t) (if (and (Entity x) (or (continuantPartOfAt y x t) (continuantPartOfAt x y t) (occurrentPartOf x y) (occurrentPartOf y x))) (not (specificallyDependsOnAt x y t)))) // axiom label in BFO2 CLIF: [013-002] (forall (x y t) (if (and (Occurrent x) (IndependentContinuant y) (specificallyDependsOnAt x y t)) (forall (t_1) (if (existsAt x t_1) (specificallyDependsOnAt x y t_1))))) // axiom label in BFO2 CLIF: [015-002] (forall (x y t) (if (specificallyDependsOnAt x y t) (exists (z) (and (IndependentContinuant z) (not (SpatialRegion z)) (specificallyDependsOnAt x z t))))) // axiom label in BFO2 CLIF: [136-001] (forall (x y z t) (if (and (specificallyDependsOnAt x y t) (specificallyDependsOnAt y z t)) (specificallyDependsOnAt x z t))) // axiom label in BFO2 CLIF: [054-002] (forall (x) (if (exists (y t) (specificallyDependsOnAt x y t)) (not (MaterialEntity x)))) // axiom label in BFO2 CLIF: [052-001] specifically depends on at some time c-part-of_st continuantPartOfAt Mary’s arm continuant_part_of Mary in the time of her life prior to her operation the Northern hemisphere of the planet Earth is a part of the planet Earth at all times at which the planet Earth exists. [copied from inverse property 'has continuant part at some time'] b has_continuant_part c at t = Def. c continuant_part_of b at t. (axiom label in BFO2 Reference: [006-001]) Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'part of continuant at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'part of continuant@en'(x,y,t) BFO 2 Reference: Immaterial entities are in some cases continuant parts of their material hosts. Thus the hold of a ship, for example, is a part of the ship; it may itself have parts, which may have names (used for example by ship stow planners, customs inspectors, and the like). Immaterial entities under both 1. and 2. can be of zero, one, two or three dimensions. We define:a(immaterial entity)[Definition: a is an immaterial entity = Def. a is an independent continuant that has no material entities as parts. (axiom label in BFO2 Reference: [028-001]) BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion. BFO2 Reference: continuant BFO2 Reference: continuantThe range for ‘t’ (as in all cases throughout this document unless otherwise specified) is: temporal region. [copied from inverse property 'has continuant part at some time'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'has continuant part at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'has continuant part@en'(x,y,t) b continuant_part_of c at t =Def. b is a part of c at t & t is a time & b and c are continuants. (axiom label in BFO2 Reference: [002-001]) continuant_part_of is antisymmetric. (axiom label in BFO2 Reference: [120-001]) continuant_part_of is reflexive (every continuant entity is a continuant_part_of itself). (axiom label in BFO2 Reference: [111-002]) continuant_part_of is transitive. (axiom label in BFO2 Reference: [110-001]) continuant_part_of satisfies unique product. (axiom label in BFO2 Reference: [122-001]) continuant_part_of satisfies weak supplementation. (axiom label in BFO2 Reference: [121-001]) if b continuant_part_of c at t and b is an independent continuant, then b is located_in c at t. (axiom label in BFO2 Reference: [047-002]) (forall (x t) (if (Continuant x) (continuantPartOfAt x x t))) // axiom label in BFO2 CLIF: [111-002] (forall (x y t) (if (and (continuantPartOfAt x y t) (IndependentContinuant x)) (locatedInAt x y t))) // axiom label in BFO2 CLIF: [047-002] (forall (x y t) (if (and (continuantPartOfAt x y t) (continuantPartOfAt y x t)) (= x y))) // axiom label in BFO2 CLIF: [120-001] (forall (x y t) (if (and (continuantPartOfAt x y t) (not (= x y))) (exists (z) (and (continuantPartOfAt z y t) (not (exists (w) (and (continuantPartOfAt w x t) (continuantPartOfAt w z t)))))))) // axiom label in BFO2 CLIF: [121-001] (forall (x y t) (if (exists (v) (and (continuantPartOfAt v x t) (continuantPartOfAt v y t))) (exists (z) (forall (u w) (iff (iff (continuantPartOfAt w u t) (and (continuantPartOfAt w x t) (continuantPartOfAt w y t))) (= z u)))))) // axiom label in BFO2 CLIF: [122-001] (forall (x y z t) (if (and (continuantPartOfAt x y t) (continuantPartOfAt y z t)) (continuantPartOfAt x z t))) // axiom label in BFO2 CLIF: [110-001] (iff (ImmaterialEntity a) (and (IndependentContinuant a) (not (exists (b t) (and (MaterialEntity b) (continuantPartOfAt b a t)))))) // axiom label in BFO2 CLIF: [028-001] part of continuant at some time c-has-part_st hasContinuantPartAt [copied from inverse property 'part of continuant at some time'] Mary’s arm continuant_part_of Mary in the time of her life prior to her operation [copied from inverse property 'part of continuant at some time'] the Northern hemisphere of the planet Earth is a part of the planet Earth at all times at which the planet Earth exists. b has_continuant_part c at t = Def. c continuant_part_of b at t. (axiom label in BFO2 Reference: [006-001]) Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'has continuant part at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'has continuant part@en'(x,y,t) [copied from inverse property 'part of continuant at some time'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'part of continuant at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'part of continuant@en'(x,y,t) [copied from inverse property 'part of continuant at some time'] BFO 2 Reference: Immaterial entities are in some cases continuant parts of their material hosts. Thus the hold of a ship, for example, is a part of the ship; it may itself have parts, which may have names (used for example by ship stow planners, customs inspectors, and the like). Immaterial entities under both 1. and 2. can be of zero, one, two or three dimensions. We define:a(immaterial entity)[Definition: a is an immaterial entity = Def. a is an independent continuant that has no material entities as parts. (axiom label in BFO2 Reference: [028-001]) [copied from inverse property 'part of continuant at some time'] BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion. [copied from inverse property 'part of continuant at some time'] BFO2 Reference: continuant [copied from inverse property 'part of continuant at some time'] BFO2 Reference: continuantThe range for ‘t’ (as in all cases throughout this document unless otherwise specified) is: temporal region. [copied from inverse property 'part of continuant at some time'] b continuant_part_of c at t =Def. b is a part of c at t & t is a time & b and c are continuants. (axiom label in BFO2 Reference: [002-001]) (iff (hasContinuantPartAt a b t) (continuantPartOfAt b a t)) // axiom label in BFO2 CLIF: [006-001] has continuant part at some time c-part-of-object_at [copied from inverse property 'has continuant part at all times'] b has_continuant_part c at t = Def. c continuant_part_of b at t. (axiom label in BFO2 Reference: [006-001]) forall(t) exists_at(y,t) -> exists_at(x,t) and 'part of continuant'(x,y,t) This is a binary version of a ternary time-indexed, instance level, relation. Unlike the rest of the temporalized relations which temporally quantify over existence of the subject of the relation, this relation temporally quantifies over the existence of the object of the relation. The relation is provided tentatively, to assess whether the GO needs such a relation. It is inverse of 'has continuant part at all times' [copied from inverse property 'has continuant part at all times'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'has continuant part at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'has continuant part@en(x,y,t)'. part of continuant at all times that whole exists c-has-part-object_at [copied from inverse property 'part of continuant at all times'] Mary’s arm continuant_part_of Mary in the time of her life prior to her operation [copied from inverse property 'part of continuant at all times'] the Northern hemisphere of the planet Earth is a part of the planet Earth at all times at which the planet Earth exists. forall(t) exists_at(y,t) -> exists_at(x,t) and 'has continuant part'(x,y,t) This is a binary version of a ternary time-indexed, instance level, relation. Unlike the rest of the temporalized relations which temporally quantify over existence of the subject of the relation, this relation temporally quantifies over the existence of the object of the relation. The relation is provided tentatively, to assess whether the GO needs such a relation. It is inverse of 'part of continuant at all times' [copied from inverse property 'part of continuant at all times'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'part of continuant at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'part of continuant@en(x,y,t)'. [copied from inverse property 'part of continuant at all times'] BFO 2 Reference: Immaterial entities are in some cases continuant parts of their material hosts. Thus the hold of a ship, for example, is a part of the ship; it may itself have parts, which may have names (used for example by ship stow planners, customs inspectors, and the like). Immaterial entities under both 1. and 2. can be of zero, one, two or three dimensions. We define:a(immaterial entity)[Definition: a is an immaterial entity = Def. a is an independent continuant that has no material entities as parts. (axiom label in BFO2 Reference: [028-001]) [copied from inverse property 'part of continuant at all times'] BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion. [copied from inverse property 'part of continuant at all times'] BFO2 Reference: continuant [copied from inverse property 'part of continuant at all times'] BFO2 Reference: continuantThe range for ‘t’ (as in all cases throughout this document unless otherwise specified) is: temporal region. [copied from inverse property 'part of continuant at all times'] b continuant_part_of c at t =Def. b is a part of c at t & t is a time & b and c are continuants. (axiom label in BFO2 Reference: [002-001]) has continuant part at all times that part exists a 'derives from' object property between an entity (in CLO case, cell line) and a disease in a patient where the entity is derived from some cell in the patient who has the disease. This is a short cut relation that represents: 'derived from' some (cell and ('part of' some 'organism' and ('has disease' some disease))) Yongqun He In most cases, the patient in the relation is used to refer human patient. However, an animal patient (or veterinary patient) can also be referred. derives from patient having disease an object property that specifies a cell line repository for a specifc cell line. SS, YH, UV, SS is in cell line repository an object property that represents a relation between a cell line cell and a disease. Asiyah Yu Lin, Yongqun He This object property is largely equivalent to the previous term 'is model for' (http://www.ebi.ac.uk/cellline#is_model_for). is disease model for a 'cell line cell derives from' object property between an entity (e.g., cell line cell in CLO) and an organism where the cell line cell is derived from some cell from the organism. In CLO, this is a short cut relation that represents: 'derived from' some (cell and ('part of' some organism)) derived from organism derived from cell has measurement unit label is about This document is about information artifacts and their representations is_about is a (currently) primitive relation that relates an information artifact to an entity. 7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. We will try to build it back up by elaborating the various subproperties that are more precisely defined. Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic. person:Alan Ruttenberg Smith, Ceusters, Ruttenberg, 2000 years of philosophy is about A person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance "Alan" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between "Alan" and the person that is being named. denotes is a primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically 2009-11-10 Alan Ruttenberg. Old definition said the following to emphasize the generic nature of this relation. We no longer have 'specifically denotes', which would have been primitive, so make this relation primitive. g denotes r =def r is a portion of reality there is some c that is a concretization of g every c that is a concretization of g specifically denotes r person:Alan Ruttenberg Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan denotes m is a quality measurement of q at t when q is a quality there is a measurement process p that has specified output m, a measurement datum, that is about q 8/6/2009 Alan Ruttenberg: The strategy is to be rather specific with this relationship. There are other kinds of measurements that are not of qualities, such as those that measure time. We will add these as separate properties for the moment and see about generalizing later From the second IAO workshop [Alan Ruttenberg 8/6/2009: not completely current, though bringing in comparison is probably important] This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details. -- From the second IAO workshop, various comments, [commented on by Alan Ruttenberg 8/6/2009] unit of measure is a quality, e.g. the length of a ruler. [We decided to hedge on what units of measure are, instead talking about measurement unit labels, which are the information content entities that are about whatever measurement units are. For IAO we need that information entity in any case. See the term measurement unit label] [Some struggling with the various subflavors of is_about. We subsequently removed the relation represents, and describes until and only when we have a better theory] a represents b means either a denotes b or a describes describe: a describes b means a is about b and a allows an inference of at least one quality of b We have had a long discussion about denotes versus describes. From the second IAO workshop: An attempt at tieing the quality to the measurement datum more carefully. a is a magnitude means a is a determinate quality particular inhering in some bearer b existing at a time t that can be represented/denoted by an information content entity e that has parts denoting a unit of measure, a number, and b. The unit of measure is an instance of the determinable quality. From the second meeting on IAO: An attempt at defining assay using Barry's "reliability" wording assay: process and has_input some material entity and has_output some information content entity and which is such that instances of this process type reliably generate outputs that describes the input. This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details. Alan Ruttenberg is quality measurement of relates a process to a time-measurement-datum that represents the duration of the process Person:Alan Ruttenberg is duration of inverse of the relation of is quality measurement of 2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship Person:Alan Ruttenberg is quality measured as relates a time stamped measurement datum to the time measurement datum that denotes the time when the measurement was taken Alan Ruttenberg has time stamp relates a time stamped measurement datum to the measurement datum that was measured Alan Ruttenberg has measurement datum is_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 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 is_specified_input_of is_specified_input_of some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. Alan Ruttenberg PERSON:Bjoern Peters is_specified_input_of has_specified_output 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 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 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 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 has category label A relation between a categorical measurement data item and the categorical label that indicates the value of that data item on the categorical scale. has category label specifies value of A relation between a value specification and an entity which the specification is about. specifies value of has value specification A relation between an information content entity and a value specification that specifies its value. PERSON: James A. Overton OBI has value specification a 'part of continuant at some time' relation that incides a genome belongs to a organism. Yongqun He, Bin Zhao is genome of organism a relation between a gene and the organism where this gene belongs to the organism in nature. It does not include a foreign gene that is transferred to an organism by a genetic engineering method. Oliver He, Yue Liu is gene of organism Bill Duncan <http://orcid.org/0000-0001-9625-1899> 2018-05-31T22:02:00Z produced by Bill Duncan <http://orcid.org/0000-0001-9625-1899> 2018-05-31T22:07:22Z provided by 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 at all times' 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 bearer_of is bearer of bearer of bearer_of is 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 has_participant is concretized as A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants. concretized by at some time http://purl.obolibrary.org/obo/obi.owl is concretized as concretizes A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant. http://purl.obolibrary.org/obo/obi.owl It is recommended to not use this if possible in OMRSE. According to OntoBee this relation has been obsoleted and replaced with 'concretization of at all times'. As of Dec. 2, 2013 iao-main still uses this relation. concretizes this catalysis function is a function of this enzyme a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. function_of is function of function 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 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 has role derives from this cell derives from this parent cell (cell division) this nucleus derives from this parent nucleus (nuclear division) a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'. derives_from derives from derives_from derives into this parent cell derives into this cell (cell division) this parent nucleus derives into this nucleus (nuclear division) a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'. derives_into derives into a relation between two independent continuants, the target and the location, in which the target is entirely within the location located in 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. has plasma membrane part x overlaps y if and only if there exists some z such that x has part z and z part of y http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) overlaps A is spatially_disjoint_from B if and only if they have no parts in common spatially disjoint from 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 develops from develops into 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. capable of c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. capable of part of x adjacent to y if and only if x and y share a boundary adjacent to 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 inverse of starts with Chris Mungall Allen starts Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p developmentally preceded by Inverse of developmentally preceded by developmentally succeeded by A mereological relationship or a topological relationship Chris Mungall Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships mereotopologically related to A relationship that holds between entities participating in some developmental process (GO:0032502) developmentally related to functionally related to x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). has developmental potential involving 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 x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y has potential to directly develop into This relation groups causal relations between material entities and causal relations between processes causally related to A relationship between a material entity and a process where the material entity has some causal role that influences the process causal agent in A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. causal relation between material entity and a process Inverse of 'causal agent in' has causal agent A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes. related via dependence to 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 (http://purl.obolibrary.org/obo/GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y) lacks_plasma_membrane_part has_disease_location has measurement value has specified numeric 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 numeric value has specified value A relation between a value specification and a literal. This is not an RDF/OWL object property. It is intended to link a value found in e.g. a database column of 'M' (the literal) to an instance of a value specification class, which can then be linked to indicate that this is about the biological gender of a human subject. OBI has specified value Bill Duncan <http://orcid.org/0000-0001-9625-1899> 2018-05-31T22:01:30Z date placed in storage entity Entity entity Julius Caesar Verdi’s Requiem the Second World War your body mass index BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) entity true continuant Continuant continuant An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] continuant true occurrent Occurrent occurrent An entity that has temporal parts and that happens, unfolds or develops through time. BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players. Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] occurrent true ic IndependentContinuant independent continuant a chair a heart a leg a molecule a spatial region an atom an orchestra. an organism the bottom right portion of a human torso the interior of your mouth A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] independent continuant true true true 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 true true true 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 true true true 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 true process Process process a process of cell-division, \ a beating of the heart a process of meiosis a process of sleeping the course of a disease the flight of a bird the life of an organism your process of aging. An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war) (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] process true disposition Disposition disposition an atom of element X has the disposition to decay to an atom of element Y certain people have a predisposition to colon cancer children are innately disposed to categorize objects in certain ways. the cell wall is disposed to filter chemicals in endocitosis and exocitosis 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 [89 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 true realizable RealizableEntity realizable entity the disposition of this piece of metal to conduct electricity. the disposition of your blood to coagulate the function of your reproductive organs the role of being a doctor the role of this boundary to delineate where Utah and Colorado meet A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] realizable entity true quality Quality quality the ambient temperature of this portion of air the color of a tomato the length of the circumference of your waist the mass of this piece of gold. the shape of your nose the shape of your nostril a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] quality true sdc SpecificallyDependentContinuant specifically dependent continuant Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key of one-sided specifically dependent continuants: the mass of this tomato of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates. the disposition of this fish to decay the function of this heart: to pump blood the mutual dependence of proton donors and acceptors in chemical reactions [79 the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction the pink color of a medium rare piece of grilled filet mignon at its center the role of being a doctor the shape of this hole. the smell of this portion of mozzarella A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] specifically dependent continuant true role Role role John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. the priest role the role of a boundary to demarcate two neighboring administrative territories the role of a building in serving as a military target the role of a stone in marking a property boundary the role of subject in a clinical trial the student role A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives. b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] role true 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 true gdc GenericallyDependentContinuant generically dependent continuant The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. the pdf file on your laptop, the pdf file that is a copy thereof on my laptop the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] generically dependent continuant true 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 true 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 true material MaterialEntity material entity a flame a forest fire a human being a hurricane a photon a puff of smoke a sea wave a tornado an aggregate of human beings. an energy wave an epidemic the undetached arm of a human being An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] material entity true 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 true 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 true anatomical structure true material anatomical entity true cell part true 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 true molecular entity Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. We are assuming that every molecular entity has to be completely connected by chemical bonds. This excludes protein complexes, which are comprised of minimally two separate molecular entities. We will follow up with Chebi to ensure this is their understanding as well molecular entity true atom A chemical entity constituting the smallest component of an element having the chemical properties of the element. atom true 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 true macromolecule A macromolecule is a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. polymer macromolecule true cell line cell A cultured cell that is part of a cell line - a stable and homogeneous population of cells with a common biological origin and propagation history in culture A cultured cell that is part of a cell line - a stable and homogeneous population of cells with a common biological origin and propagation history in culture Yongqun He, Matthew Brush, Sirarat Sarntivijai, Alexander Diehl, Jie Zheng, Yu Lin, Bjoern Peters A 'cell line cell' is a part of a cell line established through the passaging/selection of a primary cultured cells or the experimental modification of an existing cell line. New types of cell line cells are established after sufficient passaging of a primary culture to establish a stable and homogenous population that qualifies as a line (typically 1-20 passages), or following some spontaneous or experimental modification that confers novel characteristics to an existing line. A cell line cell typically has mutations of five or more genes compared to the original cell that derives the cell line cell. Some gene mutations may turn on some oncogenes. Cell line cells can be in active culture, stored in a quiescent state for future use (e.g. frozen in liquid nitrogen), or applied in experimental procedures. cell line cell true a role that inheres in a cell line repository organization. SS, YH cell line repository role true an organization that serves as a repository of cell lines. SS, YH cell line repository true cell line He, Tong-Chuan, et al., Identification of c-MYC as a target of the APC pathway. Science 281.5382 (1998): 1509-1512.: "To evaluate the transcriptional effects of APC, we studied a human colorectal cancer cell line (HT29-APC) containing a zinc-inducible APC gene and a control cell line (HT29–β-Gal) containing an analogous inducible lacZ gene". Note that common usage in the literature is often of the form "a human colorectal cancer cell line", as seen above. But such references to studies in "a line" refer to the fact that discrete populations of cells that are input into culturing or experiments, not an entire lineage of cells. It is these discrete populations that we refer to as 'cell lines'. A cultured cell population that represents a genetically stable and homogenous population of cultured cells that shares a common propagation history (i.e. has been successively passaged together in culture). A cultured cell population that represents a genetically stable and homogenous population of cultured cells that shares a common propagation history (i.e. has been successively passaged together in culture). In the spring of 2013, a working group comprised of domain experts and representatives from CLO, OBI, CL, and ReO worked to establish a consensus model and definitions of cultured cells across these efforts. This included a careful characterization of how the term 'cell line' should be defined and applied. Notes about this work and its outcomes can be found on the CLO wiki here: http://code.google.com/p/clo-ontology/wiki/Cell_Lines MB, SS, JZ, MAH, BP, CS, YH The term 'line' is used when a culture has undergone an intentional experimental process to establish a more uniform and stable population of cells (see 'establishing cell line'). This will require one or more passages, but may involve additional selection processes. Through such passaging and/or selection processes, the resulting 'line' attains some level of genetic stability and compositional homogeneity which is typically absent in primary cultures. Because of their relative homogeneity, ‘lines’ are capable of being characterized and stably propagated over a period of time. A new *type* of cell line can be established not only through the passaging/selection of a primary culture, but also through experimental modifications of existing lines (e.g. immortalization, stable genetic modifications, drug selection for a resistant subset, etc.). The definition provided here establishes the 'scale' of cell populations that qualify as cell lines - specifically those with a shared propagation history in culture. In this way, the 'cell line' class demarcates populations that represent what researchers actually use in the practice of science - e.g. as inputs to culturing, experimentation, and sharing. The definition is such that cell lines will exhibit important attributes. For example, they will have a relatively homogenous cell type composition as they have experienced similar selective pressures due to their continuous co-propagation. In addition, these populations can also be characterized by a passage number, again owing to their common passaging history.  As defined here, 'cell line' can refer to a population of cells in active culture, applied experimentally, or stored in a quiescent state for future use. cell line true LPC-1021 only one copy of the SMN2 gene; homozygous for deletion of exons 7 and 8 of the SMN1 gene Chao Pang, Oliver He, Daniel Cooper GM00232 http://lincsportal.ccs.miami.edu/cells/#/view/LPC-1021 http://web.expasy.org/cellosaurus/CVCL_Y965 GM-232 SPINAL MUSCULAR ATROPHY I; SMA1 Cell center: NeuroLINCS Cell provider: Coriell Cell Repository; Cell provider catalog number: Coriell Cell Repository GM00232 cell OMIM: 253300 RRID:CVCL_Y965 true A cell line cell that is cultured in vitro and possesses two capabilities: (1) it can self-renew, which means that it can divide indefinitely while remaining in an undifferentiated state; and (2) it is pluripotent or multipotent, which means that it can differentiate to form a specialized cell type. Yongqun He, Sirarat Sarntivijai, Alexander Diehl WEB: https://en.wikipedia.org/wiki/Stem-cell_line While stem cells hold great promise for biomedical research, the in vitro propagation and maintenance of these cells in an undifferentiated state is essential. Reference: https://www.atcc.org/~/media/7E031EF950594BC3B85A411AE1DC9684.ashx stem cell line cell true A stem cell line cell that is derived from mouse. YH mouse stem cell line cell true A mouse stem cell line cell that is derived from a mouse neural progenitor cell and capable of differentiation in vitro. YH immortalized mouse neural progenitor cell mouse neural progenitor cell line cell true 1353 http://web.expasy.org/cellosaurus/CVCL_4511 http://www.sigmaaldrich.com/catalog/product/sigma/07062902 An immortalised mouse neural progenitor cell line cell that is capable of differentiation in vitro and is established by retorviral-mediated transduction of the avian myc oncogene into mitotic progenitor cells of neonatal mouse cerrebellum. Mouse strain CD1 x C57BL/6. BAO, YH C17.2 cell BAO: BAO_0030046 true YH, AD https://en.wikipedia.org/wiki/Embryonic_stem_cell A stem cell line cell that is dervied from an embryotic stem cell, a pluripotent stem cell derived from the inner cell mass of a blastocyst, an early-stage perimplantation embryo. ES cell line cell embryonic stem cell line cell true YH, AD hES cell line cell https://en.wikipedia.org/wiki/Embryonic_stem_cell An embryonic stem cell line cell that is dervied from a cell in human embryo. hESC line cell human embryonic stem cell line cell true YH, AD https://discovery.lifemapsc.com/stem-cell-differentiation/in-vitro-cells/inner-cell-mass-homo-sapiens-line-h1-wa01-wicell-research-institute-inc H1-hESC A human ES cell line cell that expresses cell surface markers specific to undifferentiated nonhuman primate ES and human EC cells: : stage-specific embryonic antigen (SSEA)–3, SSEA-4, TRA-l-60, TRA-1- 81, and alkaline phosphatase. It has a normal 46, XY karyotype, O+ blood type. Teratomas are formed upon cell injection into SCID mice. These teratomas include cells from all three germ layers. Line H1 cell true Oliver He A primary cultured cell that is derived from fibroblast cell in vivo primary cultured fibroblast cell true Oliver He A primary cultured fibroblast cell that is from human primary cultured human fibroblast cell true YH, AD https://en.wikipedia.org/wiki/Stem-cell_line A stem cell line cell that is multipotent and is isolated and prepared from an juvenile or adult tissue. adult stem cell line cell true YH, AD https://en.wikipedia.org/wiki/Stem-cell_line An adult stem cell line cell that is isolated and prepared using bone marrow tissue and is able to generate all cells of the immune system and all blood cell types. Of the types of adult stem cells have successfully been isolated and identified, only mesenchymal stem cells can successfully be grown in culture for long periods of time. Hematopoietic stem cells are difficult to grow and propagate in vitro.[4] Identifying methods for maintaining hematopoietic stem cells in vitro is an active area of research. Reference: https://en.wikipedia.org/wiki/Stem-cell_line hematopoetic stem cell line cell true YH https://en.wikipedia.org/wiki/Stem-cell_line An adult stem cell line cell that is isolated and prepared using umbilical cord blood, amniotic fluid, and adipose tissue and can generate a number of cell types, including osteoblasts, chondrocytes, and adipocytes. MSC line cell mesenchymal stem cell line cell true YH, AD https://en.wikipedia.org/wiki/Stem-cell_line A mesenchymal stem cell line cell that is isolated and prepared using umbilical cord blood. umbilical cord mesenchymal stem cell line cell true YH, AD https://en.wikipedia.org/wiki/Embryonic_stem_cell https://en.wikipedia.org/wiki/Induced_pluripotent_stem_cell https://www.ncbi.nlm.nih.gov/pubmed/16904174 A stem cell line cell that is pluripotent and is generated from an adult somatic cell. iPS cell iPSC induced pluripotent stem cell line cell true YH, AD An induced pluripotent stem cell line cell that is derived from a human cell. human iPS cell line cell human induced pluripotent stem cell line cell true LES-1001 LINCS team, YH http://lincsportal.ccs.miami.edu/cells/#/view/LES-1001 https://discovery.lifemapsc.com/stem-cell-differentiation/in-vitro-cells/inner-cell-mass-homo-sapiens-line-h9-wa09-wicell-research-institute-inc This human ES cell line expresses cell surface markers specific to undifferentiated nonhuman primate ES and human EC cells: stage-specific embryonic antigen (SSEA)–3, SSEA-4, TRA-l-60, TRA-1- 81, and alkaline phosphatase. It has a normal 46, XX karyotype. Teratomas are formed upon cell injection into SCID mice. These teratomas include cells from all three germ layers. H9 ES cell true LES-1002 LINCS team, YH http://lincsportal.ccs.miami.edu/cells/#/view/LES-1002 https://grants.nih.gov/stem_cells/registry/current.htm?id=34 HUES 3 HUES3 ES cell true YH mES cell line cell https://en.wikipedia.org/wiki/Embryonic_stem_cell A embryotic stem cell line cell that is dervied from a cell in mouse embryo. mESC line cell mouse embryonic stem cell line cell true YH, AD https://en.wikipedia.org/wiki/Somatic_cell_nuclear_transfer#Stem_cell_research A stem cell line cell that is dervied from using the somatic cell nuclear transfer method. SCNT-derived stem cell line cell somatic cell nuclear transfer-derived stem cell line cell true YH https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3772789/ a human embryonic stem cell line cell that is derived by somatic cell nuclear transfer human embryonic stem cell line cell derived by SCNT human embryonic stem cell line cell derived by somatic cell nuclear transfer true true human fibroblast-iPS cell line cell human fibroblast-induced pluripotent stem cell line cell true Oliver He A primary cultured cell that is derived from in vivo connective tissue cell primary cultured connective tissue cell true LPC-1014 Donor subject has two copies of the SMN2 and is heterozygous for deletion of exons 7 and 8 in the SMN1 gene Daniel Cooper, Oliver He Cell center: NeuroLINCS Cell provider: Coriell Cell Repository; Cell provider catalog number: Coriell Cell Repository GM03814 cell true LPC-1015 Unclassified Daniel Cooper, Oliver He Cell center: NeuroLINCS Cell provider: Coriell Cell Repository; Cell provider catalog number: Coriell Cell Repository GM02183 cell true LPC-1016 CAG length Allele 1 = 18; Allele 2 = 17 Daniel Cooper, Oliver He Cell center: NeuroLINCS Cell provider: Coriell Cell Repository; Cell provider catalog number: Coriell Cell Repository ND30625 cell true LPC-1017 C9orf72; repeat number not indicated Daniel Cooper, Oliver He Cell center: NeuroLINCS Cell provider: Wasington University; Cell provider catalog number: Wasington University F09128 cell true LPC-1018 Daniel Cooper, Oliver He Cell center: NeuroLINCS F09229 cell true LPC-1019 C9orf72; repeat number not indicated Daniel Cooper, Oliver He Cell center: NeuroLINCS Cell provider: Wasington University; Cell provider catalog number: Wasington University F10-330 cell true LPC-1020 C9orf72; repeat number not indicated Daniel Cooper, Oliver He Cell center: NeuroLINCS Cell provider: Wasington University; Cell provider catalog number: Wasington University F09152 cell true LPC-1022 Daniel Cooper, Oliver He Cell center: NeuroLINCS Cell provider: Coriell Cell Repository; Cell provider catalog number: Coriell Cell Repository 83 Fibroblast cell true LPC-1023 donor subject has 2 copies of the SMN2 gene and is homozygous for deletion of exons 7 and 8 of the SMN1 gene Daniel Cooper, Oliver He Cell center: NeuroLINCS Cell provider: Coriell Cell Repository; Cell provider catalog number: Coriell Cell Repository GM09677 cell true LPC-1024 Daniel Cooper, Oliver He Cell center: DToxS Cell provider: ISMMS; Cell provider catalog number: ISMMS MSF01 cell true LPC-1025 Daniel Cooper, Oliver He Cell center: DToxS Cell provider: ISMMS; Cell provider catalog number: ISMMS MSF02 cell true LPC-1026 Daniel Cooper, Oliver He Cell center: DToxS Cell provider: ISMMS; Cell provider catalog number: ISMMS MSF03 cell true LPC-1028 Daniel Cooper, Oliver He Cell center: DToxS Cell provider: ISMMS; Cell provider catalog number: ISMMS MSF05 cell true LPC-1029 Daniel Cooper, Oliver He Cell center: DToxS Cell provider: ISMMS; Cell provider catalog number: ISMMS MSF06 cell true LPC-1031 Daniel Cooper, Oliver He Cell center: DToxS Cell provider: ISMMS; Cell provider catalog number: ISMMS MSF08 cell true LPC-1032 Daniel Cooper, Oliver He Cell center: DToxS Cell provider: ISMMS; Cell provider catalog number: ISMMS MSF09 cell true LPC-1033 Daniel Cooper, Oliver He Cell center: DToxS Cell provider: ISMMS; Cell provider catalog number: ISMMS MSF10 cell true LPC-1044 Daniel Cooper, Oliver He Cell center: NeuroLINCS Cell provider: Coriell Cell Repository; Cell provider catalog number: Coriell Cell Repository GM05400 cell true LPC-1054 ALS-Sporadic Daniel Cooper, Oliver He Cell center: NeuroLINCS W14-C146 cell true LPC-1055 ALS-SOD1 Daniel Cooper, Oliver He Cell center: NeuroLINCS F13-C004 cell true LPC-1056 ALS-Sporadic Daniel Cooper, Oliver He Cell center: NeuroLINCS W15-C166 cell true LPC-1057 ALS-SOD1 Daniel Cooper, Oliver He Cell center: NeuroLINCS SAB-701-022 cell true LPC-1058 ALS-Sporadic Daniel Cooper, Oliver He Cell center: NeuroLINCS W14-C138 cell true LPC-1059 ALS-Sporadic Daniel Cooper, Oliver He Cell center: NeuroLINCS W14-C152 cell true LSC-1002 Donor subject has two copies of the SMN2 and is heterozygous for deletion of exons 7 and 8 in the SMN1 gene mTeSR1, Growth Factor Reduced Matrigel Daniel Cooper, Oliver He Cell center: NeuroLINCS Cell provider: Cedars-Sinai Stem Cell Core Laboratory; Cell provider catalog number: CS14iCTR-n6 CS14iCTR-n6 cell true LSC-1003 Unclassified mTeSR1, Growth Factor Reduced Matrigel Daniel Cooper, Oliver He Cell center: NeuroLINCS Cell provider: Cedars-Sinai Stem Cell Core Laboratory; Cell provider catalog number: CS83iCTR-33n1 CS83iCTR-33n1 cell true LSC-1004 CAG length Allele 1 = 18; Allele 2 = 17 mTeSR1, Growth Factor Reduced Matrigel Daniel Cooper, Oliver He Cell center: NeuroLINCS Cell provider: Cedars-Sinai Stem Cell Core Laboratory; Cell provider catalog number: CS25iCTR-18n2 CS25iCTR-18n2 cell true LSC-1005 C9orf72; repeat number not indicated mTeSR1, Growth Factor Reduced Matrigel Daniel Cooper, Oliver He Cell center: NeuroLINCS Cell provider: Cedars-Sinai Stem Cell Core Laboratory; Cell provider catalog number: CS28iALS-n2A CS28iALS-n2A cell true LSC-1006 C9orf72; repeat number not indicated mTeSR1, Growth Factor Reduced Matrigel Daniel Cooper, Oliver He Cell center: NeuroLINCS Cell provider: Cedars-Sinai Stem Cell Core Laboratory; Cell provider catalog number: CS29iALS-n1N CS29iALS-n1N cell true LSC-1007 C9orf72; repeat number not indicated mTeSR1, Growth Factor Reduced Matrigel Daniel Cooper, Oliver He Cell center: NeuroLINCS Cell provider: Cedars-Sinai Stem Cell Core Laboratory; Cell provider catalog number: CS30iALS-n1N CS30iALS-n1N cell true LSC-1008 C9orf72; repeat number not indicated mTeSR1, Growth Factor Reduced Matrigel Daniel Cooper, Oliver He Cell center: NeuroLINCS Cell provider: Cedars-Sinai Stem Cell Core Laboratory; Cell provider catalog number: CS52iALS-n6A CS52iALS-n6A cell true LSC-1009 only one copy of the SMN2 gene; homozygous for deletion of exons 7 and 8 of the SMN1 gene mTeSR1, Growth Factor Reduced Matrigel Daniel Cooper, Oliver He Cell center: NeuroLINCS Cell provider: Cedars-Sinai Stem Cell Core Laboratory; Cell provider catalog number: CS32iSMA-n3 CS32iSMA-n3 cell true LSC-1011 Unknown mTeSR1, Growth Factor Reduced Matrigel Daniel Cooper, Oliver He Cell center: NeuroLINCS Cell provider: Cedars-Sinai Stem Cell Core Laboratory; Cell provider catalog number: CS83iSMA-n5 CS83iSMA-n5 cell true LSC-1012 donor subject has 2 copies of the SMN2 gene and is homozygous for deletion of exons 7 and 8 of the SMN1 gene mTeSR1, Growth Factor Reduced Matrigel Daniel Cooper, Oliver He Cell center: NeuroLINCS Cell provider: Cedars-Sinai Stem Cell Core Laboratory; Cell provider catalog number: CS77iSMA-n5 CS77iSMA-n5 cell true LSC-1013 none/healthy human pluripotent stem cell medium, includign mTeSR Daniel Cooper, Oliver He Cell center: DToxS MSN01-3 cell true LSC-1014 none/healthy human pluripotent stem cell medium, includign mTeSR Daniel Cooper, Oliver He Cell center: DToxS MSN03-7 cell true LSC-1015 none/healthy human pluripotent stem cell medium, includign mTeSR Daniel Cooper, Oliver He Cell center: DToxS MSN05-1 cell true LSC-1016 none/healthy human pluripotent stem cell medium, includign mTeSR Daniel Cooper, Oliver He Cell center: DToxS MSN06-7 cell true LSC-1017 none/healthy human pluripotent stem cell medium, includign mTeSR Daniel Cooper, Oliver He Cell center: DToxS MSN02-4 cell true LSC-1018 none/healthy human pluripotent stem cell medium, includign mTeSR Daniel Cooper, Oliver He Cell center: DToxS MSN08-13 cell true LSC-1019 none/healthy human pluripotent stem cell medium, includign mTeSR Daniel Cooper, Oliver He Cell center: DToxS MSN09-4 cell true LSC-1020 none/healthy human pluripotent stem cell medium, includign mTeSR Daniel Cooper, Oliver He Cell center: DToxS MSN10-1 cell true LSC-1021 Daniel Cooper, Oliver He Cell center: BROAD_T FIBRNPC cell true LSC-1022 Daniel Cooper, Oliver He Cell center: NeuroLINCS CS14isALS-Tn16 cell true LSC-1023 Daniel Cooper, Oliver He Cell center: NeuroLINCS CS04iALS-SOD1H44Rn3 cell true LSC-1024 Daniel Cooper, Oliver He Cell center: NeuroLINCS CS00iCTR-n2 cell true LSC-1025 Daniel Cooper, Oliver He Cell center: NeuroLINCS CS29iALS-C9n1 cell true LSC-1026 Daniel Cooper, Oliver He Cell center: NeuroLINCS CS30iALS-C9n1 cell true LSC-1027 Daniel Cooper, Oliver He Cell center: NeuroLINCS CS166isALS-Tn2 cell true LSC-1028 Daniel Cooper, Oliver He Cell center: NeuroLINCS CS22iALS-SOD1I113Tn2 cell true LSC-1029 Daniel Cooper, Oliver He Cell center: NeuroLINCS CS138isALS-Tn1 cell true LSC-1030 Daniel Cooper, Oliver He Cell center: NeuroLINCS CS152isALS-Tn2 cell true LSC-1031 Daniel Cooper, Oliver He Cell center: NeuroLINCS CS28iALS-C9n2 cell true LSC-1032 Daniel Cooper, Oliver He Cell center: NeuroLINCS CS52iALS-C9n6 cell true LSC-1033 Daniel Cooper, Oliver He Cell center: NeuroLINCS CS11iALS-SOD1I113Tn10 cell true cell PMID:18089833.Cancer Res. 2007 Dec 15;67(24):12018-25. "...Epithelial cells were harvested from histologically confirmed adenocarcinomas .." A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. 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 cell cell type EFO_URI: http://www.ebi.ac.uk/efo/EFO_0000324 true true primary cultured cell A cultured cell that is freshly isolated from a organismal source, or derives in culture from such a cell prior to the culture being passaged. primary cultured cell true 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 true true neuronal receptor cell (sensu Animalia) cell neuronal receptor cell true true cell migratory cranial neural crest cell true cultured cell 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 true cell migratory trunk neural crest cell true germline stem cell cell germ line stem cell true true FMA:72290 MA:0002765 VHOG:0001531 ncithesaurus:Spermatogenic_Cell cell male germ cell true cell male germ line stem cell true true Female germ cell is a germ cell that supports female gamete production. MA:0000388 VHOG:0001530 ncithesaurus:Egg cell female germ cell true cell female germ line stem cell true true A cell that will develop into a neuron often after a migration phase. BTO:0000930 FBbt:00005146 FMA:70563 cell neuroblast true true 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 true A stem cell that self-renews as well as give rise to a single mature cell type. FMA:70569 unipotent stem cell unipotential stem cell cell single fate stem cell true cell epithelial fate stem cell true 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 true true 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 true Neural stem cell is characterized as an undifferentiated cell that originates from the neuroectoderm and has the capacity both to perpetually self-renew without differentiating and to generate multiple types of lineage-restricted progenitors. BTO:0002881 CALOHA:TS-2360 FMA:86684 NSC neural stem cell cell neuronal stem cell true true 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 true true A stem cell from which all cells of the body can form. FMA:84790 totipotential stem cell cell totipotent stem cell true 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 true 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 true 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. James Malone Tomasz Adamusiak mouse embryonic fibroblast primary dermal fibroblast BTO:0000452 CL:0000057 NIFSTD:nlx_cell_20090201 BTO:0000452 CALOHA:TS-0362 FMA:63877 VHOG:0001482 cell A connective tissue cell which secretes an extracellular matrix rich in collagen and other macromolecules. A connective-tissue cell of mesenchymal origin that secretes proteins and especially molecular collagen from which the extracellular fibrillar matrix of connective tissue forms. A large, flat, oval cell found in connective tissue and responsible for the formation of fibers. These cells may be vimentin-positive, fibronectin-positive, fsp1-positive, MMP-1-positive, collagen I-positive, collagen III-positive, and alpha-SMA-negative. fibroblast EFO_URI: http://www.ebi.ac.uk/efo/EFO_0000496 URI: http://www.ebi.ac.uk/cellline#fibroblast true 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 true cell duct epithelial cell true true cell branched duct epithelial cell true cell columnar/cuboidal epithelial cell true true CALOHA:TS-1249 cell squamous epithelial cell true cell stratified epithelial cell true true A cell which moves among different tissues of the body, via blood, lymph, or other medium. cell circulating cell true BTO:0004299 lung epithelial cell cell epithelial cell of lung true cell germ line stem cell (sensu Vertebrata) true FBbt:00004861 cell germ line stem cell (sensu Nematoda and Protostomia) true FBbt:00004929 cell male germ line stem cell (sensu Nematoda and Protostomia) true true FBbt:00004873 cell female germ line stem cell (sensu Nematoda and Protostomia) true true spermatogonial stem cell cell male germ line stem cell (sensu Vertebrata) true true cell female germ line stem cell (sensu Vertebrata) true true A specialized epithelial cell involved in sensory perception. Restricted to special sense organs of the olfactory, gustatory, and vestibulocochlear receptor systems; contain sensory cells surrounded by supportive, non-receptive cells. neuroepithelial cell BTO:0004301 cell The term "neuroepithelial cell" is used to describe both this cell type and neurecto-epithelial cell (CL:0000710). sensory epithelial cell true true true Any neuron having a sensory function; an afferent neuron conveying sensory impulses. BTO:0001037 FBbt:00005124 FMA:84649 WBbt:0005759 cell sensory neuron true FMA:72552 cell of surface ectoderm surface ectoderm cell cell surface ectodermal cell true Ectoderm destined to be nervous tissue. neurectoderm cell cell neurectodermal cell true 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 true true true A specialized epithelial cell that is capable of synthesizing and secreting certain biomolecules. CALOHA:TS-2085 FMA:86494 cell glandular epithelial cell true true true A cell that specializes in controlled release of one or more substances. BTO:0003659 FMA:86916 cell secretory cell true A cell of an exocrine gland; i.e. a gland that discharges its secretion via a duct. FMA:16014 cell exocrine cell true A cell whose primary function is to shorten. cell contractile cell true 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 true true true true A somatic cell located in skeletal muscle. BTO:0004392 CALOHA:TS-2158 FMA:9727 skeletal muscle cell cell cell of skeletal muscle true cell receptor cell true A cell specialized to detect chemical substances and relay that information centrally in the nervous system. Chemoreceptors may monitor external stimuli, as in taste and olfaction, or internal stimuli, such as the concentrations of oxygen and carbon dioxide in the blood. cell chemoreceptor cell true A cell type found in the spherical or ovoid clusters of receptor cells found mainly in the epithelium of the tongue and constituting the end organs of the sense of taste. FMA:67910 taste bud cell cell taste receptor cell true true true true true true A cell whose function is determined by the generation or the reception of an electric signal. cell electrically active cell true A cell that moves by its own activities. cell motile cell true A cell of the outer of the three germ layers of the embryo. FMA:72549 ectoderm cell cell ectodermal cell true A cell of the middle germ layer of the embryo. FMA:72554 mesoblast mesoderm cell cell mesodermal cell true A cell of the inner of the three germ layers of the embryo. FMA:72555 endoderm cell cell endodermal cell true cell keratinizing barrier epithelial cell true true true cell stratified squamous epithelial cell true true cell eukaryotic cell true An epithelial cell found in the trachea. CL:1000474 FMA:74793 tracheocyte cell This class is for the vertebrate tracheal structure. For the analagous insect cell type, see 'respiratory tube epithelial cell' tracheal epithelial cell true cell keratin accumulating cell true An epidermal cell which synthesizes keratin and undergoes a characteristic change as it moves upward from the basal layers of the epidermis to the cornified (horny) layer of the skin. Successive stages of differentiation of the keratinocytes forming the epidermal layers are basal cell, spinous or prickle cell, and the granular cell. CL:0002185 BTO:0000667 CALOHA:TS-0500 FMA:62879 keratinized cell of epidermis malpighian cell cell Keratinocytes are reportedly CDw210a-negative, CDw210b-positive, CD281-positive, CD282-positive, CD285-positive, IL22Ra1-positive, Human keratinocytes are reportedly capable of secreting BD-2, BD-3, hCAP-18, CXCL1, CXCL5, CXCL8, elafin, MMP-3, NGAL, PDGF-A, S100A7, S100A8, and S100A9. Transcription factors: STAT3-positive. keratinocyte true true cell metanephric mesenchyme stem cell true A cell that is specialised to accumulate a particular substance(s). cell stuff accumulating cell true 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 true true An embryonic cell that develops into a nerve cell or neuron. cell neuroblast (sensu Vertebrata) true neuroblast cell neuroblast (sensu Nematoda and Protostomia) true A specialized mesenchymal cell that resides in the dermal papilla located at the bottom of hair follicles. This cell plays a pivotal roles in hair formation, growth, and cycling. cell Are these really all stem cells? hair follicle dermal papilla cell true cell extraembryonic cell true true A cell of the outer layer of a blastula that gives rise to the ectoderm after gastrulation. cell epiblast cell true ncithesaurus:Blastemal_Cell blastema cell cell blastemal cell true A multifate stem cell found in skeletal muscle than can differentiate into many different cell types, including muscle. Distinct cell type from satellite cell. FMA:86767 cell Multi-potency demonstrated ex vivo. At the time of writing, it is unclear whether the endogenous population differentiates into multiple cell types in vivo. multi-potent skeletal muscle stem cell true true cell hair matrix stem cell true cell stratified epithelial stem cell true An epithelial cell of the integument (the outer layer of an organism). CL:1000396 BTO:0001470 CALOHA:TS-0283 FMA:62411 cell of epidermis epithelial cell of skin cell epidermal cell true cell tracheoblast true cell nephrogenic mesenchyme stem cell true A cell whose function is determined by its response to an electric signal. cell electrically responsive cell true A cell that initiates an electrical signal and passes that signal to another cell. cell electrically signaling cell true FBbt:00005148 cell neuroepidermoblast true An epithelial fate stem cell found in flatworms. BTO:0003039 cell seam cell true FBbt:00004903 cell follicle stem cell true FBbt:00005147 cell neuroglioblast true true FBbt:00005149 cell ganglion mother cell true A neuron which conveys sensory information centrally from the periphery. FMA:87653 input neuron cell afferent neuron true The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system. BTO:0000938 CALOHA:TS-0683 FBbt:00005106 FMA:54527 VHOG:0001483 WBbt:0003679 nerve cell cell These cells are also reportedly CD4-negative and CD200-positive. They are also capable of producing CD40L and IFN-gamma. neuron neuron true true true cell animal cell true 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 true experimentally modified cell in vitro 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 true true The reproductive cell in multicellular organisms. BTO:0000535 VHOG:0001534 WBbt:0006796 cell germ cell true An elongated, spindle-shaped, cell that is located between the basal lamina and the plasmalemma of a muscle fiber. These cells are mostly quiescent, but upon activation they divide to produce cells that generate new muscle fibers. cell Skeletal muscle satellite cells are not traditionally referred to as myoblasts. They are a heterogeneous population whose division, following activiation, contributes to the formation of skeletal muscle fibers and to maintenance of the skeletal muscle statelite cell population. skeletal muscle satellite cell true true Undifferentiated; mitotic stem cell for other epithelial cell types; rounded or elliptical with little cytoplasm and few organelles; contain cytokeratin intermediate filament. BTO:0000939 FMA:62516 cell basal cell true cell neuroglioblast (sensu Nematoda) true A non-terminally differentiated cell that is capable of developing into a muscle cell. cell muscle precursor cell true true Epithelial cells derived from neural plate and neural crest. neuroepithelial cell BTO:0004301 FMA:70557 cell The term "neuroepithelial cell" is used to describe both this cell type and sensory epithelial cell (CL:0000098). neurecto-epithelial cell true true 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 true true A cell of a hematopoietic lineage. BTO:0000574 CALOHA:TS-2017 FMA:70366 FMA:83598 haematopoietic cell haemopoietic cell hemopoietic cell cell hematopoietic cell true true A hematopoietic stem cell that has plasma membrane part Kit-positive, SCA-1-positive, CD150-positive and CD34-negative. LSK stem cell Sca1-positive hematopoietic stem cell cell Cell markers are associated with mouse hematopoietic stem cell. Originally described in the dendritic cell ontology (DC_CL:0000043)(PMID:19243617). Kit and Sca1-positive hematopoietic stem cell true 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 true 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 true true A connective tissue cell found in bone. adiehl 2011-11-16T04:28:16Z cell bone cell true A hematopoietic stem cell capable of rapid replenishment of myeloerythroid progenitors and limited self renewal capability. This cell is Kit-positive, Sca1-positive, CD34-positive, CD150-positive, and is Flt3-negative. tmeehan 2010-01-08T09:19:25Z ST stem cell ST-HSC cell Markers are associated with mouse cells. These cells are also reportedly CD11b-low and CD90-low. short term hematopoietic stem cell true A hematopoietic stem cell with long term self renewal capability. This cell is Kit-positive, Sca1-positive, CD150-positive, CD90-low, CD34-negative and Flt3-negative. tmeehan 2010-01-08T09:19:28Z LT stem cell LT-HSC cell Markers are associated with mouse cells. long term hematopoietic stem cell true An epithelial cell derived from endoderm. tmeehan 2010-06-29T03:38:14Z FMA:69075 cell endo-epithelial cell true true An epithelial cell derived from ectoderm. tmeehan 2010-06-29T03:38:22Z FMA:69074 cell ecto-epithelial cell true true Epithelial cell derived from mesoderm or mesenchyme. tmeehan 2010-06-29T03:49:14Z FMA:69076 epithelial mesenchymal cell cell meso-epithelial cell true true 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 true Epithelial cells derived from general body ectoderm and ectoderm placodes. tmeehan 2010-08-26T08:31:08Z FMA:70556 cell general ecto-epithelial cell true An epithelial cell found in the lining of the stomach. tmeehan 2010-08-25T03:22:08Z CL:1000399 FMA:62948 cell epithelial cell of stomach true A mucous cell in the epithelium of the stomach. tmeehan 2010-08-25T03:38:51Z CL:1000404 FMA:63464 cell mucous cell of stomach true A stomach epithelial cell that is olumnar in form with a few short apical microvilli; relatively undifferentiated mitotic cell from which other types of gland are derived; few in number, situated in the isthmus region of the gland and base of the gastric pit. tmeehan 2010-08-25T03:57:08Z CL:1000400 FMA:62953 cell stem cell of gastric gland true true true A basally situated, mitotically active, columnar-shaped keratinocyte attached to the basement membrane. tmeehan 2010-08-26T03:12:49Z CL:1000439 FMA:70571 cell basal cell of epidermis true true true A stem cell that can give rise to the cells of the liver. tmeehan 2010-08-30T02:00:42Z FMA:86577 cell hepatic stem cell true A transient hepatic stem cell observed after liver injury with a high nuclear to cytoplasm ratio that can differentiate into mature hepatocytes and bile duct cells. Arises from more than one tissue. tmeehan 2010-08-30T02:01:49Z CL:1000036 BTO:0004270 FMA:86576 hepatic oval cell cell hepatic oval stem cell true An epithelial cell of the tracheobronchial tree. tmeehan 2010-09-02T02:09:14Z CL:1000407 FMA:66816 cell epithelial cell of tracheobronchial tree true An epithelial cell of the prostate. tmeehan 2010-09-07T01:49:29Z CL:1000295 CL:1000408 FMA:256163 FMA:66817 prostate epithelial cell cell epithelial cell of prostate true A hematopoeitic stem cell found in the blood. Normally found in very limited numbers in the peripheral circulation (less than 0.1% of all nucleated cells). tmeehan 2010-09-07T03:57:09Z BTO:0002669 FMA:86711 PBSC cell peripheral blood stem cell true true A pluripotent stem cell has the ability to form cells from all three germ layers (ectoderm, mesoderm, and endoderm). However, unlike totipotent stem cells, they cell can not generate all the cells of the whole organism such as placenta. tmeehan 2010-09-07T04:26:06Z FMA:70570 cell pluripotent stem cell true A stem cell that can differentiate into a cardiac myocyte. tmeehan 2010-09-07T04:40:32Z FMA:75620 cell primitive cardiac myocyte true true A cell that is found in a zone occupying the bottom region of the crypt; provide the source of most of the cell types of the intestinal epithelium; proliferate by mitotic division; differentiates into columnar or goblet cells. tmeehan 2010-09-08T09:21:22Z FMA:63379 stem cell of intestinal crypt of Lieberkuhn cell intestinal crypt stem cell true true An epithelial cell of the musculomembranous digestive tube extending from the mouth to the anus. tmeehan 2010-09-08T09:26:53Z cell epithelial cell of alimentary canal true The stem cell from which glial precursor cell arises from. tmeehan 2010-09-08T02:14:14Z FMA:87171 totipotent neuroepithelial stem cell cell neuroepithelial stem cell true A taste receptor cell that is characterized by morphologically identifiable synaptic contacts with the gustatory nerve fibers and expression of the synaptic membrane protein-25 (SNAP-25) and NCAM. tmeehan 2010-09-13T10:57:21Z taste bud basal cell FMA:67940 type 3 taste cell cell type III taste bud cell true true A rounded, mitotically active stem cell which is the source of new cells of the taste bud; located basally. tmeehan 2010-09-13T10:57:29Z taste bud basal cell FMA:62380 type 4 taste cell cell There is debate about the exact lineage of these cell types from this progenitor. See PMID:15738192. type IV taste receptor cell true true A cell that is part of the nervous system. tmeehan 2010-09-15T01:34:57Z CALOHA:TS-2040 FMA:70333 cell neural cell true true 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 true true A cell of the embryo. tmeehan 2010-09-15T03:39:21Z CALOHA:TS-0263 FMA:82840 FMA:82841 WBbt:0007028 cell embryonic cell true 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 true true A cell of a fetus which is suspended in the amniotic fluid. Amniocytes are considered to arise from several tissues including fetal skin, the fetal urinary tract, umbilical cord, and the inner amniotic surface. tmeehan 2010-09-20T10:13:37Z BTO:0000066 cell amniocyte true An epithelial cell of the bronchus. tmeehan 2010-09-20T02:00:00Z BTO:0002922 cell bronchial epithelial cell true An epithelial cell type that lacks the columnar shape typical for other respiratory epithelial cells. This cell type is able to differentiate into other respiratory epithelial cells in response to injury. tmeehan 2010-09-20T02:10:36Z cell basal epithelial cell of tracheobronchial tree true A stem cell located in the bulge of the hair follicle that can give rise to regenerate the new follicle with each hair cycle and to reepithelialize the epidermis during wound repair. tmeehan 2010-09-20T03:07:03Z bulge keratinocyte cell keratinocyte stem cell true true A prostate epithelial cell that is CD133-positive, CD44-positive, integrin A2beta3-high. This cell is a stem cell for the prostate epithelium. tmeehan 2010-09-20T03:21:06Z CD133-positive prostate epithelial cell cell prostate stem cell true true An undifferentiated cell of the prostate epithelium that lacks secretory activity. tmeehan 2010-09-20T03:34:10Z cell basal cell of prostate epithelium true 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 true A hematopoietic stem cell that exists during embryogenesis. tmeehan 2010-09-22T09:05:13Z cell gestational hematopoietic stem cell true A hematopoietic stem cell that resides in the fetal liver. In mice, this cell type is first observed at E10.5. This cell type is MHC-positive, HSA-positive, AA4.1-positive, CD45-positive, Sca-1 positive, CD150-positive, CD48-negative and CD244-negative. tmeehan 2010-09-22T09:08:32Z cell fetal liver hematopoietic progenitor cell true A hematopoietic stem found in the yolk sac. In mice, this cell type is Sca-1-negative, CD45-negative, MHC-negative, HSA-positive, AA4.1-positive, CD44-positive. tmeehan 2010-09-22T09:08:34Z hemangioblast precursor cell yolk sac hematopoietic stem cell true true A hematopoietic stem cell of the placenta. This cell type is first observed E10.5 This cell type may give rise to fetal liver hematopoietic stem cells. tmeehan 2010-09-22T10:30:02Z cell placental hematopoietic stem cell true A hematopoietic stem cell from the aorta-gonad-mesonephros region of the developing embryo. First seen at E10.5 in mouse embryos. May give rise to fetal liver HSC. tmeehan 2010-09-22T10:31:49Z cell AGM hematopoietic stem cell true A cell located in the outermost proliferative zone of the external germinal layer that can differentiate into astroglial cells and granule cells. This cell type is glial fibrillary acidic protein-positive and NK1-positive. tmeehan 2010-09-22T01:40:44Z cell granule cell precursor true An endo-epithelial cell of the respiratory tract. tmeehan 2010-09-23T04:38:49Z BTO:0004533 airway epithelial cell cell respiratory epithelial cell true 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 true A multi-fate stem cell that is the source of cells for growth of the mammary gland during puberty and gestation. This cell type gives rise to both the luminal and myoepithelial cell types of the gland, and have been shown to have the ability to regenerate the entire organ in mice. This cell type also plays an important role in carcinogenesis of the breast. This cell type is Lin-, CD24-positive, CD29-hi. tmeehan 2010-11-10T01:46:51Z cell mammary stem cell true A mesenchymal stem cell of the amnion membrane. tmeehan 2011-02-28T12:44:24Z amniotic membrane stem cell cell amnion mesenchymal stem cell true A mesenchymal stem cell that is part of the bone marrow. tmeehan 2011-02-28T01:47:47Z cell mesenchymal stem cell of the bone marrow true true A mesenchymal stem cell of the chorionic membrane. tmeehan 2011-02-28T03:04:35Z cell chorionic membrane mesenchymal stem cell true An epithelial cell of the intestine. tmeehan 2011-03-01T05:18:31Z cell intestinal epithelial cell true A mesenchymal stem cell that is part of Wharton's jelly. tmeehan 2011-03-01T09:51:18Z cell mesenchymal stem cell of Wharton's jelly true A mesenchymal stem cell of the umbilical cord. tmeehan 2011-03-01T09:55:12Z cell mesenchymal stem cell of umbilical cord true true A mesenchymal stem cell of adipose tissue. tmeehan 2011-03-01T09:57:17Z cell mesenchymal stem cell of adipose true A mesenchymal stem cell of liver. tmeehan 2011-03-01T09:58:51Z cell hepatic mesenchymal stem cell true true A mesenchymal stem cell of the vertebrae. tmeehan 2011-03-01T10:40:27Z cell vertebral mesenchymal stem cell true true A neural crest cell that gives rise to cells of the enteric nervous system. tmeehan 2011-03-06T07:24:35Z cell migratory enteric neural crest cell true An adult angioblastic cell released from the bone marrow, capable of blood circulation and participation in angiogenesis by differentiating into blood vessel endothelial cells. Their existence is controversial. tmeehan 2011-03-14T12:11:18Z EPC cell adult endothelial progenitor cell true tmeehan 2011-06-21T12:29:31Z cell epithelial cell of lower respiratory tract true A basal cell in the respiratory tract. tmeehan 2011-06-21T03:11:10Z airway basal cell airway basal stem cell cell respiratory basal cell true true A respiratory stem cell found at the junction of the terminal (conductive) bronchiole and the respiratory bronchiole. This cell types gives rise to alveolar cell types and Clara cells in response to lung injury. This cell type expresses markers Scgb1a1 and Sftpc. tmeehan 2011-06-21T03:26:08Z BASC basal epithelial cell of bronchioalveolar duct junction cell bronchioalveolar stem cell true true An amniotic stem cell is a mesenchymalstem cell extracted from amniotic fluid. Amniotic stem cells are able to differentiate into various tissue type such as skin, cartilage, cardiac tissue, nerves, muscle, and bone tmeehan 2011-06-21T03:55:39Z cell Not clear to me if amniotic stem cell is a different cell type from amnion mesenchymal stem cells. They are treated as distinct in the literature as isolations methods are different, so I will keep them as separate terms for now. amniotic stem cell true true An epithelial fate stem cell derived form the amnion membrane. tmeehan 2011-06-21T04:06:17Z cell amniotic epithelial stem cell true A glandular epithelial cell that is part of the stomach. tmeehan 2011-07-11T01:20:35Z CALOHA:TS-1284 FMA:86554 cell glandular cell of stomach true true A stem cell that can give rise to multiple cell types (i.e. smooth muscle, endothelial) in the developing heart. tmeehan 2011-07-11T03:15:38Z cell Discrepancy in develops from origins prevents me from making the assertion that cardioblasts give rise to all instances of cardiocytes as we state cardiac muscle cells develop from cardiac myoblast, which in turn develop from muscle stem cell. cardioblast true A multi-fate stem cell that can give rise to different retinal cell types including rod and cone cells. tmeehan 2011-08-16T02:38:01Z cell retinal progenitor cell true A neuroblast derived from a neural crest cell. tmeehan 2011-08-22T09:24:15Z cell neural crest derived neuroblast true Lymphatic progenitor cells. Ceri 2012-01-12T04:44:34Z cell Usually express Prox1, or prox1b. lymphangioblast true Mesenchymal derived lymphatic progenitor cells that give rise to the superficial lymphatics. Ceri 2012-01-12T05:01:22Z cell mesenchymal lymphangioblast true true Lymphatic progenitor cells, derived from the veins, that give rise to lymphatic endothelial cells. Ceri 2012-01-12T05:21:09Z parachordal lymphangioblast cell vascular lymphangioblast true Multi fate stem cell that gives rise to to both hepatocytes and cholangiocytes as descendants. hepatoblast true 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 true Any hematopoietic cell that is a precursor of some other hematopoietic cell type. hematopoietic precursor cell true A skeletal muscle satellite cell that divides by stem cell division. A proportion of this population undergoes symmetric stem cell division, producing two skeletal muscle satellite stem cells. The rest undergo asymmetric stem cell division - retaining their identity while budding off a daughter cell that differentiates into an adult skeletal muscle myoblast. cell skeletal muscle satellite stem cell true true A cell of the neural crest. Neural crest cells are multipotent. Premigratory neural crest cells are found at the neural plate boarder, some of which will undergo ectomesynchymal transition and delamination to form migratory neural crest cells. cell neural crest cell true true 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 true forebrain neuroblast true cell stratified keratinized epithelial stem cell true cell stratified non keratinized epithelial stem cell true A basal cell that is part of the epithelium of trachea. FMA:263118 cell basal cell of epithelium of trachea true true A basal cell found in the bronchus epithelium. CL:0002331 FMA:263120 basal cell of bronchus cell basal cell of epithelium of bronchus true true true A basal cell that is part of the epithelium of terminal bronchiole. FMA:263122 cell basal cell of epithelium of terminal bronchiole true A basal cell that is part of the epithelium of respiratory bronchiole. FMA:263124 cell basal cell of epithelium of respiratory bronchiole true A basal cell that is part of the epithelium of bronchiole. FMA:263126 cell basal cell of epithelium of lobular bronchiole true true A somatic stem cell that is part of the epidermis. FMA:70541 epidermal stem cell cell stem cell of epidermis true A basal cell that is part of the epithelium of esophagus. FMA:70731 basal cell of esophageal epithelium cell epithelial cell of stratum germinativum of esophagus true A basal cell that is part of the urothelium. FMA:84150 cell basal cell of urothelium true a respiratory stem cell found at the junction of the terminal (conductive) bronchiole and the respiratory bronchiole, which gives rise to alveolar cell types and Clara cells in response to lung injury. cl bronchioalveolar stem cells true Any basal cell of epidermis that is part of a limb. TermGenie 2014-06-25T02:28:25Z cell CL:2000033 limb basal cell of epidermis true Any mesenchymal stem cell that is part of a placenta. TermGenie 2014-10-07T17:51:11Z cell CL:2000061 http://www.sciencellonline.com/site/productInformation.php?keyword=7140 placental amniotic mesenchymal stromal cell true Any migratory neural crest cell that is part of a cardiac neural crest. TermGenie 2014-11-05T01:18:43Z cell CL:2000073 migratory cardiac neural crest cell true Any mesenchymal stem cell of the bone marrow that is part of a femur. TermGenie 2014-12-02T19:07:31Z cell CL:2000079 mesenchymal stem cell of femoral bone marrow true Any mesenchymal stem cell of adipose that is part of a abdomen. TermGenie 2014-12-02T19:10:34Z cell CL:2000080 mesenchymal stem cell of abdominal adipose true Any hair follicle dermal papilla cell that is part of a scalp. TermGenie 2014-12-02T19:10:50Z cell CL:2000083 hair follicle dermal papilla cell of scalp true Any hematopoietic stem cell that is part of a umbilical cord blood. TermGenie 2015-05-26T18:58:34Z cell CL:2000095 cord blood hematopoietic stem cell true true spinal muscular atrophy ICD9CM_2010:335.1 ICD9CM_2010:335.10 MSH2010_2010_02_22:D009134 SNOMEDCT_2010_1_31:192885003 SNOMEDCT_2010_1_31:192887006 SNOMEDCT_2010_1_31:5262007 UMLS_CUI:C0026847 URI: http://www.ebi.ac.uk/cellline#spinal_muscular_atrophy true true "degenerative disease" EXACT [NCI2004_11_17:C27090] "degenerative disorder (disorder)" EXACT [SNOMEDCT_2005_07_31:362975008] "A disease of biological process that results_in the progressive deterioration of tissue or organ function or structure, whether due to normal bodily wear or lifestyle choices." [url:http\://en.wikipedia.org/wiki/Degenerative_disease] degenerative disease NCI2009_04D:C27090 SNOMEDCT_2010_1_31:362975008 UMLS_CUI:C1285162 URI: http://www.ebi.ac.uk/cellline#degenerative_disease true "HMN (Hereditary motor Neuropathy) Proximal type I" EXACT [] "Werdnig-Hoffman disease" EXACT [SNOMEDCT_2005_07_31:155016008] "Werdnig-Hoffman disease" EXACT [SNOMEDCT_2005_07_31:267694009] "Werdnig-Hoffmann disease (disorder)" EXACT [SNOMEDCT_2005_07_31:64383006] "Werdnig-Hoffmann disease" EXACT [ICD9CM_2006:335.0] "infantile muscular atrophy" EXACT [CSP2005:2057-3620] "progressive muscular atrophy of infancy" EXACT [MTHICD9_2006:335.0] hereditary motor neuropathy proximal type I ICD9CM_2010:335.0 OMIM2009_05_01:253300 SNOMEDCT_2010_1_31:155016008 SNOMEDCT_2010_1_31:267694009 SNOMEDCT_2010_1_31:64383006 UMLS_CUI:C0043116 URI: http://www.ebi.ac.uk/cellline#hereditary_motor_neuropathy_proximal_type_I true A disease of anatomical entity that occurs in the muscular and/or skeletal system. "Musculo-skeletal disorder NOS (disorder)" EXACT [SNOMEDCT_2005_07_31:274149006] "Musculo-skeletal disorder NOS" EXACT [SNOMEDCT_2005_07_31:156881000] "Musculo-skeletal disorder NOS" EXACT [SNOMEDCT_2005_07_31:268142006] "Musculoskeletal disease" EXACT [MTH:NOCODE] "Musuloskeletal disease" EXACT [SNOMEDCT_2005_07_31:268047003] "disorder of musculoskeletal system (disorder)" EXACT [SNOMEDCT_2005_07_31:928000] "musculoskeletal disorder" EXACT [CSP2005:4000-0257] MESH:D009140 NCI:C107377 SNOMEDCT_US_2016_03_01:156881000 SNOMEDCT_US_2016_03_01:268047003 SNOMEDCT_US_2016_03_01:268142006 SNOMEDCT_US_2016_03_01:274149006 SNOMEDCT_US_2016_03_01:928000 UMLS_CUI:C0026857 disease_ontology DOID:17 musculoskeletal system disease MSH2010_2010_02_22:D009140 SNOMEDCT_2010_1_31:156881000 SNOMEDCT_2010_1_31:268047003 SNOMEDCT_2010_1_31:268142006 SNOMEDCT_2010_1_31:274149006 SNOMEDCT_2010_1_31:928000 UMLS_CUI:C0026857 URI: http://www.ebi.ac.uk/cellline#musculoskeletal_system_disease true motor neuron disease ICD9CM_2010:335.2 MSH2010_2010_02_22:D016472 SNOMEDCT_2010_1_31:155015007 SNOMEDCT_2010_1_31:192888001 SNOMEDCT_2010_1_31:192889009 SNOMEDCT_2010_1_31:192890000 SNOMEDCT_2010_1_31:37340000 UMLS_CUI:C0085084 URI: http://www.ebi.ac.uk/cellline#motor_neuron_disease true true "myelopathy" RELATED [] spinal cord disease ICD9CM_2010:336.9 MSH2010_2010_02_22:D013118 OMIM2009_05_01:MTHU005441 SNOMEDCT_2010_1_31:155020007 SNOMEDCT_2010_1_31:192908002 SNOMEDCT_2010_1_31:192913003 SNOMEDCT_2010_1_31:267587000 SNOMEDCT_2010_1_31:267695005 SNOMEDCT_2010_1_31:48522003 SNOMEDCT_2010_1_31:95648003 UMLS_CUI:C0037928 URI: http://www.ebi.ac.uk/cellline#spinal_cord_disease true "A nervous system disease that affects either the spinal cord (myelopathy) or brain (encephalopathy) of the central nervous system." [url:http\://en.wikipedia.org/wiki/Central_nervous_system_disease] central nervous system disease MSH2010_2010_02_22:D002493 NCI2009_04D:C2934 SNOMEDCT_2010_1_31:138748005 SNOMEDCT_2010_1_31:154981003 SNOMEDCT_2010_1_31:155049004 SNOMEDCT_2010_1_31:155059003 SNOMEDCT_2010_1_31:192641002 SNOMEDCT_2010_1_31:193076009 SNOMEDCT_2010_1_31:194566008 SNOMEDCT_2010_1_31:23853001 SNOMEDCT_2010_1_31:267144009 SNOMEDCT_2010_1_31:267679005 SNOMEDCT_2010_1_31:267700003 SNOMEDCT_2010_1_31:267702006 SNOMEDCT_2010_1_31:275539005 UMLS_CUI:C0007682 URI: http://www.ebi.ac.uk/cellline#central_nervous_system_disease true "A disease that involves any biological process (GO:0008150) specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms." [DO:wk\,ls] disease of biological process URI: http://www.ebi.ac.uk/cellline#disease_of_biological_process true A disease is a disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism. MESH:D004194 NCI:C2991 SNOMEDCT_US_2016_03_01:64572001 UMLS_CUI:C0012634 disease_ontology DOID:4 disease true tissue disease URI: http://www.ebi.ac.uk/cellline#tissue_disease true neuromuscular disease ICD9CM_2010:358 ICD9CM_2010:358.9 MSH2010_2010_02_22:D009468 SNOMEDCT_2010_1_31:1664005 SNOMEDCT_2010_1_31:193218007 SNOMEDCT_2010_1_31:255522009 SNOMEDCT_2010_1_31:257277002 UMLS_CUI:C0027868 URI: http://www.ebi.ac.uk/cellline#neuromuscular_disease true true hereditary degenerative disease of central nervous system SNOMEDCT_2010_1_31:192838009 SNOMEDCT_2010_1_31:192842007 UMLS_CUI:C0014887 URI: http://www.ebi.ac.uk/cellline#hereditary_degenerative_disease_of_central_nervous_system true true anterior horn cell disease ICD9CM_2010:335 ICD9CM_2010:335.9 SNOMEDCT_2010_1_31:155014006 SNOMEDCT_2010_1_31:192884004 SNOMEDCT_2010_1_31:192892008 SNOMEDCT_2010_1_31:267693003 SNOMEDCT_2010_1_31:85672005 UMLS_CUI:C0154681 URI: http://www.ebi.ac.uk/cellline#anterior_horn_cell_disease true "Neurodegenerative disease" EXACT [NCI2004_11_17:C4802] "A degenerative disease that results_in the progressive loss of structure or function of neurons, including death of neurons." [url:http\://en.wikipedia.org/wiki/Neurodegeneration] neurodegenerative disease MSH2010_2010_02_22:D019636 NCI2009_04D:C4802 UMLS_CUI:C0524851 URI: http://www.ebi.ac.uk/cellline#neurodegenerative_disease true true muscle tissue disease URI: http://www.ebi.ac.uk/cellline#muscle_tissue_disease true A disease that manifests in a defined anatomical structure. "acellular anatomical structure disease" EXACT [] "disease of anatomical set" EXACT [] "disease of anatomical structure" EXACT [] "disease of material anatomical entity" EXACT [] "disease of physical anatomical entity" EXACT [] "disease of set of heterogenous clusters" EXACT [] DOID:1 DOID:2 DOID:5 DOID:71 DOID:72 DOID:8 disease_ontology DOID:7 "A disease that manifests in a defined anatomical structure." [DO:wk\,ls, URL:http\://www2.merriam-webster.com/cgi-bin/mwmednlm?book=Medical&va=anatomic] disease of anatomical entity URI: http://www.ebi.ac.uk/cellline#disease_of_anatomical_entity true true nervous system disease ICD9CM_2010:349.9 MSH2010_2010_02_22:D009422 NCI2009_04D:C26835 SNOMEDCT_2010_1_31:118940003 SNOMEDCT_2010_1_31:154981003 SNOMEDCT_2010_1_31:155262005 SNOMEDCT_2010_1_31:192641002 SNOMEDCT_2010_1_31:267679005 SNOMEDCT_2010_1_31:286946008 UMLS_CUI:C0027765 URI: http://www.ebi.ac.uk/cellline#nervous_system_disease true "Neuropathy (disorder)" EXACT [SNOMEDCT_2005_07_31:264554005] "Neuropathy (disorder)" EXACT [SNOMEDCT_2005_07_31:386033004] "Neuropathy" EXACT [MTH:NOCODE] "Neuropathy" EXACT [SNOMEDCT_2005_07_31:193167000] "Neuropathy" EXACT [SNOMEDCT_2005_07_31:277317008] "Neuropathy" EXACT [SNOMEDCT_2005_07_31:277878001] "Neuropathy, NOS" EXACT [SNOMEDCT_2005_07_31:42658009] neuropathy NCI2009_04D:C4731 OMIM2009_05_01:MTHU016030 SNOMEDCT_2010_1_31:193167000 SNOMEDCT_2010_1_31:264554005 SNOMEDCT_2010_1_31:277317008 SNOMEDCT_2010_1_31:277878001 SNOMEDCT_2010_1_31:386033004 SNOMEDCT_2010_1_31:42658009 UMLS_CUI:C0442874 URI: http://www.ebi.ac.uk/cellline#neuropathy true osteoblast differentiation true hematopoietic progenitor cell differentiation true immune system process true production of molecular mediator of immune response true regulation of immune system process true positive regulation of immune system process true true regulation of leukocyte migration true true positive regulation of leukocyte migration true true true regulation of leukocyte chemotaxis true true positive regulation of leukocyte chemotaxis true true true antimicrobial peptide production true antimicrobial peptide secretion true peptide secretion true true developmental process involved in reproduction true true system process true cellular_component true cell true true transport true movement of cell or subcellular component true gamete generation true germ cell development true true true spermatogenesis true female gamete generation true biological_process A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. 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. GO:0000004 GO:0007582 Wikipedia:Biological_process biological process physiological process biological_process GO:0008150 Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. Note that when this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code ND, no data, is used to indicate this. biological_process true detection of chemical stimulus true 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. GO:0008151 GO:0050875 cell physiology cellular physiological process cell growth and/or maintenance biological_process GO:0009987 cellular process true peptide transport true true cell migration true stem cell division true transmission of nerve impulse true true cellular process involved in reproduction in multicellular organism true true reproductive process true signaling true cell differentiation true neuron differentiation true regulation of cell migration true positive regulation of cell migration true true epithelial cell differentiation true regulation of response to external stimulus true positive regulation of response to external stimulus true true multicellular organismal process true developmental process true regulation of localization true secretion by cell true true macromolecular complex true cardiocyte differentiation true multicellular organismal signaling true true Self-propelled movement of a cell or organism from one location to another. biological_process GO:0040011 locomotion true regulation of locomotion true positive regulation of locomotion true true MHC protein complex true MHC class II protein complex true muscle cell differentiation true amide transport true protein complex true membrane part true plasma membrane part true true cell part cell part true true fat cell differentiation true secretion true somatic stem cell division true male gamete generation true cell development true true oogenesis true true positive regulation of biological process true positive regulation of cellular process true true regulation of response to stimulus true positive regulation of response to stimulus true true multicellular organismal reproductive process true anatomical structure development true cellular developmental process true true cell motility true true regulation of biological process true regulation of cellular process true nervous system process true response to stimulus true detection of stimulus involved in sensory perception true detection of chemical stimulus involved in sensory perception true true detection of chemical stimulus involved in sensory perception of taste true regulation of chemotaxis true true positive regulation of chemotaxis true true true striated muscle cell differentiation true localization true establishment of localization true regulation of cellular component movement true true positive regulation of cellular component movement true true cell division true detection of stimulus true cardiac muscle cell differentiation true true chondroblast differentiation true biological regulation true regulation of granulocyte chemotaxis true positive regulation of granulocyte chemotaxis true true organic substance transport true nitrogen compound transport true regulation of neutrophil chemotaxis true true positive regulation of neutrophil chemotaxis true true true membrane protein complex true true plasma membrane protein complex true true regulation of neutrophil migration true positive regulation of neutrophil migration true true regulation of cell motility true true positive regulation of cell motility true true true 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 true 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 true 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 true 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 true 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 true 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. an information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity 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 information content entity true 1 1 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 true 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 true graph A diagram that presents one or more tuples of information by mapping those tuples in to a two dimensional space in a non arbitrary way. PERSON: Lawrence Hunter person:Alan Ruttenberg person:Allyson Lister OBI_0000240 group:OBI graph true 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 true 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 true 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 true 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 true 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 true material information bearer A page of a paperback novel with writing on it. The paper itself is a material information bearer, the pattern of ink is the information carrier. a brain a hard drive A material entity in which a concretization of an information content entity inheres. GROUP: IAO material information bearer true 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 true diagram A molecular structure ribbon cartoon showing helices, turns and sheets and their relations to each other in space. A figure that expresses one or more propositions PERSON: Lawrence Hunter diagram true 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 true A scalar measurement datum that is the result of measurement of length quality Alan Ruttenberg length measurement datum true A scalar measurement datum that is the result of measurement of mass quality 2009/09/28 Alan Ruttenberg. Fucoidan-use-case Person:Alan Ruttenberg mass measurement datum true 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 true 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 true line graph A line graph is a type of graph created by connecting a series of data points together with a line. PERSON:Chris Stoeckert PERSON:Melanie Courtot line chart GROUP:OBI WEB: http://en.wikipedia.org/wiki/Line_chart line graph true time stamped measurement datum true a document that denotes some identity and is concretized by the bearer of some credential role Amanda Hicks identity document true a documented identity is the aggregate of all data items about an entity. Notice that a documented identity is not itself a document since a document is intended to be understood as a whole and data items about an individual are usually scattered across different documents. Amanda Hicks is an aggregate of ICEs also an ICE? yes Is part_of the appropriate relation to use for data items and documented identities? documented identity true I order a beer and the bartender authenticates my age by looking at my DOB on my driver's license. I sign into my email account, and the system authenticates my permission to read the email by checking the password I enter against my password listed in the database. Authentication is the act of checking or verifying an identity claim (that is either tacit or explicit). Amanda Hicks authentication true a role that inheres in a concretization of an identity document and is realized by an authentication process Amanda Hicks credential role true Colonel Klink giving Sergeant Schultz an order, Jake promising Jill to take her to the junior prom A process that is carried out by a conscious being or an aggregate of conscious beings and is spontaneous, directed towards other conscious beings and aggregates thereof and needs to be perceived. Mathias Brochhausen MB: Regarding the use of the term 'sponteneous' in the definition: The term is used in the following meaning of being self generated. It does not stand in contrast to being planned. social act true Muridae Muridae true Mus musculus "Mus muscaris" RELATED misnomer [] "house mouse" EXACT genbank_common_name [] "mice C57BL/6xCBA/CaJ hybrid" RELATED misspelling [] "mouse" EXACT common_name [] house mouse mouse Mus musculus GC_ID:1 URI: http://www.ebi.ac.uk/cellline#Mus_musculus true Viruses Viruses true Euteleostomi bony vertebrates Euteleostomi true true Bacteria eubacteria Bacteria true Homininae Homininae true Archaea Archaea true Eukaryota eucaryotes eukaryotes GC_ID:1 PMID:23020233 eucaryotes eukaryotes ncbi_taxonomy Eucarya Eucaryotae Eukarya Eukaryotae eukaryotes Eukaryota true Euarchontoglires Euarchontoglires true true Glires "Rodents and rabbits" EXACT genbank_common_name [] Rodents and rabbits Glires GC_ID:1 URI: http://www.ebi.ac.uk/cellline#Glires true Simiiformes Simiiformes true Hominoidea "ape" EXACT common_name [] "apes" EXACT common_name [] ape apes Hominoidea GC_ID:1 URI: http://www.ebi.ac.uk/cellline#Hominoidea true Tetrapoda tetrapods Tetrapoda true Amniota amniotes Amniota true Theria <Mammalia> Theria Theria <Mammalia> true Opisthokonta Opisthokonta true Bilateria Bilateria true Sciurognathi Sciurognathi true Muroidea Muroidea true Murinae Murinae true Mammalia "mammals" EXACT genbank_common_name [] "mammals" RELATED blast_name [] mammals Mammalia GC_ID:1 URI: http://www.ebi.ac.uk/cellline#Mammalia true Vertebrata <Metazoa> Vertebrata vertebrates Vertebrata <Metazoa> true Craniata <chordata> Craniata Craniata <chordata> true Eutheria eutherian mammals placental mammals placentals Eutheria true Primates "Primata" RELATED synonym [] "primate" EXACT equivalent_name [] "primates" RELATED blast_name [] primate Primates GC_ID:1 URI: http://www.ebi.ac.uk/cellline#Primates true Catarrhini Catarrhini true Hominidae "Pongidae" RELATED synonym [] "great apes" EXACT common_name [] great apes Hominidae GC_ID:1 URI: http://www.ebi.ac.uk/cellline#Hominidae true Homo sapiens Homo sapiens "human" EXACT genbank_common_name [] human human being man GC_ID:1 human man ncbi_taxonomy Homo sapiens Homo sapiens GC_ID:1 URI: http://www.ebi.ac.uk/cellline#Homo_sapiens true Rodentia "rodents" EXACT genbank_common_name [] "rodents" RELATED blast_name [] rodents Rodentia GC_ID:1 URI: http://www.ebi.ac.uk/cellline#Rodentia true A measurement of the number of cells per unit volume or area. C120538 Quantitative Concept Cell Density C0162339 CDISC A measurement of the number of cells contained in a unit of volume. CELLDENS Cell Density Cell Density true A process in which blood or tissue samples are analyzed to determine their human leukocyte antigen (HLA) profiles. C71329 Laboratory Procedure HLA Typing C0242318 HLA_Typing HLA Testing HLA Typing HLA Typing true fluorescent reporter intensity A measurement datum that represents the output of a scanner measuring the intensity value for each fluorescent reporter. person:Chris Stoeckert group:OBI From the DT branch: This term and definition were originally submitted by the community to our branch, but we thought they best fit DENRIE. However we see several issues with this. First of all the name 'probe' might not be used in OBI. Instead we have a 'reporter' role. Also, albeit the term 'probe intensity' is often used in communities such as the microarray one, the name 'probe' is ambiguous (some use it to refer to what's on the array, some use it to refer to what's hybed to the array). Furthermore, this concept could possibly be encompassed by combining different OBI terms, such as the roles of analyte, detector and reporter (you need something hybed to a probe on the array to get an intensity) and maybe a more general term for 'measuring intensities'. We need to find the right balance between what is consistent with OBI and combinations of its terms and what is user-friendly. Finally, note that 'intensity' is already in the OBI .owl file and is also in PATO. Why didn't OBI import it from PATO? This might be a problem. fluorescent reporter intensity true planned process 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 planned process true 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 true ratio of collected to emitted light 10% A measurement datum measuring the amount of light collected s compared to the total amount of emitted light in the detector component of a flow cytometer instrument. The datum has a qualitative role person:Chris Stoeckert person:Kevin Clancy Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt ratio of collected to emitted light true 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 true 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 true 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 true culture medium 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 true 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 true material processing 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 true 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 true 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 true number of particles in subset 500, 200, 0 A measurement datum measuring the number of subjects in a defined subset in a flow cytometer instrument. The datum has a qualitative role person:Kevin Clancy Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt number of particles in subset true number of lost events electronic 74, 0, 14 events lost due to data acquisition electronic coincidence. A measurement datum measuring the number of analysis events lost due to errors in data acquisition electronic coincidence in a flow cytometer instrument. The datum has a qualitative role. person:Kevin Clancy Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt number of lost events electronic true parameter threshold 0.01, 0.03 A measurement datum measuring the minimal signal that must be detected to generate an electrical event, as compared to the maximal detected signal in a flow cytometer instrument. The datum has a qualitative role person:Kevin Clancy Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt parameter threshold true 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. James Malone Jie Zheng PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Philippe Rocca-Serra PERSON: Susanna Sansone Tomasz Adamusiak organisation GROUP: OBI MO_177 An organization is a continuant entity which can play 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. organization organization EFO_URI: http://www.ebi.ac.uk/efo/EFO_0002010 true number of lost events computer 0, 125, 787 events lost due to computer busy. A measurement datum recording the number of measurement events lost due to overloading of the analysis chip in a flow cytometer instrument. The datum has a qualitative role person:Kevin Clancy Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt number of lost events computer true 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 true analyte role Glucose in blood (measured in an assay to determine the concentration of glucose). A measurand 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 true 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 true interpreting 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 true 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 true 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 true 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 true 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 true 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 true 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 true 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 true material transformation objective 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 true study design execution injecting a mouse with PBS solution, weighing it, and recording the weight according to a study design. a planned process that carries out 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 true 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 true 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 true 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 true 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 true 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 true survival rate A measurement data that represents the percentage of people or animals in a study or treatment group who are alive for a given period of time after diagnosis or initiation of monitoring. Oliver He adapted from wikipedia http://en.wikipedia.org/wiki/Survival_rate survival rate true spike train datum Measurement of temporal regularity of spike train responses in auditory nerve fibers of the green treefrog A measurement datum which represents information about an ordered series of action potentials in an organism's CNS measured over time. needs more work to see exactly what the data set looks like - HP Helen Parkinson, Alan Ruttenberg spike train measurement Jessica Turner, NIF spike train datum true 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 true 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 true 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 true categorical measurement datum A measurement datum that is reported on a categorical scale Bjoern Peters nominal mesurement datum Bjoern Peters categorical measurement datum true handedness assay The Edinburgh handedness assay is a specific method of determing handedness A handedness assay measures the unequal distribution of fine motor skill between the left and right hands typically in human subjects by means of some questionnaire and scoring procedure. Helen Parkinson handedness test http://en.wikipedia.org/wiki/Handedness handedness assay true 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 true true categorical label The labels 'positive' vs. 'negative', or 'left handed', 'right handed', 'ambidexterous', or 'strongly binding', 'weakly binding' , 'not binding', or '+++', '++', '+', '-' etc. form scales of categorical labels. A label that is part of a categorical datum and that indicates the value of the data item on the categorical scale. Bjoern Peters Bjoern Peters categorical label true 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 true 1 scalar score from composite inputs A measurement datum which is the result of combining multiple datum. For example, a mean or summary score. JT: We included this because we wanted to talk about an output from a questionnaire that summarized the answers to the questionnaire, but which was not actually the answer to any single question. Person: Jessica Turner questionaire score Person: Jessica Turner JZ: can we defined it logically as the output of some data transformation, like aggragate data transformation? scalar score from composite inputs true 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 true handedness categorical measurement datum A datum used to record the answer to a self assessment of whether a person uses their left hand, right hand primarily or each hand equally PERSON:Alan Ruttenberg PERSON:Jessica Turner handedness categorical measurement datum true dose An organism has been injected 1ml of vaccine A measurement datum that measures the quantity of something that may be administered to an organism or that an organism may be exposed to. Quantities of nutrients, drugs, vaccines and toxins are referred to as doses. dose true 1 Edinburgh score A score that measures the dominance of a person's right or left hand in everyday activities. Person: Alan Ruttenberg Person:Jessica Turner PMID:5146491#Oldfield, R.C. (1971). The assessment and analysis of handedness: The Edinburgh inventory. Neuropsychologia, 9, 97-113 WEB:http://www.cse.yorku.ca/course_archive/2006-07/W/4441/EdinburghInventory.html Edinburgh score true questionnaire A document with a set of printed or written questions with a choice of answers, devised for the purposes of a survey or statistical study. JT: It plays a role in collecting data that could be fleshed out more; but I'm thinking it is, in itself, an edited document. JZ: based on textual definition of edited document, it can be defined as N&S. I prefer to leave questionnaire as a document now. We can add more restrictions in the future and use that to determine it is an edited document or not. Need to clarify if this is a document or a directive information entity (or what their connection is)) PERSON: Jessica Turner Merriam-Webster questionnaire true Edinburgh handedness assay The Edinburgh Handedness assay is an assay in which a set of questions = the Edinburgh Handedness inventory - is asked and the answers to these questions are turned into a score, used to assess the dominance of a person's right or left hand in everyday activities. The inventory can be used by an observer assessing the person, or by a person self-reporting hand use. The latter method tends to be less reliable due to a person over-attributing tasks to the dominant hand. PERSON:Jessica Turner Person:Alan Ruttenberg WEB:http://en.wikipedia.org/wiki/Edinburgh_Handedness_Inventory Edinburgh handedness assay true binding constant The predicted or measured binding affinity of a peptide to a MHC molecule can be captured in the binding constants "IC50 = 12 nM" or "t 1/2 = 30 minutes". A binding datum about the disposition of two or more material entities to form complexes which comes in the form of a scalar and unit that are utilized in equations that model the binding process 10/6/11 BP: The distinction between binding datum and binding constant is based on the later being part of an equation. That should be captured in the logical definition here, and used to make it to a defined class. PERSON: Bjoern Peters, Randi Vita, Jason Greenbaum binding constant true 3D structural organization datum The atom coordinates found in a PDB (Protein Data Bank) file, generated by X Ray crystallography or NMR. A measurement datum that describes the structural orientation of a material entity in 3D space. PERSON: Jason Greenbaum, Randi Vita, Bjoern Peters 3D structural organization datum true 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 true 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 true 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 true 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 true 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 true 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 true 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 true 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 true 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 true 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 true 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 true half life datum (t 1/2) The time it takes for 50% of a class of stochastic processes to occur. Bjoern Peters t 1/2 Bjoern Peters half life datum (t 1/2) true dose response curve A data item of paired values, one indicating the dose of a material, the other quantitating a measured effect at that dose. The dosing intervals are chosen so that effect values be interpolated by a plotting a curve. Bjoern Peters; Randi Vita dose response curve true half maximal effective concentration (EC50) Determining the potentency of a drug / antibody / toxicant by measuring a graded dose response curve, and determining the concentration of the compound where 50% of its maximal effect is observed. half maximal effective concentration (EC50) is a scalar measurement datum corresponding to the concentration of a compound which induces a response halfway between the baseline and maximum after some specified exposure time. Bjoern Peters; Randi Vita wikipedia half maximal effective concentration (EC50) true 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 true half maximal inhibitory concentration (IC50) Interpolating that at a dose of IC50=12 nM, half of the binding of a comptetitive ligand is inhibited. Half maximal inhibitory concentration (IC50) is a scalar measurement datum that measures the effectiveness of a compound to competitively inhibit a given process, and corresponds to the concentration of the compound at which it reaches half of its maximum inhibitory effect. Bjoern Peters; Randi Vita wikipedia half maximal inhibitory concentration (IC50) true 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 true minimal inhibitory concentration A scalar measurement datum that indicates the lowest concentration at which a specific compound significantly inhibits a process from occurring compared to in the absence of the compound. Created following request by Albert Goldfain PERSON:Bjoern Peters Bjoern Peters, coordinated with Albert Goldfain minimal inhibitory concentration true sequence assembly algorithm An algorithm used to assemble individual sequence reads into larger contiguous sequences (contigs). Assembly details include but are not limited to assembler type (overlap-layout-consensus, deBruijn), assembler version, and any relevant quality control information such as per cent known genes/ESTs captured. Person: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Assembly Algorithm NIAID GSCID-BRC sequence assembly algorithm true PDB file The file found in the pdb with the identifier 3pe4 http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=NO&structureId=3pe4 A 3d structural organization datum capturing the results of X-ray crystallography or NMR experiment that is formatted as specified by the Protein Databank (http://www.wwpdb.org/docs.html). A PDB file can describe the structure of multiple molecules, each of which has a different chain identifier assigned. PERSON: Bjoern Peters, Dorjee Tamang, Jason Greenbaum PDB file true equilibrium dissociation constant (KD) KD = 32 nM is the equilibrium dissociation rate found for peptide SIINFEKL binding to H-2 Kb A binding constant defined as the ratio of kon over koff (on-rate of binding divided by off-rate) PERSON: Bjoern Peters, Randi Vita IEDB equilibrium dissociation constant (KD) true equilibrium association constant (KA) KA = 10^-12 M^-1 is the equilibirum association constant maximally found for antibody binding to haptens. A binding constant defined as the ratio of koff over kon (off-rate of binding divided by on-rate) PERSON: Bjoern Peters, Randi Vita IEDB equilibrium association constant (KA) true rate measurement datum The rate of disassociation of a peptide from a complex with an MHC molecule measured by the ratio of bound and unbound peptide per unit of time. A scalar measurement datum that represents the number of events occuring over a time interval PERSON: Bjoern Peters, Randi Vita IEDB rate measurement datum true equilibrium dissociation constant (KD) approximated by IC50 A measurement of an IC50 value under specific assay conditions approximates KD, namely the binding reaction is at an equilibrium, there is a single population of sites on the receptor that competitor and ligand are binding to, and the concentration of the receptor must be much less than the KD for the competitor and the ligand. In this case, according to Cheng and Prussoff, KD = IC50 / (1 + Lstot / KDs), in which Lstot is the total concentration of the labeled competitor and KDs is the KD value of that competitor. PERSON: Bjoern Peters, Randi Vita http://dx.doi.org/10.1016/0006-2952(73)90196-2 equilibrium dissociation constant (KD) approximated by IC50 true true 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 true equilibrium dissociation constant (KD) approximated by EC50 A measurement of an EC50 value under specific assay conditions approximates KD, namely the binding reaction is at an equilibrium, and the concentration of the receptor must be much less than the KD for the ligand. PERSON: Bjoern Peters, Randi Vita Assay Development: Fundamentals and Practices, By Ge Wu, page 74 equilibrium dissociation constant (KD) approximated by EC50 true true half life of binding datum The 45 minute period in which one half of the complexes formed by peptide ligand bound to a HLA-A*0201molecule disassociate. A half life datum of the time it takes for 50% of bound complexes in an ensemble to disassociate in absence of re-association. PERSON: Bjoern Peters, Randi Vita IEDB half life of binding datum true true 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 true PDB file chain The 'D' chain in the PDB file 2BSE identifies the heavy chain of the antibody in the protein:antibody complex A 3D structural organization datum that is part of a PDB file and has a specific chain identifier that identifies the entire information on a subset of the material entities PERSON: Bjoern Peters, Dorjee Tamang, Jason Greenbaum IEDB PDB file chain true binding off rate measurement datum (koff) A rate measurement datum of how quickly bound complexes disassociate PERSON: Bjoern Peters, Randi Vita IEDB binding off rate measurement datum (koff) true true binding on rate measurement datum (kon) A rate measurement datum of how quickly bound complexes form PERSON: Bjoern Peters, Randi Vita IEDB binding on rate measurement datum (kon) true true specimen collection time measurement datum A time measurement datum that is the measure of the time when the specimens are collected. Person: Chris Stoeckert, Jie Zheng collection date NIAID GSCID-BRC metadata working group Specimen Collection Date NIAID GSCID-BRC specimen collection time measurement datum true latitude coordinate measurement datum A measurement datum that is the measure of the latitude coordinate of a site. Person: Chris Stoeckert, Jie Zheng latitude NIAID GSCID-BRC metadata working group Specimen Collection Location - Latitude NIAID GSCID-BRC latitude coordinate measurement datum true longitude coordinate measurement datum A measurement datum that is the measure of the longitude coordinate of a site. Person: Chris Stoeckert, Jie Zheng longitude NIAID GSCID-BRC metadata working group Specimen Collection Location - Longitude NIAID GSCID-BRC longitude coordinate measurement datum true 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 true 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 true sequence assembly process A data transformation that assembles two or more individual sequence reads into contiguous sequences (i.e., contigs). PRS/AGB: changed to restrictions by adding 2 possible specified outputs (N50 and genome coverage) for sequence assembly. Alejandra Gonzalez-Beltran PERSON: Jie Zheng, Chris Stoeckert Philippe Rocca-Serra NIAID GSCID-BRC metadata working group NIAID GSCID-BRC sequence assembly process true number of errors Gigascience. 2012 Dec 27;1(1):18. doi: 10.1186/2047-217X-1-18. PMID: 23587118. see table2 a data item that is the number of times that a given process failed, as an integer Alejandra Gonzalez-Beltran Philippe Rocca-Serra PRS, AGB number of errors true true random access memory size Gigascience. 2012 Dec 27;1(1):18. doi: 10.1186/2047-217X-1-18. PMID: 23587118. "However, the error correction module in SOAPdenovo was designed for short Illumina reads (35-50 bp), which consumes an excessive amount of computational time and memory on longer reads, for example, over 150 GB memory running for two days using 40-fold 100 bp paired-end Illumina HiSeq 2000 reads" random access memory size is a scalar measurement datum which denotes the amount of physical memory know as random access memory present of a computer or required by a computational process or data transformation Alejandra Gonzalez-Beltran Philippe Rocca-Serra PRS, AGB random access memory size true random access memory Random-access memory (RAM) is a form of computer data storage. A random-access device allows stored data to be accessed directly in any random order. In contrast, other data storage media such as hard disks, CDs, DVDs and magnetic tape, as well as early primary memory types such as drum memory, read and write data only in a predetermined order, consecutively, because of mechanical design limitations. Therefore, the time to access a given data location varies significantly depending on its physical location Alejandra Gonzalez-Beltran Philippe Rocca-Serra RAM http://en.wikipedia.org/wiki/RAM last accessed: 2013-12-02 random access memory true reagent A biological or chemical entity that bears a reagent role in virtue of it being intended for application in a scientific technique to participate in (or have molecular parts that participate in) a chemical reaction that facilitates the generation of data about some distinct entity, or the generation of some distinct material specified output. 2013-6-5 MHB: Clarifications regarding the distinction between reagetns and devices were made at the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For examples, see editor note on OBI:device. PERSON:Matthew Brush PERSON:Matthew Brush (copied from ReO) Reagents are distinguished from devices/instruments that also serve as facilitators in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in or have parts that participate in some chemical interaction or reaction during their intended participation in some technique. By contrast, devices do not participate in a chemical reaction/interaction during the technique. Reagents are distinguished from study subjects/evaluants in that study subjects and evaluants are that about which conclusions are drawn and knowledge is sought in an investigation - while reagents, by definition, are not. It should be noted, however, that reagent and study subject/evaluant roles can be borne by instances of the same type of material entity - but a given instance can only realize one of these roles in the execution of a given assay. For example, taq polymerase can bear a reagent role or an evaluant role. In a DNA sequencing assay aimed at generating sequence data about some plasmid, the reagent role of the taq polymerase is realized. In an assay to evaluate the quality of the taq polymerase itself, the evaluant/study subject role of the taq is realized, but not the reagent role since the taq is the subject about which data is generated. In regard to the statement that reagents are 'distinct' from the specified outputs of a technique: note that a reagent may be incorporated into a material output of a technique, as long as the IDENTITY of this output is distinct from that of the bearer of the reagent role. For example, dNTPs input into a PCR are reagents that become part of the material output of this technique, but this output has a new identity (ie that of a 'nucleic acid molecule') that is distinct from the identity of the dNTPs that comprise it. Similarly, a biotin molecule input into a cell labeling technique are reagents that become part of the specified output, but the identity of the output is that of some modified cell specimen which shares identity with the input unmodified cell specimen, and not with the biotin label. Thus, we see that an important criteria of 'reagent-ness' is that it is a facilitator, and not the primary focus of an investigation or material processing technique (ie not the specified subject/evaluant about which knowledge is sought, or the specified output material of the technique). reagent true 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 true testable hypothesis that fucoidan has a small statistically significant effect on AT3 level but no useful clinical effect as in-vivo anticoagulant, a paraphrase of part of the last paragraph of the discussion section of the paper 'Pilot clinical study to evaluate the anticoagulant activity of fucoidan', by Lowenthal et. al.PMID:19696660 An information content entity that expresses an assertion that is intended to be tested. In the Philly 2013 workshop, we recognized the limitations of "hypothesis textual entity", and we introduced this as more general. The need for the 'textual entity' term going forward is up for future debate. Group:2013 Philly Workshop group hypothesis Group:2013 Philly Workshop group testable hypothesis true 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 true cell freezing medium culture media or serum + 10% DMSO is often used as cell freezing media. 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 true computation run time Gigascience. 2012 Dec 27;1(1):18. doi: 10.1186/2047-217X-1-18. PMID: 23587118. See Table 4 computation run time is a time measurement datum which corresponds the time expressed in second, minute, hour necessary for a computer program to complete a process execution, for example genome assembly. It is an important metrics as it indicates the resource occupancy and computer program efficiency. Alejandra Gonzalez-Beltran Philippe Rocca-Serra computation run time datum PRS,AGB computation run time true mass value specification A value specification that specifies the mass of some thing. PERSON:Bjoern Peters mass value specification true categorical value specification A value specification that is specifies one category out of a fixed number of nominal categories PERSON:Bjoern Peters categorical value specification true 1 1 scalar value specification A value specification that consists of two parts: a numeral and a unit label PERSON:Bjoern Peters scalar value specification true 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 true genome coverage Gigascience. 2012 Dec 27;1(1):18. doi: 10.1186/2047-217X-1-18. PMID: 23587118. "The genome coverage increased from 81.16% to 93.91%" A data item that is the total number of bases in reads, divided by genome size, assumed to be the reference size (for instance of 3.10 Gb for human and 2.73 Gb for mouse) and refers to the percentage of the genome that is contained in the assembly based on size estimates; these are usually based on cytological techniques. Genome coverage of 90–95% is generally considered to be good, as most genomes contain a considerable fraction of repetitive regions that are difficult to sequence. So it is not a cause for concern if the genome coverage of an assembly is a bit less than 100%. Alejandra Gonzalez-Beltran Philippe Rocca-Serra A beginner's guide to eukaryotic genome annotation. Yandell M, Ence D. Nat Rev Genet. 2012 Apr 18;13(5):329-42. doi: 10.1038/nrg3174. PMID: 22510764 genome coverage true N50 Gigascience. 2012 Dec 27;1(1):18. doi: 10.1186/2047-217X-1-18. PMID: 23587118. "Here, the contig and scaffold N50 of the YH genome were ~20.9 kbp and ~22 Mbp" the weighted median item size or N50 is a weighted median of the lengths of items, equal to the length of the longest item i such that the sum of the lengths of items greater than or equal in length to i is greater than or equal to half the length of all of the items. With regard to assemblies the items are typically contigs or scaffolds. It therefore denotes the ability of the software to create contigs and provides information about the resulting sequence assembly Alejandra Gonzalez-Beltran Philippe Rocca-Serra weighted median item size adapted from: "http://genome.cshlp.org/content/21/12/2224.full?sid=74019122-f944-4ccc-bffe-d16fdd0e7d6c" (from table 7) and from "http://www.nature.com/nrg/journal/v14/n3/full/nrg3367.html" N50 true contig N50 Gigascience. 2012 Dec 27;1(1):18. doi: 10.1186/2047-217X-1-18. PMID: 23587118. "Here, the contig and scaffold N50 of the YH genome were ~20.9 kbp and ~22 Mbp" N50 statistic computed for the contigs produced by the assembly process. A contig N50 is calculated by first ordering every contig by length from longest to shortest. Next, starting from the longest contig, the lengths of each contig are summed, until this running sum equals one-half of the total length of all contigs in the assembly. The contig N50 of the assembly is the length of the shortest contig in this list. Alejandra Gonzalez-Beltran Philippe Rocca-Serra adapted from: nature:http://www.nature.com/nrg/journal/v13/n5/box/nrg3174_BX1.html contig N50 true scaffold N50 Gigascience. 2012 Dec 27;1(1):18. doi: 10.1186/2047-217X-1-18. PMID: 23587118. "Here, the contig and scaffold N50 of the YH genome were ~20.9 kbp and ~22 Mbp" N50 statistic computed for the scaffold produced by the assembly process. The method for computing the value is similar to that of contig N50 but uses scaffold information instead of contig information Alejandra Gonzalez-Beltran Philippe Rocca-Serra adapted from: nature:http://www.nature.com/nrg/journal/v13/n5/box/nrg3174_BX1.html scaffold N50 true RNA Integrity Number value specification A value specification that specifies the value of the RNA Integrity Number as a real value between 1 (most degraded) and 10 (most intact). Chris Stoeckert, Bjoern Peters RIN value specification OBI RNA Integrity Number value specification true temperature value specification A value specification that specifies the temperature of some thing. Chris Stoeckert OBI temperature value specification true volume value specification A value specification that specifies the volume of some thing. Chris Stoeckert OBI volume value specification true tissue section thickness A length measurement datum that is the result of an assay measuring the thickness of a tissue section. Chris Stoeckert, Helena Ellis NCI BBRB, OBIB NCI BBRB tissue section thickness true histologic grade according to AJCC 7th edition G4: Undifferentiated G1:Well differentiated A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the American Joint Committee on Cancer (AJCC) 7th Edition grading system. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB histologic grade according to AJCC 7th edition true histologic grade according to the Fuhrman Nuclear Grading System A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the Fuhrman Nuclear Grading System. Chris Stoeckert, Helena Ellis Histologic Grade (Fuhrman Nuclear Grading System) NCI BBRB, OBI NCI BBRB histologic grade according to the Fuhrman Nuclear Grading System true histologic grade for ovarian tumor A categorical value specification that is a histologic grade assigned to a ovarian tumor. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB histologic grade for ovarian tumor true histologic grade for ovarian tumor according to a two-tier grading system A histologic grade for ovarian tumor that is from a two-tier histological classification of tumors. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB histologic grade for ovarian tumor according to a two-tier grading system true histologic grade for ovarian tumor according to the World Health Organization A histologic grade for ovarian tumor that is from a histological classification by the World Health Organization (WHO). Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB histologic grade for ovarian tumor according to the World Health Organization true pathologic primary tumor stage for colon and rectum according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of colorectal cancer following the rules of the TNM American Joint Committee on Cancer (AJCC) version 7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. Chris Stoeckert, Helena Ellis pT: Pathologic spread colorectal primary tumor (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic primary tumor stage for colon and rectum according to AJCC 7th edition true pathologic primary tumor stage for lung according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM American Joint Committee on Cancer (AJCC) version 7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. Chris Stoeckert, Helena Ellis pT: Pathologic spread lung primary tumor (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic primary tumor stage for lung according to AJCC 7th edition true pathologic primary tumor stage for kidney according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. Chris Stoeckert, Helena Ellis pT: Pathologic spread kidney primary tumor (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic primary tumor stage for kidney according to AJCC 7th edition true pathologic primary tumor stage for ovary according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. Chris Stoeckert, Helena Ellis pT: Pathologic spread ovarian primary tumor (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic primary tumor stage for ovary according to AJCC 7th edition true pathologic lymph node stage for colon and rectum according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of colorectal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes. Chris Stoeckert, Helena Ellis pN: Pathologic spread colon lymph nodes (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic lymph node stage for colon and rectum according to AJCC 7th edition true pathologic lymph node stage for lung according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes. Chris Stoeckert, Helena Ellis pN: Pathologic spread colon lymph nodes (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic lymph node stage for lung according to AJCC 7th edition true pathologic lymph node stage for kidney according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes. Chris Stoeckert, Helena Ellis pN: Pathologic spread kidney lymph nodes (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic lymph node stage for kidney according to AJCC 7th edition true pathologic lymph node stage for ovary according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes. Chris Stoeckert, Helena Ellis pN: Pathologic spread ovarian lymph nodes (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic lymph node stage for ovary according to AJCC 7th edition true pathologic distant metastases stage for colon according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of colon cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. Chris Stoeckert, Helena Ellis M: colon distant metastases (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic distant metastases stage for colon according to AJCC 7th edition true pathologic distant metastases stage for lung according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. Chris Stoeckert, Helena Ellis M: lung distant metastases (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic distant metastases stage for lung according to AJCC 7th edition true pathologic distant metastases stage for kidney according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. Chris Stoeckert, Helena Ellis M: kidney distant Metastases (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic distant metastases stage for kidney according to AJCC 7th edition true pathologic distant metastases stage for ovary according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. Chris Stoeckert, Helena Ellis M: ovarian distant metastases (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic distant metastases stage for ovary according to AJCC 7th edition true clinical tumor stage group according to AJCC 7th edition A categorical value specification that is an assessment of the stage of a cancer according to the American Joint Committee on Cancer (AJCC) v7 staging systems. Chris Stoeckert, Helena Ellis Clinical tumor stage group (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB clinical tumor stage group according to AJCC 7th edition true International Federation of Gynecology and Obstetrics cervical cancer stage value specification A categorical value specification that is an assessment of the stage of a gynecologic cancer according to the International Federation of Gynecology and Obstetrics (FIGO) staging systems. Chris Stoeckert, Helena Ellis Clinical FIGO stage NCI BBRB, OBI NCI BBRB International Federation of Gynecology and Obstetrics cervical cancer stage value specification true International Federation of Gynecology and Obstetrics ovarian cancer stage value specification A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the FIGO classification system. Chris Stoeckert, Helena Ellis Pathologic Tumor Stage Grouping for ovarian cancer (FIGO) NCI BBRB, OBI NCI BBRB International Federation of Gynecology and Obstetrics ovarian cancer stage value specification true performance status value specification A categorical value specification that is an assessment of a participant's performance status (general well-being and activities of daily life). Chris Stoeckert, Helena Ellis Performance Status Scale https://en.wikipedia.org/wiki/Performance_status NCI BBRB performance status value specification true Eastern Cooperative Oncology Group score value specification A performance status value specification designed by the Eastern Cooperative Oncology Group to assess disease progression and its affect on the daily living abilities of the patient. Chris Stoeckert, Helena Ellis ECOG score NCI BBRB, OBI NCI BBRB Eastern Cooperative Oncology Group score value specification true Karnofsky score vaue specification A performance status value specification designed for classifying patients 16 years of age or older by their functional impairment. Chris Stoeckert, Helena Ellis Karnofsky Score NCI BBRB, OBI NCI BBRB Karnofsky score vaue specification true number of pregnancies A measurement datum of the total number of pregnancies a woman has had. Chris Stoeckert, Helena Ellis NCI BBRB, OBIB NCI BBRB number of pregnancies true number of live births A measurement datum of the total number of live births a female has had. Chris Stoeckert, Helena Ellis NCI BBRB, OBIB NCI BBRB number of live births true age when gave birth to first child An age measurement datum performed on a female when her first biological child was born. Chris Stoeckert, Helena Ellis NCI BBRB, OBIB NCI BBRB age when gave birth to first child true measurand role A role borne by a material entity and realized in an assay which achieves the objective to measure the magnitude/concentration/amount of the measurand in the entity bearing evaluant role. Person: Alan Ruttenberg, Jie Zheng https://en.wiktionary.org/wiki/measurand https://github.com/obi-ontology/obi/issues/778 measurand role true age since culture seeding measurement datum An age measurement datum that is the result of the measurement of the age of a cell since cultured (the process of seeding cells onto a culture dish). Stephen A. Fisher, Junhyong Kim, Dan Berrios age of culture age since culture seeding measurement datum true sequence read length measurement datum A measurement datum that is the result of the measurement of the number of bases in a DNA or RNA sequence. Stephen A. Fisher, Junhyong Kim, Dan Berrios read length, read length measurement datum sequence read length measurement datum true sequencing library input quantity measurement datum A scalar measurement datum that indicates the amount of sequencing library used as input for a sequencer. Stephen A. Fisher, Junhyong Kim library input amount sequencing library input quantity measurement datum true specimen harvest quantity A scalar measurement datum that indicates the amount of specimen collected. Stephen A. Fisher, Junhyong Kim, Dan Berrios harvest quantity specimen harvest quantity true minimum age value specification A value specifcation that specifies the youngest age when specifying an age range. Mathias Brochhausen minimum age value specification true maximum age value specification A value specifcation that specifies the oldest age when specifying an age range. Mathias Brochhausen maximum age value specification true 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 true 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 true 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 true 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 true 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 true 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 true 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 true 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 true 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 true 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 true 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 true donor A T cell line from a PPD(+) donor. A role which inheres in an organism or part thereof from which any part including cell, organ or tissue is removed with the intention that the donated part will be placed into another organism and/or cultured in vitro. IEDB donor role IEDB Definition modified by HP to deal with the case where an organ may be removed for donation but is not transplanted as intended. donor true A genome is a material entity that represents the entirety of an organism's hereditary information. The genome includes both the genes and the non-coding sequences of the DNA and RNA. Oliver He Book: Eugene Nester, Denise Anderson, C. Evans Roberts, Jr., Microbiology (Companion Site): A Human Perspective, 7th Edition. Mcgraw Hill, October 18, 2011. ISBN-13: 978-0073375311 WEB: http://en.wikipedia.org/wiki/Genome genome true A gene is a material entity that represents the entire DNA sequence required for synthesis of a functional protein or RNA molecule. Oliver He WEB: http://www.ncbi.nlm.nih.gov/books/NBK21640/ In addition to the coding regions (exons), a gene includes transcription-control regions and sometimes introns. Although the majority of genes encode proteins, some encode tRNAs, rRNAs, and other types of RNA. gene true a disposition that a gene can be used as a blueprint for generating a new form of product such as protein. Yongqun He WEB: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/objects/entrezgene/entrezgene.asn YH: According to NCBI Gene project, there are two gene types: unknown (0) , tRNA (1) , rRNA (2) , snRNA (3) , scRNA (4) , snoRNA (5) , protein-coding (6) , pseudo (7) , transposon (8) , miscRNA (9) , ncRNA (10) , other (255). Therefore, we have generated corresponding gene dispositions. Note that we don't use the term "gene type" here to differentiate the meanings of "type" and "disposition". gene disposition true a gene disposition that a gene can be used as a blueprint for generating a protein (i.e., a gene encodes for a protein). Yongqun He WEB: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/objects/entrezgene/entrezgene.asn protein-coding gene disposition true a gene disposition that represents the disposition of gene being "pseudo", i.e., the gene is a pseudogene. Yongqun He WEB: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/objects/entrezgene/entrezgene.asn pseudo gene disposition true The genome of an organism of Eukaryota Yue Liu, Bin Zhao, Oliver He 2759 genome of Eukaryota true The genome of an organism of Homo sapiens Yue Liu, Bin Zhao, Oliver He 9606 genome of Homo sapiens true A gene of an organism of Eukaryota Yue Liu, Bin Zhao, Oliver He 2759 gene of Eukaryota true A gene of an organism of Homo sapiens Yue Liu, Bin Zhao, Oliver He 9606 gene of Homo sapiens true A gene of Homo sapiens that has a protein-coding gene disposition Bin Zhao, Oliver He 9606 protein-coding gene of Homo sapiens true A gene of Homo sapiens that has a pseudo gene disposition Bin Zhao, Oliver He 9606 pseudo gene of Homo sapiens true Bin Zhao, Yue Liu, Oliver He AAT6 ACTSA MYMY5 WEB: http://www.ncbi.nlm.nih.gov/gene https://www.ncbi.nlm.nih.gov/pubmed/28117838 ACTA2 actin, alpha 2, smooth muscle, aorta 59 GIG46 10q23.3 20140408 9606 10 protein-coding Official from a nomenclature committee GO_0005524 (EC: IEA); GO_0005615 (EC: IDA); GO_0005737 (EC: IDA, PMID: 12355421); GO_0005829 (EC: TAS); GO_0006936 (EC: TAS); GO_0008217 (EC: IEA); GO_0009615 (EC: IEP, PMID: 16548883); GO_0014829 (EC: IEA); GO_0015629 (EC: IEA); GO_0030485 (EC: IEA); GO_0043234 (EC: IDA, PMID: 18468998); GO_0072144 (EC: IEP, PMID: 17464107) PMID: 1540415; 1555776; 1907279; 1939373; 1969628; 1991513; 2022339; 2295650; 2398629; 2612915; 2701935; 3842206; 6330528; 6725286; 7780165; 8138584; 8997639; 9512352; 9546431; 9841925; 10341211; 10556093; 10628374; 11037796; 11580270; 11707283; 11812134; 12119014; 12355421; 12477932; 12777385; 14530271; 14627618; 14694110; 15032605; 15164054; 15342556; 15489334; 15555551; 15588509; 15618548; 15703204; 15862967; 16051665; 16115228; 16289162; 16385451; 16526095; 16548883; 16573163; 17360745; 17411366; 17464107; 17504171; 17626241; 17786474; 17994018; 18443296; 18468998; 18775311; 18781797; 19261809; 19285011; 19409525; 19531499; 19639585; 19639654; 19654303; 19683985; 19745835; 19788615; 19883584; 19913121; 20128380; 20132408; 20147394; 20237496; 20301299; 20381122; 20618440; 20628086; 20628268; 20639865; 20689142; 20694011; 20734336; 20876399; 20970362; 20972266; 21131735; 21139048; 21145461; 21212136; 21233699; 21248741; 21288906; 21343850; 21477997; 21496259; 21530503; 21553326; 21612641; 21617610; 21815248; 21890473; 21906983; 21917091; 21923909; 21937134; 21937873; 21963094; 21987572; 21996542; 22001912; 22004035; 22053931; 22133903; 22138123; 22232431; 22395512; 22460095; 22465675; 22479424; 22505724; 22535526; 22543453; 22619371; 22790431; 22810585; 22831780; 22939629; 22946110; 22960022; 22989508; 23000965; 23020218; 23068445; 23116162; 23182716; 23246001; 23770605; 23788249; 23794425; 23982059; 24244333 actin, alpha 2, smooth muscle, aorta Ensembl:ENSG00000107796 HGNC:130 HPRD:00031 MIM:102620 Vega:OTTHUMG00000018700 Other designations: actin, aortic smooth muscle|alpha-cardiac actin|cell growth-inhibiting gene 46 protein This gene is upregulated at neural stem cell stage. Ref: https://www.ncbi.nlm.nih.gov/pubmed/28117838 ACTA2 true Bin Zhao, Yue Liu, Oliver He ANK SPH1 SPH2 WEB: http://www.ncbi.nlm.nih.gov/gene ANK1 ankyrin 1, erythrocytic 286 8p11.1 20140408 9606 8 protein-coding Official from a nomenclature committee GO_0005198 (EC: NAS, PMID: 9430667); GO_0005200 (EC: TAS, PMID: 8640229); GO_0005515 (EC: IPI, PMID: 12527750); GO_0005634 (EC: IEA); GO_0005829 (EC: TAS); GO_0005856 (EC: NAS, PMID: 1833445); GO_0005886 (EC: IDA, PMID: 379653); GO_0005886 (EC: NAS, PMID: 9430667); GO_0006779 (EC: IEA); GO_0006887 (EC: NAS, PMID: 1833445); GO_0006888 (EC: IDA, PMID: 18768923); GO_0007010 (EC: NAS, PMID: 9430667); GO_0007165 (EC: IEA); GO_0007411 (EC: TAS); GO_0008093 (EC: IDA, PMID: 379653); GO_0008093 (EC: TAS, PMID: 11427698); GO_0010638 (EC: IEA); GO_0014731 (EC: IDA, PMID: 379653); GO_0015672 (EC: IEA); GO_0016323 (EC: NAS, PMID: 12409278); GO_0016529 (EC: IEA); GO_0019899 (EC: IPI); GO_0019899 (EC: TAS, PMID: 11427698); GO_0030018 (EC: IEA); GO_0030507 (EC: IDA, PMID: 379653); GO_0030507 (EC: IPI, PMID: 8159688); GO_0030507 (EC: NAS, PMID: 8640229); GO_0030673 (EC: IEA); GO_0030863 (EC: IEA); GO_0031430 (EC: IEA); GO_0042383 (EC: IEA); GO_0045199 (EC: TAS, PMID: 11427698); GO_0045211 (EC: IEA); GO_0048821 (EC: IEA); GO_0051117 (EC: IPI, PMID: 8159688); GO_0072661 (EC: IMP, PMID: 18768923) PMID: 379653; 492324; 1689849; 1833445; 2137557; 2141335; 2968981; 2970468; 2971657; 6449514; 7505012; 8125298; 8159688; 8227202; 8385102; 8640229; 8681137; 8703812; 9024692; 9235914; 9430667; 9519902; 9587054; 9628825; 9804856; 10893266; 10910934; 11222639; 11372755; 11427698; 12019270; 12130521; 12409278; 12444090; 12456646; 12477932; 12527750; 12543979; 12631729; 12719424; 15040428; 15051494; 15489334; 15929114; 16580865; 16597699; 16718373; 16762928; 16962094; 17128827; 17207965; 17520478; 17716929; 17720975; 18768923; 18987618; 20379614; 20479128; 20858683; 21071415; 21099109; 21177872; 21493712; 22348230; 22424883; 22456796; 22573887; 22968456; 23013433; 23457408 ankyrin 1, erythrocytic Ensembl:ENSG00000029534 HGNC:492 HPRD:01693 MIM:612641 Vega:OTTHUMG00000150281 Other designations: ANK-1|ankyrin-1|ankyrin-R|erythrocyte ankyrin This gene is upregulated at neural stem cell stage. Ref: https://www.ncbi.nlm.nih.gov/pubmed/28117838 ANK1 true Bin Zhao, Yue Liu, Oliver He SM22 SMCC TAGLN1 WS3-10 WEB: http://www.ncbi.nlm.nih.gov/gene TAGLN transgelin 6876 11q23.2 20140408 9606 11 protein-coding Official from a nomenclature committee GO_0003779 (EC: IEA); GO_0005515 (EC: IPI); GO_0005737 (EC: IEA); GO_0007517 (EC: TAS, PMID: 9615232); GO_0030855 (EC: IDA) PMID: 1520290; 1872880; 7788527; 8117285; 8125298; 9242426; 9276683; 9384215; 9615232; 11053353; 11773051; 12200029; 12477932; 12521938; 15489334; 16009940; 17082327; 17305610; 17353931; 17629319; 18245174; 18291675; 18378184; 18446369; 19011151; 19188659; 19329940; 19724680; 19796641; 19848416; 19913121; 20012321; 20066125; 20098441; 20336793; 20379614; 20540360; 20628086; 20705054; 20707403; 21044950; 21051832; 21092460; 21139048; 21677441; 21763649; 21943158; 22245152; 22257561; 22365974; 22939629; 23138394; 23174934; 23331552; 23538046; 23824909 transgelin Ensembl:ENSG00000149591 HGNC:11553 HPRD:02891 MIM:600818 Vega:OTTHUMG00000167067 Other designations: 22 kDa actin-binding protein|SM22-alpha|smooth muscle protein 22-alpha|transgelin variant 2 This gene is upregulated at neural stem cell stage. Ref: https://www.ncbi.nlm.nih.gov/pubmed/28117838 TAGLN true Bin Zhao, Yue Liu, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene VGF VGF nerve growth factor inducible 7425 7q22.1 20140408 9606 7 protein-coding Official from a nomenclature committee GO_0001541 (EC: IEA); GO_0002021 (EC: IEA); GO_0003674 (EC: ND); GO_0005184 (EC: IEA); GO_0005615 (EC: IDA, PMID: 15706611); GO_0006091 (EC: IEA); GO_0008083 (EC: IEA); GO_0009409 (EC: IEA); GO_0019953 (EC: IEA); GO_0030073 (EC: IEA); GO_0030133 (EC: IEA); GO_0031410 (EC: IDA, PMID: 17440014); GO_0032868 (EC: IEA); GO_0042593 (EC: IEA); GO_0042742 (EC: IEA); GO_0051591 (EC: IEP, PMID: 10381005) PMID: 8125298; 9084409; 9344675; 10381005; 12477932; 15706611; 16481598; 17440014; 17684500; 18432310; 19598235; 20164831; 20471433; 20631166; 21151573; 21621608; 22808091; 24244333; 24250222; 24457600 VGF nerve growth factor inducible Other designations: neuro-endocrine specific protein VGF|neurosecretory protein VGF This gene is upregulated at neural stem cell stage. Ref: https://www.ncbi.nlm.nih.gov/pubmed/28117838 VGF true Bin Zhao, Yue Liu, Oliver He MST092 MST106 MST129 MSTP032 MSTP092 MSTP106 MSTP129 WEB: http://www.ncbi.nlm.nih.gov/gene RGS5 regulator of G-protein signaling 5 8490 RP11-267N12.3 1q23.1 20140408 9606 1 protein-coding Official from a nomenclature committee GO_0005096 (EC: IBA); GO_0005737 (EC: IDA); GO_0005886 (EC: IBA); GO_0007165 (EC: IEA); GO_0008277 (EC: TAS, PMID: 10471929); GO_0038032 (EC: IEA); GO_0043547 (EC: IBA); GO_0043547 (EC: TAS, PMID: 10471929) PMID: 9079700; 9747037; 10471929; 11009569; 11076863; 11230166; 11253162; 12477932; 14755443; 15342556; 15459006; 15489334; 15489336; 15670159; 16293795; 16344560; 16381901; 16710414; 17100651; 17220356; 17762159; 17939118; 18029348; 18262772; 18676680; 19170196; 19488044; 19536175; 19564336; 19625176; 19692168; 19863299; 20379614; 20453000; 20627871; 20643937; 21105200; 21278382; 21393447; 21780128; 21832049; 21881522; 22130514; 23464602; 23868206; 24009623; 24124411; 24297163 regulator of G-protein signaling 5 Ensembl:ENSG00000143248 Ensembl:ENSG00000232995 HGNC:10001 HPRD:04471 MIM:603276 Vega:OTTHUMG00000034441 This gene is upregulated at neural stem cell stage. Ref: https://www.ncbi.nlm.nih.gov/pubmed/28117838 RGS5 true Bin Zhao, Yue Liu, Oliver He GABABR2 GPR51 GPRC3B HG20 HRIHFB2099 WEB: http://www.ncbi.nlm.nih.gov/gene GABBR2 gamma-aminobutyric acid (GABA) B receptor, 2 9568 9q22.1-q22.3 20140408 9606 9 protein-coding Official from a nomenclature committee GO_0004965 (EC: IDA, Qualifier: contributes_to, PMID: 9872316); GO_0005515 (EC: IPI, PMID: 16724110); GO_0005737 (EC: IEA); GO_0005886 (EC: TAS); GO_0005887 (EC: IDA, PMID: 9872316); GO_0007186 (EC: TAS, PMID: 9872316); GO_0007194 (EC: TAS, PMID: 10328880); GO_0007214 (EC: IDA, PMID: 9872316); GO_0007268 (EC: TAS); GO_0030054 (EC: IEA); GO_0038039 (EC: IPI, PMID: 9872316); GO_0043005 (EC: IEA); GO_0045211 (EC: IEA) PMID: 2834384; 7494864; 9872316; 9872317; 10075644; 10087195; 10328880; 10727622; 10773016; 11087824; 11850456; 11854302; 12477932; 14625043; 14961561; 14966130; 14978362; 15164053; 15489334; 15660124; 15822905; 16169070; 16724110; 16829628; 17145756; 17185339; 18482426; 18577758; 18978678; 19002745; 19086053; 19308021; 19336370; 19744961; 19763258; 20379614; 20424473; 20467438; 20557420; 20583170; 20634891; 20734064; 21303731; 21724853; 21971078; 22169202; 22613715; 22660477; 23726511; 23864651 gamma-aminobutyric acid (GABA) B receptor, 2 Ensembl:ENSG00000136928 HGNC:4507 HPRD:09552 MIM:607340 Vega:OTTHUMG00000020345 Other designations: G protein-coupled receptor 51|G-protein coupled receptor 51|GABA-B receptor 2|GABA-B receptor, R2 subunit|GABA-B-R2|GABA-BR2|gamma-aminobutyric acid B receptor 2|gamma-aminobutyric acid type B receptor subunit 2|gb2 This gene is upregulated at neural stem cell stage. Ref: https://www.ncbi.nlm.nih.gov/pubmed/28117838 GABBR2 true Bin Zhao, Yue Liu, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene COL5A3 collagen, type V, alpha 3 50509 19p13.2 20140408 9606 19 protein-coding Official from a nomenclature committee GO_0005201 (EC: NAS, PMID: 10722718); GO_0005518 (EC: NAS, PMID: 10722718); GO_0005576 (EC: TAS); GO_0005588 (EC: NAS, PMID: 10722718); GO_0005788 (EC: TAS); GO_0007160 (EC: IEA); GO_0007411 (EC: TAS); GO_0008201 (EC: IEA); GO_0022617 (EC: TAS); GO_0030198 (EC: TAS); GO_0030199 (EC: NAS, PMID: 10722718); GO_0030574 (EC: TAS); GO_0043394 (EC: IEA); GO_0043588 (EC: NAS, PMID: 10722718) PMID: 1571108; 1916105; 6501291; 7115902; 7346227; 8535602; 9443080; 10722718; 11423559; 15136578; 15316020; 19012342 collagen, type V, alpha 3 Other designations: collagen alpha-3(V) chain|pro-(alpha)3(V) collagen This gene is upregulated at neural stem cell stage. Ref: https://www.ncbi.nlm.nih.gov/pubmed/28117838 COL5A3 true Bin Zhao, Yue Liu, Oliver He CLR19.9 NALP2 NBS1 PAN1 PYPAF2 WEB: http://www.ncbi.nlm.nih.gov/gene https://www.ncbi.nlm.nih.gov/pubmed/28117838 NLRP2 NLR family, pyrin domain containing 2 55655 XXbac-BPG230H20.8 19q13.42 20140408 9606 19 protein-coding Official from a nomenclature committee GO_0005515 (EC: IPI, PMID: 15030775); GO_0005524 (EC: IEA); GO_0005737 (EC: IDA, PMID: 15030775); GO_0032090 (EC: IPI, PMID: 15030775); GO_0043280 (EC: IDA, PMID: 15030775); GO_0050718 (EC: IDA, PMID: 15030775) PMID: 8125298; 11250163; 11270363; 12019269; 12387869; 12477932; 12563287; 14702039; 15030775; 15456791; 15489334; 15817483; 16344560; 17046979; 17178784; 17420470; 17435760; 18056399; 18285453; 18369178; 18772453; 19074885; 19103770; 19300480; 19534089; 19900269; 20403135; 20800603; 21832049; 21906983; 21976665; 22909446; 23128233; 23360675; 23625868; 23644288 NLR family, pyrin domain containing 2 Ensembl:ENSG00000022556 HGNC:22948 HPRD:14805 MIM:609364 Vega:OTTHUMG00000167763 Other designations: NACHT, LRR and PYD containing protein 2|NACHT, LRR and PYD domains-containing protein 2|NACHT, leucine rich repeat and PYD containing 2|PYRIN domain and NACHT domain-containing protein 1|PYRIN-containing APAF1-like protein 2|nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 2|nucleotide-binding site protein 1 This gene is upregulated at neural stem cell stage and at iPSC stage. Ref: https://www.ncbi.nlm.nih.gov/pubmed/28117838 NLRP2 true Bin Zhao, Yue Liu, Oliver He CBP PAG WEB: http://www.ncbi.nlm.nih.gov/gene PAG1 phosphoprotein associated with glycosphingolipid microdomains 1 55824 8q21.13 20140408 9606 8 protein-coding Official from a nomenclature committee GO_0005070 (EC: NAS, PMID: 10790433); GO_0005515 (EC: IPI, PMID: 10790433); GO_0005886 (EC: IDA, PMID: 10790433); GO_0005886 (EC: TAS); GO_0007165 (EC: TAS, PMID: 10790433); GO_0007173 (EC: TAS); GO_0009967 (EC: NAS, PMID: 10790433); GO_0016021 (EC: IEA); GO_0035556 (EC: IDA, PMID: 10790433); GO_0042169 (EC: IDA, PMID: 10790433); GO_0045121 (EC: IDA, PMID: 10790433); GO_0050852 (EC: TAS); GO_0050863 (EC: IDA, PMID: 10790433); GO_0050868 (EC: IEA) PMID: 9334312; 10790433; 11163757; 11684085; 12477932; 12665526; 14665621; 14702039; 15489334; 16160011; 16413409; 16636672; 16947079; 17143285; 17389760; 18056706; 18070987; 19581936; 19913121; 20379614; 20388373; 20561033; 20628086; 21092590; 21156787; 21388951; 21822266; 22027792; 22659621; 22994656; 23022100; 23671581 phosphoprotein associated with glycosphingolipid microdomains 1 Ensembl:ENSG00000076641 HGNC:30043 HPRD:05772 HPRD:16944 MIM:605767 Vega:OTTHUMG00000164592 Other designations: Csk-binding protein|phosphoprotein associated with glycosphingolipid-enriched microdomains 1|transmembrane adapter protein PAG|transmembrane adaptor protein PAG|transmembrane phosphoprotein Cbp This gene is upregulated at neural stem cell stage. Ref: https://www.ncbi.nlm.nih.gov/pubmed/28117838 PAG1 true Bin Zhao, Yue Liu, Oliver He CPI17-like KEPI NY-BR-81 WEB: http://www.ncbi.nlm.nih.gov/gene PPP1R14C protein phosphatase 1, regulatory (inhibitor) subunit 14C 81706 6q24.3-q25.3 20140408 9606 6 protein-coding Official from a nomenclature committee GO_0004865 (EC: IEA); GO_0005737 (EC: IEA); GO_0016020 (EC: IEA); GO_0042325 (EC: IEA) PMID: 11564868; 11812771; 11948623; 12477932; 12747765; 14574404; 14702039; 15489334; 16449650; 19132087; 19475667; 20592344; 21946350; 22939629; 23284291 protein phosphatase 1, regulatory (inhibitor) subunit 14C Ensembl:ENSG00000198729 HGNC:14952 HPRD:17890 MIM:613242 Vega:OTTHUMG00000015818 Other designations: PKC-potentiated PP1 inhibitory protein|kinase C-enhanced PP1 inhibitor|kinase-enhanced PP1 inhibitor|protein phosphatase 1 regulatory subunit 14C|serologically defined breast cancer antigen NY-BR-81 This gene is upregulated at neural stem cell stage. Ref: https://www.ncbi.nlm.nih.gov/pubmed/28117838 PPP1R14C true Bin Zhao, Yue Liu, Oliver He CEACAM3 R29124_1 WEB: http://www.ncbi.nlm.nih.gov/gene CEACAM21 carcinoembryonic antigen-related cell adhesion molecule 21 90273 UNQ3098/PRO10075 19q13.2 20140408 9606 19 protein-coding Official from a nomenclature committee GO_0016021 (EC: IEA) PMID: 12477932; 12975309; 14702039; 21682944; 23065704 carcinoembryonic antigen-related cell adhesion molecule 21 Ensembl:ENSG00000007129 HGNC:28834 HPRD:10179 Vega:OTTHUMG00000151062 This gene is upregulated at neural stem cell stage. Ref: https://www.ncbi.nlm.nih.gov/pubmed/28117838 CEACAM21 true Bin Zhao, Yue Liu, Oliver He UNQ26 bet WEB: http://www.ncbi.nlm.nih.gov/gene DNER delta/notch-like EGF repeat containing 92737 UNQ262/PRO299 2q36.3 20140408 9606 2 protein-coding Official from a nomenclature committee GO_0001764 (EC: NAS, PMID: 11950833); GO_0004888 (EC: TAS, PMID: 11950833); GO_0005112 (EC: IEA); GO_0005509 (EC: NAS, PMID: 11950833); GO_0005515 (EC: IPI, PMID: 11950833); GO_0005769 (EC: IDA, PMID: 11950833); GO_0005886 (EC: IDA, PMID: 11950833); GO_0006897 (EC: NAS, PMID: 11950833); GO_0007219 (EC: TAS); GO_0007220 (EC: IEA); GO_0007416 (EC: NAS, PMID: 11950833); GO_0007417 (EC: IEP, PMID: 11950833); GO_0010001 (EC: IEA); GO_0016021 (EC: IEA); GO_0030276 (EC: TAS, PMID: 11950833); GO_0030425 (EC: IDA, PMID: 11950833); GO_0043025 (EC: IEA); GO_0048741 (EC: IEA) PMID: 9847074; 11950833; 11997712; 12477932; 12975309; 15489334; 15815621; 16344560; 16740002; 20070733; 20237496; 20367751; 23284291; 23382691; 24101674 delta/notch-like EGF repeat containing Ensembl:ENSG00000187957 HGNC:24456 HPRD:09531 MIM:607299 Vega:OTTHUMG00000153637 Other designations: H_NH0150O02.1|WUGSC:H_NH0150O02.1|delta and Notch-like epidermal growth factor-related receptor|delta-notch-like EGF repeat-containing transmembrane This gene is upregulated at neural stem cell stage. Ref: https://www.ncbi.nlm.nih.gov/pubmed/28117838 DNER true Bin Zhao, Yue Liu, Oliver He WEB: http://www.ncbi.nlm.nih.gov/gene EEF1A1P16 eukaryotic translation elongation factor 1 alpha 1 pseudogene 16 387845 12p12.3 20140408 9606 12 pseudo Official from a nomenclature committee eukaryotic translation elongation factor 1 alpha 1 pseudogene 16 This gene is upregulated at iPSC stage. Ref: https://www.ncbi.nlm.nih.gov/pubmed/28117838 EEF1A1P16 true An ethnic identity datum that is the output of an ethnic identification process that uses OMB terminology for ethnicity or terminology that is mapped the OMB ethnicity terms. Amanda Hicks OMB ethnic identity datum true A racial identity is an information content entity that is the output of some racial identitification process and is intended to be a truthful statement about the genetic or cultural race of a person. Unlike data items they are not necessilary contributed or acquired by a reliable method. racial identity datum true racial identification process true An ethnic identity datum is an information content entity that is the output of some ethnic identitification process and is intended to be a truthful statement about the cultural or national heritage of a person. Unlike data items they are not necessilary contributed or acquired by a reliable method. Amanda Hicks ethnic identity datum true ethnic identification process true An OMB ethnic identity datum that indicates the person identified is of Cuban, Mexican, Puerto Rican, South or Central American, or other Spanish culture or origin regardless of race. Amanda Hicks hispanic or latino identity datum true An OMB ethnic identity datum that indicates the person identified is not of Cuban, Mexican, Puerto Rican, South or Central American, or other Spanish culture or origin regardless of race. Amanda Hicks not hispanic or latino identity datum true An identity datum is an information content entity that is the output of some identitification process and is intended to be a truthful statement about a person's social identity. Unlike data items they are not necessilary contributed or acquired by a reliable method. Amanda Hicks identity datum true A gender identity is an information content entity that is the output of some gender identitification process and is intended to be a truthful statement about a person's subjective sense of their gender. Unlike data items they are not necessilary contributed or acquired by a reliable method. Amanda Hicks gender identity datum true Amanda Hicks identification process true true gender identification process true a gender identity datum resulting from a gender identification process in which ‘female’ is selected based on the participant's subjective sense of gender Amanda Hicks female gender identity datum true a gender identity datum resulting from a gender identification process in which ‘male’ is selected based on the participant's subjective sense of gender Amanda Hicks male gender identity datum true A racial identity that is the output of a racial identification process that uses OMB terminology for race or terminology that is mapped the OMB race terms and that indicates that the subject of the identity has origins in any of the original peoples of North and South America (including Central America), and maintains tribal affiliation or community attachment. Amanda Hicks American Indian or Alaska Native identity datum true A racial identity that is the output of a racial identification process that uses OMB terminology for race or terminology that is mapped the OMB race terms and that indicates that the subject of the identity has origins in any of the original peoples of the Far East, Southeast Asia, or the Indian subcontinent. Amanda Hicks Asian identity datum true A racial identity that is the output of a racial identification process that uses OMB terminology for race or terminology that is mapped the OMB race terms and that indicates that the subject of the identity has origins in any of the black racial groups of Africa. Amanda Hicks black or African American identity datum true A racial identity that is the output of a racial identification process that uses OMB terminology for race or terminology that is mapped the OMB race terms and that indicates that the subject of the identity has origins in any of the original peoples of Hawaii, Guam, Samoa, or other Pacific Islands. Amanda Hicks Native Hawaiian or other Pacific Islander identity datum true A racial identity that is the output of a racial identification process that uses OMB terminology for race or terminology that is mapped the OMB race terms and that indicates that the subject of the identity has origins in any of the original peoples of Europe, the Middle East, or North Africa. Amanda Hicks white identity datum true A racial identity that is the output of a racial identification process that uses OMB terminology for race or terminology that is mapped the OMB race terms. Amanda Hicks OMB racial identity datum true A measurement datum that records how many times a cell culture has been subcultured. Bill Duncan <http://orcid.org/0000-0001-9625-1899> 2018-05-31T21:47:04Z cell cutlture passage number true gene marker role true stem cell marker process true neural stem cell marker process true iPSC marker process true Bill Duncan <http://orcid.org/0000-0001-9625-1899> 2018-05-31T22:04:02Z stem cell producer true Bill Duncan <http://orcid.org/0000-0001-9625-1899> 2018-05-31T22:05:33Z stem cell provider true Bill Duncan <http://orcid.org/0000-0001-9625-1899> 2018-05-31T22:44:27Z age of donor at time of donation true Bill Duncan <http://orcid.org/0000-0001-9625-1899> 2018-05-31T22:49:56Z cell line testing laboratory true Bill Duncan <http://orcid.org/0000-0001-9625-1899> 2018-05-31T23:01:40Z feeder cell role true Bill Duncan <http://orcid.org/0000-0001-9625-1899> 2018-05-31T23:03:57Z feeder cell true true Bill Duncan <http://orcid.org/0000-0001-9625-1899> 2018-05-31T23:05:48Z feeder cell preparation protocol true Bill Duncan <http://orcid.org/0000-0001-9625-1899> 2018-05-31T23:08:01Z source cell storage/master cell banking protocol true Bill Duncan <http://orcid.org/0000-0001-9625-1899> 2018-05-31T23:09:23Z source cell procurement protocol true Bill Duncan <http://orcid.org/0000-0001-9625-1899> 2018-05-31T23:10:11Z material transferring protocol true Bill Duncan <http://orcid.org/0000-0001-9625-1899> 2018-05-31T23:10:35Z cell passage protocol true Bill Duncan <http://orcid.org/0000-0001-9625-1899> 2018-05-31T23:11:25Z establishment protocol (molecular induction protocol) true Bill Duncan <http://orcid.org/0000-0001-9625-1899> 2018-05-31T23:12:12Z cell culture protocol true Bill Duncan <http://orcid.org/0000-0001-9625-1899> 2018-06-05T17:59:34Z donor true Bill Duncan <http://orcid.org/0000-0001-9625-1899> 2018-06-05T19:08:22Z TeSR true Bill Duncan <http://orcid.org/0000-0001-9625-1899> 2018-06-05T19:08:39Z DMEM true Bill Duncan <http://orcid.org/0000-0001-9625-1899> 2018-06-05T19:08:58Z F12 true Bill Duncan <http://orcid.org/0000-0001-9625-1899> 2018-06-05T19:15:48Z cell culture additive role true Bill Duncan <http://orcid.org/0000-0001-9625-1899> 2018-06-05T19:18:35Z cell culture medium additive true Bill Duncan <http://orcid.org/0000-0001-9625-1899> 2018-06-05T19:24:37Z concentration measurment datum true age A time quality inhering in a bearer by virtue of how long the bearer has existed. age true biological sex James Malone Jie Zheng Tomasz Adamusiak biological sex http://mged.sourceforge.net/ontologies/MGEDOntology.owl#sex MO_680 NCIt:C28421 PATO:0000047 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. Term applied to any organism able to undergo sexual reproduction in order to differentiate the individuals or types involved. Sexual reproduction is defined as the ability to exchange genetic material with the potential of recombinant progeny. The assemblage of physical properties or qualities by which male is distinguished from female; the physical difference between male and female; the distinguishing peculiarity of male or female. biological sex sex EFO_URI: http://www.ebi.ac.uk/efo/EFO_0000695 true length A 1-D extent quality which is equal to the distance between two points. length true mass A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter. mass true temperature A physical quality of the thermal energy of a system. temperature true behavioral quality An organismal quality inhering in a bearer by virtue of the bearer's behavior aggregate of the responses or reactions or movements in a given situation. behavioral quality true James Malone Jie Zheng Tomasz Adamusiak http://mged.sourceforge.net/ontologies/MGEDOntology.owl#male CARO:0000027 MO_652 PATO:0000384 A biological sex quality inhering in an individual or a population whose sex organs contain only male gametes. male true volume A 3-D extent quality inhering in a bearer by virtue of the bearer's amount of 3-dimensional space it occupies. volume true quality of a single physical entity A physical object quality which inheres in a single-bearer. quality of a single physical entity true physical object quality physical object quality true cellular quality true cellular potency cellular potency true unipotent true multipotent multipotent true pluripotent pluripotent true organismal quality organismal quality true handedness A behavioral quality inhering ina bearer by virtue of the bearer's unequal distribution of fine motor skill between its left and right hands or feet. handedness true left handedness Handedness where the organism preferentially uses the left hand or foot for tasks requiring the use of a single hand or foot or a dominant hand or foot. left handedness true right handedness Handedness where the organism preferentially uses the right hand or foot for tasks requiring the use of a single hand or foot or a dominant hand or foot. right handedness true ambidextrous handedness Handedness where the organism exhibits no overall dominance in the use of right or left hand or foot in the performance of tasks that require one hand or foot or a dominant hand or foot. ambidextrous handedness true An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA. protein true 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. B-lymphocyte surface antigen B4 CD19 T-cell surface antigen Leu-12 differentiation antigen CD19 CD19 molecule true 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 hematopoietic progenitor cell antigen CD34 CD34 molecule true 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 T-cell differentiation antigen L3T4 T-cell surface antigen T4/Leu-3 T-cell surface glycoprotein CD4 CD4 molecule true An integrin alpha that contains an A domain. A hallmark of this class is the presence of a von Willebrand factor type A domain (Pfam:PF00092) (I-domain) of approximately 200 amino acid residues at the N terminus, which confers divalent cation binding properties. Unlike other integrin alpha proteins, they do not undergo proteolytic cleavage. integrin alpha with I domain integrin alpha with A domain true 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. T200 CD45 L-CA PTPRC leukocyte common antigen ly-5 lymphocyte antigen 5 receptor-type tyrosine-protein phosphatase C true 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. CD11 antigen-like family member B CD11b CR-3 alpha chain ITGAM cell surface glycoprotein MAC-1 subunit alpha leukocyte adhesion receptor MO1 neutrophil adherence receptor CR3A integrin alpha-M true 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 exons 4(A), 5(B), and 6(C). Example: UniProtKB:P08575-1. CD45R CD45RABC PTPRC/iso:CD45R B220 receptor-type tyrosine-protein phosphatase C isoform CD45R true A protein with a core domain composition consisting of an extracellular N-terminal domain that adopts an immunoglobulin fold, a transmembrane domain, and an intracellular C-terminal domain with a single copy of the Immunoreceptor tyrosine-based activation motif (Pfam:PF02189) (ITAM). It constitutes the invariant subunit of the T cell antigen receptor (TCR). TCR is a surface receptor on T cells responsible for recognizing MHC-restricted antigens and initiating the cellular immune response. CD3 subunit with Ig-like domain CD3 subunit with immunoglobulin domain true A CD3 subunit with immunoglobulin domain that is a translation product of the human CD3E gene or a 1:1 ortholog thereof. CD3E CD3e T-cell surface antigen T3/Leu-4 epsilon chain T3E CD3 epsilon true A protein with a domain composition consisting of a large extracellular domain, including five Ig-like C2-type domains followed by two copies of the Fibronectin type-III domain (Pfam:PF00041), a single-pass transmembrane domain and a short cytoplasmic C-terminal domain. neural cell adhesion molecule true A neural cell adhesion molecule that is involved in neuronal development, synaptic plasticity, and regeneration. neural cell adhesion molecule NCAM true A neural cell adhesion molecule NCAM that is a translation product of the human NCAM1 gene or a 1:1 ortholog thereof. CD56 N-CAM-1 NCAM-1 NCAM1 NCAM neural cell adhesion molecule 1 true A protein that is a translation product of the human CD2 gene or a 1:1 ortholog thereof. CD2 LFA-2 LFA-3 receptor T-cell surface antigen CD2 T-cell surface antigen T11/Leu-5 T-cell surface glycoprotein CD2 erythrocyte receptor ly-37 lymphocyte antigen 37 rosette receptor SRBC CD2 molecule true 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. CD8A CD8a T-cell surface glycoprotein Lyt-2 T-lymphocyte differentiation antigen T8/Leu-2 Lyt-2 Lyt2 MAL T-cell surface glycoprotein CD8 alpha chain true A protein that contains the ADP-ribosyl cyclase domain (Pfam:PF02267). ADP-ribosyl cyclase true A protein that is a translation product of the human MS4A1 gene or a 1:1 ortholog thereof. B-cell differentiation antigen Ly-44 B-cell surface antigen CD20 B-lymphocyte antigen CD20 B-lymphocyte surface antigen B1 Bp35 CD20 MS4A1 leukocyte surface antigen Leu-16 lymphocyte antigen 44 Ly-44 Ms4a2 membrane-spanning 4-domains subfamily A member 1 true A protein that is a translation product of the human CD44 gene or a 1:1 ortholog thereof. CD44 CD44 antigen CDw44 ECMR-III GP90 lymphocyte homing/adhesion receptor HUTCH-I PGP-1 epican extracellular matrix receptor III heparan sulfate proteoglycan hermes antigen hyaluronate receptor ly-24 lymphocyte antigen 24 phagocytic glycoprotein 1 phagocytic glycoprotein I LHR MDU2 MDU3 MIC4 PGP-I CD44 molecule true A protein that is a translation product of the human CD48 gene or a 1:1 ortholog thereof. B-lymphocyte activation marker BLAST-1 BCM1 surface antigen BLAST-1 CD48 CD48 antigen HM48-1 MRC OX-45 surface antigen TCT.1 leukocyte antigen MEM-102 sgp-60 BCM1 BLAST1 Bcm-1 CD48 molecule true A protein that has a core domain structure of signal sequence, propeptide, five Cadherin domains (Pfam:PF00028), a transmembrane region, and a Cadherin cytoplasmic region (Pfam:PF01049). Cadherins function as adhesion molecules that mediate Ca2+-dependent cell-cell adhesion in solid tissues. cadherin true A protein that is a translation product of the human ENG gene or a 1:1 ortholog thereof. CD105 ENG cell surface MJ7/18 antigen END Edg endoglin true 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 true An ADP-ribosyl cyclase that is a translation product of the human CD38 gene or a 1:1 ortholog thereof. CD38 I-19 NIM-R5 antigen T10 cADPr hydrolase 1 cyclic ADP-ribose hydrolase 1 ADP-ribosyl cyclase 1 true A cadherin that is a translation product of the human CDH5 gene or a 1:1 ortholog thereof. 7B4 antigen CD144 CDH5 VE-cadherin vascular endothelial cadherin cadherin-5 true An immunoglobulin gamma Fc receptor II/III/IV that is a translation product of the mouse Fcgr3 gene or a 1:1 ortholog thereof. CD16 Fc-gamma RIII FcRIII Fcgr3 IgG Fc receptor III low affinity immunoglobulin gamma Fc region receptor III true A protein with core architecture consisting of one Prominin (Pfam:PF05478) domain. The prominins are an emerging family of proteins that, among the multispan membrane proteins, display a novel topology. Mouse and human prominin and prominin-like 1 are predicted to contain five membrane spanning domains, with an N-terminal domain exposed to the extracellular space followed by four, alternating small cytoplasmic and large extracellular, loops and a cytoplasmic C-terminal domain. prominin true A prominin that is a translation product of the human PROM1 gene or a 1:1 ortholog thereof. CD133 PROM1 antigen AC133 antigen AC133 homolog prominin-like protein 1 PROML1 Prom prominin-1 true A protein that is a translation product of the human NT5E gene or a 1:1 ortholog thereof. 5'-NT CD73 NT5E ecto-5'-nucleotidase NT5 NTE 5'-nucleotidase true 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 true A protein with core architecture consisting of asignal sequence, 5 Ig-like domains, followed by a transmembrane sequence, followed by a Protein tyrosine kinase domain (Pfam:PF07714). However, only 1-3 of the Ig domains are detected by the Pfam HMMs in most of the sequences. Pfam:PF00047 is most common, but other members of the Ig domain clan, Pfam:PF07679 and Pfam:PF07686 can be identified instead. The fourth Ig domain lacks the disulfide-bonded cysteines. CSF-1/PDGF receptor-type tyrosine-protein kinase true A protein that is a translation product of the human SLAMF1 gene or a 1:1 ortholog thereof. CD150 CDw150 IPO-3 SLAMF1 SLAM SLAM family member 1 true A protein that is a translation product of the human CD5 gene or a 1:1 ortholog thereof. CD5 Lyt-1 ly-1 lymphocyte antigen 1 lymphocyte antigen T1/Leu-1 LEU1 T-cell surface glycoprotein CD5 true A protein that is a translation product of the human THY1 gene or a 1:1 ortholog thereof. CD90 CDw90 THY1 Thy-1 antigen Thy-1 Thy-1 membrane glycoprotein true A protein that is a translation product of the human IL7R gene or a 1:1 ortholog thereof. CD127 CDw127 IL-7 receptor subunit alpha IL-7R subunit alpha IL-7R-alpha IL-7RA IL7R interleukin-7 receptor subunit alpha true 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 true A protein that is a translation product of the human CD14 gene or a 1:1 ortholog thereof. CD14 monocyte differentiation antigen CD14 myeloid cell-specific leucine-rich glycoprotein CD14 molecule true A protein that is a translation product of the human CD33 gene or a 1:1 ortholog thereof. CD33 gp67 myeloid cell surface antigen CD33 sialic acid-binding Ig-like lectin 3 siglec-3 SIGLEC3 CD33 molecule true A protein that is a translation product of the human CD244 gene or a 1:1 ortholog thereof. CD244 NAIL NK cell activation-inducing ligand NK cell type I receptor protein 2B4 NKR2B4 non-MHC restricted killing associated 2B4 Nmrk natural killer cell receptor 2B4 true A protein that is a translation product of the human CD24 gene or a 1:1 ortholog thereof. CD24 HSA M1/69-J11D heat stable antigen R13-Ag X62 heat stable antigen ly-52 lymphocyte antigen 52 nectadrin small cell lung carcinoma cluster 4 antigen CD24A signal transducer CD24 true A protein with core architecture consisting of a signal sequence, a Lectin C-type domain (Pfam:PF00059), 5 or 6 EGF-like domains (Pfam:PF00008, Pfam:PF09064, or Pfam:PF07645), a transmembrane region, and a small cytoplasmic region (36-51 amino acids). thrombomodulin-like receptor true A protein that is a translation product of the human TFRC gene or a 1:1 ortholog thereof. p90 CD71 T9 TFRC TfR TfR1 Trfr TR transferrin receptor protein 1 true A protein with core architecture consisting of a signal sequence, followed by 7 Ig-like domains (Pfam:PF00047, Pfam:PF07679, or Pfam:PF07686), a transmembrane region, and a cytoplasmic Protein tyrosine kinase domain. vascular endothelial growth factor receptor true A CSF-1/PDGF receptor-type tyrosine-protein kinase that is a translation product of the human FLT3 gene or a 1:1 ortholog thereof. CD135 FLK-2 FLT-3 FLT3 Fms-like tyrosine kinase 3 fetal liver kinase 2 stem cell tyrosine kinase 1 tyrosine-protein kinase FLT3 tyrosine-protein kinase receptor FLT3 tyrosine-protein kinase receptor flk-2 STK-1 STK1 receptor-type tyrosine-protein kinase FLT3 true A thrombomodulin-like receptor that is a translation product of the human CD93 gene or a 1:1 ortholog thereof. C1q/MBL/SPA receptor C1qR C1qR(p) C1qRp CD93 CDw93 cell surface antigen AA4 complement component 1 q subcomponent receptor 1 ly-68 lymphocyte antigen 68 matrix-remodeling-associated protein 4 Aa4 C1QR1 Ly68 MXRA4 complement component C1q receptor true 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. CD117 KIT SCFR proto-oncogene c-Kit tyrosine-protein kinase Kit Sl mast/stem cell growth factor receptor true A vascular endothelial growth factor receptor that is a translation product of the human KDR gene or a 1:1 ortholog thereof. CD309 FLK-1 KDR VEGFR-2 fetal liver kinase 1 kinase NYK kinase insert domain receptor protein-tyrosine kinase receptor flk-1 FLK1 vascular endothelial growth factor receptor 2 true A protein that is the translation product of any of the LY6 genes (LY6A-LY6I). ly-6-like protein true A KLRB1-like protein that is a translation product of the mouse Klrb1c gene or a 1:1 ortholog thereof. CD161 antigen-like family member C CD161c Klrb1c NK1.1 NKR-P1 40 NKR-P1.9 NKR-P1C ly-55c lymphocyte antigen 55c natural killer cell surface protein P1-40 Ly55c Nkrp1c killer cell lectin-like receptor subfamily B member 1C true A ly-6-like protein that is a translation product of the mouse Ly6g gene or a 1:1 ortholog thereof. Ly6g ly-6G ly-6G.1 lymphocyte antigen 6G true A ly-6-like protein that is a translation product of the mouse Ly6a gene or a 1:1 ortholog thereof. Ly6a T-cell-activating protein ly-6A.2/Ly-6E.1 stem cell antigen 1 Ly6 SCA-1 TAP lymphocyte antigen 6A-2/6E-1 true A protein that is a translation product of the mouse Ly76 gene or a 1:1 ortholog thereof. Ly76 ter-119 ter119 lymphocyte antigen 76 true A protein that is a translation product of the human TAL1 gene or a 1:1 ortholog thereof. T-cell leukemia/lymphoma protein 5 TAL-1 TAL1 bHLHa17 class A basic helix-loop-helix protein 17 stem cell protein SCL TCL5 T-cell acute lymphocytic leukemia protein 1 true An organic amino compound that is a polymer of amino acid chain components (unmodified amino-acid residues and/or modified amino-acid residues linked by peptide bonds or derivatives of such bonds. peptide polypeptide amino acid chain true A protein that is composed of a long N-terminal extracellular domain, a transmembrane domain and a short cytoplasmic C-terminal domain. The N-terminal domain contains beta-propeller repeats (interrupted by an A domain in a subset of integrins alpha), while the C-terminal domain contains a GFFxR motif. integrin alpha true region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. primary structure of sequence macromolecule sequence region true supercontig One or more contigs that have been ordered and oriented using end-read information. Contains gaps that are filled with N's. supercontig true contig A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases. contig true sequence_assembly A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences. sequence_assembly true assembly A region of the genome of known length that is composed by ordering and aligning two or more different regions. assembly true Any portion of the organ that covers that body and consists of a layer of epidermis and a layer of dermis. portion of skin region of skin skin skin region skin zone zone of skin true true Any hollow cylindrical anatomical structure containing a lumen through which substances are transported. anatomical tube duct tube true Major subdivision of an organism that protrudes from the body[DOS, CARO]. appendages extremitaet extremity limbs/digits/tail appendage true A thin layer of loose connective tissue which lies beneath the epithelium and together with the epithelium constitutes the mucosa[WP]. The lamina propria contains capillaries and a central lacteal (lymph vessel) in the small intestine, as well as lymphoid tissue. Lamina propria also contains glands with the ducts opening on to the mucosal epithelium, that secrete mucus and serous secretions. lamina propria mucosa lamina propria mucosae tunica propria lamina propria true The head is the anterior-most division of the body [GO]. head (volume) adult head cephalic area head true A tubular structure that contains, conveys body fluid, such as blood or lymph. vessel true A tubular structure that transports secreted or excreted substances. anatomical duct exocrine duct exocrine gland duct ducts duct true Organ component adjacent to an organ cavity and which consists of a maximal aggregate of organ component layers. wall wall of organ organ wall anatomical wall true Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. AAO:0010825 AEO:0000003 BILA:0000003 CARO:0000003 EHDAA2:0003003 EMAPA:0 FBbt:00007001 FMA:305751 FMA:67135 GAID:781 HAO:0000003 MA:0003000 MESH:D000825 TAO:0000037 TGMA:0001823 VHOG:0001759 WBbt:0000100 XAO:0003000 ZFA:0000037 biological structure connected biological structure uberon UBERON:0000061 biological structure connected biological structure anatomical structure true Anatomical structure that performs a specific function or group of functions [WP]. anatomical unit body organ element organ true A part of an organ that constitutes a distinct modular sub-unit. In some cases, the organ may also contain other sub-units of identical or similar types, in other cases this may be a distinct entity. organ region with fixed fiat boundary organ segment segment of organ organ subunit true A multicellular structure that is a part of an organ. cardinal organ part regional part of organ organ part true Anatomical structure that is part of the respiratory system. In mammals consists of upper and lower tracts respiratory tract true true An section of a respiratory tract. respiratory tract subdivision of respiratory tract proximo-distal subdivision of respiratory tract true true Any part or collection of parts of the central or peripheral nervous system. Parts may span both CNS and PNS. part of nervous system regional part of nervous system true Anatomical cluster consisting of the skeletal elements and articular elements that are part of an individual subdivision of the organism. skeletal system subdivision skeletal system part subdivision of skeletal system true The surface (external) layer of ectoderm which begins to proliferate shortly after separation from the neuroectoderm. surface (external) ectoderm surface ectoderm external ectoderm true true An anatomical structure that develops from the endoderm and the mesoderm. mixed endoderm/mesoderm-derived structure true true The organs associated with producing offspring in the gender that produces spermatozoa. genitalia of male organism male genital system male genitalia male genitals male organism genitalia male organism reproductive system reproductive system of male organism male genital organ male genital tract male reproductive tract systema genitale masculinum male reproductive system true A spherical embryonic mass of blastomeres formed before the blastula and resulting from cleavage of the fertilized ovum. morula (2-16 cells) morula true A mass of cells that develop into the body of the embryo and some extraembryonic tissues ICM early embryoblast embryoblast embryoblastus; massa cellularis interna; pluriblastus senior pluriblast inner cell mass true the mesectodermal cell layer arising from the trophectoderm that erodes the uterine mucosa and contributes to the formation of the placenta trophoblast layer massa cellularis externa trophoblastus trophoderm trophoblast true A flattened, almost circular bilaminar plate of cells formed when the inner cell mass (aka embryoblast) forms two epithelial layers, each of a distinct lineage, separated by an extracellular basement membrane: the external (dorsal) layer is called the epiblast and the internal (ventral) layer is called the hypoblast (aka primitive endoderm); together, they compose the bilaminar embryonic disc. embryonic disc embryonic shield germinal disc germinal disk bilaminary embryonic disc bilaminary germ disc bilaminar disk bilaminar disc true portion of neural crest that develops from the dorsal neural tube. It overlaps the vagal neural crest and migrates to populate the pharyngeal arches 3, 4 and 6 (producing structures in the head) and to the heart, forming connective tissue that separates the great vessels of the heart. [Wikipedia] cardiac neural crest complex complexus cristae neuralis cardiacus cardiac neural crest true true true The epithelial layer of the lung. epithelial tissue of lung epithelium of lung lung epithelial tissue pulmonary epithelium lung epithelium true A tube in the respiratory system. Examples: bronchus, bronchiole, trachea. segment of tracheobronchial tree respiratory conducting tube segment of tracheobronchial tree tracheobronchial tree segment respiratory tube true true Structure derived from foregut that becomes a lung[GO]. gemma pulmonalis gemma respiratoria lung bud primary lung bud respiratory diverticulum lung bud true true anterior region of body true posterior region of body true membrane membranous organ component membranous layer true 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. bowel intestinal tract intestine true Common chamber into which the intestines and excretory system opens. Arises during development in all vertebrates, but in many it becomes subdivided, lost or incorporated into other structures cloacal chamber vent cloaca true true endoderm-lined chamber that develops as pouch-like dilation of the caudal end of the hindgut and receives the allantois ventrally and two mesonephric ducts laterally; caudally it ends blindly at the cloacal membrane formed by the union of proctodeal (anal pit) ectoderm and cloacal endoderm, with no intervening mesoderm[MP]. cloaca embryonic cloaca true the ventral part of the cloaca remaining after septation of the rectum, which further develops into part of the bladder, part of the prostatic part of the male urethra and the urethra and vestibule in females urogenital sinus UGS fetal UGS sinus urogenitalis primitive urogenital sinus true The pair of anatomical structures comprised of a left lung and right lung. lungs lungs pair pulmones set of lungs pair of lungs true Organ that functions in gaseous exchange between an organism and its environment. In plants, microorganisms, and many small animals, air or water makes direct contact with the organism's cells or tissue fluids, and the processes of diffusion supply the organism with dioxygen (O2) and remove carbon dioxide (CO2). In larger animals the efficiency of gaseous exchange is improved by specialized respiratory organs, such as lungs and gills, which are ventilated by breathing mechanisms. apparatus respiratorius organ breathing organ organ of apparatus respiratorius organ of respiratory system respiratory organ respiratory system organ gas exchange organ respiration organ true Amniotic fluid is a bodily fluid consisting of watery liquid surrounding and cushioning a growing fetus within the amnion. It allows the fetus to move freely without the walls of the uterus being too tight against its body. Buoyancy is also provided. The composition of the fluid changes over the course of gestation. Initially, amniotic fluid is similar to maternal plasma, mainly water with electrolytes. As the fetus develops, proteins, carbohydrates, lipids, phospholipids originating from the lungs, fetal cells, and urea are deposited in the fluid. acqua amnii liquor amnii amniotic fluid true A fluid that is composed of blood plasma and erythrocytes. portion of blood vertebrate blood whole blood blood true true Circulating fluid that is part of the hemolymphoid system. Blood, lymph, interstitial fluid or its analogs. blood or blood analog circulating fluid haemolymphatic fluid true the thin innermost layer of the extraembryonic membranes that contains the amniotic fluid; the membrane forms a closed sac in which the embryo and later, the fetus, is suspended and protected amnios amnion true true true Organism at the blastula stage - an early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence. blastula embryo blastosphere blastula true An embryo that is at the late embryonic stage; this stage covers late steps of the embryogenesis with a fully formed embryo still developing before birth or egg hatching. fetus embryo late growth stage embryo late stage late embryo true The branched tubular glands found in the mucosa of the fundus and body of the stomach which contain parietal cells that secrete hydrochloric acid and zymogenic cells that produce pepsin. gastric gland true true The wall of the digestive tract. This encompasses all parts of the digestive tract with the exception of the lumen (cavity). digestive tract wall wall of digestive tract wall of gut wall of alimentary tract gut wall true A gland that is part of the intestinal mucosa. Examples include the intestinal crypts, duodenal gland[cjm]. bowel mucosa gland bowel mucosa of organ gland bowel mucous membrane gland bowel organ mucosa gland gland of bowel mucosa gland of bowel mucosa of organ gland of bowel mucous membrane gland of bowel organ mucosa gland of intestinal mucosa gland of intestine mucosa gland of intestine mucosa of organ gland of intestine mucous membrane gland of intestine organ mucosa gland of mucosa of bowel gland of mucosa of intestine gland of mucosa of organ of bowel gland of mucosa of organ of intestine gland of mucous membrane of bowel gland of mucous membrane of intestine gland of organ mucosa of bowel gland of organ mucosa of intestine glandula intestinalis intestinal mucosa gland intestine mucosa gland intestine mucosa of organ gland intestine mucous membrane gland intestine organ mucosa gland mucosa of bowel gland mucosa of intestine gland mucosa of organ of bowel gland mucosa of organ of intestine gland mucous membrane of bowel gland mucous membrane of intestine gland organ mucosa of bowel gland organ mucosa of intestine gland glandulae intestinales intestinal gland true A lining of mostly endodermal origin, covered in epithelium, which is involved in absorption and secretion. They line various body cavities that are exposed to the external environment and internal organs. It is at several places continuous with skin: at the nostrils, the lips, the ears, the genital area, and the anus. The sticky, thick fluid secreted by the mucous membranes and gland is termed mucus. The term mucous membrane refers to where they are found in the body and not every mucous membrane secretes mucus[WP] mucosa of organ mucosa of organ part mucosal region mucous membrane organ mucosa region of mucosa tunica mucosa mucosa true functional part of an organ in the body. This is in contrast to the stroma, which refers to the structural tissue of organs, being exactly, connective tissues. parenchyma true The mammalian blastocyst is a hollow ball of cells containing two cell types, the inner cell mass and the trophectoderm[GO]. blastocystis blastula blastocyst true true An epithelial tissue layer that lines much of the urinary tract, including the renal pelvis, the ureters, the bladder, and parts of the urethra. transitional epithelium epithelium transitionale transitional epithelium uroepithelium urothelium true true The part of the hindlimb between pelvis and the knee, corresponding to the femur. hind limb stylopod hind limb stylopodium hind propodium hindlimb propodium hindlimb stylopod hindlimb stylopodium proximal segment of free lower limb stylopod of hind limb stylopod of hindlimb stylopod of lower limb thigh upper leg femur hindlimb stylopod true true A mucosa that is part of a respiratory airway. mucosa of organ of trachea mucosa of organ of windpipe mucosa of trachea mucosa of windpipe mucous membrane of trachea mucous membrane of windpipe organ mucosa of trachea organ mucosa of windpipe trachea mucosa trachea mucosa of organ trachea mucous membrane trachea organ mucosa tracheal mucous membrane tunica mucosa (tracheae) tunica mucosa tracheae windpipe mucosa windpipe mucosa of organ windpipe mucous membrane windpipe organ mucosa tracheal mucosa true The subdivision of the musculoskeletal system that consists of all the muscles of the body[VSAO, modified]. muscle system muscle system of body muscular system musculature system set of all muscles set of muscles of body vertebrate muscular system muskelsystem musculature of body true The outer covering of the calvaria. It is composed of several layers: SKIN; subcutaneous connective tissue; the occipitofrontal muscle which includes the tendonous galea aponeurotica; Loose connective tissue; and the pericranium (the PERIOSTEUM of the SKULL). scalpus scalp true true A mucosa that is part of a bronchus [Automatically generated definition]. bronchi mucosa bronchi mucosa of organ bronchi mucous membrane bronchi organ mucosa bronchial trunk mucosa bronchial trunk mucosa of organ bronchial trunk mucous membrane bronchial trunk organ mucosa bronchus mucosa bronchus mucosa of organ bronchus mucous membrane bronchus organ mucosa mucosa of bronchi mucosa of bronchial trunk mucosa of bronchus mucosa of organ of bronchi mucosa of organ of bronchial trunk mucosa of organ of bronchus mucous membrane of bronchi mucous membrane of bronchial trunk mucous membrane of bronchus organ mucosa of bronchi organ mucosa of bronchial trunk organ mucosa of bronchus tunica mucosa bronchi bronchial mucosa true true A mesodermal signaling center of the hair follicle consisting of closely packed specialized mesenchymal fibroblasts. Framed by the enlarged bulb matrix in anagen. dermal papillae follicular papilla dermal papilla cell hair follicle dermal papilla hair papilla papilla corii papilla dermatis papilla dermis papilla of corium papillae dermis skin papilla dermal papilla true true 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. body fluid or substance body substance organism substance portion of body substance portion of organism substance organism substance true Non-material anatomical entity of three dimensions, that is generated by morphogenetic or other physiologic processes; is surrounded by one or more anatomical structures; contains one or more organism substances or anatomical structures. lumen space lumen space anatomical spaces anatomical space true Anatomical entity that has mass. AAO:0010264 AEO:0000006 BILA:0000006 CARO:0000006 EHDAA2:0003006 FBbt:00007016 FMA:67165 HAO:0000006 TAO:0001836 TGMA:0001826 VHOG:0001721 uberon UBERON:0000465 material anatomical entity true Anatomical entity that has no mass. immaterial physical anatomical entity immaterial anatomical entity true Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function. system body system connected anatomical system organ system anatomical systems anatomical system true Anatomical structure that is an individual member of a species and consists of more than one cell. TODO - split body and mc organism? body continues after death stage organismal AAO:0010026 AEO:0000191 BILA:0000012 BSA:0000038 BTO:0000042 CARO:0000012 EFO:0002906 EHDAA2:0003103 EHDAA2:0003191 EHDAA:1 EHDAA:9178 EMAPA:25765 EV:0100016 FBbt:00000001 FMA:256135 HAO:0000012 TADS:0000001 TAO:0001094 TGMA:0001832 VHOG:0000671 WBbt:0007833 XAO:0003004 ZFA:0001094 galen:Organism ncithesaurus:Whole_Organism multi-cellular organism organism whole organism animal uberon Koerper body whole body UBERON:0000468 organism multi-cellular organism animal Koerper body whole body whole organism multicellular organism true The organs and associated structures associated with bearing offspring in a female animal. female organism genitalia female organism reproductive system genitalia of female organism reproductive system of female organism female genital system female genital tract female genitalia female genitals female reproductive tract gynaecological tissue systema genitale femininum female reproductive system true 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. anatomic region body part body region cardinal body part organism subdivision true Anatomical structure that consists of cell parts and cell substances and together does not constitute a cell or a tissue. acellular anatomical structures acellular anatomical structure true Anatomical group that has its parts adjacent to one another. anatomical cluster true 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. extra-embryonic structure extraembryonic structures extraembryonic tissue extraembryonic structure true 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. changed label and definition to reflect CARO2 AAO:0000607 AAO:0010054 AEO:0000043 BILA:0000043 CALOHA:TS-2090 CARO:0000043 EHDAA2:0003043 EMAPA:35868 FBbt:00007003 FMA:9637 HAO:0000043 MA:0003002 MESH:D014024 TAO:0001477 TGMA:0001844 UMLS:C0040300 VHOG:0001757 WBbt:0005729 XAO:0003040 ZFA:0001477 galen:Tissue portion of tissue tissue portion simple tissue uberon UBERON:0000479 portion of tissue tissue portion simple tissue tissue true 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 structures multi-tissue structure true 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]. epithelial tissue portion of epithelium epithelium true Unilaminar epithelium, which consists of a single layer of columnar cells. Examples: ciliated columnar epithelium, gastric epithelium, microvillus columnar epithelium.[FMA] columnar epithelium columnar epithlium epithelium simplex columnare simple columnar epithelium simple columnar epithelia simple columnar epithelium true true Epithelium which consists of more than one layer of epithelial cells that may or may not be in contact with a basement membrane. Examples: keratinized stratified squamous epithelium, ciliated stratified columnar epithelium.[FMA] stratified epithelium laminated epithelium multilaminar epithelium true Epithelium which consists of a single layer of epithelial cells. Examples: endothelium, mesothelium, glandular squamous epithelium.[FMA] simple epithelium unilaminar epithelia unilaminar epithelium true Interstitial fluid is a bodily fluid consisting of a solution which bathes and surrounds the cells of multicellular animals. It is the main component of the extracellular fluid, which also includes plasma and transcellular fluid. intercellular fluid tissue fluid interstitial fluid true Subdivision of trunk that lies between the head and the abdomen. thorax anterior subdivision of trunk upper body upper trunk thoracic segment of trunk true true The subdivision of the vertebrate body between the thorax and pelvis. The ventral part of the abdomen contains the abdominal cavity and visceral organs. The dorsal part includes the abdominal section of the vertebral column. abdominopelvic region abdominopelvis adult abdomen belly celiac region abdomen true 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. embryonic organism developing organism developmental tissue embryo true 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. embryonic tissue germinal layer primary germ layer embryonic germ layer embryonic germ layers germ layer true Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue. embryonic ectoderm ectoderm true Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut. entoderm endoderm true The middle germ layer of the embryo, between the endoderm and ectoderm. embryonic mesoderm entire mesoderm mesodermal mantle mesoderm true 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 chamber anterior intestine gaster mesenteron ventriculus stomach true true A myogenic muscular circulatory organ found in the vertebrate cardiovascular system composed of chambers of cardiac muscle. It is the primary circulatory organ. chambered heart vertebrate heart branchial heart Herz@de cardium heart true true true true true Anatomical system that consists of the glands and parts of glands that produce endocrine secretions and help to integrate and control bodily metabolic activity. endocrine glandular system endocrine system systema endocrinum endocrine system true 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]. encephalon suprasegmental levels of nervous system suprasegmental structures synganglion the brain brain true true The portion of the hindlimb that contains both the stylopod and zeugopod. tetrapod leg lower extremity leg true true Endochondral longbone connecting the pelvic girdle with posterior zeugopodium skeleton.[VSAO, modified]. thigh bone femoral bone mesomere 1 of pevlic appendage os femorale os femoris os longissimum proximal metapterygial mesomere of pelvic appendage proximal metapterygial mesomere of pelvic fin femur true true true true Anatomical cluster that consists of two or more adjacent skeletal structures, which may be interconnected by various types of tissue[VSAO]. articulation joint articular joint joints skeletal joint true Anatomical system that has as its parts the organs concerned with reproduction. Geschlechtsorgan animal reproductive system genital system genital tract genitalia organa genitalia reproductive tissue reproductive tract systemata genitalia reproductive system true Reproductive organ that produces and releases eggs (ovary) or sperm (testis). gonada gonads gonad true A tube or collection of tubes in an animal from the ovaries to the outside of the body. ovarian duct ovarian tube uterine tube female reproductive tracts oviducts tuba uterina tuba uterinae tubular parts of female reproductive system oviduct true true the female muscular organ of gestation in which the developing embryo or fetus is nourished until birth uterus true The outer epithelial layer of the skin that is superficial to the dermis. epidermis skin vertebrate epidermis skin epidermis true true Functional system which consists of structures involved in respiration. apparatus respiratorius respiratory system Atmungssystem apparatus respiratorius systema respiratorium respiratory system true An airway through which respiratory air passes in organisms. airway airways respiratory airway true Anatomical system that has as its parts the organs devoted to the ingestion, digestion, and assimilation of food and the discharge of residual wastes. alimentary system alimentary tract gastrointestinal system gut digestive system true The renal system in an anatomical system that maintains fluid balance and contributes to electrolyte balance, acid/base balance, and disposal of nitrogenous waste products.. excretory system renal system systema urinaria systema urinarium urinary system urinary tract renal or urinary system renal/urinary system renal system true organ system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells, etc. to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis[WP]. systema cardiovasculare circulatory system true Portion of connective tissue composed of adipocytes enmeshed in areolar tissue fat fat tissue fatty tissue adipose bodyfat fatty depot adipose tissue true A subdivision of the muscular system corresponding to a subdisivision of an organism. muscle group muscles set musculature musculi set of muscles set of skeletal muscles muscle system muscles musculature system musculature true The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organism, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO]. neurological system nerve net systema nervosum nervous system true The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. In invertebrates it includes central ganglia plus nerve cord. CNS systema nervosum centrale cerebrospinal axis neuraxis central nervous system true true 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]. saccus vitellinus vesicula umbilicalis yolk sac true true true Anterior subdivision of a digestive tract. praeenteron proenteron foregut true Tube that connects the pharynx to the stomach. In mammals, the oesophagus connects the buccal cavity with the stomach. The stratified squamous non-keratinised epithelium lining the buccal cavity is continued through the pharynx down into the oesophagus. The lowest part of the oesophagus (ca. 2 cm) is lined with gastric mucosa and covered by peritoneum. The main body of the oesophagus is lined with small, simple mucous glands. Each gland opens into the lumen by a long duct which pierces the muscularis mucosae (Wilson and Washington, 1989). A sphincter is situated at the point where the oesophagus enters the stomach to prevent gastro-oesophageal reflux, i.e. to prevent acidic gastric contents from reaching stratified epithelia of the oesophagus, where they can cause inflammation and irritation (Wilson and Washington, 1989; Brown et al., 1993). gullet oesophagus esophagus true true true Middle subdivision of a digestive tract[CJM]. In vertebrates: The middle part of the alimentary canal from the stomach, or entrance of the bile duct, to, or including, the large intestine[GO]. mesenteron midgut true The caudalmost subdivision of a digestive tract. metenteron hindgut true Primordia are populations of contiguous cells that are morphologically distinct and already correspond in extent to a later organ/tissue[FBbt, Hartenstein, V. (2004)]. bud future organ placode primordia rudiment primordium true In the developing vertebrate, the neural tube is the embryo's precursor to the central nervous system, which comprises the brain and spinal cord. The neural groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or neural canal (which strictly speaking is the center of the neural tube), the ectodermal wall of which forms the rudiment of the nervous system. [WP,unvetted]. neural primordium presumptive central nervous system tubus neuralis neural tube true true true true 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. AAO:0010841 AEO:0000000 BILA:0000000 CARO:0000000 EHDAA2:0002229 FBbt:10000000 FBbt_root:00000000 FMA:62955 HAO:0000000 MA:0000001 TAO:0100000 TGMA:0001822 UMLS:C1515976 XAO:0000000 ZFA:0100000 uberon UBERON:0001062 anatomical entity true A zone of skin that is part of a head [Automatically generated definition]. adult head zone of skin head skin head zone of skin zone of skin of adult head zone of skin of head skin of head true An anatomical wall that is part of a esophagus [Automatically generated definition]. anatomical wall of esophagus anatomical wall of gullet anatomical wall of oesophagus esophageal wall esophagus anatomical wall esophagus wall gullet anatomical wall gullet wall oesophagus anatomical wall oesophagus wall wall of gullet wall of oesophagus wall of esophagus true Subdivision of skeletal system that consists of all the vertebra and associated skeletal elements and joints in the body[modified from VSAO]. spine backbone vertebral column skeleton columna vertebralis dorsal spine spinal column vertebral region vertebral column true Muscle tissue that consists primarily of skeletal muscle fibers. skeletal muscle skeletal muscle system somatic muscle skeletal muscle tissue true the layered structure that makes up the stomach, typiclly consists of a serous coat, a muscular coat, a mucous membrane, and other tissue layers in between anatomical wall of stomach anatomical wall of ventriculus gastric wall stomach anatomical wall stomach wall ventriculus anatomical wall ventriculus wall wall of ventriculus wall of stomach true The triangular region on the periphery of the liver lobules that contain a bile duct and a terminal branch of the hepatic artery and portal vein, and may also include a lymphatic vessel. portal lobule true true The functional unit of the liver, consisting of a mass of hepatocytes from adjacent liver lobules aligned around the hepatic arterioles and portal venules just as they anastomose into sinusoids. liver acinus portal acinus hepatic acinus true true A complex network of conduits that begins with the canals of Hering (intralobar bile duct) and progressively merges into a system of interlobular, septal, and major ducts which then coalesce to form the extrahepatic bile ducts, which finally deliver bile to the intestine, and in some species to the gallbladder. biliary tract biliary tree true true An artery that supplies the liver. arteria hepatica propria arteria hepatica hepatic artery true The mucosal layer that lines the stomach. gastric mucosa gastric mucous membrane mucosa of organ of stomach mucosa of organ of ventriculus mucosa of ventriculus mucous membrane of stomach mucous membrane of ventriculus organ mucosa of stomach organ mucosa of ventriculus stomach mucosa stomach mucosa of organ stomach mucous membrane stomach organ mucosa tunica mucosa (gaster) tunica mucosa gastricae ventriculus mucosa ventriculus mucosa of organ ventriculus mucous membrane ventriculus organ mucosa Magenschleimhaut tunica mucosa gastris mucosa of stomach true Mucosal layer that lines the intestine. bowel mucosa bowel mucosa of organ bowel mucous membrane bowel organ mucosa intestine mucosa intestine mucosa of organ intestine mucous membrane intestine organ mucosa mucosa of bowel mucosa of intestine mucosa of organ of bowel mucosa of organ of intestine mucous membrane of bowel mucous membrane of intestine organ mucosa of bowel organ mucosa of intestine tunica mucosa intestini intestinal mucosa true The canals that carry bile in the liver between the intralobular ducts and the biliary ductules; interlobular bile ducts are part of the interlobular portal triad. interlobular ductule interlobular bile duct true An anatomical wall that is part of a intestine [Automatically generated definition]. anatomical wall of bowel anatomical wall of intestine bowel anatomical wall bowel wall intestinal wall intestine anatomical wall intestine wall wall of bowel bowel wall wall of intestine true The organism subdivision that includes the pelvic girdle skeleton and associated soft tissue. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). Examples: There are only two instances in an organism, right and left pectoral girdle regions. girdle - pelvic pelvic girdle pelvic girdle region true true The epithelial layer of the stomach . epithelial tissue of stomach epithelial tissue of ventriculus epithelium of ventriculus stomach epithelial tissue stomach epithelium ventriculus epithelial tissue ventriculus epithelium gastric epithelium epithelium of stomach true true true true Epithelial layer that lines the intestine. bowel epithelial tissue bowel epithelium epithelial tissue of bowel epithelial tissue of intestine epithelium of bowel epithelium of intestine intestine epithelial tissue villous epithelium intestine epithelium intestinal epithelium true true true true A multi-organ-part structure that consists of three vessels of the portal lobule including the bile duct, a terminal branch of the hepatic artery and portal vein, and may also include a lymphatic vessel trias hepatica trias hepatica portal triad true true The functional units of the liver including the lobules. hepatic parenchyma liver parenchyme parenchyma of liver hepatic parenchyme liver parenchyma true true the tubules located between the bile canaliculi and interlobular bile ducts near the outer edge of a classic liver lobule canal of Herring cholangiole ductus interlobularis bilifer canal of Hering canals of Hering duct of Herring intrahepatic bile ductule intralobular bile duct true true The anus and surrounding regions. Encompasses both internal and external regions, where present posterior posterior end of organism anal region true Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system. skeleton system set of all bones and joints Skelettsystem skeletal system true Subdivision of skeleton consisting of all skeletal elements in an hindlimb region. bones of lower limb free lower limb skeleton hind limb skeleton hind-limb skeleton hindlimb skeleton lower limb skeleton ossa membri inferioris set of bones of lower limb skeleton of free lower limb skeleton of lower limb hindlimb skeleton true true The hip region is located lateral to the gluteal region (i.e. the buttock), inferior to the iliac crest, and overlying the greater trochanter of the thigh bone. In adults, three of the bones of the pelvis have fused into the hip bone which forms part of the hip region. The hip joint, scientifically referred to as the acetabulofemoral joint (art. coxae), is the joint between the femur and acetabulum of the pelvis and its primary function is to support the weight of the body in both static (e.g. standing) and dynamic (e.g. walking or running) postures. [WP,modified]. hip region regio coxae coxa hip true Skeletal element that is composed of bone tissue. bone organ bone bones bone element true A tube extending from the mouth to the anus. gut digestive tube enteric tract alimentary canal alimentary tract digestive canal gut tube digestive tract true The segment of the respiratory tract that starts proximally with the trachea and includes all distal structures including the lungs[WP,modified] lower respiratory tract true true 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]. muscle muscle organ true true true An epithelial tube or tree of tibes that transports blood away from the heart[modified from AEO definition]. arterial subtree arterial tree organ part arteries arterial system arterial vessel artery true Any of the tubular branching vessels that carry blood from the capillaries toward the heart. venous subtree venous vessel venous tree organ part vascular element vena venae vein true The most anterior region the brain including both the telencephalon and diencephalon. FB prosencephalon forebrain true the epithelial lining of the trachea which contains numerous ciliated cells epithelial tissue of trachea epithelial tissue of windpipe epithelium of windpipe trachea epithelial tissue trachea epithelium tracheal epithelium windpipe epithelial tissue windpipe epithelium epithelium of trachea true An epithelium that is part of a respiratory bronchiole [Automatically generated definition]. bronchiolus respiratorius epithelial tissue bronchiolus respiratorius epithelium epithelial tissue of bronchiolus respiratorius epithelial tissue of respiratory bronchiole epithelium of bronchiolus respiratorius respiratory bronchiole epithelial tissue respiratory bronchiole epithelium epithelium of respiratory bronchiole true An epithelium that lines a terminal bronchiole. bronchiolus terminalis epithelial tissue bronchiolus terminalis epithelium epithelial tissue of bronchiolus terminalis epithelial tissue of terminal bronchiole epithelium of bronchiolus terminalis epithelium of terminal bronchiole terminal bronchiole epithelial tissue terminal bronchiole epithelium terminal bronchiole epithelium true The liquid component of blood, in which erythrocytes are suspended. plasma portion of plasma blood plasm portion of blood plasma blood plasma true the epithelial layer that lines the luminal space of the esophagus epithelial tissue of esophagus epithelial tissue of gullet epithelial tissue of oesophagus epithelium of gullet epithelium of oesophagus esophageal epithelium esophagus epithelial tissue esophagus epithelium gullet epithelial tissue gullet epithelium oesophagus epithelial tissue oesophagus epithelium epithelium of esophagus true true A vessel through which blood circulates in the body. vascular element region of vascular tree organ vascular tree organ region vas sanguineum blood vessel true true the tubular intestinal glands found in the mucosal membranes intestinal gland Lieberkuhn crypt Lieberkuhn gland Lieberkuhn's gland Lieberkuhn's glands crypt of Lieberkuhn crypt of Lieberkühn crypts of Lieberkühn follicles of lieberkuhn intestinal crypt intestinal crypts lieberkuhn crypt intestinal gland of Lieberkuhn crypt of Lieberkuhn true 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. allantoic placenta eutherian placenta placenta true true true The upper layer of the dermis beneath the epidermis, composed of dense irregular connective tissue[ncit,modified]. corpus papillary dermis papillary layer papillary dermis papillary layer papillary layer of dermis stratum papillare stratum papillare (dermis) stratum papillare corii stratum papillare dermis superficial dermis dermal papillary layer stratum papillare papillary layer of dermis true true A vein that conducts blood from the digestive organs, spleen, pancreas, and gallbladder to the liver[BTO]. portal venous tree organ part portal vein true the deepest layer of the epidermis, which is composed of dividing stem cells and anchoring cells Malpighian layer rete Malphighii rete Malpighii stratum Malpighi stratum basale stratum germinosum basal cell layer of epidermis basal epidermal layer epidermal basal stratum epidermis stratum basale stratum basalis of epidermis stratum germinativum stratum germinosum of epidermis basal cell layer of skin basal layer of epidermis epidermis basal layer epidermis sensorial layer epidermis stratum germinativum stratum basale of epidermis true true true An epithelium that is part of a bronchus [Automatically generated definition]. bronchi epithelial tissue bronchi epithelium bronchial epithelium bronchial trunk epithelial tissue bronchial trunk epithelium bronchus epithelial tissue bronchus epithelium epithelial tissue of bronchi epithelial tissue of bronchial trunk epithelial tissue of bronchus epithelium of bronchi epithelium of bronchial trunk epithelium of bronchus true Muscle tissue that contains fibers that are divided by transverse bands into striations. striated muscle striated muscle tissue true Respiration organ that develops as an oupocketing of the esophagus. pulmo lung true true true true An interconnected tubular multi-tissue structure contains fluid that is actively transported around the organism[ZFA]. Examples: vasculature of lung, vasculature of face. vascular network vasculature true Anatomical structure that is part of an embryo. developing embryonic structure embryonic anatomical structure developing structure embryonale Struktur embryonic structures embryonic structure true An epithelium that is part of a bronchiole [Automatically generated definition]. bronchiolar epithelium bronchiole epithelial tissue bronchiole epithelium epithelial tissue of bronchiole epithelial tissue of lobular bronchiole epithelium of lobular bronchiole lobular bronchiole epithelial tissue lobular bronchiole epithelium epithelium of bronchiole true true true The dermis is a layer of skin between the epidermis (with which it makes up the skin) and subcutaneous tissues, and is composed of two layers, the papillary and reticular dermis[WP]. vertebrate dermis corium cutis dermis true true true 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]. hypoderm vertebrate hypodermis sub-tegumental tissue subcutaneous tissue subcutis subtegumental tissue superficial fascia tela subcutanea hypodermis true true The postcranial subdivision of skeleton structural components forming the long axis of the vertebrate body; in Danio, consisting of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins; in human consists of the bones of the vertebral column, the thoracic cage and the pelvis[ZFA+FMA]. axial skeleton post-cranial axial skeleton postcranial axial skeleton true Subdivision of skeleton which which consists of all the skeletal elements in in the pectoral and pelvic appendage complexes[cjm]. appendicular skeleton entire appendicular skeleton paired fin skeleton skeleton appendiculare appendicular skeleton true The organ covering the body that consists of the dermis and epidermis. entire skin skin organ entire integument integument integumental organ pelt skin skin of body true true true Organism subdivision which is the part of the body posterior to the cervical region (or head, when cervical region not present) and anterior to the caudal region. Includes the sacrum when present. thoracolumbar region torso trunk region Rumpf trunk true A paired appendage that is evolved from a paired fin. The extent of this structure includes autopod, stylopod and zeugopod regions when present, but excludes the girdle and its parts. free limb limb sensu Vertebrata pentadactyl limb tetrapod limb flipper extremities extremity limb true A (free) limb that is connected to a pelvic girdle region. The extent of this structure includes autopod, stylopod and zeugopod regions when present, but excludes the pelvic girdle and its parts. free lower limb hind limb hind-limb hindlimb inferior member lower limb membrum inferius free part of lower limb lower extremity membrum inferius pelvic appendage hindlimb true true 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]. iecur jecur liver true true true true true Lung which consists of the right upper lobe, middle lobe and right lower lobe.[FMA] right lung true Lung which consists of the left upper lobe and left lower lobe.[FMA] left lung true the upper conducting airways of the lung; these airways arise from the terminus of the trachea bronchi bronchial trunk bronchial tissue bronchus true the conducting airway of the lungs found terminal to the bronchi; these structures contain neither cartilage nor mucous-secreting glands; the epithelium of the bronchioles becomes thinner with each branching lobular bronchiole bronchioli bronchiolus bronchiole true the last conducting structure of non-respiratory bronchioles; after this point, the airways have alveoli in their walls bronchiolus terminalis bronchioli terminalis terminal bronchiole tube terminal bronchiole true A bronchiole that is the first segment of the respiratory zone. bronchiolus respiratorii bronchiolus respiratorius respiratory bronchiole true Anatomical cluster consisting of the hematopoietic system and the lymphoid system, or its analogs. hematolymphoid system lymphomyeloid complex haemolymphoid system hemolymphoid system true The dermis, epidermis and hypodermis. dermis plus epidermis plus hypodermis integumentum commune skin and subcutaneous tissue skin plus hypodermis the integument Hautsystem@de dermal system dermoid system skin tegument vertebrate integument integument true Anatomical system that consists of the muscular and skeletal systems. musculo-skeletal system musculoskeletal system true Joint in which the articulating bones or cartilages are connected by an articular capsule which encloses a synovial membrane and a synovial cavity. Examples: Temporomandibular joint, knee joint.[FMA] articulatio synoviale diarthroses diarthrosis diarthrosis joint diarthrodial joints synovial joint true Organ system subdivision that consists of the organs and ducts that are involved in the production and transportation of bile. In most species this is the gallbladder and the bile ducts (biliary tree). biliary apparatus biliary tract biliary system true Somites are spheres of epithelial cells that form sequentially along the anterior-posterior axis of the embryo through mesenchymal to epithelial transition of the presomitic mesoderm. mesodermal cluster epimere epimere mesoderm epithelial somite somites somitic mesoderm somitus somite true true Anatomical system that consists of the glands and parts of glands that produce exocrine secretions and help to integrate and control bodily metabolic activity. Exocrine glands are glands that secrete their products (hormones) into ducts (duct glands). They are the counterparts to endocrine glands, which secrete their products (hormones) directly into the bloodstream (ductless glands) or release hormones (paracrines) that affect only target cells nearby the release site. [Wikipedia]. exocrine glandular system exocrine system true The connecting cord from the developing embryo to the placenta. chorda umbilicalis funiculus umbilicalis birth cord connecting stalk funiculus umbilicalis yolk stalk umbilical cord true 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]. NC crista neuralis neural crest material neural crest true true true Embryonic ectoderm that gives rise to nervous tissue. neural ectoderm neuroectoderm epithelium tubi neuralis; neuroectoderma neuaral ectoderm presumptive central nervous system ventral neurogenic region neurectoderm true true The lower segment of the trunk, inferioposterior to the abdomen proper, in the transition area between the trunk and the lower limbs. lesser pelvis pelvic region pelvis pelvis region true pelvis pelvic region of trunk true 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 ducted gland glandula exocrina exocrine gland true 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. male prostate prostate prostata prostate gland true true Endocrine glands are glands of the endocrine system that secrete their products directly into the circulatory system rather than through a duct.[WP, modified]. ductless gland glandula endocrina ductless gland glandulae endocrinae endocrine gland true the soft tissue that fills the cavities of bones medulla ossea medulla ossium medulla of bone medullary bone bone marrow true true true Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance. One of the four types of tissue in traditional classifications. It is largely a category of exclusion rather than one with a precise definition, but there are certain characteristics shared by all or most tissues in this category, such as involvement in structure and support, derived from mesoderm, and characterized largely by the traits of non-living tissue.[AAO] Portion of tissue that consists of mesodermally derived cells and intercellular matrix comprised of protein fibers and carbohydrates, which supports, ensheathes and binds together other tissues.[TAO] Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.[VSAO] MA also has set of connective tissues AAO:0000098 BTO:0000421 CALOHA:TS-2009 EFO:0000952 EMAPA:35251 FMA:9640 GAID:100 MA:0000011 MAT:0000301 MESH:D003238 MIAA:0000301 OpenCyc:Mx4rv-aBgZwpEbGdrcN5Y29ycA TAO:0001641 UMLS:C0009780 VSAO:0000017 XAO:0001017 ZFA:0001632 galen:ConnectiveTissue portion of connective tissue textus connectivus uberon Bindegewebe UBERON:0002384 portion of connective tissue textus connectivus Bindegewebe connective tissue true Muscle tissue is a contractile tissue made up of actin and myosin fibers[GO]. muscular tissue portion of muscle tissue textus muscularis muscle tissue true true Anatomical system that is involved in the production of hematopoietic cells. haematological system haemopoietic system organa haemopoietica Blutbildungssystem haematopoietic system hematological system hematolymphoid system hemopoietic system hematopoietic system true true Lymph is the fluid that is formed when interstitial fluid enters the conduits of the lymphatic system through lymph capillaries[WP]. lympha lymph true Any of the ducts that form the biliary tree, carrying bile from the liver to the small intestine. bile tube biliary duct gall duct hepatic duct bile duct true true 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 true The ossified form of a vertebral element, a skeletal element that forms around the notochord and is part of the vertebral column. vertebra bone vertebrae vertebra true true true Connected anatomical system that forms a barrier between an animal and its environment. In vertebrates, the integumental system consists of the epidermis, dermis plus associated glands and adnexa such as hair and scales. In invertebrates, the integumental system may include cuticle. integumentary system body surface dermal system external covering of organism integumentum commune organism surface surface integumental system true The abdominal segment of the torso. abdomen/pelvis/perineum lower body lower trunk lumbar region abdominal segment of trunk true true Skeletal tissue that is avascular, rich in glycosaminoglycans (GAGs) and typically includes chondrocytes within isolated lacunae. Cartilage tissue is deposited by chondroblasts. cartilage tissue cartilaginous tissue chondrogenic tissue cartilage cartilages portion of cartilage tissue cartilage tissue true The part of the digestive system that contains the liver and the biliary system hepaticobiliary system liver and biliary system liver/biliary system hepatobiliary system true A bone that is part of a limb [Automatically generated definition]. bone of extremity bone of limb free limb bone limb bone true true true The lymphatic system in vertebrates is a network of conduits that carry a clear fluid called lymph. It also includes the lymphoid tissue through which the lymph travels. Lymphoid tissue is found in many organs, particularly the lymph nodes, and in the lymphoid follicles associated with the digestive system such as the tonsils. The system also includes all the structures dedicated to the circulation and production of lymphocytes, which includes the spleen, thymus, bone marrow and the lymphoid tissue associated with the digestive system[WP]. lymphatic system lymphatic circulatory system lymphatic drainage system systema lymphoideum lymphoid system true A mucosa that is part of a esophagus [Automatically generated definition]. esophageal mucosa esophageal mucous membrane esophagus mucosa esophagus mucous membrane lamina muscularis mucosae oesophageae mucosa of esophagus mucosa of oesophagus mucous membrane of esophagus mucous membrane of oesophagus oesophageal mucosa oesophagus mucosa oesophagus mucous membrane tunica mucosa esophagi tunica mucosa oesophageae tunica mucosa oesophagi muscularis mucosae of oesophagus tunica mucosa oesophagi esophagus mucosa true The proximal free limb segment. Includes as parts the stylopod skeleton. proximal part of limb propodium proximal free limb segment stylopodial limb segment stylopodium proximal segment of free limb stylopod true Skeletal tissue with a collagen-rich extracellular matrix vascularized, mineralized with hydroxyapatite and typically including osteocytes located in lacunae that communicate with one another by cell processes (in canaliculi). Bone is deposited by osteoblasts. calcium tissue osseous tissue osteogenic tissue mineralized bone tissue bone portion of bone tissue bone tissue true Long bone is a limb bone that is subcylindrical and has a shaft with periosteum separating the ends of the bones. Long bones are present only in the limbs[VSAO:wd]. os longum long bone true Replacement bone that forms within cartilage. ossified chondrogenic bone cartilaginous bone endochondral bones endochondral bone true true the thick fibrous membrane that closely invests the entire surface of a bone except the articular cartilage at synovial joints periosteum true A major subdivision of a mature or developing limb, including both skeletal elements (or the mesenchyme that gives rise to the skeletal elements) and associated tissues, such as muscle, connective tissue, integument. Examples: autopod region, zeugopod region, stylopod region, metapodial region, arm region. Excludes the limb girdles. free limb segment segment of limb subdivision of limb extremity part limb region region of limb limb segment true an organ that functions as a secretory or excretory organ glandular organ Druese glandula gland true In amniote animal embryology, the epiblast is a tissue type derived either from the inner cell mass in mammals or the blastodisc in birds and reptiles. It lies above the hypoblast. In mammalian embryogenesis, the columnar cells of the epiblast are adjacent to the trophoblast, while the cuboidal cells of the hypoblast are closer to the blastocoele. The epiblast, whilst referred to as the primary ectoderm, differentiates to form all three layers of the trilaminar germ disc in a process called gastrulation[WP]. The outer of the two layers of the blastoderm that form during gastrulation, corresponding to primitive ectoderm during gastrulation and to the definitive ectoderm after gastrulation[ZFA] epiblast blastocyst ectoblast epiblastus primitive ectoderm epiblast (generic) true 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. anatomical structure of brain biological structure of brain brain anatomical structure brain biological structure brain part neuraxis segment neuroanatomical region segment of brain regional part of brain true true The portion of neural plate anterior to the mid-hindbrain junction. anterior neural plate pre-chordal neural plate true true Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. segmental plate unsegmented paraxial mesoderm PSM presumptive somite mesoderm somitogenic mesoderm somitomeric mesoderm unsegmented mesenchyme presomitic mesoderm true Blood islands are structures in the developing embryo which lead to many different parts of the circulatory system. They primarily derive from plexuses formed from angioblasts. Within them, vacuoles appear through liquefaction of the central part of the syncytium into plasma. The lumen of the blood vessels thus formed is probably intracellular. The flattened cells at the periphery form the endothelium. The nucleated red blood corpuscles develop either from small masses of the original angioblast left attached to the inner wall of the lumen or directly from the flat endothelial cells. In either case the syncytial mass thus formed projects from and is attached to the wall of the vessel. Such a mass is known as a blood island and hemoglobin gradually accumulates within it. Later the cells on the surface round up, giving the mass a mulberry-like appearance. Then the red blood cells break loose and are carried away in the plasma. Such free blood cells continue to divide. Blood islands have been seen in the area vasculosa in the omphalomesenteric vein and arteries, and in the dorsal aorta[WP, unvetted]. ventral lateral plate mesoderm blood islands VBI caudal hematopoietic tissue posterior ICM posterior blood island ventral blood island blood island true The intermediate mesoderm is located between the lateral mesoderm and the paraxial mesoderm. It develops into the kidney and gonads. IM intermediate mesenchyme intermediate plate intermediate plate mesoderm mesenchyma intermedium intermediate mesoderm true A region of embryonic ectodermal cells that lie directly above the notochord. During neurulation, they change shape and produce an infolding of the neural plate (the neural fold) that then seals to form the neural tube[XAO]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium[ZFA] lamina neuralis presumptive central nervous system neural plate true true true The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO] paraxial mesenchyme somitic mesoderm mesoderma paraxiale paraxial mesoderm true true true anterior neural tube true Portion of the middle of the three primary germ layers of the embryo that resides on the periphery of the embryo, is continuous with the extra-embryonic mesoderm, splits into two layers enclosing the intra-embryonic coelom, and gives rise to body wall structures[MP]. LPM lateral mesoderm lateral plate lateral plate mesenchyme mesoderma laminae lateralis lateral plate mesoderm true true true true A transitional population of migrating mesenchymal cells that derive from somites and that will become muscle cells. myomeres muscle plate myomere myotome region myotomes myotomus myotome true Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline to form the heart rudiment or cone. cardiac field fused heart primordium heart primordium true Ventral somitic compartment that is a precursor of the axial skeleton[XAO]. Sclerotomes eventually differentiate into the vertebrae and most of the skull. The caudal (posterior) half of one sclerotome fuses with the rostral (anterior) half of the adjacent one to form each vertebra. From their initial location within the somite, the sclerotome cells migrate medially towards the notochord. These cells meet the sclerotome cells from the other side to form the vertebral body. From this vertebral body, sclerotome cells move dorsally and surround the developing spinal cord, forming the vertebral arch[WP]. sclerotomes sclerotomus sclerotome true true Gonochoristic organism that can produce female gametes. female human body female female organism true Gonochoristic organism that can produce male gametes. male human body male male organism true Anatomical structure that overlaps the outer epithelial layer and is adjacent to the space surrounding the organism. anatomical surface feature surface feature surface region surface structures surface structure true 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. organ compound organ true Portion of tissue consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage[XAO]. A mesh-like cell arrangement, less compact than an epithelium[ZFA]. The part of the embryonic mesoderm, consisting of loosely packed, unspecialized cells set in a gelatinous ground substance, from which connective tissue, bone, cartilage, and the circulatory and lymphatic systems develop[BTO]. mesenchymal tissue mesenchyme tissue portion of mesenchymal tissue portion of mesenchyme tissue mesenchyma mesenchyme true the outermost extraembryonic membrane chorion (vertebrates) embryonic chorion fetal chorion uterine chorion chorion frondosum chorionic sac chorion true true true The trachea is the portion of the airway that attaches to the bronchi as it branches [GO:dph]. cartilaginous trachea vertebrate trachea windpipe tracheal tubule trachea true An organ involved in reproduction genital organ reproductive system organ sex organ genitalia reproductive organ true true amnion ectoderm amnionic ectoderm amnion epithelium amniotic ectoderm true true true true An endoderm that is part of a foregut [Automatically generated definition]. foregut endoderm endoderm of foregut true true true A mesenchyme that is part of a amnion. amnion mesenchyme amnion mesoderm amnionic mesoderm mesenchyme of amnion amnionic mesenchyme amnionic mesoderm amniotic mesoderm true true true A mesenchyme that is part of a chorion. chorion mesenchyme chorion mesoderm chorionic mesenchyme mesenchyme of chorion mesenchyme of chorion (vertebrates) chorionic mesenchyme true true true A gland that is part of a foregut [Automatically generated definition]. foregut gland gland of foregut true A layer of epithelial cells on the surface of the mucosa. lamina epithelialis mucosa lamina epithelialis mucosae epithelium of mucosa true An epithelium that is part of a hindgut [Automatically generated definition]. epithelial tissue of hindgut hindgut epithelial tissue hindgut epithelium epithelium of hindgut true A extraembryonic structure that develops_from a ectoderm and is part of a chorion. chorion ectoderm chorion epithelium chorionic epithelium chorionic ectoderm true A gland that is part of a digestive tract [Automatically generated definition]. digestive tract gland gland of digestive tract gland of lower gastrointestinal tract gut gland lower gastrointestinal tract gland gland of digestive tract true true A gelatinous substance within the umbilical cord, largely made up of mucopolysaccharides (hyaluronic acid and chondroitin sulfate). It also contains some fibroblasts and macrophages. It is derived from Extra Embryonic Mesoderm[WP] Wharton's jelly umbilical cord mesenchyme mesenchyme of umbilical cord true true true 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) bone of hind limb bone of hindlimb bone of inferior member bone of lower extremity bone organ of hind limb bone organ of hindlimb bone organ of lower extremity hind limb bone hind limb bone organ hindlimb bone organ hindlimb bone true true true A blood vessel that is part of the arterial system. Includes artery, arteriole and aorta. arterial blood vessel true A long bone that is part of a limb [Automatically generated definition]. long bone of limb limb long bone true true A long bone that is part of a hindlimb [Automatically generated definition]. hind limb long bone inferior member long bone long bone of hind limb long bone of hindlimb long bone of inferior member long bone of lower extremity lower extremity long bone hindlimb long bone true true Passages external to the liver for the conveyance of bile. These include the common bile duct and the common hepatic duct. bile duct extrahepatic part extrahepatic biliary system extrahepatic bile duct true Passages within the liver for the conveyance of bile. Includes right and left hepatic ducts even though these may join outside the liver to form the common hepatic duct. bile duct intrahepatic part intrahepatic biliary system intrahepatic bile duct true Portion of tissue in the nervous system which consists of neurons and glial cells, and may also contain parts of the vasculature. nerve tissue nervous tissue portion of neural tissue neural tissue true A region of the fetal urogenital sinus epithelium destined to become the prostate[GO]. prostate ductal progenitor prostatic bud prostate gland bud prostate primordium prostate bud true true A bone that is part of a hindlimb stylopod [Automatically generated definition]. femur upper leg bone true Mesenchyme that is part of a developing hindlimb [Automatically generated definition]. hind limb mesenchyme inferior member mesenchyme lower extremity mesenchyme mesenchyme of hind limb mesenchyme of hindlimb mesenchyme of inferior member mesenchyme of lower extremity hindlimb mesenchyme true A small endodermal thickening in the foregut adjacent to the transverse septum. Invaginates forming the hepatic diverticulum. embryological hepatic plate primordium of the liver hepatic plate liver bud liver endoderm liver primordium true true true true true 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 or endothelial tube epithelial tube true true A blood vessel that carries blood from the capillaries toward the heart segment of venous tree organ venous tree organ segment venous blood vessel true A duct that is part of a digestive system [Automatically generated definition]. duct of digestive system duct of gastrointestinal system gastrointestinal system duct digestive system duct true An epithelium that lines the lumen of the digestive tract. digestive tract epithelial tissue epithelial tissue of digestive tract epithelial tissue of gut epithelium of digestive tract epithelium of gut gastrodermis gut epithelial tissue gut epithelium alimentary tract epithelium digestive tract epithelium true Any of the organized aggregations of cells that function as secretory or excretory organs and are associated with reproduction. genitalia gland gland of genitalia gland of reproductive system reproductive gland reproductive system gland sex gland reproductive gland true true A transitional population of migrating mesenchymal cells that derive from somites and that will become dermal cells. cutis plate dermatomal mesenchyme epimere mesoderm mesenchyma dermatomiale dermatome true Any tube, opening or passage that connects two distinct anatomical spaces. foramen foramina opening ostia ostium anatomical conduit true An anatomical structure that develops (entirely or partially) from the endoderm. endoderm-derived structure true An anatomical structure that develops (entirely or partially) from the mesoderm. mesodermal derivative mesoderm-derived structure true An anatomical structure that develops (entirely or partially) from the ectoderm. ectodermal deriviative ectoderm-derived structure true Anatomical system that has as its parts the organs concerned with the production and excretion of urine and those concerned with reproduction. urogenital system GU tract UG tract Urogenitalsystem genito-urinary system genitourinary tract urogenital tract genitourinary system true true The first recognizable structure derived from the heart field myocardial plate cardiac crescent cardiogenic crescent heart rudiment cardiogenic plate true A specific region of the lateral mesoderm that will form the primary beating heart tube. In mammals the primary heart field gives rise to the left ventricle. first heart field primary heart field FHF PHF heart field primary heart field true true true true An epithelial tube that will give rise to the mature heart. embryonic heart tube endocardial heart tube endocardial tube heart tube true true true A cardiac chamber surrounds an enclosed cavity within the heart chamber of heart heart chamber cardiac chamber true true A thick plate of mesodermal tissue that occupies the space between the thoracic cavity and yolk stalk in the early embryo, forming a transverse partition partially separating the coelomic cavity into thoracic and abdominal portions. It gives rise to the central tendon of the diaphragm[VHOG]. transverse septum septum transversum true The internal genitalia are the internal sex organs such as the uterine tube, the uterus and the vagina in female mammals, and the testis, seminal vesicle, ejaculatory duct and prostate in male mammals internal genitalia internal genitals internal reproductive organ internal sex organ internal genitalia true A portions of the gut that is derived from endoderm. endodermal gut gut endoderm endodermal part of digestive tract true true Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body. set of all bones set of bones of body skeleton true The bilaminar epithelium formed from the myotome and dermatome. dermamyotome dermomyotomes dermomyotome true true A cone-like structure that is formed when myocardial progenitor cells of the heart field fuse at the midline. The heart rudiment is the first structure of the heart tube. heart cone rudimentary heart heart rudiment true A membranous sac that develops from the posterior part of the alimentary canal in the embryos of mammals, birds, and reptiles, and it is important in the formation of the umbilical cord and placenta in mammals[VHOG]. allantoic bud allantois true true outermost layer of cells in the blastodermic vesicle, which will develop into the trophoblast layer and then contact the endometrium and take part in establishing the embryo's means of nutrition trophectoderm true true An outgrowth on the lateral trunk of the embryo that develops into a limb. The limb bud is divided into ectoderm and mesenchyme[cjm, modified from MP]. limb buds limbbud gemmae membrorum limb bud true multilayered ectodermal region at the distal tip of a limb or fin bud necessary for the proper development of the underlying mesenchyme[MP,modified]. Along with the zone of polarizing activity, it is a crucial organizing region during limb development[WP]. apical epidermal ridge AER crista ectodermalis apicalis apical ectodermal ridge true An outgrowth on the lateral trunk of the embryo that develops into a limb or paired fin. The limb/fin bud is divided into ectoderm and mesenchyme[cjm, modified from MP]. limb - fin bud paired appendage bud paired limb/fin bud paired limb/fin bud true true A bone that is part of an appendage [Automatically generated definition]. appendage bone bone of appendage bone of free segment of appendicular skeleton bone of free limb or fin true true The collection of all skeletal elements in an individual limb. free limb skeleton limb skeleton set of bones of limb skeleton of limb true true Anatomical system that has as its parts the heart and blood vessels. CV system Herz und Gefaesssystem cardiovascular system true A network of blunt ended vessels lacking direct connection to the blood vascular system. These vessels collect and drain fluids and macromolecules from interstitial spaces throughout the animal. They derive from a subpopulation of endothelial cells and have walls that are much thinner than the blood carrying vessels. Lymphatic vessels are usually classified as either superficial or deep. lymphatic trunks and ducts lymphatic vasculature lymphatic vessel network lymphatic vessels set set of lymphatic vessels trunci et ductus lymphatici lymph vessels lymph vasculature true true A vascular network consisting of blood vessels. blood vascular network set of blood vessels blood system blood vessel system blood vessels blood vasculature true The part of the cardiovascular system consisting of all arteries. arterial system true The part of the cardiovascular system consisting of all venous vessels. In vertebrates with a double circulation, this can be divided into systemic and pulmonary portions. vein system venous system true the polygonal structure of the liver that consists of hepatocytes radiating outward from a hepatic vein hepatic lobule lobuli hepatici lobulus hepaticus lobules of liver lobuli hepatis liver lobule true true An appendage that is part of an appendage girdle complex. girdle-associated appendage limb or fin limb/fin pectoral or pelvic appendage pelvic/pectoral appendage jointed paired lateral appendage paired appendage paired limb/fin true Paired appendage that consists of the posterior appendicular skeleton and associated soft and hard tissues, but excludes the pelvic girdle and its associated soft and hard tissues. posterior appendage hindlimb/pelvic fin pelvic appendage pelvic limb/fin posterior limb/fin posterior paired appendage pelvic appendage true The embryo and its adnexa (appendages or adjunct parts) or associated membranes (i.e. the products of conception) The conceptus includes all structures that develop from the zygote, both embryonic and extraembryonic. It includes the embryo as well as the embryonic part of the placenta and its associated membranes - amnion, chorion (gestational sac), and yolk sac[WP]. embryo plus adnexa conceptus true Organism at the gastrula stage. gastrula embryo blastocystis trilaminaris tri-laminar disc tri-laminar disk trilaminar blastocyst trilaminar blastoderm trilaminar disc trilaminar disk trilaminar germ gastrula true A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO] skeletal tissue true Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles. skeletal element true Anatomical system that consists of all the joints of the body. joint system set of all joints of body set of all joints set of joints of body articular system true the mucous membrane lining the respiratory tract apparatus respiratorius mucosa apparatus respiratorius mucosa of organ apparatus respiratorius mucous membrane mucosa of apparatus respiratorius mucosa of organ of apparatus respiratorius mucosa of organ of respiratory system mucosa of respiratory system mucous membrane of apparatus respiratorius mucous membrane of respiratory system respiratory system mucosa of organ respiratory system mucous membrane laryngeal mucous membrane respiratory mucosa respiratory tract mucosa respiratory system mucosa true A mucosa that is part of a gastrointestinal system. digestive tract mucosa gut mucosa gut mucuous membrane mucosa of gut gastrointestinal system mucosa true 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 epithelial tissue of respiratory tract epithelium of respiratory tract respiratory tract epithelial tissue airway epithelium respiratory epithelium respiratory tract epithelium true true true An epithelium that is part of a respiratory system [Automatically generated definition]. apparatus respiratorius epithelial tissue apparatus respiratorius epithelium epithelial tissue of apparatus respiratorius epithelial tissue of respiratory system epithelium of apparatus respiratorius epithelium of respiratory system respiratory system epithelial tissue respiratory system epithelium true An epithelium that is part of a digestive system [Automatically generated definition]. digestive system epithelial tissue digestive system epithelium epithelial tissue of digestive system epithelial tissue of gastrointestinal system epithelium of digestive system epithelium of gastrointestinal system gastrointestinal system epithelial tissue gastrointestinal system epithelium true An epithelium that is part of a lower respiratory tract [Automatically generated definition]. epithelial tissue of lower respiratory tract epithelium of lower respiratory tract lower respiratory tract epithelial tissue lower respiratory tract epithelium true Layer of lateral plate mesoderm that forms the future body wall - underlies the ectoderm[WP]. outer layer of lateral plate mesoderm parietal mesoderm somatic mesoderm somatic layer of lateral plate mesoderm true Layer of lateral plate mesoderm that forms the circulatory system and future gut wall - overlies endoderm[WP]. visceral mesoderm inner layer of lateral plate mesoderm splanchnic mesoderm splanchnic layer of lateral plate mesoderm true A structure created during embryogenesis when the lateral mesoderm splits into two layers - the outer (or somatic) layer becomes applied to the inner surface of the ectoderm, and with it forms the somatopleure.[WP]. somatopleure true The fetal urogenital sinus (from which the prostate derives) is a simple cylinder of stratified basal epithelium, surrounded by mesenchyme and positioned between the embryonic bladder and pelvic urethra UGE epithelium of urogenital sinus urogenital sinus epithelium true Anatomical cluster that connects two or more adjacent skeletal elements or hardened body parts. joint articulation true The region of the digestive tract extending from the mouth cavity through pharynx esophagus stomach and duodenum. upper GI tract upper gastrointestinal tract upper digestive tract true hepatic diverticulum biliary bud true true true true A proximal-distal subdivision of the digestive tract. alimentary system subdivision intestinal tract segment of intestinal tract subdivision of alimentary system subdivision of digestive tract true A part of a wall of an organ that forms a layer. organ component layer true A mucosa that is part of a bronchiole [Automatically generated definition]. bronchiole mucosa bronchiole mucosa of organ bronchiole mucous membrane bronchiole organ mucosa lobular bronchiole mucosa lobular bronchiole mucosa of organ lobular bronchiole mucous membrane lobular bronchiole organ mucosa mucosa of lobular bronchiole mucosa of organ of bronchiole mucosa of organ of lobular bronchiole mucous membrane of bronchiole mucous membrane of lobular bronchiole organ mucosa of bronchiole organ mucosa of lobular bronchiole mucosa of bronchiole true The median dorsal longitudinal groove formed in the embryo by the neural plate after the appearance of the neural folds. neural groove true One of the two elevated edges of the neural groove[GO,MP]. medullary fold neural fold true true true true true A solid rod of neurectoderm derived from the neural keel. The neural rod is roughly circular in cross section. Neural rod formation occurs during primary neurulation in teleosts[GO]. An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube[ZFIN]. neural tube rod neural rod true Muscle structures are contractile cells, tissues or organs that are found in multicellular organisms[GO]. musculus muscle muscle element muscle structure true A bud is a protrusion that forms from an epithelial sheet by localized folding. epithelial bud true Any anatomical structure that is part of the reproductive system. reproductive system element reproductive system structure reproductive structure true An epithelial sheet bent on a linear axis. epithelial fold true An organ or element that is in the abdomen. Examples: spleen, intestine, kidney, abdominal mammary gland. abdomen organ abdomen element true An organ or element that is part of the adbominal segment of the organism. This region can be further subdivided into the abdominal cavity and the pelvic region. abdominal segment organ abdominal segment element true 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 organ trunk region element true An organ or element that is in the thoracic cavity. Examples: lung, heart, longus colli. thoracic cavity organ thoracic cavity element true An organ that part of the thoracic segment region. This region can be further subdividied chest and thoracic cavity regions. upper body organ thoracic segment organ true Mesenchyme that is part of a developing hindlimb stylopod [Automatically generated definition]. upper leg mesenchyme true Mesenchyme that is part of a developing trunk. trunk and cervical mesenchyme trunk mesenchyme true true A portion of tissue that is part of an embryo. portion of embryonic tissue developing tissue embryonic tissue true Portion of tissue that is contiguous with the embryo and is comprised of portions of tissue or cells that will not contribute to the embryo. extra-embryonic tissue extraembryonic tissue true A sex gland that is part of a male reproductive system. accessory sex gland male reproductive gland true The part of the digestive system that excludes the hepatobiliary system. GI tract alimentary system alimentary tract gastro-intestinal system gastrointestinal (GI) tract gastrointestinal system gastrointestinal tract alimentary part of gastrointestinal system true A limb bud that develops into a hindlimb. hind limb bud posterior limb bud leg bud limb bud - hindlimb hindlimb bud true true A limb bud that develops into a hindlimb or pelvic fin. hindlimb/pelvic fin bud pelvic fin bud pelvic fin buds pelvic appendage bud true developing structure developmental structure developmental tissue developing anatomical structure true Vagal neural crest is adjacent to the first seven somites gives rise to both ganglionic and ectomesenchymal derivatives[ZFA]. VNC enteric neural crest post-otic neural crest vagal neural crest true true Multi-tissue structure that arises from the heart rudiment and will become the heart tube. primitive heart tube early primitive heart tube primitive heart tube true true Portion of tissue that gives rise to the immature gonad. future gonad gonadal primordium primitive gonad undifferentiated gonad immature gonad gonad primordium true A pair of lateral diverticula just over the liver rudiment representing the primordia of the lungs, formed by the floor of the foregut just anterior to the liver diverticulum. lateral diverticula lung diverticulum lung endoderm lung primordium true Intrinsic membrane that arises from embryonic germ layers and grow to surround the developing embryo. extraembryonic membrane true . extra-embryonic mesoderm extraembryonic mesenchyme extraembryonic mesoderm true true true A acellular anatomical structure that is the bounding layer of a anatomical structure. acellular membrane true An acellular membrane that is part of the epithelium, lies adjacent to the epithelial cells, and is the fusion of the the basal lamina and the reticular lamina. basement membrane of connective tissue membrana basalis basement membrane basement membrane of epithelium true fetal uterus embryonic uterus true In the circulatory system of animals, a portal venous system occurs when a capillary bed drains into another capillary bed through veins, without first going through the heart. Both capillary beds and the blood vessels that connect them are considered part of the portal venous system. They are relatively uncommon as the majority of capillary beds drain into veins which then drain into the heart, not into another capillary bed. Portal venous systems are considered venous because the blood vessels that join the two capillary beds are either veins or venules. Examples of such systems include the hepatic portal system and the hypophyseal portal system. Unqualified, 'portal venous system' often refers to the hepatic portal system. For this reason, 'portal vein' most commonly refers to the hepatic portal vein[WP]. portal venous system portal system true A delimited region of dense mesenchyme within looser mesenchyme. mesenchyme condensation developing mesenchymal condensation true true Cell condensation that is an aggregation of mesenchymal cells that are committed to differentiate into chondroblasts and chondrocytes. cartilage condensation cartilagenous condensation chondrogenic condensation cartilaginous condensation true A delimited region of dense mesenchyme within looser mesenchyme whose cells are committed to become chondroblasts. pre-chondrogenic condensation precartilage condensation precartilagenous condensation prechondrogenic condensation pre-cartilage condensation true true A bone that is part of the region of the hindlimb that includes the zeugopod and stylopod. Examples: patella, femur, tibia. Counter-examples: any pes phalanx leg bone true Epithelium that derives from the endoderm. Examples: urothelium, transitional epithelium of ureter, epithelium of prostatic gland.[FMA] endoderm-derived epithelium endoepithelium endo-epithelium true true Subdivision of skeleton which consists of cranial skeleton, set of all vertebrae, set of all ribs and sternum[FMA, modified]. skeleton axiale axial skeleton plus cranial skeleton true A sheet of somatopleure that grows upward over the embryo and eventually meets in the midline enclosing the embryo, eventually giving rise to the amnion and chorion[Kardong]. amnionic fold amniotic fold true A collection of two or more connected limb segments. Examples: arm (comprising stylopod and zeugopod regions). multi-limb segment region true A femur endochondral element that is composed primarily of a pre-cartilage condensation. femoral pre-cartilage condensation femur pre-cartilage condensation true true true true An anatomical junctions that overlaps the foregut and midgut. foregut-midgut junction true The embryonic precursor of the brain. brain rudiment presumptive brain encephalon embryonic brain future brain true A presumptive structure that has the potential to develop into a forebrain. future prosencephalon presumptive forebrain presumptive prosencephalon prosencephalon future forebrain true Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not. fluid body fluid bodily fluid true An organ system subdivision that is a network of vessels capable of removing accumulating protein and fluid from the interstitial space and returning it to the vascular space. In some species, this network is connected to the immune system via lymph nodes and lymphocyte-producing organs, with the whole being the lymphoid system. lymphatic system lymphatic tree system lymporeticular system lymphatic part of lymphoid system true The pharynx is the part of the digestive system immediately posterior to the mouth[GO]. anterior part of foregut pharyngeal tube pharynx true Presumptive structure of the blastula that will develop into endoderm. presumptive endoderm true future blood presumptive blood true Portion of embryonic tissue determined by fate mapping to become a structure. future structure presumptive structures presumptive structure true Presumptive structure of the blastula that will develop into ectoderm. presumptive epidermis presumptive ectoderm true Presumptive structure of the blastula that will develop into mesoderm. presumptive mesoderm true A sheet of extracellular matrix. aponeuroses aponeurotic aponeurosis true The galea aponeurotica (epicranial aponeurosis, aponeurosis epicranialis) is a tough layer of dense fibrous tissue which covers the upper part of the cranium; behind, it is attached, in the interval between its union with the Occipitales, to the external occipital protuberance and highest nuchal lines of the occipital bone; in front, it forms a short and narrow prolongation between its union with the Frontales. On either side it gives origin to the Auriculares anterior and superior; in this situation it loses its aponeurotic character, and is continued over the temporal fascia to the zygomatic arch as a layer of laminated areolar tissue. It is closely connected to the integument by the firm, dense, fibro-fatty layer which forms the superficial fascia of the scalp: it is attached to the pericranium by loose cellular tissue, which allows the aponeurosis, carrying with it the integument to move through a considerable distance. aponeurosis epicranialis aponeurosis of epicranius epicranial aponeurosis epicranius aponeurosis galea aponeurotica cranial aponeurosis epicranial aponeurosis galea aponeurosis galea aponeurotica; aponeurosis epicranialis galeal aponeurosis epicranial aponeurosis true An epithelium that is composed primarily of secretory cells. glandular epithelium true Loose connective tissue located at the outer and inner layers of organs. Examples: submucosal connective tissue, tunica adventitia of artery, papillary dermis, superficial fascia of dorsum of hand. loose areolar connective tissue areolar tissue loose connective tissue areolar connective tissue true The distalmost portion of the digestive tract, derived from the hindgut, and terminating with the anus. rectum rectal part of digestive tract terminal section of digestive tract terminal part of digestive tract true A glandular epithelium that lines the stomach. The stomach's glandular epithelium is characterized by the presence of gastric glands. epithelium of gastric gland gastric gland epithelium stomach glandular epithelium true true Any gland that is part of the digestive system. digestive gland digestive system gland true true Simple columnar epithelium that constitutes the secretory part of a gland. Examples: epithelium of stomach, luminal epithelium of lactiferous duct.[FMA] glandular columnar epithelium true true stomach mucosa that is lined with glandular epithelium and part of a stomach glandular region. stomach glandular region glandular mucous membrane stomach glandular region mucosa true The vascular cord is the primordial vasculature that will develop into blood vessels by the process of tubulogenesis[GO]. The vascular cord is composed of angioblast or vascular endothelial cells in a solid linear mass called a cord. The cord then undergoes tubulogenesis to form the lumen of the vessels[ZFA]. vascular cord true The splanchnic mesoderm in the cardiogenic region where the heart develops; it gives rise to endocardial heart tubes that fuse to form the primordial cardiac tube, the heart primordium[web]. Two migratory heart primordia that move ventrally during the course of neurulation, and then fuse[XAO]. cardiogenic splanchnopleure cardiac mesoderm cardiogenic mesoderm cardiogenic region heart primordia cardiogenic splanchnic mesoderm true true Organism at the cleavage stage. cleaving embryo true future digestive tract future digestive tube future gut primitive gut embryonic digestive tube primordial digestive tube primordial gut presumptive gut true A hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood or analogs[GO,modified]. dorsal tube heart adult heart primary circulatory organ true An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. presumptive central nervous system neural keel true 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. arbor tracheobronchialis tracheobronchial system tracheobronchial tree true true true The collection of all skeletal elements in a pelvic appendage region. pelvic appendage skeleton true A presumptive structure that has the potential to develop into a presomitic mesoderm. presumptive segmental plates presumptive segmental plate true A presumptive structure that has the potential to develop into a neural plate. prospective neuroectoderm prospective vegetal ectoderm presumptive neural plate true The part of the blastula that has the potential to develop into a paraxial mesoderm. future paraxial mesenchyme future paraxial mesoderm presumptive paraxial mesoderm true 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]. epidermis epidermis (sensu Metazoa) outer epidermal layer outer epithelial layer hypoderm hypodermis outer epithelium true true Outermost layer of cells surrounding the embryo. EVL enveloping layer enveloping layer of ectoderm true true true An epithelial tube that is open at one end only. epithelial sac true true An epithelial tube open at both ends that allows fluid flow. epithelial tube open at both ends true A closed epithelium with a lumen. epithelial vesicle true Mesenchyme with little extracellular matrix. dense mesenchyme tissue true Mesenchymal cells that are migrating. migrating mesenchyme population true 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 true true Epithelium bearing vibratile cilia on the free surface. ciliated epithelium true An anatomical structure that connects two structures junction anatomical junction anatomical junction true Anlagen are populations of contiguous cells, typically arranged in one plane, that are morphologically indistinct, but that already correspond in extent to a later organ/tissue. field developmental field future organ organ field anlage true true Anatomical system that consists of all blood and lymph vessels. Gefaesssystem@de vascular system true A bridge of mesoderm connecting the caudal end of the young embryo with the trophoblastic tissues; the precursor of the umbilical cord. connecting stalk true The anteriormost subdivision of the body that includes the head, jaws, pharyngeal region and the neck (if present). In vertebrates this is the subdivision that includes the cervical vertebrae. cephalic area cephalic part of animal cephalic region head and neck head or neck craniocervical region true An organism subdivision that encompasses the region containing the pectoral or pelvic girdle. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). girdle girdle region fin girdle fin girdle region limb girdle limb girdle region appendage girdle region true Skeletal subdivision consisting of a set of bones linking the axial series to the hindlimb zeugopodium and offering anchoring areas for hindlimb and caudal musculature. pelvic girdle skeleton skeletal parts of pelvic girdle skeleton of pelvic girdle pelvic girdle pelvic girdle skeleton true true Skeletal element that is composed of cartilage tissue and may be permanent or transient. cartilage organ cartilaginous element chondrogenic element cartilage cartilage element true The irregular bones are bones which, from their peculiar form, cannot be grouped as long bone, short bone, flat bone or sesamoid bone. Irregular bones serve various purposes in the body, such as protection of nervous tissue, affording multiple anchor points for skeletal muscle attachment (as with the sacrum), and maintaining pharynx and trachea support, and tongue attachment (such as the hyoid bone). They consist of cancellous tissue enclosed within a thin layer of compact bone. The irregular bones are: the vertebrC&, sacrum, coccyx, temporal, sphenoid, ethmoid, zygomatic, maxilla, mandible, palatine, inferior nasal concha, and hyoid. os irregulare os irregulare irregular bone true bone of hip region true An embryonic structure that is derived from the inner cell mass and lies above the hypoblast and gives rise to the three primary germ layers embryonic epiblast inner cell mass derived epiblast true A limb segment that is part of a hindlimb. free lower limb segment free lower limb subdivision segment of free lower limb subdivision of free lower limb lower limb segment true An out-pocket of thickened ventral foregut epithelium adjacent to the developing heart. Constitutes the first morphological sign of the embryonic liver. The anterior portion of the hepatic diverticulum gives rise to the liver and intrahepatic biliary tree, while the posterior portion forms the gall bladder and extrahepatic bile ducts. liver diverticulum diverticulum hepaticum hepatic diverticulum true true true true true liver bud true true true true The part of the airway consisting of a respiratory bronchiole and all of its branches acinus pulmonaris arbor alveolaris lobulus pulmonis primarius primary pulmonary lobule respiratory lobule pulmonary acinus true respiratory primordium true Sum total of mesenchyme in the embryo. entire embryonic mesenchyme true An epithelium that is part of a foregut-midgut junction. epithelium of foregut-midgut junction true true true An endoderm that is part of a anal region. anal membrane endodermal component true true An endoderm that is part of a foregut-midgut junction. endoderm of foregut-midgut junction true region of trunk trunk subdivision subdivision of trunk true trunk and cervical paraxial mesenchyme trunk paraxial mesenchyme trunk paraxial mesoderm true The primordial embryonic connective tissue of the developing limbs, autopods and digits, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to limb connective tissue, bone and musculature in conjunction with myotome cells. limb mesoderm limb mesenchyme true The many-lobed berry cluster of cells that is the terminous of a gland where the secretion is produced is acinar in form. acinus acini glandular acinus true An epithelium that is part of a embryonic cloaca. cloacal epithelium embryonic cloacal epithelium true true true A specific region of the urogenital sinus epithelium into the area in which the prostate gland will develop. prostate primordium prostate field true true true true Branch or outpocketing of the digestive tract. diverticulum of gut intestinal pouch digestive tract diverticulum true true pouch diverticulum sac true A division of the stomach. The stomach can be divided based on mucosal histology (glandular epithelium and gastric glands) and the relative position and type of gastric gland. gastric zone region of stomach section of stomach zone of stomach true ALPM anterior lateral plate mesoderm true true lobulus lobule true An anatomical structure that has more than one cell as a part. CARO:0010000 FBbt:00100313 multicellular structure uberon UBERON:0010000 multicellular structure multicellular anatomical structure true An organ of the digestive tract that is capable of retaining and storing food food storage organ true Mesenchyme that has the potential to develop into a dermis. future dermis true A femur endochondral element that is composed primarily of cartilage tissue. femoral cartilage condensation femur cartilage element true true true true 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 gland male accessory reproductive gland male accessory sex gland true An anatomical structure that has some part that develops from the neural crest. structure with developmental contribution from neural crest true germ layer / neural crest true true Mesenchyme that is part of a extraembryonic membrane. extraembryonic membrane mesenchyme true true true A skeletal element that has the potential to participate in endochondral ossification, and may participate in intramembranous ossification. endochondral replacement element endochondral element true The smallest anatomical unit of the lung, measuring 0.50 to 2.00 cm in diameter. Each lobule is composed of 4-8 terminal bronchioles and their distal alveolar ducts and sacs. The lobules are separated by fibrous interlobular septa. lobulus pulmonis pulmonary lobule true true Epithelium composed of cells that develops from the ectoderm[FMA,modified]. ectoderm-derived epithelium ecto-epithelium true true Mesenchyme that develops_from a somatopleure. mesenchyme from somatopleure true true true A simple columnar epithelium that looks stratified but is not, because its cells are arranged with their nuclei at different levels. pseudostratified columnar epithelium true 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. epithelium pseudostratificatum columnare ciliatum (trachea et bronchi) pseudostratified ciliated columnar epithelium true true An appendage segment that is part of a limb/fin. limb/fin segment paired limb/fin segment true An organism subdivision that includes both an appendage and its associated girdle region. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). appendage complex appendage-girdle complex appendage/girdle complex girdle plus limb or fin limb appendage girdle complex true true Appendage girdle complex that when present, encompasses the pelvic appendicular skeleton and the pelvic girdle. pelvic appendage/girdle complex pelvic girdle plus pelvic limb or fin pelvic girdle plus posterior limb or fin lower limb lower limb and pelvic girdle lower limb and pelvis pelvic complex true Skeletal subdivision that is a segment of the limb skeleton. limb skeleton subdivision true The subdivision of the skeleton of either the pectoral or pelvic girdle. skeleton of girdle girdle skeleton true A bone that is part of an appendage girdle complex (i.e. any bone in a limb, fin or girdle). bone of extended limb/fin region limb bone bone of appendage girdle complex true A bone that is part of a pelvic complex. Examples: pubis, ischium, fot phalanx, any tarsal bone, any bone of the pelvic fin or girdle. hindlimb bone bone of pelvic complex true A major subdivision of an organism that divides an organism along an axis perpedicular to the main body anterior-posterior axis. In vertebrates, this is typically a fin or limb segment. In insects, this includes segments of appendages such as antennae, as well as segments of the insect leg. appendage segment appendicular segment subdivision of organism along appendicular axis true A skeletal element that is part of a limb and composed of cartilage tissue. limb cartilage element true true A skeletal element that is part of a limb and composed of pre-cartilage tissue. limb bone pre-cartilage condensation true A cartilaginous condensation that has the potential to develop into a hindlimb bone. hindlimb cartilage condensation hindlimb cartilage element true true A pre-cartilage condensation that has the potential to develop into a hindlimb bone. hindlimb pre-cartilage condensation hindlimb pre-cartilage condensation true true Anatomical cluster consisting of the skeletal elements (i.e. bone elements, cartilage elements, cartilage condensations) that are part of an individual subdivision of the organism. Excludes joints. skeletal subdivision subdivision of skeleton (in vivo) subdivision of skeleton true Skeletal element that forms around the notochord and is part of the vertebral column. vertebra skeletal element vertebra element vertebra endochondral element vertebral endochondral element vertebral element true The cartilaginous form of a vertebral element, a skeletal element that forms around the notochord and is part of the vertebral column. vertebral cartilage condensation vertebra cartilage element true true The pre-cartilaginous form of a vertebral element, a skeletal element that forms around the notochord and is part of the vertebral column. vertebral pre-cartilage condensation vertebra pre-cartilage condensation true Joint in which the articulating bones or cartilages are connected by ligaments or fibrocartilage without an intervening synovial cavity. Examples: sagittal suture, inferior tibiofibular syndesmosis, costochondral joint, pubic symphysis. solid joint nonsynovial joint true Subdivision of the skeletal system which consists of the axial skeleton plus associated joints. axial skeletal system true Subdivision of the skeletal system which consists of the postcranial axial skeleton plus associated joints. axial skeletal system post-cranial axial skeletal system postcranial axial skeletal system true A subdivision of an anatomical system. organ system subdivision true Subdivision of the skeletal system which consists of the appendicular skeleton plus associated joints. appendicular skeletal system true basal cell layer of skin outer epithelium of body embryonic skin basal layer true true The collection of all skeletal elements in an individual limb or fin. limb/fin skeleton skeletal parts of limb/fin skeleton of limb/fin paired limb/fin skeleton true true Proximal element of a free limb skeleton consisting of the femur and humerus in the forelimb stylopodium and hindlimb stylopodium respectively[VSAO, modified]. stylopodium skeleton mesomere 1 propodial skeleton propodium proximal metapterygial mesomere stylopod stylopodium stylopodial skeleton true true Anatomical structure that is an aggregation of similar cells from which cartilages and bones form, and from which chondrogenesis and osteogenesis are initiated during repair and/or regeneration. (Hall and Miyake 1995). cell condensation true A major subdivision of an organism that divides an organism along its main body axis (typically anterio-posterior axis). In vertebrates, this is based on the vertebral column. axial subdivision of organism body segment main body segment subdivision of organism along main body axis true A cardiovascular system that is part of a conceptus. conceptus cardiovascular system embryonic circulatory system fetal circulatory system embryonic cardiovascular system true Connective tissue, which consists of a population of connective tissue cells, the intercellular matrix of which contains an irregular network of collagen and elastic fiber bundles. Examples: areolar tissue, mucoid tissue, connective tissue of peritoneum, connective tissue of fibrous pericardium. irregular connective tissue true Irregular connective tissue is an irregular connective tissue, the intercellular matrix of which contains a dense irregular network of collagen and elastic fiber bundles. Examples: connective tissue of peritoneum, connective tissue of fibrous pericardium. irregular dense connective tissue typus irregularis (textus connectivus collagenosus compactus) dense irregular connective tissue true true Dense connective tissue is mainly composed of collagen type I. Crowded between the collagen fibers are rows of fibroblasts, fiber-forming cells, that manufacture the fibers. Dense connective tissue forms strong, rope-like structures such as tendons and ligaments. Tendons attach skeletal muscles to bones; ligaments connect bones to bones at joints. Ligaments are more stretchy and contain more elastic fibers than tendons. Dense connective tissue also make up the lower layers of the skin (dermis), where it is arranged in sheets dense connective tissue true Irregular connective tissue, the intercellular matrix of which contains a sparse irregular network of collagen and elastic fiber bundles. Examples: areolar tissue, neuroglial tissue, mucoid tissue. textus connectivus collagenosus laxus textus connectivus laxus loose connective tissue true An acinus that is part of a exocrine gland. exocrine gland acinus acinus of exocrine gland true collection of collagen fibrils true A region of the stomach that is lined with glandular epithelium. glandular stomach stomach glandular region true blood that remains in the placenta and in the attached umbilical cord after childbirth[WP]. cord blood fetal blood umbilical cord blood umbilical cord blood true A zone of skin that is part of a craniocervical region. head or neck skin true An epithelium that consists of columnar epithelial cells. Columnar epithelia are epithelial cells whose heights are at least four times their width. Columnar epithelia are divided into simple (or unilayered), and the rarer stratified (or multi-layered).[WP, modified] columnar epithelium true Epithelium that derives from the mesoderm. [Automatically generated definition]. mesoderm-derived epithelium mesoepithelium meso-epithelium true true internal anal region true Blood-forming tissue, consisting of reticular fibers and cells. haemopoietic tissue hematopoietic tissue hemopoietic tissue textus haemopoieticus bone marrow tissue hematopoietic tissue true true The collection of all skeletal elements in a pelvic complex - i.e. the combination of free limb or fin plus pelvic girdle. bones of lower limb lower limb skeleton ossa membri inferioris pelvic complex skeleton set of bones of lower limb skeleton of posterior limb/fin and girdle skeleton of pelvic complex true An epithelium that is part of a cloaca. cloacal endoderm cloacal epithelium true true true true A section through the tube or network of tubes that connects the ovaries to the outside of the body. subdivision of oviduct subdivision of uterine tube uterine tube zone zone of uterine tube subdivision of fallopian tube subdivision of oviduct true true subdivision of tube true An anatomical space which is the lumen of some anatomical conduit and connects two or more spaces together[FMA,modified]. foramen space anatomical conduit space true A principle subdivision of an organism that includes all structures along the primary axis, typically the anterior-posterior axis, from head to tail, including structures of the body proper where present (for example, ribs), but excluding appendages. main body axis true The region of the organism associated with the visceral organs. body whole body body proper true A organ component layer that is part of a integumental system. layer of skin skin layer integumentary system layer true Any of the organs or elements that are part of the digestive system. Examples: tongue, esophagus, spleen, crop, lunge feeding organ, tooth elements. digestive organ digestive system organ digestive system element true Subdivision of skeletal system that consists of all skeletal elements in the thoracic region of the trunk. In most vertebrates this is the rib cage and sternum. skeleton of thorax thoracic part of axial skeleton thoracic skeleton thoracic skeleton true A duct that is located between lobules, within the thin connective tissue septa that separate lobules. All interlobular ducts are excretory. interlobular duct true 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 skeletal muscle organ true A portion of tissue that will develop into vasculature. primordial vasculature true A hindlimb bone or its cartilage or pre-cartilage precursor. hindlimb bone skeletal element hindlimb endochondral element true A femur bone or its cartilage or pre-cartilage precursor. femur skeletal element femur element femur endochondral element true A limb bone or its cartilage or pre-cartilage precursor. limb bone skeletal element limb bone endochondral element limb endochondral element true true Any structure that is placed on one side of the left-right axis of a bilaterian. lateral structure true A hollow, muscular organ, which, by contracting rhythmically, contributes to the circulation of lymph, blood or analogs. Examples: a chambered vertebrate heart; the tubular peristaltic heart of ascidians; the dorsal vessel of an insect; the lymoh heart of a reptile. heart cardiac pump heart or heart like organ circulatory vessel cardiac structure circulatory organ true heart/pericardium heart plus pericardium true portion of heterogeneous tissue heterogeneous tissue true A epithelium that is part of a foregut. foregut epithelium true Primordium that develops into the central nervous system future CNS presumptive central nervous system future central nervous system true Primordium that develops into the nervous system presumptive nervous system future nervous system true The part of the conceptus that may be lost before birth or will be discarded at birth, or when the embryo becomes an independent organism. extra-embryonic component extraembryonic component entire extraembryonic component true An embryonic anatomical entity that will turn into one or more other anatomical entities, perhaps with other anatomical entities, later in development. transitional anatomical structure true A mesenchyme-derived anatomical entity undergoing a transtion to become another structure. developing mesenchymal structure true skeletal musculature true lymphomyeloid tissue true An multicellular anatomical structure that has subparts of multiple organs as a part. anatomical cluster multi organ part structure true A cluster of cells, largely surrounded by a morphological boundary. cell cluster true A collection of anatomical structures that are alike in terms of their morphology or developmental origin. anatomical collection true organ sector organ zonal region organ zone organ region with floating fiat boundary zone of organ true duct epithelium ductal epithelium epithelial layer of duct true excretory duct true An region of the mesoderm that includes anterior lateral mesoderm of the first heart field plus contiguous pharyngeal mesoderm that gives rise to second-heart-field-derived regions of the heart and branchiomeric muscles. cardiopharyngeal field true true true true Structures of the dermis, epidermis, glands and pigment cells recognizable on the external surfaces of the integument. external integument structure true length unit A unit which is a standard measure of the distance between two points. length unit true mass unit A unit which is a standard measure of the amount of matter/energy of a physical object. mass unit true time unit A unit which is a standard measure of the dimension in which events occur in sequence. time unit true temperature unit A unit which is a standard measure of the average kinetic energy of the particles in a sample of matter. temperature unit true concentration unit A unit which represents a standard measurement of how much of a given substance there is mixed with another substance. concentration unit true 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 true James Malone Tomasz Adamusiak ALS ALS (Amyotrophic Lateral Sclerosis) AMYOTROPHIC SCLEROSIS Amyotrophic Lateral Sclerosis, Guam Form Amyotrophic lateral sclerosis (disorder) Dementia With Amyotrophic Lateral Sclerosis Disease, Lou-Gehrigs GEHRIGS DIS Gehrig Disease Gehrigs Disease Guam Form of Amyotrophic Lateral Sclerosis LOU GEHRIG DIS LOU GEHRIGS DIS Lateral Scleroses, Amyotrophic Lou Gehrig Disease Lou Gehrig's disease MOTOR NEURON DIS AMYOTROPHIC LATERAL SCLEROSIS Motor Neuron Disease, Amyotrophic Lateral Sclerosis Motor neuron disease, bulbar amyotrophic lateral sclerosis DOID:332 GeneRIF:11675877 GeneRIF:11854284 GeneRIF:11854285 GeneRIF:11860274 GeneRIF:11943600 GeneRIF:11951178 GeneRIF:11991808 GeneRIF:11996514 GeneRIF:12039658 GeneRIF:12125045 GeneRIF:12127151 GeneRIF:12138710 GeneRIF:12153483 GeneRIF:12210393 GeneRIF:12217886 GeneRIF:12230304 GeneRIF:12235108 GeneRIF:12270696 GeneRIF:12393885 GeneRIF:12437574 GeneRIF:12441104 GeneRIF:12442272 GeneRIF:12446576 GeneRIF:12448348 GeneRIF:12458194 GeneRIF:12475980 GeneRIF:12480087 GeneRIF:12502789 GeneRIF:12528821 GeneRIF:12584731 GeneRIF:12614934 GeneRIF:12641746 GeneRIF:12644909 GeneRIF:12659845 GeneRIF:12677446 GeneRIF:12679596 GeneRIF:12694394 GeneRIF:12707786 GeneRIF:12730211 GeneRIF:12770687 GeneRIF:12783432 GeneRIF:12843244 GeneRIF:12847526 GeneRIF:12866199 GeneRIF:12870272 GeneRIF:12875980 GeneRIF:12915461 GeneRIF:12972170 GeneRIF:13129803 GeneRIF:13678668 GeneRIF:14506936 GeneRIF:14511332 GeneRIF:14596848 GeneRIF:14597108 GeneRIF:14642651 GeneRIF:14675609 GeneRIF:14676054 GeneRIF:14734542 GeneRIF:14970233 GeneRIF:14978393 GeneRIF:14985749 GeneRIF:14989597 GeneRIF:14991384 GeneRIF:15006704 GeneRIF:15019581 GeneRIF:15030390 GeneRIF:15033789 GeneRIF:15037546 GeneRIF:15048885 GeneRIF:15069187 GeneRIF:15076751 GeneRIF:15094483 GeneRIF:15106121 GeneRIF:15109247 GeneRIF:15126567 GeneRIF:15184633 GeneRIF:15233913 GeneRIF:15264227 GeneRIF:15313203 GeneRIF:15326253 GeneRIF:15330338 GeneRIF:15350647 GeneRIF:15388334 GeneRIF:15465081 GeneRIF:15475574 GeneRIF:15488469 GeneRIF:15509539 GeneRIF:15546588 GeneRIF:15557516 GeneRIF:15568021 GeneRIF:15623718 GeneRIF:15634772 GeneRIF:15652414 GeneRIF:15657392 GeneRIF:15657798 GeneRIF:15672551 GeneRIF:15691826 GeneRIF:15753080 GeneRIF:15776280 GeneRIF:15789135 GeneRIF:15829169 GeneRIF:15837590 GeneRIF:15910777 GeneRIF:15978558 GeneRIF:16005901 GeneRIF:16020530 GeneRIF:16114275 ICD9:335.20 MSH:D000690 NCIt:C34373 NIFSTD:birnlex_12566 SNOMEDCT:86044005 A degenerative disorder affecting upper MOTOR NEURONS in the brain and lower motor neurons in the brain stem and SPINAL CORD. Disease onset is usually after the age of 50 and the process is usually fatal within 3 to 6 years. Clinical manifestations include progressive weakness, atrophy, FASCICULATION, hyperreflexia, DYSARTHRIA, dysphagia, and eventual paralysis of respiratory function. Pathologic features include the replacement of motor neurons with fibrous ASTROCYTES and atrophy of anterior SPINAL NERVE ROOTS and corticospinal tracts (MeSH). A degenerative disorder affecting upper MOTOR NEURONS in the brain and lower motor neurons in the brain stem and SPINAL CORD. Disease onset is usually after the age of 50 and the process is usually fatal within 3 to 6 years. Clinical manifestations include progressive weakness, atrophy, FASCICULATION, hyperreflexia, DYSARTHRIA, dysphagia, and eventual paralysis of respiratory function. Pathologic features include the replacement of motor neurons with fibrous ASTROCYTES and atrophy of anterior SPINAL NERVE ROOTS and corticospinal tracts. (From Adams et al., Principles of Neurology, 6th ed, pp1089-94) An autosomal dominant inherited form of amyloidosis. amyotrophic lateral sclerosis URI: http://www.ebi.ac.uk/cellline#amyotrophic_lateral_sclerosis true true James Malone A disease is a disposition that describes states of disease associated with a particular sample and/or organism. disease true tissue, organ, system, sperm, blood or body location (arm). James Malone Jie Zheng Tomasz Adamusiak MO_954 The part of organism's anatomy or substance arising from an organism from which the biomaterial was derived, excludes cells. E.g. tissue, organ, system, sperm, blood or body location (arm). organism part URI: http://www.ebi.ac.uk/cellline#organism_part true James Malone motor system muscle muscle system muscles musculature musculature system muscule system AAO:0000307 BTO:0001485 EV:0100146 FBbt:00005069 MA:0000015 MAT:0000025 MFO:0002100 TADS:0000324 TAO:0000548 WBbt:0005737 ZFA:0000548 The bodily system that is composed of skeletal, smooth, and cardiac muscle tissue and functions in movement of the body or of materials through the body, maintenance of posture, and heat production. muscular system URI: http://www.ebi.ac.uk/cellline#muscular_system true James Malone Tomasz Adamusiak AAO:0000324 BTO:0001484 EHDAA:826 EMAPA:16469 EV:0100162 FBbt:00005093 FMAID:7157 MA:0000016 MAT:0000026 NIFSTD:birnlex_844 SAEL:71 TAO:0000396 WBbt:0005735 XAO:0000177 ZFA:0000396 A regulatory system of the body that consists of neurons and neuroglial cells. The nervous system is divided into two parts, the central nervous system (CNS) and the peripheral nervous system (PNS). A regulatory system of the body that consists of neurons and neuroglial cells. The nervous system is divided into two parts, the central nervous system (CNS) and the peripheral nervous system (PNS). (Source: BioGlossary, www.Biology-Text.com) All the nerve centers and nerve fibers in the central, visceral and peripheral nervous systems. The nervous system is essentially a biological information highway, and is responsible for controlling all the biological processes and movement in the body, and can also receive information and interpret it via electrical signals which are used in this nervous system. It consists of the Central Nervous System (CNS), essentially the processing area and the Peripheral Nervous System which detects and sends electrical impulses that are used in the nervous system. nervous system URI: http://www.ebi.ac.uk/cellline#nervous_system true James Malone Tomasz Adamusiak CNS Cerebrospinal axis Neuraxis BTO:0000227 EHDAA:828 EMAPA:16470 EV:0100163 FMAID:55675 MA:0000167 MAT:0000457 NIFSTD:birnlex_1099 TAO:0000012 ZFA:0000012 Organ with organ cavity which consists of gray matter and white matter. Examples: There is only one neuraxis. The brain and spinal cord. The brain and spinal cord. Kimmel et al, 1995. The central nervous system is that part of the nervous system that consists of the brain and spinal cord. The central nervous system (CNS) is one of the two major divisions of the nervous system. The other is the peripheral nervous system (PNS) which is outside the brain and spinal cord. central nervous system URI: http://www.ebi.ac.uk/cellline#central_nervous_system true Tomasz Adamusiak muscular disease DOID:423 myopathy URI: http://www.ebi.ac.uk/cellline#muscular_disease true Bill Duncan <http://orcid.org/0000-0001-9625-1899> 2018-06-02T03:01:08Z obsolete class true http://www.lincsproject.org/LINCS/centers/data-and-signature-generating-centers/lincs-pccse The LINCS Proteomic Characterization Center for Signaling and Epigenetics at the Broad Institute PCCSE http://lincsproject.org/LINCS/centers/data-and-signature-generating-centers/lincs-transcriptomics https://www.broadinstitute.org/ BROAD_T example to be eventually removed example to be eventually removed 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 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 right handed right handed ambidexterous ambidexterous left handed left handed Edingburgh handedness inventory The Edinburgh Handedness Inventory is a set of questions used to assess the dominance of a person's right or left hand in everyday activities. PERSON:Alan Ruttenberg PERSON:Jessica Turner PMID:5146491#Oldfield, R.C. (1971). The assessment and analysis of handedness: The Edinburgh inventory. Neuropsychologia, 9, 97-113 WEB:http://www.cse.yorku.ca/course_archive/2006-07/W/4441/EdinburghInventory.html Edingburgh handedness inventory axiom holds for all times ## Elucidation This is used when the statement/axiom is assumed to hold true 'eternally' ## How to interpret (informal) First the "atemporal" FOL is derived from the OWL using the standard interpretation. This axiom is temporalized by embedding the axiom within a for-all-times quantified sentence. The t argument is added to all instantiation predicates and predicates that use this relation. ## Example Class: nucleus SubClassOf: part_of some cell forall t : forall n : instance_of(n,Nucleus,t) implies exists c : instance_of(c,Cell,t) part_of(n,c,t) ## Notes This interpretation is *not* the same as an at-all-times relation axiom holds for all times en Ontology for Biomedical Investigations Advisors for this project come from the IFOMIS group, Saarbruecken and from the Co-ODE group in Manchester Alan Ruttenberg Allyson Lister Barry Smith Bill Bug Bjoern Peters Carlo Torniai Chris Mungall Chris Stoeckert Chris Taylor Christian Bolling Cristian Cocos Daniel Rubin Daniel Schober Dawn Field Dirk Derom Elisabetta Manduchi Eric Deutsch Frank Gibson Gilberto Fragoso Helen C. Causton Helen Parkinson Holger Stenzhorn James A. Overton James Malone Jay Greenbaum Jeffrey Grethe Jennifer Fostel Jessica Turner Jie Zheng Joe White John Westbrook Kevin Clancy Larisa Soldatova Lawrence Hunter Liju Fan Luisa Montecchi Matthew Brush Matthew Pocock Melanie Courtot Melissa Haendel Mervi Heiskanen Monnie McGee Norman Morrison Philip Lord Philippe Rocca-Serra Pierre Grenon Richard Bruskiewich Richard Scheuermann Robert Stevens Ryan R. Brinkman Stefan Wiemann Susanna-Assunta Sansone Tanya Gray Tina Hernandez-Boussard Trish Whetzel Yongqun He 2009-07-31 The Ontology for Biomedical Investigations (OBI) is build in a collaborative, international effort and will serve as a resource for annotating biomedical investigations, including the study design, protocols and instrumentation used, the data generated and the types of analysis performed on the data. This ontology arose from the Functional Genomics Investigation Ontology (FuGO) and will contain both terms that are common to all biomedical investigations, including functional genomics investigations and those that are more domain specific. OWL-DL An ontology for the annotation of biomedical and functional genomics experiments. Ontology for Biomedical Investigation http://creativecommons.org/licenses/by/4.0/ Please cite the OBI consortium http://purl.obolibrary.org/obo/obi where traditional citation is called for. However it is adequate that individual terms be attributed simply by use of the identifying PURL for the term, in projects that refer to them. 2017-02-22 2018-05-23 See PMID:15693950, PMID:12799354, PMID:20123131, PMID:21208450; Contact Alexander Diehl, addiehl@buffalo.edu, University at Buffalo. Caty Chung Stephan Schurer Asiyah Yu Lin 2018-01-26 Draft version James Malone Alexander Diehl Jie Zheng Yongqun "Oliver" He (YH) Uma Vempati Jiangan Xie Hiroshi Masuya Alex Ade Daniel Cooper The Cell Line Ontology. Yue Liu OWL-DL Helen Parkinson Sirarat Sarntivijai An ontology for the domain of cell lines and cell line cells 2.1.135 CLO: Cell Line Ontology Matthew Brush Allen Xiang Vision Release: 1.0.59 Yue Liu Yongqun "Oliver" He (YH) A biological ontology in the area of genes and genomes. OGG is a biological ontology in the area of genes and genomes. OGG uses the Basic Formal Ontology (BFO) as its upper level ontology. This OGG document contains the genes and genomes of a list of selected organisms, including human, two viruses (HIV and influenza virus), and bacteria (B. melitensis strain 16M, E. coli strain K-12 substrain MG1655, M. tuberculosis strain H37Rv, and P. aeruginosa strain PAO1). More OGG information for other organisms (e.g., mouse, zebrafish, fruit fly, yeast, etc.) may be found in other OGG subsets. OGG: Ontology of Genes and Genomes 12-01-2016 OWL-DL Bin Zhao This ontology grew out of efforts to represent the reality underlying the demographic information required by the US federal government's "meaningful use" criteria for electronic medical records and a presentation by Dr. William Hogan at the Electronic Health Record of the Future conference in Buffalo, NY http://ontology.buffalo.edu/EHR/Demographics_Hogan_Buffalo_2010_09_22.ppt William Hogan Mathias Brochhausen Amanda Hicks 2017-06-08 Swetha Garimalla The Ontology of Medically Related Social Entities Daniel Welch Shariq Tariq