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cmungall committed Jul 29, 2017
1 parent f00bd8b commit bcd5c5ac8020886755c868d0fa8fe74f8e3d3fed
Showing with 29 additions and 74 deletions.
  1. +4 −6 cl-basic.obo
  2. +5 −11 cl-basic.owl
  3. +5 −11 cl.obo
  4. +6 −29 cl.owl
  5. +4 −6 src/ontology/cl-basic.obo
  6. +5 −11 src/ontology/cl-basic.owl
View
@@ -4464,6 +4464,8 @@ name: cardiac muscle myoblast
namespace: cell
alt_id: CL:0000714
def: "A precursor cell destined to differentiate into cardiac muscle cell." [GOC:tfm, MESH:A11.635.470]
synonym: "cardiac muscle progenitor cell" EXACT []
synonym: "cardiomyocyte progenitor cell" EXACT []
xref: FMA:84797
is_a: CL:0002494 ! cardiocyte
is_a: CL:0010021 ! cardiac myoblast
@@ -9698,11 +9700,11 @@ id: CL:0001044
name: effector CD4-positive, alpha-beta T cell
namespace: cell
def: "A CD4-positive, alpha-beta T cell with the phenotype CCR7-negative, CD45RA-positive." [GOC:add, PMID:22343568]
comment: This cell type is compatible with the HIPC Lyoplate markers for 'effector CD4+ T cell'. The functional characteristics of this cell type currently undefined in CL, which affects its proper placement within the hierarchy.
synonym: "effector CD4+ T cell" BROAD [PMID:22343568]
synonym: "effector CD4-positive, alpha-beta T lymphocyte" EXACT []
synonym: "effector CD4-positive, alpha-beta T-cell" EXACT []
synonym: "effector CD4-positive, alpha-beta T-lymphocyte" EXACT []
synonym: "This cell type is compatible with the HIPC Lyoplate markers for 'effector CD4+ T cell'. The functional characteristics of this cell type currently undefined in CL, which affects its proper placement within the hierarchy." EXACT []
is_a: CL:0000624 ! CD4-positive, alpha-beta T cell
is_a: CL:0000911 ! effector T cell
@@ -10001,8 +10003,8 @@ is_a: CL:0000136 ! fat cell
[Term]
id: CL:0001071
name: group 3 innate lymphoid cell
namespace: An innate lymphoid cell that constituitively expresses RORgt and is capable of expressing IL17A and/or IL-22. {xref="GOC:add", xref="GOC:dsd", xref="PMID:23348417", xref="PMID:23292121"}
namespace: cell
def: "An innate lymphoid cell that constituitively expresses RORgt and is capable of expressing IL17A and/or IL-22." [GOC:add, GOC:dsd, PMID:23292121, PMID:23348417]
synonym: "ILC3" EXACT []
is_a: CL:0001065 ! innate lymphoid cell
property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0001-9990-8331
@@ -22361,10 +22363,6 @@ is_a: CL:2000029 ! central nervous system neuron
created_by: TermGenie
creation_date: 2015-12-03T16:42:40Z
[Typedef]
id: RO:0002161
name: never in taxon
[Typedef]
id: has_completed
name: has_completed
View
@@ -341,14 +341,6 @@
<!-- http://purl.obolibrary.org/obo/RO_0002161 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002161">
<rdfs:label>never in taxon</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/cl#has_completed -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/cl#has_completed">
@@ -9417,6 +9409,8 @@ Covers cells actively being cultured or stored in a quiescent state for future u
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A precursor cell destined to differentiate into cardiac muscle cell.</obo:IAO_0000115>
<oboInOwl:hasAlternativeId rdf:datatype="http://www.w3.org/2001/XMLSchema#string">CL:0000714</oboInOwl:hasAlternativeId>
<oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FMA:84797</oboInOwl:hasDbXref>
<oboInOwl:hasExactSynonym>cardiac muscle progenitor cell</oboInOwl:hasExactSynonym>
<oboInOwl:hasExactSynonym>cardiomyocyte progenitor cell</oboInOwl:hasExactSynonym>
<oboInOwl:hasOBONamespace rdf:datatype="http://www.w3.org/2001/XMLSchema#string">cell</oboInOwl:hasOBONamespace>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">cardiac muscle myoblast</rdfs:label>
</owl:Class>
@@ -20950,11 +20944,11 @@ radial glial cells acting as neural progenitors throughout life.</rdfs:comment>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CL_0000911"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A CD4-positive, alpha-beta T cell with the phenotype CCR7-negative, CD45RA-positive.</obo:IAO_0000115>
<oboInOwl:hasBroadSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">effector CD4+ T cell</oboInOwl:hasBroadSynonym>
<oboInOwl:hasExactSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This cell type is compatible with the HIPC Lyoplate markers for &apos;effector CD4+ T cell&apos;. The functional characteristics of this cell type currently undefined in CL, which affects its proper placement within the hierarchy.</oboInOwl:hasExactSynonym>
<oboInOwl:hasExactSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">effector CD4-positive, alpha-beta T lymphocyte</oboInOwl:hasExactSynonym>
<oboInOwl:hasExactSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">effector CD4-positive, alpha-beta T-cell</oboInOwl:hasExactSynonym>
<oboInOwl:hasExactSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">effector CD4-positive, alpha-beta T-lymphocyte</oboInOwl:hasExactSynonym>
<oboInOwl:hasOBONamespace rdf:datatype="http://www.w3.org/2001/XMLSchema#string">cell</oboInOwl:hasOBONamespace>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This cell type is compatible with the HIPC Lyoplate markers for &apos;effector CD4+ T cell&apos;. The functional characteristics of this cell type currently undefined in CL, which affects its proper placement within the hierarchy.</rdfs:comment>
<rdfs:label>effector CD4-positive, alpha-beta T cell</rdfs:label>
</owl:Class>
<owl:Axiom>
@@ -21702,16 +21696,16 @@ radial glial cells acting as neural progenitors throughout life.</rdfs:comment>
<owl:Class rdf:about="http://purl.obolibrary.org/obo/CL_0001071">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CL_0001065"/>
<obo:IAO_0000115>An innate lymphoid cell that constituitively expresses RORgt and is capable of expressing IL17A and/or IL-22.</obo:IAO_0000115>
<dc:creator rdf:resource="http://orcid.org/0000-0001-9990-8331"/>
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2017-01-31T20:21:26Z</dc:date>
<oboInOwl:hasExactSynonym>ILC3</oboInOwl:hasExactSynonym>
<oboInOwl:hasOBONamespace>An innate lymphoid cell that constituitively expresses RORgt and is capable of expressing IL17A and/or IL-22.</oboInOwl:hasOBONamespace>
<oboInOwl:hasOBONamespace>cell</oboInOwl:hasOBONamespace>
<rdfs:label>group 3 innate lymphoid cell</rdfs:label>
</owl:Class>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/CL_0001071"/>
<owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasOBONamespace"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
<owl:annotatedTarget>An innate lymphoid cell that constituitively expresses RORgt and is capable of expressing IL17A and/or IL-22.</owl:annotatedTarget>
<oboInOwl:hasDbXref>GOC:add</oboInOwl:hasDbXref>
<oboInOwl:hasDbXref>GOC:dsd</oboInOwl:hasDbXref>
View
16 cl.obo
@@ -1,5 +1,5 @@
format-version: 1.2
data-version: releases/2017-04-14
data-version: releases/2017-07-29
subsetdef: ubprop:upper_level "abstract upper-level terms not directly useful for analysis"
synonymtypedef: HUMAN_PREFERRED "preferred term when talking about an instance of this class in Homo sapiens"
synonymtypedef: LATIN "latin term"
@@ -2140,13 +2140,10 @@ xref: VHOG:0001679
is_a: CL:0000147 {is_inferred="true"} ! pigment cell
is_a: CL:0002371 ! somatic cell
intersection_of: CL:0000147 ! pigment cell
intersection_of: CL:0000147 ! pigment cell
intersection_of: develops_from CL:0000541 ! melanoblast
intersection_of: has_part GO:0042470 ! melanosome
intersection_of: never_in_taxon NCBITaxon:6237 ! Caenorhabditis
relationship: develops_from CL:0000541 ! melanoblast
relationship: has_part GO:0042470 ! melanosome
relationship: never_in_taxon NCBITaxon:6237 ! Caenorhabditis
[Term]
id: CL:0000149
@@ -5511,6 +5508,8 @@ name: cardiac muscle myoblast
namespace: cell
alt_id: CL:0000714
def: "A precursor cell destined to differentiate into cardiac muscle cell." [GOC:tfm, MESH:A11.635.470]
synonym: "cardiac muscle progenitor cell" EXACT []
synonym: "cardiomyocyte progenitor cell" EXACT []
xref: FMA:84797
is_a: CL:0002494 ! cardiocyte
is_a: CL:0010021 ! cardiac myoblast
@@ -13531,11 +13530,11 @@ id: CL:0001044
name: effector CD4-positive, alpha-beta T cell
namespace: cell
def: "A CD4-positive, alpha-beta T cell with the phenotype CCR7-negative, CD45RA-positive." [GOC:add, PMID:22343568]
comment: This cell type is compatible with the HIPC Lyoplate markers for 'effector CD4+ T cell'. The functional characteristics of this cell type currently undefined in CL, which affects its proper placement within the hierarchy.
synonym: "effector CD4+ T cell" BROAD [PMID:22343568]
synonym: "effector CD4-positive, alpha-beta T lymphocyte" EXACT []
synonym: "effector CD4-positive, alpha-beta T-cell" EXACT []
synonym: "effector CD4-positive, alpha-beta T-lymphocyte" EXACT []
synonym: "This cell type is compatible with the HIPC Lyoplate markers for 'effector CD4+ T cell'. The functional characteristics of this cell type currently undefined in CL, which affects its proper placement within the hierarchy." EXACT []
is_a: CL:0000624 ! CD4-positive, alpha-beta T cell
is_a: CL:0000911 ! effector T cell
intersection_of: CL:0000911 ! effector T cell
@@ -14021,8 +14020,8 @@ relationship: part_of UBERON:0001347 ! white adipose tissue
[Term]
id: CL:0001071
name: group 3 innate lymphoid cell
namespace: An innate lymphoid cell that constituitively expresses RORgt and is capable of expressing IL17A and/or IL-22. {xref="GOC:add", xref="GOC:dsd", xref="PMID:23348417", xref="PMID:23292121"}
namespace: cell
def: "An innate lymphoid cell that constituitively expresses RORgt and is capable of expressing IL17A and/or IL-22." [GOC:add, GOC:dsd, PMID:23292121, PMID:23348417]
synonym: "ILC3" EXACT []
is_a: CL:0001065 ! innate lymphoid cell
intersection_of: CL:0001065 ! innate lymphoid cell
@@ -75681,11 +75680,6 @@ xref: RO:0002212
is_a: regulates ! regulates
inverse_of: negatively_regulated_by ! negatively regulated by
[Typedef]
id: never_in_taxon
name: never in taxon
xref: RO:0002161
[Typedef]
id: occurs_in
name: occurs in
View
35 cl.owl
@@ -12,7 +12,7 @@
xmlns:obo="http://purl.obolibrary.org/obo/"
xmlns:dc="http://purl.org/dc/elements/1.1/">
<owl:Ontology rdf:about="http://purl.obolibrary.org/obo/cl.owl">
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/cl/releases/2017-04-14/cl.owl"/>
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/cl/releases/2017-07-29/cl.owl"/>
<owl:imports rdf:resource="http://purl.obolibrary.org/obo/cl/imports/pato_import.owl"/>
<owl:imports rdf:resource="http://purl.obolibrary.org/obo/cl/imports/clo_import.owl"/>
<owl:imports rdf:resource="http://purl.obolibrary.org/obo/cl/imports/ro_import.owl"/>
@@ -373,14 +373,6 @@
<!-- http://purl.obolibrary.org/obo/RO_0002161 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002161">
<rdfs:label>never in taxon</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0002211 -->
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002211">
@@ -6062,17 +6054,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/CL_0000147"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0002161"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_6237"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CL_0000147"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CL_0002371"/>
<rdfs:subClassOf>
@@ -6081,12 +6062,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GO_0042470"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0002161"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_6237"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0002202"/>
@@ -14600,6 +14575,8 @@ Covers cells actively being cultured or stored in a quiescent state for future u
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A precursor cell destined to differentiate into cardiac muscle cell.</obo:IAO_0000115>
<oboInOwl:hasAlternativeId rdf:datatype="http://www.w3.org/2001/XMLSchema#string">CL:0000714</oboInOwl:hasAlternativeId>
<oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FMA:84797</oboInOwl:hasDbXref>
<oboInOwl:hasExactSynonym>cardiac muscle progenitor cell</oboInOwl:hasExactSynonym>
<oboInOwl:hasExactSynonym>cardiomyocyte progenitor cell</oboInOwl:hasExactSynonym>
<oboInOwl:hasOBONamespace rdf:datatype="http://www.w3.org/2001/XMLSchema#string">cell</oboInOwl:hasOBONamespace>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">cardiac muscle myoblast</rdfs:label>
</owl:Class>
@@ -42428,11 +42405,11 @@ radial glial cells acting as neural progenitors throughout life.</rdfs:comment>
</rdfs:subClassOf>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A CD4-positive, alpha-beta T cell with the phenotype CCR7-negative, CD45RA-positive.</obo:IAO_0000115>
<oboInOwl:hasBroadSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">effector CD4+ T cell</oboInOwl:hasBroadSynonym>
<oboInOwl:hasExactSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This cell type is compatible with the HIPC Lyoplate markers for &apos;effector CD4+ T cell&apos;. The functional characteristics of this cell type currently undefined in CL, which affects its proper placement within the hierarchy.</oboInOwl:hasExactSynonym>
<oboInOwl:hasExactSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">effector CD4-positive, alpha-beta T lymphocyte</oboInOwl:hasExactSynonym>
<oboInOwl:hasExactSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">effector CD4-positive, alpha-beta T-cell</oboInOwl:hasExactSynonym>
<oboInOwl:hasExactSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">effector CD4-positive, alpha-beta T-lymphocyte</oboInOwl:hasExactSynonym>
<oboInOwl:hasOBONamespace rdf:datatype="http://www.w3.org/2001/XMLSchema#string">cell</oboInOwl:hasOBONamespace>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This cell type is compatible with the HIPC Lyoplate markers for &apos;effector CD4+ T cell&apos;. The functional characteristics of this cell type currently undefined in CL, which affects its proper placement within the hierarchy.</rdfs:comment>
<rdfs:label>effector CD4-positive, alpha-beta T cell</rdfs:label>
</owl:Class>
<owl:Axiom>
@@ -44139,16 +44116,16 @@ radial glial cells acting as neural progenitors throughout life.</rdfs:comment>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/PR_000003455"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115>An innate lymphoid cell that constituitively expresses RORgt and is capable of expressing IL17A and/or IL-22.</obo:IAO_0000115>
<dc:creator rdf:resource="http://orcid.org/0000-0001-9990-8331"/>
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2017-01-31T20:21:26Z</dc:date>
<oboInOwl:hasExactSynonym>ILC3</oboInOwl:hasExactSynonym>
<oboInOwl:hasOBONamespace>An innate lymphoid cell that constituitively expresses RORgt and is capable of expressing IL17A and/or IL-22.</oboInOwl:hasOBONamespace>
<oboInOwl:hasOBONamespace>cell</oboInOwl:hasOBONamespace>
<rdfs:label>group 3 innate lymphoid cell</rdfs:label>
</owl:Class>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/CL_0001071"/>
<owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasOBONamespace"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
<owl:annotatedTarget>An innate lymphoid cell that constituitively expresses RORgt and is capable of expressing IL17A and/or IL-22.</owl:annotatedTarget>
<oboInOwl:hasDbXref>GOC:add</oboInOwl:hasDbXref>
<oboInOwl:hasDbXref>GOC:dsd</oboInOwl:hasDbXref>
View
@@ -4464,6 +4464,8 @@ name: cardiac muscle myoblast
namespace: cell
alt_id: CL:0000714
def: "A precursor cell destined to differentiate into cardiac muscle cell." [GOC:tfm, MESH:A11.635.470]
synonym: "cardiac muscle progenitor cell" EXACT []
synonym: "cardiomyocyte progenitor cell" EXACT []
xref: FMA:84797
is_a: CL:0002494 ! cardiocyte
is_a: CL:0010021 ! cardiac myoblast
@@ -9698,11 +9700,11 @@ id: CL:0001044
name: effector CD4-positive, alpha-beta T cell
namespace: cell
def: "A CD4-positive, alpha-beta T cell with the phenotype CCR7-negative, CD45RA-positive." [GOC:add, PMID:22343568]
comment: This cell type is compatible with the HIPC Lyoplate markers for 'effector CD4+ T cell'. The functional characteristics of this cell type currently undefined in CL, which affects its proper placement within the hierarchy.
synonym: "effector CD4+ T cell" BROAD [PMID:22343568]
synonym: "effector CD4-positive, alpha-beta T lymphocyte" EXACT []
synonym: "effector CD4-positive, alpha-beta T-cell" EXACT []
synonym: "effector CD4-positive, alpha-beta T-lymphocyte" EXACT []
synonym: "This cell type is compatible with the HIPC Lyoplate markers for 'effector CD4+ T cell'. The functional characteristics of this cell type currently undefined in CL, which affects its proper placement within the hierarchy." EXACT []
is_a: CL:0000624 ! CD4-positive, alpha-beta T cell
is_a: CL:0000911 ! effector T cell
@@ -10001,8 +10003,8 @@ is_a: CL:0000136 ! fat cell
[Term]
id: CL:0001071
name: group 3 innate lymphoid cell
namespace: An innate lymphoid cell that constituitively expresses RORgt and is capable of expressing IL17A and/or IL-22. {xref="GOC:add", xref="GOC:dsd", xref="PMID:23348417", xref="PMID:23292121"}
namespace: cell
def: "An innate lymphoid cell that constituitively expresses RORgt and is capable of expressing IL17A and/or IL-22." [GOC:add, GOC:dsd, PMID:23292121, PMID:23348417]
synonym: "ILC3" EXACT []
is_a: CL:0001065 ! innate lymphoid cell
property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0001-9990-8331
@@ -22361,10 +22363,6 @@ is_a: CL:2000029 ! central nervous system neuron
created_by: TermGenie
creation_date: 2015-12-03T16:42:40Z
[Typedef]
id: RO:0002161
name: never in taxon
[Typedef]
id: has_completed
name: has_completed
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