diff --git a/uberon_edit.obo b/uberon_edit.obo index 05a52b6268..8fc7eb5077 100644 --- a/uberon_edit.obo +++ b/uberon_edit.obo @@ -1626,7 +1626,7 @@ relationship: connects UBERON:0000061 {minCardinality="2"} ! anatomical structur [Term] id: UBERON:0006800 name: anatomical line -def: "Non-material anatomical entity of one dimension, which forms a boundary of an anatomical surface or is a modulation of an anatomical surface." [CARO:MAH] +def: "Non-material anatomical entity of one dimension, which forms a boundary of an anatomical surface or is a modulation of an anatomical surface." [http://orcid.org/0000-0001-9114-8737] subset: upper_level xref: HAO:0000008 ! anatomical line xref: ZFA:0001689 ! anatomical line @@ -5551,7 +5551,7 @@ xref: UMLS:C0004799 {source="ncithesaurus:Basement_Membrane"} [Term] id: UBERON:0000482 name: basal lamina of epithelium -def: "Acellular anatomical structure that consists of a thin sheet of fibrous proteins that underlie and support the cells of an epithelium. It separates the cells of an epithelium from any underlying tissue." [CARO:MAH] +def: "Acellular anatomical structure that consists of a thin sheet of fibrous proteins that underlie and support the cells of an epithelium. It separates the cells of an epithelium from any underlying tissue." [http://orcid.org/0000-0001-9114-8737] property_value: curator_notes "this class represents a continuous sheet of basal lamina which can underlie multiple epithelial cells over large regions. In contrast, the GO class 'basal lamina' represents a portion of substance on the scale of a single cell." xsd:string xref: Wikipedia:Basal_lamina subset: uberon_slim @@ -12556,7 +12556,7 @@ is_obsolete: true [Term] id: UBERON:0000463 name: organism substance -def: "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." [CARO:MAH] +def: "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." [http://orcid.org/0000-0001-9114-8737] subset: upper_level synonym: "body fluid or substance" EXACT [MA:0002450] synonym: "portion of body substance" EXACT [FMA:9669] @@ -12661,7 +12661,7 @@ intersection_of: located_in UBERON:0005906 ! serous sac [Term] id: UBERON:0000464 name: anatomical space -def: "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." [CARO:MAH] +def: "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." [http://orcid.org/0000-0001-9114-8737] subset: upper_level synonym: "lumen" BROAD [] synonym: "lumen space" EXACT [] @@ -12688,7 +12688,7 @@ synonym: "anatomical spaces" RELATED PLURAL [ZFA:0001643] [Term] id: UBERON:0000465 name: material anatomical entity -def: "Anatomical entity that has mass." [CARO:MAH] +def: "Anatomical entity that has mass." [http://orcid.org/0000-0001-9114-8737] subset: upper_level xref: BILA:0000006 xref: CARO:0000006 ! material anatomical entity @@ -12706,7 +12706,7 @@ xref: VHOG:0001721 ! material anatomical entity [Term] id: UBERON:0000466 name: immaterial anatomical entity -def: "Anatomical entity that has no mass." [CARO:MAH] +def: "Anatomical entity that has no mass." [http://orcid.org/0000-0001-9114-8737] subset: upper_level synonym: "immaterial physical anatomical entity" EXACT [FMA:67112] xref: BILA:0000007 @@ -12771,7 +12771,7 @@ synonym: "anatomical systems" RELATED PLURAL [ZFA:0001439] [Term] id: UBERON:0000468 name: multicellular organism -def: "Anatomical structure that is an individual member of a species and consists of more than one cell." [CARO:0000012, CARO:MAH, Wikipedia:Multi-cellular_organism] +def: "Anatomical structure that is an individual member of a species and consists of more than one cell." [CARO:0000012, http://orcid.org/0000-0001-9114-8737, Wikipedia:Multi-cellular_organism] xref: Wikipedia:Multi-cellular_organism property_value: editor_note "TODO - split body and mc organism? body continues after death stage" xsd:string subset: uberon_slim @@ -12819,7 +12819,7 @@ subset: pheno_slim [Term] id: UBERON:0000470 name: cell part -def: "Anatomical structure that is a direct part of the cell." [CARO:MAH] +def: "Anatomical structure that is a direct part of the cell." [http://orcid.org/0000-0001-9114-8737] property_value: editor_note "TODO - move metadata to GO and obsolete this class once homes have been found for existing children. Note the inconsistency between the usage of the label 'cell component' in GO and CARO" xsd:string subset: upper_level synonym: "cell component" RELATED [CARO:0000014] @@ -12842,7 +12842,7 @@ property_value: seeAlso https://github.com/obophenotype/uberon/issues/489 [Term] id: UBERON:0000471 name: compound organ component -def: "Multi-tissue structure that is part of a compound organ." [CARO:0000019, CARO:MAH] +def: "Multi-tissue structure that is part of a compound organ." [CARO:0000019, http://orcid.org/0000-0001-9114-8737] property_value: curator_notes "this class was introduced for consistency with CARO, however, it has yet to be used in this or other ontologies. It may be retired in the future" xsd:string subset: upper_level xref: BILA:0000019 @@ -12862,7 +12862,7 @@ synonym: "compound organ components" RELATED PLURAL [ZFA:0001489] [Term] id: UBERON:0000472 name: simple organ -def: "Multi-tissue structure that is not part of a compound organ." [CARO:0000021, CARO:MAH] +def: "Multi-tissue structure that is not part of a compound organ." [CARO:0000021, http://orcid.org/0000-0001-9114-8737] property_value: curator_notes "this class was introduced for consistency with CARO, however, it has yet to be used in this or other ontologies. It may be retired in the future" xsd:string subset: upper_level xref: BILA:0000021 @@ -13221,7 +13221,7 @@ subset: pheno_slim [Term] id: UBERON:0000475 name: organism subdivision -def: "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." [CARO:0000032, CARO:MAH, CARO:DOS] +def: "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." [CARO:0000032, http://orcid.org/0000-0001-9114-8737, CARO:DOS] xref: Wikipedia:Body_part property_value: editor_note "Reflects CARO2. todo - check the inclusion of FMA 'cardinal body part here', and check child terms for consistency" xsd:string subset: uberon_slim @@ -13281,7 +13281,7 @@ relationship: has_part UBERON:0001021 ! nerve [Term] id: UBERON:0000476 name: acellular anatomical structure -def: "Anatomical structure that consists of cell parts and cell substances and together does not constitute a cell or a tissue." [CARO:MAH] +def: "Anatomical structure that consists of cell parts and cell substances and together does not constitute a cell or a tissue." [http://orcid.org/0000-0001-9114-8737] subset: vertebrate_core xref: BILA:0000040 xref: CARO:0000040 ! acellular anatomical structure @@ -13335,7 +13335,7 @@ is_a: UBERON:0034925 ! anatomical collection [Term] id: UBERON:0000480 name: anatomical group -def: "Anatomical structure consisting of at least two non-overlapping organs, multi-tissue aggregates or portion of tissues or cells of different types that does not constitute an organism, organ, multi-tissue aggregate, or portion of tissue." [CARO:0000054, CARO:MAH] +def: "Anatomical structure consisting of at least two non-overlapping organs, multi-tissue aggregates or portion of tissues or cells of different types that does not constitute an organism, organ, multi-tissue aggregate, or portion of tissue." [CARO:0000054, http://orcid.org/0000-0001-9114-8737] property_value: editor_note "Obsoleted in v2 of CARO [https://github.com/obophenotype/caro/issues/2]" xsd:string subset: upper_level xref: BILA:0000054 @@ -13355,7 +13355,7 @@ xref: VHOG:0001724 ! anatomical group [Term] id: UBERON:0000477 name: anatomical cluster -def: "Anatomical group that has its parts adjacent to one another." [CARO:MAH] +def: "Anatomical group that has its parts adjacent to one another." [http://orcid.org/0000-0001-9114-8737] property_value: editor_note "Will be obsoleted in CARO v2 [https://github.com/obophenotype/caro/issues/3]" xsd:string subset: upper_level xref: BILA:0000041 @@ -13401,7 +13401,7 @@ xref: EMAPA:16042 ! extraembryonic component [Term] id: UBERON:0000478 name: extraembryonic structure -def: "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." [CARO:DOS, CARO:MAH, https://cedar.bio.indiana.edu/trac/env/ontologies/ticket/279] +def: "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." [CARO:DOS, http://orcid.org/0000-0001-9114-8737, https://cedar.bio.indiana.edu/trac/env/ontologies/ticket/279] comment: see also conceptus extraembryonic component in EHDAA2. subset: uberon_slim subset: vertebrate_core @@ -13485,7 +13485,7 @@ subset: pheno_slim [Term] id: UBERON:0000481 name: multi-tissue structure -def: "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." [CARO:0000055, CARO:MAH] +def: "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." [CARO:0000055, http://orcid.org/0000-0001-9114-8737] subset: upper_level xref: BILA:0000055 xref: CARO:0000055 ! multi-tissue structure @@ -13539,7 +13539,7 @@ subset: pheno_slim [Term] id: UBERON:0000483 name: epithelium -def: "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]." [CARO:MAH, Wikipedia:Epithelium] +def: "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]." [http://orcid.org/0000-0001-9114-8737, Wikipedia:Epithelium] xref: Wikipedia:Epithelium subset: uberon_slim subset: vertebrate_core @@ -13593,7 +13593,7 @@ xref: UMLS:C0682577 {source="ncithesaurus:Cuboidal_Epithelium"} [Term] id: UBERON:0000484 name: simple cuboidal epithelium -def: "Unilaminar epithelium that consists of a single layer of cuboidal cells." [CARO:MAH, Wikipedia:Simple_cuboidal_epithelium] +def: "Unilaminar epithelium that consists of a single layer of cuboidal cells." [http://orcid.org/0000-0001-9114-8737, Wikipedia:Simple_cuboidal_epithelium] xref: Wikipedia:Simple_cuboidal_epithelium property_value: editor_note "needs to be synchronized with CL - there is no distinct cuboidal cell in CL" xsd:string subset: uberon_slim @@ -13627,7 +13627,7 @@ relationship: has_part CL:0000075 ! columnar/cuboidal epithelial cell [Term] id: UBERON:0000485 name: simple columnar epithelium -def: "Unilaminar epithelium, which consists of a single layer of columnar cells. Examples: ciliated columnar epithelium, gastric epithelium, microvillus columnar epithelium.[FMA]" [CARO:MAH, Wikipedia:Simple_columnar_epithelium, FMA:FMA] +def: "Unilaminar epithelium, which consists of a single layer of columnar cells. Examples: ciliated columnar epithelium, gastric epithelium, microvillus columnar epithelium.[FMA]" [http://orcid.org/0000-0001-9114-8737, Wikipedia:Simple_columnar_epithelium, FMA:FMA] xref: Wikipedia:Simple_columnar_epithelium subset: uberon_slim subset: vertebrate_core @@ -13657,7 +13657,7 @@ synonym: "simple columnar epithelia" RELATED PLURAL [ZFA:0001496] [Term] id: UBERON:0000486 name: multilaminar epithelium -def: "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]" [CARO:MAH, Wikipedia:Stratified_epithelium, FMA:FMA] +def: "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]" [http://orcid.org/0000-0001-9114-8737, Wikipedia:Stratified_epithelium, FMA:FMA] xref: Wikipedia:Stratified_epithelium subset: uberon_slim subset: vertebrate_core @@ -13678,13 +13678,13 @@ is_a: UBERON:0000483 ! epithelium xref: AAO:0010059 ! multilaminar epithelium xref: SCTID:309044005 ! Multilaminar epithelium xref: XAO:0004006 ! multilaminar epithelium -property_value: external_definition "Epithelium that consists of more than one layer of epithelial cells.[CARO]" xsd:string {ontology="CARO", external_class="CARO:0000069", date_retrieved="2012-06-20", source="CARO:MAH", source="FMA:45562"} +property_value: external_definition "Epithelium that consists of more than one layer of epithelial cells.[CARO]" xsd:string {ontology="CARO", external_class="CARO:0000069", date_retrieved="2012-06-20", source="http://orcid.org/0000-0001-9114-8737", source="FMA:45562"} xref: UMLS:C0682575 {source="ncithesaurus:Stratified_Epithelium"} [Term] id: UBERON:0000487 name: simple squamous epithelium -def: "Unilaminar epithelium which consists of a single layer of squamous cells. Examples: pulmonary alveolar epithelium, endothelium.[FMA]" [CARO:MAH, Wikipedia:Simple_squamous_epithelium, FMA:45565] +def: "Unilaminar epithelium which consists of a single layer of squamous cells. Examples: pulmonary alveolar epithelium, endothelium.[FMA]" [http://orcid.org/0000-0001-9114-8737, Wikipedia:Simple_squamous_epithelium, FMA:45565] xref: Wikipedia:Simple_squamous_epithelium subset: uberon_slim subset: vertebrate_core @@ -13704,7 +13704,7 @@ intersection_of: has_part CL:0000076 ! squamous epithelial cell xref: AAO:0010066 ! simple squamous epithelium xref: XAO:0004010 ! simple squamous epithelium property_value: foaf-depicted_by http://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg -property_value: external_definition "Unilaminar epithelium that consists of a single layer of squamous cells.[CARO]" xsd:string {ontology="CARO", external_class="CARO:0000070", date_retrieved="2012-06-20", source="CARO:MAH", source="FMA:45565"} +property_value: external_definition "Unilaminar epithelium that consists of a single layer of squamous cells.[CARO]" xsd:string {ontology="CARO", external_class="CARO:0000070", date_retrieved="2012-06-20", source="http://orcid.org/0000-0001-9114-8737", source="FMA:45565"} xref: UMLS:C0836133 {source="ncithesaurus:Simple_Squamous_Epithelium"} synonym: "simple squamous epithelia" RELATED PLURAL [ZFA:0001498] @@ -13760,7 +13760,7 @@ xref: FMA:45568 ! keratinized stratified squamous epithelium [Term] id: UBERON:0000488 name: atypical epithelium -def: "Epithelium that consists of epithelial cells not arranged in one ore more layers." [CARO:MAH] +def: "Epithelium that consists of epithelial cells not arranged in one ore more layers." [http://orcid.org/0000-0001-9114-8737] subset: vertebrate_core synonym: "heterogenous epithelium" EXACT [] xref: BILA:0000071 @@ -13845,7 +13845,7 @@ xref: CALOHA:TS-0682 [Term] id: UBERON:0000489 name: cavitated compound organ -def: "Compound organ that contains one or more macroscopic anatomical spaces." [CARO:MAH] +def: "Compound organ that contains one or more macroscopic anatomical spaces." [http://orcid.org/0000-0001-9114-8737] property_value: curator_notes "this class was introduced for consistency with CARO, however, it has yet to be used in this or other ontologies. It may be retired in the future" xsd:string subset: upper_level xref: BILA:0000072 @@ -13869,7 +13869,7 @@ synonym: "cavitated compound organs" RELATED PLURAL [ZFA:0001490] [Term] id: UBERON:0000490 name: unilaminar epithelium -def: "Epithelium which consists of a single layer of epithelial cells. Examples: endothelium, mesothelium, glandular squamous epithelium.[FMA]" [CARO:MAH, FMA:45561] +def: "Epithelium which consists of a single layer of epithelial cells. Examples: endothelium, mesothelium, glandular squamous epithelium.[FMA]" [http://orcid.org/0000-0001-9114-8737, FMA:45561] property_value: editor_note "consider adding disjointness axiom between unilaminar and multilaminar - but note that this will render EHDAA2:0003244 (chorionic trophoblast) unsatisfiable" xsd:string subset: vertebrate_core synonym: "simple epithelium" EXACT [FMA:45561] @@ -13888,14 +13888,14 @@ is_a: UBERON:0000483 ! epithelium xref: AAO:0010062 ! unilaminar epithelium xref: SCTID:309043004 ! Unilaminar epithelium xref: XAO:0004007 ! unilaminar epithelium -property_value: external_definition "Epithelium that consists of a single layer of epithelial cells.[CARO]" xsd:string {ontology="CARO", external_class="CARO:0000073", date_retrieved="2012-06-20", source="CARO:MAH", source="FMA:45561"} +property_value: external_definition "Epithelium that consists of a single layer of epithelial cells.[CARO]" xsd:string {ontology="CARO", external_class="CARO:0000073", date_retrieved="2012-06-20", source="http://orcid.org/0000-0001-9114-8737", source="FMA:45561"} xref: UMLS:C0682574 {source="ncithesaurus:Simple_Epithelium"} synonym: "unilaminar epithelia" RELATED PLURAL [ZFA:0001495] [Term] id: UBERON:0000491 name: solid compound organ -def: "Compound organ that does not contain macroscopic anatomical spaces." [CARO:MAH] +def: "Compound organ that does not contain macroscopic anatomical spaces." [http://orcid.org/0000-0001-9114-8737] property_value: curator_notes "this class was introduced for consistency with CARO, however, it has yet to be used in this or other ontologies. It may be retired in the future. Note also that we place the FMA class 'solid organ' here, and the FMA includes many glands plus the liver as solid organs, which some may find confusing" xsd:string subset: upper_level synonym: "solid organ" RELATED [FMA:55670] @@ -22599,7 +22599,7 @@ subset: efo_slim [Term] id: UBERON:0001062 name: anatomical entity -def: "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." [CARO:MAH, FMA:62955] +def: "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." [http://orcid.org/0000-0001-9114-8737, FMA:62955] subset: upper_level xref: XAO:0000000 ! Xenopus anatomical entity xref: BILA:0000000 @@ -94554,7 +94554,7 @@ subset: efo_slim [Term] id: UBERON:0007197 ! hermaphroditic organism name: hermaphroditic organism -def: "multicellular organism that can produce both male and female gametes." [CARO:MAH] +def: "multicellular organism that can produce both male and female gametes." [http://orcid.org/0000-0001-9114-8737] synonym: "dioecious organism" RELATED [BILA:0000029] synonym: "hermaphrodite" RELATED [WBbt:0007849] xref: CARO:0000029 @@ -164493,7 +164493,7 @@ subset: organ_slim [Term] id: UBERON:0006983 name: anatomical point -def: "Non-material anatomical entity of zero dimension, which forms a boundary of an anatomical line or surface." [CARO:MAH] +def: "Non-material anatomical entity of zero dimension, which forms a boundary of an anatomical line or surface." [http://orcid.org/0000-0001-9114-8737, FMA:9658] subset: upper_level xref: CARO:0000009 xref: BILA:0000009 ! anatomical point