omo-full.obo

format-version: 1.2
data-version: omo/releases/2023-11-02/omo-full.owl
synonymtypedef: OMO:0003000 "abbreviation"
synonymtypedef: OMO:0003001 "ambiguous synonym"
synonymtypedef: OMO:0003002 "dubious synonym"
synonymtypedef: OMO:0003003 "layperson synonym"
synonymtypedef: OMO:0003004 "plural form"
synonymtypedef: OMO:0003005 "UK spelling synonym"
synonymtypedef: OMO:0003006 "misspelling"
synonymtypedef: OMO:0003007 "misnomer"
synonymtypedef: OMO:0003008 "previous name"
synonymtypedef: OMO:0003009 "legal name"
synonymtypedef: OMO:0003010 "International Nonproprietary Name"
synonymtypedef: OMO:0003011 "latin term"
synonymtypedef: OMO:0003012 "acronym"
ontology: omo/omo-full
property_value: defaultLanguage "en" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Adam Goldstein" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Alan Ruttenberg" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Albert Goldfain" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Barry Smith" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Bjoern Peters" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Carlo Torniai" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Chris Mungall" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Chris Stoeckert" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Christian A. Boelling" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Darren Natale" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "David Osumi-Sutherland" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Gwen Frishkoff" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Holger Stenzhorn" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "James A. Overton" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "James Malone" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Jennifer Fostel" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Jie Zheng" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Jonathan Rees" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Larisa Soldatova" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Lawrence Hunter" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Mathias Brochhausen" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Matt Brush" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Melanie Courtot" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Michel Dumontier" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Paolo Ciccarese" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Pat Hayes" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Philippe Rocca-Serra" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Randy Dipert" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Ron Rudnicki" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Satya Sahoo" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Sivaram Arabandi" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Werner Ceusters" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "William Duncan" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "William Hogan" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Yongqun (Oliver) He" xsd:string
property_value: http://purl.org/dc/elements/1.1/description "An ontology specifies terms that are used to annotate ontology terms for all OBO ontologies. The ontology was developed as part of Information Artifact Ontology (IAO)." xsd:string
property_value: http://purl.org/dc/elements/1.1/title "OBO Metadata Ontology" xsd:string
property_value: http://purl.org/dc/terms/license https://creativecommons.org/publicdomain/zero/1.0/
property_value: owl:versionInfo "2023-11-02" xsd:string

[Term]
id: IAO:0000027
name: data item
is_a: IAO:0000030 ! information content entity
property_value: IAO:0000111 "data item" xsd:string

[Term]
id: IAO:0000030
name: information content entity
is_a: BFO:0000031
property_value: IAO:0000111 "information content entity" xsd:string

[Term]
id: IAO:0000078
name: curation status specification
def: "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." []
is_a: IAO:0000102 ! data about an ontology part
property_value: IAO:0000111 "curation status specification" xsd:string
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000116 "Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)" xsd:string
property_value: IAO:0000117 "PERSON:Bill Bug" xsd:string
property_value: IAO:0000119 "GROUP:OBI:<http://purl.obolibrary.org/obo/obi>" xsd:string
property_value: IAO:0000119 "OBI_0000266" xsd:string

[Term]
id: IAO:0000102
name: data about an ontology part
def: "Data about an ontology part is a data item about a part of an ontology, for example a term" []
is_a: IAO:0000027 ! data item
property_value: IAO:0000111 "data about an ontology part" xsd:string
property_value: IAO:0000117 "Person:Alan Ruttenberg" xsd:string

[Term]
id: IAO:0000225
name: obsolescence reason specification
def: "The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value." []
is_a: IAO:0000102 ! data about an ontology part
property_value: IAO:0000111 "obsolescence reason specification" xsd:string
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000116 "The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology." xsd:string
property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string
property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string

[Term]
id: IAO:0000409
name: denotator type
def: "A denotator type indicates how a term should be interpreted from an ontological perspective." []
is_a: IAO:0000102 ! data about an ontology part
property_value: IAO:0000111 "denotator type" xsd:string
property_value: IAO:0000112 "The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are \"natural kinds\" and the latter arbitrary collections of entities." xsd:string
property_value: IAO:0000117 "Alan Ruttenberg" xsd:string
property_value: IAO:0000119 "Barry Smith, Werner Ceusters" xsd:string

[Term]
id: IAO:8000000
name: ontology module
is_a: IAO:0000102 ! data about an ontology part
property_value: IAO:0000111 "ontology module" xsd:string
property_value: IAO:0000116 "I have placed this under 'data about an ontology part', but this can be discussed. I think this is OK if 'part' is interpreted reflexively, as an ontology module is the whole ontology rather than part of it." xsd:string
property_value: IAO:0000118 "ontology file" xsd:string
property_value: IAO:0000232 "This class and it's subclasses are applied to OWL ontologies. Using an rdf:type triple will result in problems with OWL-DL. I propose that dcterms:type is instead used to connect an ontology URI with a class from this hierarchy. The class hierarchy is not disjoint, so multiple assertions can be made about a single ontology." xsd:string

[Term]
id: IAO:8000001
name: base ontology module
def: "An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies." []
is_a: IAO:8000000 ! ontology module
property_value: IAO:0000111 "base ontology module" xsd:string
property_value: seeAlso https://github.com/INCATools/ontology-starter-kit/issues/50

[Term]
id: IAO:8000002
name: editors ontology module
def: "An ontology module that is intended to be directly edited, typically managed in source control, and typically not intended for direct consumption by end-users." []
is_a: IAO:8000000 ! ontology module
property_value: IAO:0000111 "editors ontology module" xsd:string
property_value: IAO:0000118 "source ontology module" xsd:string

[Term]
id: IAO:8000003
name: main release ontology module
def: "An ontology module that is intended to be the primary release product and the one consumed by the majority of tools." []
is_a: IAO:8000000 ! ontology module
property_value: IAO:0000111 "main release ontology module" xsd:string
property_value: IAO:0000116 "TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module" xsd:string

[Term]
id: IAO:8000004
name: bridge ontology module
def: "An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module." []
is_a: IAO:8000000 ! ontology module
property_value: IAO:0000111 "bridge ontology module" xsd:string
property_value: seeAlso https://github.com/obophenotype/uberon/wiki/inter-anatomy-ontology-bridge-ontologies

[Term]
id: IAO:8000005
name: import ontology module
def: "A subset ontology module that is intended to be imported from another ontology." []
is_a: IAO:8000006 ! subset ontology module
property_value: IAO:0000111 "import ontology module" xsd:string
property_value: IAO:0000116 "TODO: add axioms that indicate this is the output of a module extraction process." xsd:string
property_value: IAO:0000118 "import file" xsd:string
property_value: seeAlso http://robot.obolibrary.org/extract

[Term]
id: IAO:8000006
name: subset ontology module
def: "An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms." []
is_a: IAO:8000000 ! ontology module
property_value: IAO:0000111 "subset ontology module" xsd:string
property_value: IAO:0000118 "ontology slim" xsd:string
property_value: IAO:0000118 "subset ontology" xsd:string
property_value: seeAlso http://robot.obolibrary.org/filter
property_value: seeAlso http://www.geneontology.org/page/go-slim-and-subset-guide

[Term]
id: IAO:8000007
name: curation subset ontology module
def: "A subset ontology that is intended as a whitelist for curators using the ontology. Such a subset will exclude classes that curators should not use for curation." []
is_a: IAO:8000006 ! subset ontology module
property_value: IAO:0000111 "curation subset ontology module" xsd:string

[Term]
id: IAO:8000008
name: analysis subset ontology module
def: "An ontology module that is intended for usage in analysis or discovery applications." []
is_a: IAO:8000006 ! subset ontology module
property_value: IAO:0000111 "analysis ontology module" xsd:string

[Term]
id: IAO:8000009
name: single layer subset ontology module
def: "A subset ontology that is largely comprised of a single layer or strata in an ontology class hierarchy. The purpose is typically for rolling up for visualization. The classes in the layer need not be disjoint." []
is_a: IAO:8000006 ! subset ontology module
property_value: IAO:0000111 "single layer ontology module" xsd:string
property_value: IAO:0000118 "ribbon subset" xsd:string

[Term]
id: IAO:8000010
name: exclusion subset ontology module
def: "A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes." []
is_a: IAO:8000006 ! subset ontology module
property_value: IAO:0000111 "exclusion subset ontology module" xsd:string
property_value: IAO:0000118 "antislim" xsd:string

[Term]
id: IAO:8000011
name: external import ontology module
def: "An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach." []
is_a: IAO:8000005 ! import ontology module
property_value: IAO:0000111 "external import ontology module" xsd:string
property_value: IAO:0000118 "external import" xsd:string

[Term]
id: IAO:8000012
name: species subset ontology module
def: "A subset ontology that is crafted to either include or exclude a taxonomic grouping of species." []
is_a: IAO:8000006 ! subset ontology module
property_value: IAO:0000111 "species subset ontology module" xsd:string
property_value: IAO:0000118 "taxon subset" xsd:string
property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints

[Term]
id: IAO:8000013
name: reasoned ontology module
def: "An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available." []
is_a: IAO:8000000 ! ontology module
property_value: IAO:0000111 "reasoned ontology module" xsd:string
property_value: seeAlso http://robot.obolibrary.org/reason

[Term]
id: IAO:8000014
name: generated ontology module
def: "An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV." []
is_a: IAO:8000000 ! ontology module
property_value: IAO:0000111 "generated ontology module" xsd:string
property_value: IAO:0000116 "TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process" xsd:string

[Term]
id: IAO:8000015
name: template generated ontology module
def: "An ontology module that is automatically generated from a template specification and fillers for slots in that template." []
is_a: IAO:8000014 ! generated ontology module
property_value: IAO:0000111 "template generated ontology module" xsd:string
property_value: seeAlso http://robot.obolibrary.org/template
property_value: seeAlso https://doi.org/10.1186/s13326-017-0126-0
property_value: seeAlso https://github.com/dosumis/dead_simple_owl_design_patterns/

[Term]
id: IAO:8000016
name: taxonomic bridge ontology module
is_a: IAO:8000004 ! bridge ontology module
property_value: IAO:0000111 "taxonomic bridge ontology module" xsd:string

[Term]
id: IAO:8000017
name: ontology module subsetted by expressivity
is_a: IAO:8000006 ! subset ontology module
property_value: IAO:0000111 "ontology module subsetted by expressivity" xsd:string

[Term]
id: IAO:8000018
name: obo basic subset ontology module
def: "A subset ontology that is designed for basic applications to continue to make certain simplifying assumptions; many of these simplifying assumptions were based on the initial version of the Gene Ontology, and have become enshrined in many popular and useful tools such as term enrichment tools.\n\nExamples of such assumptions include: traversing the ontology graph ignoring relationship types using a naive algorithm will not lead to cycles (i.e. the ontology is a DAG); every referenced term is declared in the ontology (i.e. there are no dangling clauses).\n\nAn ontology is OBO Basic if and only if it has the following characteristics:\nDAG\nUnidirectional\nNo Dangling Clauses\nFully Asserted\nFully Labeled\nNo equivalence axioms\nSingly labeled edges\nNo qualifier lists\nNo disjointness axioms\nNo owl-axioms header\nNo imports" []
is_a: IAO:8000017 ! ontology module subsetted by expressivity
property_value: IAO:0000111 "obo basic subset ontology module" xsd:string
property_value: seeAlso 6.2

[Term]
id: IAO:8000019
name: ontology module subsetted by OWL profile
is_a: IAO:8000017 ! ontology module subsetted by expressivity
property_value: IAO:0000111 "ontology module subsetted by OWL profile" xsd:string

[Term]
id: IAO:8000020
name: EL++ ontology module
is_a: IAO:8000019 ! ontology module subsetted by OWL profile
property_value: IAO:0000111 "EL++ ontology module" xsd:string