From 931153be446b9c29d577cbca33c33ad1ad43968e Mon Sep 17 00:00:00 2001 From: "alida.avola@icloud.com" Date: Tue, 3 Dec 2024 19:12:00 +0000 Subject: [PATCH 1/2] NTR-PVALB-GABAergic-neurons-of-the-substantia-nigra Fixes #2761 --- src/ontology/cl-edit.owl | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index 4b26c3b6a..ee695db85 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -3090,6 +3090,7 @@ Declaration(Class(obo:CL_4042034)) Declaration(Class(obo:CL_4042035)) Declaration(Class(obo:CL_4042036)) Declaration(Class(obo:CL_4042037)) +Declaration(Class(obo:CL_4042038)) Declaration(Class(obo:CL_4042039)) Declaration(Class(obo:CL_4042040)) Declaration(Class(obo:CL_4047006)) @@ -31163,8 +31164,8 @@ EquivalentClasses(obo:CL_4030033 ObjectIntersectionOf(obo:CL_0000115 ObjectSomeV AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:18757316") Annotation(oboInOwl:hasDbXref "PMID:21364219") Annotation(oboInOwl:hasDbXref "PMID:34044844") Annotation(oboInOwl:hasDbXref "PMID:37834236") obo:IAO_0000115 obo:CL_4030034 "A multiciliated epithelial cell located in the respiratory tract epithelium, characterized by a columnar shape and motile cilia on its apical surface. This cell develops through a highly orchestrated process, transitioning from a basal progenitor via an intermediate deuterosomal cell stage that generates centrioles essential for ciliogenesis.") AnnotationAssertion(terms:date obo:CL_4030034 "2023-01-25T11:06:01Z"^^xsd:dateTime) AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_4030034 "ciliated cell of the respiratory tract") -AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_4030034 "respiratory multiciliated cell") AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_4030034 "respiratory ciliated cell") +AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_4030034 "respiratory multiciliated cell") AnnotationAssertion(rdfs:label obo:CL_4030034 "respiratory tract multiciliated cell") EquivalentClasses(obo:CL_4030034 ObjectIntersectionOf(obo:CL_0000075 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0004802) ObjectSomeValuesFrom(obo:BFO_0000051 obo:GO_0031514) ObjectSomeValuesFrom(obo:RO_0000053 obo:PATO_0010007))) SubClassOf(obo:CL_4030034 ObjectSomeValuesFrom(obo:RO_0002207 obo:CL_4033044)) @@ -32877,6 +32878,15 @@ SubClassOf(obo:CL_4042037 ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_0002435 SubClassOf(obo:CL_4042037 ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0061534)) SubClassOf(obo:CL_4042037 ObjectSomeValuesFrom(obo:RO_0002292 obo:PR_000015665)) +# Class: obo:CL_4042038 (pvalb GABAergic neuron of the striatum) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:17177263") Annotation(oboInOwl:hasDbXref "PMID:37843977") obo:IAO_0000115 obo:CL_4042038 "An interneuron of the substantia nigra that expresses parvalbumin. This neuron is involved in motor control and behaviour.") +AnnotationAssertion(terms:contributor obo:CL_4042038 ) +AnnotationAssertion(terms:date obo:CL_4042038 "2024-12-03T19:10:41Z"^^xsd:dateTime) +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:37843977") oboInOwl:hasNarrowSynonym obo:CL_4042038 "SNr-PV+") +AnnotationAssertion(rdfs:label obo:CL_4042038 "pvalb GABAergic neuron of the striatum"@en) +SubClassOf(obo:CL_4042038 obo:CL_0002613) + # Class: obo:CL_4042039 (caudal ganglionic eminence derived neuron) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:12593982") Annotation(oboInOwl:hasDbXref "PMID:12637172") Annotation(oboInOwl:hasDbXref "PMID:20130169") Annotation(oboInOwl:hasDbXref "https://www.ncbi.nlm.nih.gov/books/NBK98190/") obo:IAO_0000115 obo:CL_4042039 "A neuron of the central nervous system that develops from a caudal ganglionic eminence.") From 5231a62bfe0bce080af9ad4c38c4917aa0309a6c Mon Sep 17 00:00:00 2001 From: "alida.avola@icloud.com" Date: Wed, 4 Dec 2024 16:41:55 +0000 Subject: [PATCH 2/2] NTR-PVALB-GABAergic-neurons-of-the-substantia-nigra --- src/mappings/zfa.sssom.tsv | 2 +- src/ontology/cl-edit.owl | 36 + src/ontology/components/cellxgene_subset.owl | 640 +++- src/ontology/components/clm-cl.owl | 2734 +++++++++++++++++- src/ontology/imports/merged_import.owl | 355 ++- src/ontology/imports/uberon_terms.txt | 3 +- src/patterns/definitions.owl | 4 +- src/templates/cellxgene_subset.tsv | 1404 +++++---- 8 files changed, 4386 insertions(+), 792 deletions(-) diff --git a/src/mappings/zfa.sssom.tsv b/src/mappings/zfa.sssom.tsv index 4b142d1ee..73e0ec794 100644 --- a/src/mappings/zfa.sssom.tsv +++ b/src/mappings/zfa.sssom.tsv @@ -20,7 +20,7 @@ ZFA:0005238 juxtaglomerular cell semapv:crossSpeciesExactMatch CL:0000648 kidney ZFA:0005239 micropylar cell semapv:crossSpeciesExactMatch CL:0007022 micropylar cell semapv:UnspecifiedMatching ZFA:0005240 Kolmer-Agduhr neuron semapv:crossSpeciesExactMatch CL:0005007 Kolmer-Agduhr neuron semapv:UnspecifiedMatching ZFA:0005241 polychromatophilic erythroblast semapv:crossSpeciesExactMatch CL:0000550 polychromatophilic erythroblast semapv:UnspecifiedMatching -ZFA:0005242 multi-ciliated epithelial cell semapv:crossSpeciesExactMatch CL:0005012 multi-ciliated epithelial cell semapv:UnspecifiedMatching +ZFA:0005242 multi-ciliated epithelial cell semapv:crossSpeciesExactMatch CL:0005012 multiciliated epithelial cell semapv:UnspecifiedMatching ZFA:0005243 single ciliated epithelial cell semapv:crossSpeciesExactMatch CL:0005013 single ciliated epithelial cell semapv:UnspecifiedMatching ZFA:0005244 auditory epithelial support cell semapv:crossSpeciesExactMatch CL:0005014 auditory epithelial supporting cell semapv:UnspecifiedMatching ZFA:0005245 xanthoblast semapv:crossSpeciesExactMatch CL:0005002 xanthoblast semapv:UnspecifiedMatching diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index ee695db85..240f2425e 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -3093,6 +3093,9 @@ Declaration(Class(obo:CL_4042037)) Declaration(Class(obo:CL_4042038)) Declaration(Class(obo:CL_4042039)) Declaration(Class(obo:CL_4042040)) +Declaration(Class(obo:CL_4042041)) +Declaration(Class(obo:CL_4042042)) +Declaration(Class(obo:CL_4042043)) Declaration(Class(obo:CL_4047006)) Declaration(Class(obo:CL_4047007)) Declaration(Class(obo:CL_4047011)) @@ -3242,6 +3245,7 @@ Declaration(Class(obo:UBERON_0000424)) Declaration(Class(obo:UBERON_0001004)) Declaration(Class(obo:UBERON_0001335)) Declaration(Class(obo:UBERON_0001786)) +Declaration(Class(obo:UBERON_0001875)) Declaration(Class(obo:UBERON_0001881)) Declaration(Class(obo:UBERON_0002197)) Declaration(Class(obo:UBERON_0002222)) @@ -32908,6 +32912,38 @@ SubClassOf(obo:CL_4042040 obo:CL_0000540) SubClassOf(obo:CL_4042040 ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_0002420)) SubClassOf(obo:CL_4042040 ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0061535)) +# Class: obo:CL_4042041 (pvalb GABAergic neuron of the basal ganglia) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:16131542") obo:IAO_0000115 obo:CL_4042041 "An interneuron of the central nervous system with its soma in the basal ganglia expressing parvalbumin. This neuron is involved in motor control and behaviour.") +AnnotationAssertion(terms:contributor obo:CL_4042041 ) +AnnotationAssertion(terms:date obo:CL_4042041 "2024-12-04T16:11:11Z"^^xsd:dateTime) +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:16131542") rdfs:comment obo:CL_4042041 "Developmental deficits in pvalb GABAergic neurons of the basal ganglia are associated to with Tourette Syndrome.") +AnnotationAssertion(rdfs:label obo:CL_4042041 "pvalb GABAergic neuron of the basal ganglia"@en) +SubClassOf(obo:CL_4042041 obo:CL_0011005) +SubClassOf(obo:CL_4042041 ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_0002420)) +SubClassOf(obo:CL_4042041 ObjectSomeValuesFrom(obo:RO_0002292 obo:PR_000013502)) + +# Class: obo:CL_4042042 (pvalb GABAergic neuron of the globus pallidus) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:23044920") Annotation(oboInOwl:hasDbXref "PMID:26905595") Annotation(oboInOwl:hasDbXref "PMID:29917235") obo:IAO_0000115 obo:CL_4042042 "A GABAergic neuron of the central nervous system expressing parvalbumin with soma location in a globus pallidus.") +AnnotationAssertion(terms:contributor obo:CL_4042042 ) +AnnotationAssertion(terms:date obo:CL_4042042 "2024-12-04T16:15:02Z"^^xsd:dateTime) +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:23044920") Annotation(oboInOwl:hasDbXref "PMID:26905595") Annotation(oboInOwl:hasDbXref "PMID:29917235") rdfs:comment obo:CL_4042042 "Pvalb GABAergic neuron compromise 40% of all the interneurons in the globus pallidus (GP). They are predominantly localised in the globus pallidus external segment. They exhibit fast-firing spontaneous acting, project to the subthalamic nucleus and the internal segment of the GP and also innervate the striatum.") +AnnotationAssertion(rdfs:label obo:CL_4042042 "pvalb GABAergic neuron of the globus pallidus"@en) +SubClassOf(obo:CL_4042042 obo:CL_0011005) +SubClassOf(obo:CL_4042042 ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_0001875)) +SubClassOf(obo:CL_4042042 ObjectSomeValuesFrom(obo:RO_0002292 obo:PR_000013502)) + +# Class: obo:CL_4042043 (MEIS2 expressing GABAergic neuron of the thalamus) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:39048816") obo:IAO_0000115 obo:CL_4042043 "A GABAergic neuron expressing homeobox protein Meis2 located in a thalamus.") +AnnotationAssertion(terms:contributor obo:CL_4042043 ) +AnnotationAssertion(terms:date obo:CL_4042043 "2024-12-04T16:38:28Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label obo:CL_4042043 "MEIS2 expressing GABAergic neuron of the thalamus"@en) +SubClassOf(obo:CL_4042043 obo:CL_0011005) +SubClassOf(obo:CL_4042043 ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_0010225)) +SubClassOf(obo:CL_4042043 ObjectSomeValuesFrom(obo:RO_0002292 obo:PR_000010317)) + # Class: obo:CL_4047006 (fetal artery endothelial cell) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:34497389") obo:IAO_0000115 obo:CL_4047006 "An endothelial cell that lines an artery in the fetal circulatory system.") diff --git a/src/ontology/components/cellxgene_subset.owl b/src/ontology/components/cellxgene_subset.owl index 7966e3926..30cd7f839 100644 --- a/src/ontology/components/cellxgene_subset.owl +++ b/src/ontology/components/cellxgene_subset.owl @@ -7,12 +7,11 @@ Prefix(rdfs:=) Ontology( - -Annotation(owl:versionInfo "2024-06-13") + +Annotation(owl:versionInfo "2024-12-04") Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -30,6 +29,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -44,6 +44,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -52,6 +53,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -97,32 +99,40 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -133,7 +143,9 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -141,7 +153,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -174,6 +185,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -199,6 +211,15 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -255,6 +276,8 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -276,8 +299,10 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -285,6 +310,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -339,14 +365,18 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -359,6 +389,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -380,8 +411,11 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -403,6 +437,8 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -411,14 +447,17 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) +Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -433,23 +472,29 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -464,18 +509,28 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -488,6 +543,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -527,7 +583,11 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -535,14 +595,21 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -551,6 +618,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -578,6 +646,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -603,6 +672,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -633,8 +703,10 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -644,18 +716,23 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -668,6 +745,8 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -684,9 +763,16 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -696,6 +782,38 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(AnnotationProperty()) @@ -711,10 +829,6 @@ AnnotationAssertion( ) -# Class: () - -AnnotationAssertion( ) - # Class: () AnnotationAssertion( ) @@ -783,6 +897,10 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -839,6 +957,10 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -871,6 +993,10 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -1051,6 +1177,10 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -1059,10 +1189,22 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -1075,10 +1217,6 @@ AnnotationAssertion( ) -# Class: () - -AnnotationAssertion( ) - # Class: () AnnotationAssertion( ) @@ -1095,10 +1233,6 @@ AnnotationAssertion( ) -# Class: () - -AnnotationAssertion( ) - # Class: () AnnotationAssertion( ) @@ -1111,6 +1245,10 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -1119,6 +1257,14 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -1139,6 +1285,10 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -1147,6 +1297,10 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -1155,6 +1309,10 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -1195,10 +1353,18 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -1227,10 +1393,6 @@ AnnotationAssertion( ) -# Class: () - -AnnotationAssertion( ) - # Class: () AnnotationAssertion( ) @@ -1359,6 +1521,10 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -1459,6 +1625,42 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -1683,6 +1885,14 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -1767,6 +1977,10 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -1775,6 +1989,10 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -1803,6 +2021,10 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -2019,6 +2241,10 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -2027,6 +2253,10 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -2051,6 +2281,14 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -2099,6 +2337,10 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -2183,6 +2425,14 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -2191,6 +2441,10 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -2275,6 +2529,14 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -2307,6 +2569,14 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -2331,14 +2601,18 @@ AnnotationAssertion( ) -# Class: () +# Class: () -AnnotationAssertion( ) +AnnotationAssertion( ) # Class: () AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -2395,6 +2669,10 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -2407,6 +2685,10 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -2431,6 +2713,10 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -2447,6 +2733,10 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -2455,6 +2745,10 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -2463,6 +2757,10 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -2519,6 +2817,10 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -2527,6 +2829,10 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -2551,6 +2857,10 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -2563,10 +2873,38 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -2615,6 +2953,10 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -2771,10 +3113,26 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -2803,10 +3161,22 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -2815,6 +3185,10 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -2823,10 +3197,18 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -2835,6 +3217,10 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -2867,6 +3253,10 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -2975,6 +3365,10 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -3075,6 +3469,10 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -3195,6 +3593,10 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -3203,6 +3605,10 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -3239,6 +3645,10 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -3251,6 +3661,10 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -3271,6 +3685,14 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -3287,6 +3709,10 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -3335,6 +3761,14 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -3399,18 +3833,46 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -3447,5 +3909,133 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + ) \ No newline at end of file diff --git a/src/ontology/components/clm-cl.owl b/src/ontology/components/clm-cl.owl index 902854fff..45fc34afd 100644 --- a/src/ontology/components/clm-cl.owl +++ b/src/ontology/components/clm-cl.owl @@ -1,14 +1,2732 @@ - - + xmlns:dcterms="http://purl.org/dc/terms/" + xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> + + + + None + + Cell Markers Ontology + 2024-12-02 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + description + + + + + + + + license + + + + + + + + title + + + + + + + + + + + + + + + + + + + + + + + + + has characterizing marker set + + + + + + + + + + + + + + TAC1 + + + + + + + + + STAB1 + + + + + + + + + TLL1 + + + + + + + + + MSR1 + + + + + + + + + TNC + + + + + + + + + ROS1 + + + + + + + + + TNIP3 + + + + + + + + + HOMER3 + + + + + + + + + FCGR2B + + + + + + + + + BPIFB2 + + + + + + + + + KCNK2 + + + + + + + + + SEMA5B + + + + + + + + + HMOX1 + + + + + + + + + PVALB + + + + + + + + + CHGA + + + + + + + + + ACTA2 + + + + + + + + + PRR4 + + + + + + + + + ST8SIA4 + + + + + + + + + PLCH1 + + + + + + + + + SMYD1 + + + + + + + + + MYB + + + + + + + + + CCN2 + + + + + + + + + ONECUT2 + + + + + + + + + NPY + + + + + + + + + SFTPA1 + + + + + + + + + CHST8 + + + + + + + + + F13A1 + + + + + + + + + LAMP5 + + + + + + + + + HIGD1B + + + + + + + + + AOC3 + + + + + + + + + TOP2A + + + + + + + + + GRP + + + + + + + + + HCRTR2 + + + + + + + + + SULF1 + + + + + + + + + POU2F3 + + + + + + + + + NUSAP1 + + + + + + + + + LUM + + + + + + + + + RXRG + + + + + + + + + DPT + + + + + + + + + THSD7B + + + + + + + + + VIP + + + + + + + + + TAGLN + + + + + + + + + CHST9 + + + + + + + + + GLYATL2 + + + + + + + + + SST + + + + + + + + + KIT + + + + + + + + + BSND + + + + + + + + + CXCL5 + + + + + + + + + HPGD + + + + + + + + + PCLAF + + + + + + + + + MS4A8 + + + + + + + + + MYO5B + + + + + + + + + SCARA5 + + + + + + + + + FABP4 + + + + + + + + + KCNK3 + + + + + + + + + KRT15 + + + + + + + + + RRM2 + + + + + + + + + THEMIS + + + + + + + + + ANKRD36C + + + + + + + + + CD248 + + + + + + + + + GPR149 + + + + + + + + + UBE2C + + + + + + + + + ASCL3 + + + + + + + + + ADAMTSL1 + + + + + + + + + CA8 + + + + + + + + + C1orf194 + + + + + + + + + ARSJ + + + + + + + + + C6orf58 + + + + + + + + + POU3F1 + + + + + + + + + DMBT1 + + + + + + + + + RELN + + + + + + + + + APOD + + + + + + + + + NPSR1-AS1 + + + + + + + + + LYPD2 + + + + + + + + + PLCG2 + + + + + + + + + PRC1 + + + + + + + + + RORB + + + + + + + + + COL5A2 + + + + + + + + + AGER + + + + + + + + + SERPINB4 + + + + + + + + + MUC5AC + + + + + + + + + LINC00298 + + + + + + + + + PEG10 + + + + + + + + + LINC00507 + + + + + + + + + + + + + + + + + + + + + + + 0.85 + NS forest marker set of alveolar adventitial fibroblast (Human Lung). + + + + + + + + + + + + + + + + + + + + + + + 0.70 + NS forest marker set of alveolar type 1 fibroblast cell (Human Lung). + + + + + + + + + + + + + + + + + + + + + + + 0.80 + NS forest marker set of alveolar macrophage (Human Lung). + + + + + + + + + + + + + + + + + + + + + + + 0.67 + NS forest marker set of CCL3-positive alveolar macrophage (Human Lung). + + + + + + + + + + + + + + + + + + + + + + + 0.41 + NS forest marker set of metallothionein-positive alveolar macrophage (Human Lung). + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.26 + NS forest marker set of cycling alveolar macrophage (Human Lung). + + + + + + + + + + + + + + + 0.85 + NS forest marker set of pulmonary alveolar type 1 cell (Human Lung). + + + + + + + + + + + + + + + 0.95 + NS forest marker set of pulmonary alveolar type 2 cell (Human Lung). + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.61 + NS forest marker set of cycling pulmonary alveolar type 2 cell (Human Lung). + + + + + + + + + + + + + + + + + + + + + + + 0.55 + NS forest marker set of bronchial goblet cell (Human Lung). + + + + + + + + + + + + + + + + + + + + + + + 0.81 + NS forest marker set of nasal mucosa goblet cell (Human Lung). + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.46 + NS forest marker set of lung interstitial macrophage (Human Lung). + + + + + + + + + + + + + + + + + + + + + + + 0.82 + NS forest marker set of pulmonary ionocyte (Human Lung). + + + + + + + + + + + + + + + + + + + + + + + 0.86 + NS forest marker set of ciliated columnar cell of tracheobronchial tree (Human Lung). + + + + + + + + + + + + + + + + + + + + + + + 0.94 + NS forest marker set of lung neuroendocrine cell (Human Lung). + + + + + + + + + + + + + + + + + + + + + + + 0.58 + NS forest marker set of pulmonary interstitial fibroblast (Human Lung). + + + + + + + + + + + + + + + + + + + + + + + 0.84 + NS forest marker set of lung pericyte (Human Lung). + + + + + + + + + + + + + + + + + + + + + + + 0.46 + NS forest marker set of airway submucosal gland collecting duct epithelial cell (Human Lung). + + + + + + + + + + + + + + + 0.93 + NS forest marker set of mucus secreting cell of bronchus submucosal gland (Human Lung). + + + + + + + + + + + + + + + + + + + + + + + 0.75 + NS forest marker set of serous secreting cell of bronchus submucosal gland (Human Lung). + + + + + + + + + + + + + + + + + + + + + + + 0.69 + NS forest marker set of tracheobronchial smooth muscle cell (Human Lung). + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.62 + NS forest marker set of respiratory suprabasal cell (Human Lung). + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.56 + NS forest marker set of brush cell of tracheobronchial tree (Human Lung). + + + + + + + + + + + + + + + + + + + + + + + 0.799748111 + NS forest marker set of chandelier pvalb GABAergic cortical interneuron (Human Brain). + + + + + + + + + + + + + + + + + + + + + + + 0.670149932 + NS forest marker set of L2/3 intratelencephalic projecting glutamatergic neuron (Human Brain). + + + + + + + + + + + + + + + + + + + + + + + 0.720108696 + NS forest marker set of L4 intratelencephalic projecting glutamatergic neuron (Human Brain). + + + + + + + + + + + + + + + + + + + + + + + 0.815891473 + NS forest marker set of L5 extratelencephalic projecting glutamatergic cortical neuron (Human Brain). + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.764261336 + NS forest marker set of L5 intratelencephalic projecting glutamatergic neuron (Human Brain). + + + + + + + + + + + + + + + + + + + + + + + 0.899288218 + NS forest marker set of L5/6 near-projecting glutamatergic neuron (Human Brain). + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.631898455 + NS forest marker set of L6 corticothalamic-projecting glutamatergic cortical neuron (Human Brain). + + + + + + + + + + + + + + + + + + + + + + + 0.641695703 + NS forest marker set of L6 intratelencephalic projecting glutamatergic neuron (Human Brain). + + + + + + + + + + + + + + + + + + + + + + + 0.877752028 + NS forest marker set of L6 intratelencephalic projecting Car3 glutamatergic neuron (Human Brain). + + + + + + + + + + + + + + + + + + + + + + + 0.819940964 + NS forest marker set of L6b glutamatergic neuron of the primary motor cortex (Human Brain). + + + + + + + + + + + + + + + + + + + + + + + 0.814687838 + NS forest marker set of lamp5 GABAergic cortical interneuron (Human Brain). + + + + + + + + + + + + + + + + + + + + + + + 0.821678322 + NS forest marker set of Lamp5 Lhx6 neuron (Human Brain). + + + + + + + + + + + + + + + + + + + + + + + 0.724125093 + NS forest marker set of Pax6 (Human Brain). + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.691998764 + NS forest marker set of pvalb GABAergic cortical interneuron (Human Brain). + + + + + + + + + + + + + + + + + + + + + + + 0.628943702 + NS forest marker set of sncg GABAergic cortical interneuron (Human Brain). + + + + + + + + + + + + + + + + + + + + + + + 0.842367005 + NS forest marker set of sst GABAergic cortical interneuron (Human Brain). + + + + + + + + + + + + + + + 0.894026187 + NS forest marker set of sst chodl GABAergic cortical interneuron (Human Brain). + + + + + + + + + + + + + + + 0.855531344 + NS forest marker set of VIP GABAergic cortical interneuron (Human Brain). + + + + + + + + + + + + + + + The marker set MSR1, FABP4 can identify the Human cell type alveolar macrophage in the Lung with a confidence of 0.80 (NS-Forest FBeta value). + + + + + The marker set MSR1, FABP4 can identify the Human cell type alveolar macrophage in the Lung with a confidence of 0.80 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + + + + + + + + + + + + + + + The marker set AGER can identify the Human cell type pulmonary alveolar type 1 cell in the Lung with a confidence of 0.85 (NS-Forest FBeta value). + + + + + The marker set AGER can identify the Human cell type pulmonary alveolar type 1 cell in the Lung with a confidence of 0.85 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + + + + + + + + + + + + + + + The marker set SFTPA1 can identify the Human cell type pulmonary alveolar type 2 cell in the Lung with a confidence of 0.95 (NS-Forest FBeta value). + + + + + The marker set SFTPA1 can identify the Human cell type pulmonary alveolar type 2 cell in the Lung with a confidence of 0.95 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + + + + + + + + + + + + + + + The marker set POU2F3, HOMER3, MYB can identify the Human cell type brush cell of tracheobronchial tree in the Lung with a confidence of 0.56 (NS-Forest FBeta value). + + + + + The marker set POU2F3, HOMER3, MYB can identify the Human cell type brush cell of tracheobronchial tree in the Lung with a confidence of 0.56 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + + + + + + + + + + + + + + + The marker set C1orf194, MS4A8 can identify the Human cell type ciliated columnar cell of tracheobronchial tree in the Lung with a confidence of 0.86 (NS-Forest FBeta value). + + + + + The marker set C1orf194, MS4A8 can identify the Human cell type ciliated columnar cell of tracheobronchial tree in the Lung with a confidence of 0.86 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + + + + + + + + + + + + + + + The marker set DPT, APOD can identify the Human cell type pulmonary interstitial fibroblast in the Lung with a confidence of 0.58 (NS-Forest FBeta value). + + + + + The marker set DPT, APOD can identify the Human cell type pulmonary interstitial fibroblast in the Lung with a confidence of 0.58 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + + + + + + + + + + + + + + + The marker set LYPD2, MUC5AC can identify the Human cell type nasal mucosa goblet cell in the Lung with a confidence of 0.81 (NS-Forest FBeta value). + + + + + The marker set LYPD2, MUC5AC can identify the Human cell type nasal mucosa goblet cell in the Lung with a confidence of 0.81 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + + + + + + + + + + + + + + + The marker set HIGD1B, KCNK3 can identify the Human cell type lung pericyte in the Lung with a confidence of 0.84 (NS-Forest FBeta value). + + + + + The marker set HIGD1B, KCNK3 can identify the Human cell type lung pericyte in the Lung with a confidence of 0.84 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + + + + + + + + + + + + + + + The marker set ASCL3, BSND can identify the Human cell type pulmonary ionocyte in the Lung with a confidence of 0.82 (NS-Forest FBeta value). + + + + + The marker set ASCL3, BSND can identify the Human cell type pulmonary ionocyte in the Lung with a confidence of 0.82 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + + + + + + + + + + + + + + + The marker set ACTA2, TAGLN can identify the Human cell type tracheobronchial smooth muscle cell in the Lung with a confidence of 0.69 (NS-Forest FBeta value). + + + + + The marker set ACTA2, TAGLN can identify the Human cell type tracheobronchial smooth muscle cell in the Lung with a confidence of 0.69 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + + + + + + + + + + + + + + + The marker set CHGA, GRP can identify the Human cell type lung neuroendocrine cell in the Lung with a confidence of 0.94 (NS-Forest FBeta value). + + + + + The marker set CHGA, GRP can identify the Human cell type lung neuroendocrine cell in the Lung with a confidence of 0.94 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + + + + + + + + + + + + + + + The marker set PLCG2, ANKRD36C can identify the Human cell type bronchial goblet cell in the Lung with a confidence of 0.55 (NS-Forest FBeta value). + + + + + The marker set PLCG2, ANKRD36C can identify the Human cell type bronchial goblet cell in the Lung with a confidence of 0.55 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + + + + + + + + + + + + + + + The marker set LINC00298, KIT can identify the Human cell type lamp5 GABAergic cortical interneuron in the Brain with a confidence of 0.814687838 (NS-Forest FBeta value). + + + + + The marker set LINC00298, KIT can identify the Human cell type lamp5 GABAergic cortical interneuron in the Brain with a confidence of 0.814687838 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + + + + + + + + + + + + + + + The marker set RXRG, THSD7B can identify the Human cell type sncg GABAergic cortical interneuron in the Brain with a confidence of 0.628943702 (NS-Forest FBeta value). + + + + + The marker set RXRG, THSD7B can identify the Human cell type sncg GABAergic cortical interneuron in the Brain with a confidence of 0.628943702 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + + + + + + + + + + + + + + + The marker set VIP can identify the Human cell type VIP GABAergic cortical interneuron in the Brain with a confidence of 0.855531344 (NS-Forest FBeta value). + + + + + The marker set VIP can identify the Human cell type VIP GABAergic cortical interneuron in the Brain with a confidence of 0.855531344 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + + + + + + + + + + + + + + + The marker set SST, PLCH1 can identify the Human cell type sst GABAergic cortical interneuron in the Brain with a confidence of 0.842367005 (NS-Forest FBeta value). + + + + + The marker set SST, PLCH1 can identify the Human cell type sst GABAergic cortical interneuron in the Brain with a confidence of 0.842367005 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + + + + + + + + + + + + + + + The marker set PVALB, TAC1, MYO5B can identify the Human cell type pvalb GABAergic cortical interneuron in the Brain with a confidence of 0.691998764 (NS-Forest FBeta value). + + + + + The marker set PVALB, TAC1, MYO5B can identify the Human cell type pvalb GABAergic cortical interneuron in the Brain with a confidence of 0.691998764 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + + + + + + + + + + + + + + + The marker set GPR149, CA8 can identify the Human cell type chandelier pvalb GABAergic cortical interneuron in the Brain with a confidence of 0.799748111 (NS-Forest FBeta value). + + + + + The marker set GPR149, CA8 can identify the Human cell type chandelier pvalb GABAergic cortical interneuron in the Brain with a confidence of 0.799748111 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + + + + + + + + + + + + + + + The marker set CHST8, POU3F1 can identify the Human cell type L5 extratelencephalic projecting glutamatergic cortical neuron in the Brain with a confidence of 0.815891473 (NS-Forest FBeta value). + + + + + The marker set CHST8, POU3F1 can identify the Human cell type L5 extratelencephalic projecting glutamatergic cortical neuron in the Brain with a confidence of 0.815891473 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + + + + + + + + + + + + + + + The marker set SEMA5B, ADAMTSL1, SULF1 can identify the Human cell type L6 corticothalamic-projecting glutamatergic cortical neuron in the Brain with a confidence of 0.631898455 (NS-Forest FBeta value). + + + + + The marker set SEMA5B, ADAMTSL1, SULF1 can identify the Human cell type L6 corticothalamic-projecting glutamatergic cortical neuron in the Brain with a confidence of 0.631898455 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + + + + + + + + + + + + + + + The marker set CCN2, ROS1 can identify the Human cell type L6b glutamatergic neuron of the primary motor cortex in the Brain with a confidence of 0.819940964 (NS-Forest FBeta value). + + + + + The marker set CCN2, ROS1 can identify the Human cell type L6b glutamatergic neuron of the primary motor cortex in the Brain with a confidence of 0.819940964 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + + + + + + + + + + + + + + + The marker set NPY can identify the Human cell type sst chodl GABAergic cortical interneuron in the Brain with a confidence of 0.894026187 (NS-Forest FBeta value). + + + + + The marker set NPY can identify the Human cell type sst chodl GABAergic cortical interneuron in the Brain with a confidence of 0.894026187 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + + + + + + + + + + + + + + + The marker set AOC3, LUM can identify the Human cell type alveolar type 1 fibroblast cell in the Lung with a confidence of 0.70 (NS-Forest FBeta value). + + + + + The marker set AOC3, LUM can identify the Human cell type alveolar type 1 fibroblast cell in the Lung with a confidence of 0.70 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + + + + + + + + + + + + + + + The marker set SCARA5, CD248 can identify the Human cell type alveolar adventitial fibroblast in the Lung with a confidence of 0.85 (NS-Forest FBeta value). + + + + + The marker set SCARA5, CD248 can identify the Human cell type alveolar adventitial fibroblast in the Lung with a confidence of 0.85 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + + + + + + + + + + + + + + + The marker set ONECUT2, COL5A2 can identify the Human cell type L2/3 intratelencephalic projecting glutamatergic neuron in the Brain with a confidence of 0.670149932 (NS-Forest FBeta value). + + + + + The marker set ONECUT2, COL5A2 can identify the Human cell type L2/3 intratelencephalic projecting glutamatergic neuron in the Brain with a confidence of 0.670149932 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + + + + + + + + + + + + + + + The marker set RORB, ST8SIA4 can identify the Human cell type L4 intratelencephalic projecting glutamatergic neuron in the Brain with a confidence of 0.720108696 (NS-Forest FBeta value). + + + + + The marker set RORB, ST8SIA4 can identify the Human cell type L4 intratelencephalic projecting glutamatergic neuron in the Brain with a confidence of 0.720108696 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + + + + + + + + + + + + + + + The marker set ARSJ, RORB, KCNK2 can identify the Human cell type L5 intratelencephalic projecting glutamatergic neuron in the Brain with a confidence of 0.764261336 (NS-Forest FBeta value). + + + + + The marker set ARSJ, RORB, KCNK2 can identify the Human cell type L5 intratelencephalic projecting glutamatergic neuron in the Brain with a confidence of 0.764261336 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + + + + + + + + + + + + + + + The marker set LINC00507, THEMIS can identify the Human cell type L6 intratelencephalic projecting glutamatergic neuron in the Brain with a confidence of 0.641695703 (NS-Forest FBeta value). + + + + + The marker set LINC00507, THEMIS can identify the Human cell type L6 intratelencephalic projecting glutamatergic neuron in the Brain with a confidence of 0.641695703 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + + + + + + + + + + + + + + + The marker set NPSR1-AS1, TLL1 can identify the Human cell type L5/6 near-projecting glutamatergic neuron in the Brain with a confidence of 0.899288218 (NS-Forest FBeta value). + + + + + The marker set NPSR1-AS1, TLL1 can identify the Human cell type L5/6 near-projecting glutamatergic neuron in the Brain with a confidence of 0.899288218 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + + + + + + + + + + + + + + + The marker set SMYD1, THEMIS can identify the Human cell type L6 intratelencephalic projecting Car3 glutamatergic neuron in the Brain with a confidence of 0.877752028 (NS-Forest FBeta value). + + + + + The marker set SMYD1, THEMIS can identify the Human cell type L6 intratelencephalic projecting Car3 glutamatergic neuron in the Brain with a confidence of 0.877752028 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + + + + + + + + + + + + + + + The marker set PRR4, C6orf58 can identify the Human cell type serous secreting cell of bronchus submucosal gland in the Lung with a confidence of 0.75 (NS-Forest FBeta value). + + + + + The marker set PRR4, C6orf58 can identify the Human cell type serous secreting cell of bronchus submucosal gland in the Lung with a confidence of 0.75 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + + + + + + + + + + + + + + + The marker set BPIFB2 can identify the Human cell type mucus secreting cell of bronchus submucosal gland in the Lung with a confidence of 0.93 (NS-Forest FBeta value). + + + + + The marker set BPIFB2 can identify the Human cell type mucus secreting cell of bronchus submucosal gland in the Lung with a confidence of 0.93 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + + + + + + + + + + + + + + + The marker set GLYATL2, DMBT1 can identify the Human cell type airway submucosal gland collecting duct epithelial cell in the Lung with a confidence of 0.46 (NS-Forest FBeta value). + + + + + The marker set GLYATL2, DMBT1 can identify the Human cell type airway submucosal gland collecting duct epithelial cell in the Lung with a confidence of 0.46 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + + + + + + + + + + + + + + + The marker set TNIP3, CXCL5 can identify the Human cell type CCL3-positive alveolar macrophage in the Lung with a confidence of 0.67 (NS-Forest FBeta value). + + + + + The marker set TNIP3, CXCL5 can identify the Human cell type CCL3-positive alveolar macrophage in the Lung with a confidence of 0.67 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + + + + + + + + + + + + + + + The marker set HMOX1, HPGD can identify the Human cell type metallothionein-positive alveolar macrophage in the Lung with a confidence of 0.41 (NS-Forest FBeta value). + + + + + The marker set HMOX1, HPGD can identify the Human cell type metallothionein-positive alveolar macrophage in the Lung with a confidence of 0.41 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + + + + + + + + + + + + + + + The marker set F13A1, STAB1, FCGR2B can identify the Human cell type lung interstitial macrophage in the Lung with a confidence of 0.46 (NS-Forest FBeta value). + + + + + The marker set F13A1, STAB1, FCGR2B can identify the Human cell type lung interstitial macrophage in the Lung with a confidence of 0.46 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + + + + + + + + + + + + + + + The marker set TNC, KRT15, SERPINB4 can identify the Human cell type respiratory suprabasal cell in the Lung with a confidence of 0.62 (NS-Forest FBeta value). + + + + + The marker set TNC, KRT15, SERPINB4 can identify the Human cell type respiratory suprabasal cell in the Lung with a confidence of 0.62 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + + + + + + + + + + + + + + + The marker set PCLAF, RRM2, UBE2C, NUSAP1 can identify the Human cell type cycling alveolar macrophage in the Lung with a confidence of 0.26 (NS-Forest FBeta value). + + + + + The marker set PCLAF, RRM2, UBE2C, NUSAP1 can identify the Human cell type cycling alveolar macrophage in the Lung with a confidence of 0.26 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + + + + + + + + + + + + + + + The marker set PEG10, PRC1, TOP2A can identify the Human cell type cycling pulmonary alveolar type 2 cell in the Lung with a confidence of 0.61 (NS-Forest FBeta value). + + + + + The marker set PEG10, PRC1, TOP2A can identify the Human cell type cycling pulmonary alveolar type 2 cell in the Lung with a confidence of 0.61 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + + + + + + + + + + + + + + + The marker set CHST9, LAMP5 can identify the Human cell type Lamp5 Lhx6 neuron in the Brain with a confidence of 0.821678322 (NS-Forest FBeta value). + + + + + The marker set CHST9, LAMP5 can identify the Human cell type Lamp5 Lhx6 neuron in the Brain with a confidence of 0.821678322 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + + + + + + + + + + + + + + + The marker set RELN, HCRTR2 can identify the Human cell type http://purl.obolibrary.org/obo/CL_4042032 in the Brain with a confidence of 0.724125093 (NS-Forest FBeta value). + + + + + The marker set RELN, HCRTR2 can identify the Human cell type http://purl.obolibrary.org/obo/CL_4042032 in the Brain with a confidence of 0.724125093 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + + + + + + + + + + + + + + sequence_collection + + + + + + - - diff --git a/src/ontology/imports/merged_import.owl b/src/ontology/imports/merged_import.owl index cb150f83d..2f2ea25d2 100644 --- a/src/ontology/imports/merged_import.owl +++ b/src/ontology/imports/merged_import.owl @@ -7,8 +7,8 @@ Prefix(rdfs:=) Ontology( - -Annotation(owl:versionInfo "2024-11-21") + +Annotation(owl:versionInfo "2024-12-04") Declaration(Class()) Declaration(Class()) @@ -2527,6 +2527,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -9959,6 +9960,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -10179,6 +10181,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -11925,6 +11928,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -13867,6 +13871,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -14123,6 +14128,7 @@ Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) +Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) @@ -14267,6 +14273,7 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -14323,8 +14330,8 @@ We don't have definitions of 'meaning' or 'expression' or 'property'. For 'refer 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."@en) -AnnotationAssertion(rdfs:label "definition") AnnotationAssertion(rdfs:label "definition"@en) +AnnotationAssertion(rdfs:label "definition") # Annotation Property: (editor note) @@ -14345,15 +14352,15 @@ AnnotationAssertion( "true"^^xsd:boolean) AnnotationAssertion( "term_tracker_item") AnnotationAssertion(rdfs:comment "The 'tracker item' can associate a tracker with a specific ontology term."@en) -AnnotationAssertion(rdfs:label "term tracker item") AnnotationAssertion(rdfs:label "term tracker item"@en) +AnnotationAssertion(rdfs:label "term tracker item") # Annotation Property: (expand expression to) AnnotationAssertion( "A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones"@en) AnnotationAssertion(rdfs:label "expand expression to"@en) -# Annotation Property: (preferred_root) +# Annotation Property: (has ontology root term) AnnotationAssertion( "Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root."@en) AnnotationAssertion( "IAO:0000700") @@ -14361,15 +14368,15 @@ AnnotationAssertion( "has_ontology_root_term") AnnotationAssertion( "true"^^xsd:boolean) AnnotationAssertion( "has_ontology_root_term") -AnnotationAssertion(rdfs:label "has ontology root term") AnnotationAssertion(rdfs:label "has ontology root term"@en) +AnnotationAssertion(rdfs:label "has ontology root term") # Annotation Property: (term replaced by) AnnotationAssertion( "Use on obsolete terms, relating the term to another term that can be used as a substitute"@en) AnnotationAssertion(rdfs:comment "Add as annotation triples in the granting ontology"@en) -AnnotationAssertion(rdfs:label "term replaced by") AnnotationAssertion(rdfs:label "term replaced by"@en) +AnnotationAssertion(rdfs:label "term replaced by") # Annotation Property: (defined by construct) @@ -14807,7 +14814,7 @@ AnnotationAssertion( "database_cross_reference") AnnotationAssertion(rdfs:label "has cross-reference") -# Annotation Property: (has_exact_synonym) +# Annotation Property: (has exact synonym) AnnotationAssertion( "An alternative label for a class or property which has the exact same meaning than the preferred name/primary label.") AnnotationAssertion( "https://github.com/information-artifact-ontology/ontology-metadata/issues/20") @@ -14815,7 +14822,7 @@ AnnotationAssertion(rdfs:label "has_exact_synonym") AnnotationAssertion(rdfs:seeAlso "https://github.com/information-artifact-ontology/ontology-metadata/issues/20") -# Annotation Property: (has_narrow_synonym) +# Annotation Property: (has narrow synonym) AnnotationAssertion( "An alternative label for a class or property which has a more specific meaning than the preferred name/primary label.") AnnotationAssertion( "https://github.com/information-artifact-ontology/ontology-metadata/issues/19") @@ -14868,12 +14875,12 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "part_of") -AnnotationAssertion(rdfs:label "part of") AnnotationAssertion(rdfs:label "part of"@en) +AnnotationAssertion(rdfs:label "part of") AnnotationAssertion(rdfs:seeAlso ) AnnotationAssertion(rdfs:seeAlso ) -AnnotationAssertion(rdfs:seeAlso "http://www.obofoundry.org/ro/#OBO_REL:part_of") AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Part_of"^^xsd:anyURI) +AnnotationAssertion(rdfs:seeAlso "http://www.obofoundry.org/ro/#OBO_REL:part_of") SubObjectPropertyOf( ) InverseObjectProperties( ) TransitiveObjectProperty() @@ -14893,8 +14900,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "has_part") -AnnotationAssertion(rdfs:label "has part") AnnotationAssertion(rdfs:label "has part"@en) +AnnotationAssertion(rdfs:label "has part") SubObjectPropertyOf( ) TransitiveObjectProperty() @@ -14907,8 +14914,8 @@ AnnotationAssertion( "preceded_by") AnnotationAssertion( ) AnnotationAssertion( "preceded_by") -AnnotationAssertion(rdfs:label "preceded by") AnnotationAssertion(rdfs:label "preceded by"@en) +AnnotationAssertion(rdfs:label "preceded by") SubObjectPropertyOf( ) InverseObjectProperties( ) TransitiveObjectProperty() @@ -14923,8 +14930,8 @@ AnnotationAssertion( "precedes") AnnotationAssertion( ) AnnotationAssertion( "precedes") -AnnotationAssertion(rdfs:label "precedes") AnnotationAssertion(rdfs:label "precedes"@en) +AnnotationAssertion(rdfs:label "precedes") SubObjectPropertyOf( ) TransitiveObjectProperty() ObjectPropertyDomain( ) @@ -14941,8 +14948,8 @@ AnnotationAssertion( ) AnnotationAssertion( "occurs_in") AnnotationAssertion(rdfs:comment "Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant") -AnnotationAssertion(rdfs:label "occurs in") AnnotationAssertion(rdfs:label "occurs in"@en) +AnnotationAssertion(rdfs:label "occurs in") AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Occurs_in"^^xsd:anyURI) InverseObjectProperties( ) ObjectPropertyDomain( ) @@ -14990,8 +14997,8 @@ AnnotationAssertion( "external") AnnotationAssertion( "bearer_of") AnnotationAssertion( "bearer_of") -AnnotationAssertion(rdfs:label "bearer of") AnnotationAssertion(rdfs:label "has characteristic"@en) +AnnotationAssertion(rdfs:label "bearer of") InverseFunctionalObjectProperty() ObjectPropertyRange( ) @@ -15002,8 +15009,8 @@ AnnotationAssertion( "external") AnnotationAssertion( "participates_in") AnnotationAssertion( "participates_in") -AnnotationAssertion(rdfs:label "participates in") AnnotationAssertion(rdfs:label "participates in"@en) +AnnotationAssertion(rdfs:label "participates in") InverseObjectProperties( ) ObjectPropertyDomain( ) ObjectPropertyRange( ) @@ -15016,8 +15023,8 @@ AnnotationAssertion( "external") AnnotationAssertion( "has_participant") AnnotationAssertion( "has_participant") -AnnotationAssertion(rdfs:label "has participant") AnnotationAssertion(rdfs:label "has participant"@en) +AnnotationAssertion(rdfs:label "has participant") ObjectPropertyDomain( ) ObjectPropertyRange( ) @@ -15124,8 +15131,8 @@ AnnotationAssertion( ) AnnotationAssertion( "bounding_layer_of") AnnotationAssertion(rdfs:comment "A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane.") -AnnotationAssertion(rdfs:label "bounding layer of") AnnotationAssertion(rdfs:label "bounding layer of"@en) +AnnotationAssertion(rdfs:label "bounding layer of") SubObjectPropertyOf( ) ObjectPropertyDomain( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) ObjectPropertyRange( ) @@ -15170,8 +15177,8 @@ AnnotationAssertion( "immediately_preceded_by") AnnotationAssertion( "immediately_preceded_by") AnnotationAssertion(rdfs:comment "X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)"@en) -AnnotationAssertion(rdfs:label "immediately preceded by") AnnotationAssertion(rdfs:label "immediately preceded by"@en) +AnnotationAssertion(rdfs:label "immediately preceded by") SubObjectPropertyOf( ) InverseObjectProperties( ) @@ -15183,8 +15190,8 @@ AnnotationAssertion( ) AnnotationAssertion( "immediately_precedes") AnnotationAssertion(rdfs:comment "X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)"@en) -AnnotationAssertion(rdfs:label "immediately precedes") AnnotationAssertion(rdfs:label "immediately precedes"@en) +AnnotationAssertion(rdfs:label "immediately precedes") SubObjectPropertyOf( ) # Object Property: (has soma location) @@ -15290,8 +15297,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "overlaps") -AnnotationAssertion(rdfs:label "overlaps") AnnotationAssertion(rdfs:label "overlaps"@en) +AnnotationAssertion(rdfs:label "overlaps") SubObjectPropertyOf( ) SymmetricObjectProperty() @@ -15412,8 +15419,8 @@ AnnotationAssertion( "has_component") AnnotationAssertion( ) AnnotationAssertion( "has_component") -AnnotationAssertion(rdfs:label "has component") AnnotationAssertion(rdfs:label "has component"@en) +AnnotationAssertion(rdfs:label "has component") AnnotationAssertion(rdfs:seeAlso ) SubObjectPropertyOf( ) @@ -15477,8 +15484,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "regulates") -AnnotationAssertion(rdfs:label "regulates") AnnotationAssertion(rdfs:label "regulates"@en) +AnnotationAssertion(rdfs:label "regulates") SubObjectPropertyOf( ) InverseObjectProperties( ) TransitiveObjectProperty() @@ -15496,8 +15503,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "negatively_regulates") -AnnotationAssertion(rdfs:label "negatively regulates") AnnotationAssertion(rdfs:label "negatively regulates"@en) +AnnotationAssertion(rdfs:label "negatively regulates") SubObjectPropertyOf( ) SubObjectPropertyOf( ) InverseObjectProperties( ) @@ -15512,8 +15519,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "positively_regulates") -AnnotationAssertion(rdfs:label "positively regulates") AnnotationAssertion(rdfs:label "positively regulates"@en) +AnnotationAssertion(rdfs:label "positively regulates") SubObjectPropertyOf( ) SubObjectPropertyOf( ) InverseObjectProperties( ) @@ -15527,8 +15534,8 @@ AnnotationAssertion( "capable_of") AnnotationAssertion( ) AnnotationAssertion( "capable_of") -AnnotationAssertion(rdfs:label "capable of") AnnotationAssertion(rdfs:label "capable of"@en) +AnnotationAssertion(rdfs:label "capable of") SubObjectPropertyOf( ) ObjectPropertyDomain( ) ObjectPropertyRange( ) @@ -15540,8 +15547,8 @@ AnnotationAssertion( "external") AnnotationAssertion( "capable_of_part_of") AnnotationAssertion( "capable_of_part_of") -AnnotationAssertion(rdfs:label "capable of part of") AnnotationAssertion(rdfs:label "capable of part of"@en) +AnnotationAssertion(rdfs:label "capable of part of") AnnotationAssertion(rdfs:seeAlso ) SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -15564,8 +15571,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "adjacent_to") -AnnotationAssertion(rdfs:label "adjacent to") AnnotationAssertion(rdfs:label "adjacent to"@en) +AnnotationAssertion(rdfs:label "adjacent to") SubObjectPropertyOf( ) ObjectPropertyDomain( ) ObjectPropertyRange( ) @@ -15602,8 +15609,8 @@ AnnotationAssertion( "starts_with") AnnotationAssertion( ) AnnotationAssertion( "starts_with") -AnnotationAssertion(rdfs:label "starts with") AnnotationAssertion(rdfs:label "starts with"@en) +AnnotationAssertion(rdfs:label "starts with") SubObjectPropertyOf( ) SubObjectPropertyOf( ) TransitiveObjectProperty() @@ -15638,8 +15645,8 @@ AnnotationAssertion( "ends_with") AnnotationAssertion( ) AnnotationAssertion( "ends_with") -AnnotationAssertion(rdfs:label "ends with") AnnotationAssertion(rdfs:label "ends with"@en) +AnnotationAssertion(rdfs:label "ends with") SubObjectPropertyOf( ) SubObjectPropertyOf( ) TransitiveObjectProperty() @@ -15652,8 +15659,8 @@ AnnotationAssertion( "has_start_location") AnnotationAssertion( ) AnnotationAssertion( "has_start_location") -AnnotationAssertion(rdfs:label "has start location") AnnotationAssertion(rdfs:label "has start location"@en) +AnnotationAssertion(rdfs:label "has start location") SubObjectPropertyOf( ) ObjectPropertyDomain( ) ObjectPropertyRange( ) @@ -15666,8 +15673,8 @@ AnnotationAssertion( "has_end_location") AnnotationAssertion( ) AnnotationAssertion( "has_end_location") -AnnotationAssertion(rdfs:label "has end location") AnnotationAssertion(rdfs:label "has end location"@en) +AnnotationAssertion(rdfs:label "has end location") SubObjectPropertyOf( ) ObjectPropertyDomain( ) ObjectPropertyRange( ) @@ -15683,8 +15690,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "has_input") -AnnotationAssertion(rdfs:label "has input") AnnotationAssertion(rdfs:label "has input"@en) +AnnotationAssertion(rdfs:label "has input") AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Has_input"^^xsd:anyURI) SubObjectPropertyOf( ) InverseObjectProperties( ) @@ -15701,8 +15708,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "has_output") -AnnotationAssertion(rdfs:label "has output") AnnotationAssertion(rdfs:label "has output"@en) +AnnotationAssertion(rdfs:label "has output") AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Has_output"^^xsd:anyURI) SubObjectPropertyOf( ) InverseObjectProperties( ) @@ -15816,8 +15823,8 @@ AnnotationAssertion( "external") AnnotationAssertion( "results_in_developmental_progression_of") AnnotationAssertion( "results_in_developmental_progression_of") -AnnotationAssertion(rdfs:label "results in developmental progression of") AnnotationAssertion(rdfs:label "results in developmental progression of"@en) +AnnotationAssertion(rdfs:label "results in developmental progression of") AnnotationAssertion(rdfs:seeAlso ) SubObjectPropertyOf( ) ObjectPropertyDomain( ) @@ -15833,8 +15840,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "results_in_development_of") -AnnotationAssertion(rdfs:label "results in development of") AnnotationAssertion(rdfs:label "results in development of"@en) +AnnotationAssertion(rdfs:label "results in development of") SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -15847,8 +15854,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "results_in_formation_of") -AnnotationAssertion(rdfs:label "results in formation of") AnnotationAssertion(rdfs:label "results in formation of anatomical entity"@en) +AnnotationAssertion(rdfs:label "results in formation of") SubObjectPropertyOf( ) SubObjectPropertyOf( ) InverseObjectProperties( ) @@ -15863,8 +15870,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "results_in_morphogenesis_of") -AnnotationAssertion(rdfs:label "results in morphogenesis of") AnnotationAssertion(rdfs:label "results in morphogenesis of"@en) +AnnotationAssertion(rdfs:label "results in morphogenesis of") SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -15878,8 +15885,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "results_in_maturation_of") -AnnotationAssertion(rdfs:label "results in maturation of") AnnotationAssertion(rdfs:label "results in maturation of"@en) +AnnotationAssertion(rdfs:label "results in maturation of") SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -15931,8 +15938,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "results_in_acquisition_of_features_of") -AnnotationAssertion(rdfs:label "results in acquisition of features of") AnnotationAssertion(rdfs:label "results in acquisition of features of"@en) +AnnotationAssertion(rdfs:label "results in acquisition of features of") SubObjectPropertyOf( ) SubObjectPropertyOf( ) ObjectPropertyRange( ) @@ -15977,8 +15984,8 @@ AnnotationAssertion( "external") AnnotationAssertion( "regulates_levels_of") AnnotationAssertion( "regulates_levels_of") -AnnotationAssertion(rdfs:label "regulates levels of") AnnotationAssertion(rdfs:label "regulates levels of"@en) +AnnotationAssertion(rdfs:label "regulates levels of") SubObjectPropertyOf( ) ObjectPropertyDomain( ) ObjectPropertyRange( ) @@ -15991,8 +15998,8 @@ AnnotationAssertion( "regulated_by") AnnotationAssertion( ) AnnotationAssertion( "regulated_by") -AnnotationAssertion(rdfs:label "regulated by") AnnotationAssertion(rdfs:label "regulated by"@en) +AnnotationAssertion(rdfs:label "regulated by") SubObjectPropertyOf( ) TransitiveObjectProperty() ObjectPropertyDomain( ) @@ -16006,8 +16013,8 @@ AnnotationAssertion( "negatively_regulated_by") AnnotationAssertion( ) AnnotationAssertion( "negatively_regulated_by") -AnnotationAssertion(rdfs:label "negatively regulated by") AnnotationAssertion(rdfs:label "negatively regulated by"@en) +AnnotationAssertion(rdfs:label "negatively regulated by") SubObjectPropertyOf( ) # Object Property: (positively regulated by) @@ -16018,8 +16025,8 @@ AnnotationAssertion( "positively_regulated_by") AnnotationAssertion( ) AnnotationAssertion( "positively_regulated_by") -AnnotationAssertion(rdfs:label "positively regulated by") AnnotationAssertion(rdfs:label "positively regulated by"@en) +AnnotationAssertion(rdfs:label "positively regulated by") SubObjectPropertyOf( ) # Object Property: (related via localization to) @@ -16039,8 +16046,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "has_target_start_location") -AnnotationAssertion(rdfs:label "has target start location") AnnotationAssertion(rdfs:label "has target start location"@en) +AnnotationAssertion(rdfs:label "has target start location") SubObjectPropertyOf( ) # Object Property: (has target end location) @@ -16053,8 +16060,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "has_target_end_location") -AnnotationAssertion(rdfs:label "has target end location") AnnotationAssertion(rdfs:label "has target end location"@en) +AnnotationAssertion(rdfs:label "has target end location") SubObjectPropertyOf( ) # Object Property: (results in transport along) @@ -16064,8 +16071,8 @@ AnnotationAssertion( "external") AnnotationAssertion( "results_in_transport_along") AnnotationAssertion( "results_in_transport_along") -AnnotationAssertion(rdfs:label "results in transport along") AnnotationAssertion(rdfs:label "results in transport along"@en) +AnnotationAssertion(rdfs:label "results in transport along") SubObjectPropertyOf( ) # Object Property: (results in transport across) @@ -16076,8 +16083,8 @@ AnnotationAssertion( "results_in_transport_across") AnnotationAssertion( ) AnnotationAssertion( "results_in_transport_across") -AnnotationAssertion(rdfs:label "results in transport across") AnnotationAssertion(rdfs:label "results in transport across"@en) +AnnotationAssertion(rdfs:label "results in transport across") SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -16087,8 +16094,8 @@ AnnotationAssertion( "external") AnnotationAssertion( "results_in_growth_of") AnnotationAssertion( "results_in_growth_of") -AnnotationAssertion(rdfs:label "results in growth of") AnnotationAssertion(rdfs:label "results in growth of"@en) +AnnotationAssertion(rdfs:label "results in growth of") SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -16098,8 +16105,8 @@ AnnotationAssertion( "external") AnnotationAssertion( "results_in_transport_to_from_or_in") AnnotationAssertion( "results_in_transport_to_from_or_in") -AnnotationAssertion(rdfs:label "results in transport to from or in") AnnotationAssertion(rdfs:label "results in transport to from or in"@en) +AnnotationAssertion(rdfs:label "results in transport to from or in") SubObjectPropertyOf( ) # Object Property: (member of) @@ -16133,8 +16140,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "output_of") -AnnotationAssertion(rdfs:label "output of") AnnotationAssertion(rdfs:label "output of"@en) +AnnotationAssertion(rdfs:label "output of") SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -16252,8 +16259,8 @@ AnnotationAssertion( "external") AnnotationAssertion( "causally_downstream_of") AnnotationAssertion( "causally_downstream_of") -AnnotationAssertion(rdfs:label "causally downstream of") AnnotationAssertion(rdfs:label "causally downstream of"@en) +AnnotationAssertion(rdfs:label "causally downstream of") SubObjectPropertyOf( ) SubObjectPropertyOf( ) InverseObjectProperties( ) @@ -16287,8 +16294,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "causally_upstream_of") -AnnotationAssertion(rdfs:label "causally upstream of") AnnotationAssertion(rdfs:label "causally upstream of"@en) +AnnotationAssertion(rdfs:label "causally upstream of") SubObjectPropertyOf( ) SubObjectPropertyOf( ) TransitiveObjectProperty() @@ -16642,8 +16649,8 @@ AnnotationAssertion( ) AnnotationAssertion( "produces") AnnotationAssertion(rdfs:comment "Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue.") -AnnotationAssertion(rdfs:label "produces") AnnotationAssertion(rdfs:label "produces"@en) +AnnotationAssertion(rdfs:label "produces") InverseObjectProperties( ) ObjectPropertyDomain( ) ObjectPropertyRange( ) @@ -16656,8 +16663,8 @@ AnnotationAssertion( "produced_by") AnnotationAssertion( ) AnnotationAssertion( "produced_by") -AnnotationAssertion(rdfs:label "produced by") AnnotationAssertion(rdfs:label "produced by"@en) +AnnotationAssertion(rdfs:label "produced by") ObjectPropertyDomain( ) ObjectPropertyRange( ) @@ -16737,8 +16744,8 @@ AnnotationAssertion( "external") AnnotationAssertion( "has_small_molecule_activator") AnnotationAssertion( "has_small_molecule_activator") -AnnotationAssertion(rdfs:label "has small molecule activator") AnnotationAssertion(rdfs:label "has small molecule activator"@en) +AnnotationAssertion(rdfs:label "has small molecule activator") SubObjectPropertyOf( ) InverseObjectProperties( ) @@ -16754,8 +16761,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "acts_on_population_of") -AnnotationAssertion(rdfs:label "acts on population of") AnnotationAssertion(rdfs:label "acts on population of"@en) +AnnotationAssertion(rdfs:label "acts on population of") SubObjectPropertyOf( ) # Object Property: (is small molecule regulator of) @@ -16787,8 +16794,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "results_in_fusion_of") -AnnotationAssertion(rdfs:label "results in fusion of") AnnotationAssertion(rdfs:label "results in fusion of"@en) +AnnotationAssertion(rdfs:label "results in fusion of") SubObjectPropertyOf( ) # Object Property: (has synaptic IO in region) @@ -16812,6 +16819,16 @@ AnnotationAssertion(rdfs:label "has SubObjectPropertyOf( ) ObjectPropertyDomain( ) +# Object Property: (has characterizing marker set) + +AnnotationAssertion( "A relation that applies between a cell type and a set of markers that can be used to uniquely identify that cell type.") +AnnotationAssertion( "C has_characterizing_marker_set y iff: C is a cell type and y is a collection of genes or proteins whose expression is sufficient to distinguish cell type C from most or all other cell types.") +AnnotationAssertion( ) +AnnotationAssertion( "has marker gene combination") +AnnotationAssertion( "has marker signature set") +AnnotationAssertion(rdfs:label "has characterizing marker set") +ObjectPropertyDomain( ) + # Object Property: (different in magnitude relative to) AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.") @@ -17071,7 +17088,7 @@ SubClassOf( ) -# Class: (cell) +# Class: () DisjointClasses( ) DisjointClasses( ) @@ -40185,6 +40202,18 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (globus pallidus development) + +AnnotationAssertion(Annotation( "GOC:cls") Annotation( "GOC:dgh") Annotation( "GOC:dph") Annotation( "GOC:jid") Annotation( "GO_REF:0000021") Annotation( "ISBN:0878937420") "The progression of the globus pallidus over time from its initial formation until its mature state. The globus pallidus is one of the basal ganglia involved with control of voluntary movement in the brain.") +AnnotationAssertion(Annotation( "PMID:16271465") "pallidum development") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0021759") +AnnotationAssertion(rdfs:label "globus pallidus development") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (limbic system development) AnnotationAssertion(Annotation( "GOC:cls") Annotation( "GOC:dgh") Annotation( "GOC:dph") Annotation( "GOC:jid") Annotation( "GO_REF:0000021") Annotation( "ISBN:0878937420") "The progression of the limbic system over time from its initial formation until its mature state. The limbic system is a collection of structures in the brain involved in emotion, motivation and emotional aspects of memory.") @@ -69077,6 +69106,9 @@ AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0051932") AnnotationAssertion(rdfs:label "synaptic transmission, GABAergic") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (catecholamine transport) @@ -112266,6 +112298,7 @@ SubClassOf( (Saccharomycotina) AnnotationAssertion( "GC_ID:1") +AnnotationAssertion( "PMID:38895705") AnnotationAssertion(Annotation( ) "true yeasts") AnnotationAssertion( "ncbi_taxonomy") AnnotationAssertion( "NCBITaxon:147537") @@ -112986,6 +113019,7 @@ SubClassOf( (Saccharomycetes) AnnotationAssertion( "GC_ID:1") +AnnotationAssertion( "PMID:38895705") AnnotationAssertion( "ncbi_taxonomy") AnnotationAssertion(Annotation( ) "Hemiascomycetes") AnnotationAssertion( "NCBITaxon:4891") @@ -112995,6 +113029,7 @@ SubClassOf( (Saccharomycetales) AnnotationAssertion( "GC_ID:1") +AnnotationAssertion( "PMID:38895705") AnnotationAssertion( "ncbi_taxonomy") AnnotationAssertion(Annotation( ) "Endomycetales") AnnotationAssertion(Annotation( ) "budding yeasts") @@ -113057,6 +113092,7 @@ AnnotationAssertion( ) "Candida robusta") AnnotationAssertion(Annotation( ) "Mycoderma cerevisiae") AnnotationAssertion(Annotation( ) "Saccharomyces capensis") +AnnotationAssertion(Annotation( ) "Saccharomyces cerevisiae (Desm.) Meyen ex E.C. Hansen, 1883") AnnotationAssertion(Annotation( ) "Saccharomyces diastaticus") AnnotationAssertion(Annotation( ) "Saccharomyces italicus") AnnotationAssertion(Annotation( ) "Saccharomyces oviformis") @@ -130766,7 +130802,6 @@ AnnotationAssertion( "WBbt:0005739") AnnotationAssertion( "Wikipedia:Head") AnnotationAssertion( "XAO:0003024") -AnnotationAssertion( "ZFA:0001114") AnnotationAssertion( "galen:Head") AnnotationAssertion(Annotation( "FMA:7154") "head (volume)") AnnotationAssertion( "adult head") @@ -138025,7 +138060,7 @@ AnnotationAssertion( "ZFA:0000560") AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "ovarian duct") AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "ovarian tube") -AnnotationAssertion( "uterine tube") +AnnotationAssertion( "uterine tube") AnnotationAssertion( "uberon") AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "female reproductive tracts") AnnotationAssertion(Annotation( "ZFA:0000560") Annotation( ) "oviducts") @@ -138527,7 +138562,6 @@ AnnotationAssertion(Annotation( "Wikipedia:Acoelomorpha") ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( "AAO:0000959") AnnotationAssertion( "CALOHA:TS-2103") AnnotationAssertion( "VHOG:0001248") @@ -138535,7 +138569,6 @@ AnnotationAssertion( "uberon") AnnotationAssertion(Annotation( "Wikipedia:Circulatory_system") Annotation( ) "systema cardiovasculare") AnnotationAssertion( "UBERON:0001009") -AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "circulatory system") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg"^^xsd:anyURI) @@ -154177,6 +154210,50 @@ SubClassOf(Annotation( "FMA SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (globus pallidus) + +AnnotationAssertion(Annotation( "BIRNLEX:1234") "Subcortical nucleus, functionally part of the basal ganglia, which consists of two segments the external (or lateral) and internal (or medial) separated by the medial medullary lamina in primates. In rodents, The globus pallidus lateral is separated from the medial segment by the fibers of the internal capsule/cerebral peduncle.") +AnnotationAssertion( "BAMS:GP") +AnnotationAssertion( "BIRNLEX:1234") +AnnotationAssertion( "BTO:0002246") +AnnotationAssertion( "CALOHA:TS-2013") +AnnotationAssertion( "DHBA:10342") +AnnotationAssertion( "EFO:0000905") +AnnotationAssertion( "EMAPA:35380") +AnnotationAssertion( "EV:0100188") +AnnotationAssertion( "FMA:61835") +AnnotationAssertion( "GAID:668") +AnnotationAssertion( "HBA:4293") +AnnotationAssertion( "MA:0000890") +AnnotationAssertion( "MAT:0000510") +AnnotationAssertion( "MESH:D005917") +AnnotationAssertion( "NCIT:C12449") +AnnotationAssertion( "PBA:10097") +AnnotationAssertion( "SCTID:362361005") +AnnotationAssertion(Annotation( "BIRNLEX:1234") Annotation( "ncithesaurus:Globus_Pallidus") "UMLS:C0017651") +AnnotationAssertion( "Wikipedia:Globus_pallidus") +AnnotationAssertion(Annotation( "BIRNLEX:1234") "neuronames:231") +AnnotationAssertion(Annotation( "BIRNLEX:1234") "pale body") +AnnotationAssertion(Annotation( "Wikipedia:Globus_pallidus") "paleostriatum") +AnnotationAssertion( "uberon") +AnnotationAssertion(Annotation( "NeuroNames:231") "globus pallidus (Burdach)") +AnnotationAssertion(Annotation( "NeuroNames:231") Annotation( ) "nucleus pallidus") +AnnotationAssertion(Annotation( "Wikipedia:Globus_pallidus") "pallidium") +AnnotationAssertion(Annotation( "BIRNLEX:1234") Annotation( "GO:0021759") Annotation( "Wikipedia:Globus_pallidus") "pallidum") +AnnotationAssertion( "UBERON:0001875") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "BTO and MA are inconsistent w.r.t striatum and pallidum being non-overlapping as in ABA. Note that we have pallidum as part_of basal gangion, so we can make the direct link to basal ganglion. ISBN:1588900649 says: ... a derivative of the diencephalon, seperates as a result of growing fibers of theinternal capsule and is finally displaced into telencephalon. only a small medial remnannt remains, the entopeduncular nucleus. The globus pallidus should be regarded as part of the subthalamus") +AnnotationAssertion(rdfs:label "globus pallidus") +AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/e/ee/Brain_structure.gif"^^xsd:anyURI) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) +SubClassOf(Annotation( "BTO-weakened") ObjectSomeValuesFrom( )) +SubClassOf(Annotation( "GO") Annotation( "ISBN:1588900649") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (amygdala) AnnotationAssertion(Annotation( "BIRNLEX:1241") "Subcortical brain region lying anterior to the hippocampal formation in the temporal lobe and anterior to the temporal horn of the lateral ventricle in some species. It is usually subdivided into several groups. Functionally, it is not considered a unitary structure (MM).") @@ -157908,6 +157985,7 @@ SubClassOf( ) SubClassOf( ) SubClassOf(Annotation( "some species only have a single lung") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -161725,6 +161803,35 @@ SubClassOf(Annotation( "FMA SubClassOf(Annotation( "Wikipedia") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (lentiform nucleus) + +AnnotationAssertion(Annotation( "Wikipedia:Lentiform_nucleus") "The lentiform nucleus or lenticular nucleus comprises the putamen and the globus pallidus within the basal ganglia. It is a large, cone-shaped mass of gray matter just lateral to the internal capsule. [WP,unvetted].") +AnnotationAssertion( "TODO - add parts") +AnnotationAssertion( "BTO:0002250") +AnnotationAssertion( "EMAPA:18208") +AnnotationAssertion( "EMAPA:19147") +AnnotationAssertion( "EV:0100186") +AnnotationAssertion( "FMA:77615") +AnnotationAssertion( "MA:0000896") +AnnotationAssertion( "NCIT:C32977") +AnnotationAssertion( "SCTID:279319002") +AnnotationAssertion(Annotation( "ncithesaurus:Lenticular_Nucleus") "UMLS:C0162342") +AnnotationAssertion( "Wikipedia:Lentiform_nucleus") +AnnotationAssertion( "neuronames:1234") +AnnotationAssertion(Annotation( "BTO:0002250") "nucleus lenticularis") +AnnotationAssertion(Annotation( "BTO:0002250") "nucleus lentiformis") +AnnotationAssertion( "uberon") +AnnotationAssertion(Annotation( "BTO:0002250") "lenticular nucleus") +AnnotationAssertion(Annotation( "Wikipedia:Lentiform_nucleus") Annotation( ) "nucleus lentiformis") +AnnotationAssertion( "UBERON:0002263") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "lentiform nucleus") +AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/f/fc/Gray741.png"^^xsd:anyURI) +SubClassOf( ) +SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (olfactory bulb) AnnotationAssertion(Annotation( "BTO:0000961") Annotation( "Wikipedia:Olfactory_bulb") "A bulbous anterior projection of the olfactory lobe that is the place of termination of the olfactory nerves and is especially well developed in lower vertebrates (as fishes)[BTO].") @@ -162820,7 +162927,6 @@ AnnotationAssertion( "SCTID:361348008") AnnotationAssertion( "TAO:0001438") AnnotationAssertion(Annotation( "ncithesaurus:Cavity") "UMLS:C0333343") -AnnotationAssertion( "ZFA:0001438") AnnotationAssertion( "galen:BodyCavity") AnnotationAssertion(Annotation( "EHDAA2:0000267") "coelomic cavity") AnnotationAssertion(Annotation( "EHDAA2:0000267") "coelomic cavity lumen") @@ -164228,6 +164334,7 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (tonsil) AnnotationAssertion(Annotation( "MGI:cwg") Annotation( "MP:0002380") "Either of the two small almond-shaped masses of lymph tissue found on either side of the oropharynx.") +AnnotationAssertion( ) AnnotationAssertion( "BTO:0001387") AnnotationAssertion( "CALOHA:TS-1053") AnnotationAssertion( "EFO:0001401") @@ -164248,6 +164355,7 @@ AnnotationAssertion( "BTO:0001387") "Mandel") AnnotationAssertion( "UBERON:0002372") AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "tonsil") @@ -166126,6 +166234,7 @@ DisjointClasses( (lymphoid system) AnnotationAssertion(Annotation( "Wikipedia:Lymphoid_system") "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].") +AnnotationAssertion( ) AnnotationAssertion( "EHDAA2:0001043") AnnotationAssertion( "EHDAA:8677") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37664") @@ -166148,6 +166257,7 @@ AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "lymphatic drainage system") AnnotationAssertion(Annotation( "Wikipedia:Lymphoid_system") Annotation( ) "systema lymphoideum") AnnotationAssertion( "UBERON:0002465") +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "lymphoid system") @@ -167160,7 +167270,7 @@ SubClassOf( "EHDAA2") ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "PMID:16313389") ObjectSomeValuesFrom( )) +SubClassOf(Annotation( "PMID:16313389") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "http://tolweb.org/Chordata/2499") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "PMID:16313389") ObjectSomeValuesFrom( )) @@ -172149,6 +172259,7 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (mucosa of rectum) AnnotationAssertion(Annotation( "OBOL:automatic") "A mucosa that is part of a rectum [Automatically generated definition].") +AnnotationAssertion( ) AnnotationAssertion( "CALOHA:TS-2107") AnnotationAssertion( "EMAPA:27081") AnnotationAssertion( "FMA:15033") @@ -172165,6 +172276,7 @@ AnnotationAssertion(Annotation( "OBOL:automatic") "rectum organ mucosa") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0003346") +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "mucosa of rectum") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -178396,6 +178508,7 @@ SubClassOf(Annotation( "Wik AnnotationAssertion(Annotation( "MGI:smb") Annotation( "MP:0003574") Annotation( "http://orcid.org/0000-0002-6601-2165") "Initial section of the oviduct through which the ova pass from the ovary to the uterus.") AnnotationAssertion( ) +AnnotationAssertion(Annotation( "https://sourceforge.net/p/geneontology/ontology-requests/8397/") "mammalian oviduct") AnnotationAssertion(Annotation( ) "salpinges") AnnotationAssertion( "salpinx") AnnotationAssertion( "CALOHA:TS-0732") @@ -178411,10 +178524,9 @@ AnnotationAssertion( "ncithesaurus:Fallopian_Tube") "UMLS:C0015560") AnnotationAssertion( "Wikipedia:Fallopian_tube") AnnotationAssertion( "galen:FallopianTube") -AnnotationAssertion(Annotation( "https://sourceforge.net/p/geneontology/ontology-requests/8397/") "mammalian oviduct") AnnotationAssertion( "uterine tube (sensu Mammalia)") AnnotationAssertion( "uberon") -AnnotationAssertion( "fallopian tubes") +AnnotationAssertion(Annotation( ) "fallopian tubes") AnnotationAssertion(Annotation( "EHDAA2:0000504") "female paramesonephric duct") AnnotationAssertion(Annotation( "EMAPA:35660") "paramesonephric duct of female") AnnotationAssertion(Annotation( "Wikipedia:Fallopian_tube") Annotation( ) "tuba uterina") @@ -183154,7 +183266,6 @@ AnnotationAssertion( "pharyngeal arch artery") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/8/84/Gray473.png"^^xsd:anyURI) SubClassOf( ) -SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -184782,7 +184893,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (arterial system) AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "The part of the cardiovascular system consisting of all arteries.") -AnnotationAssertion( ) AnnotationAssertion( "BTO:0004690") AnnotationAssertion( "EHDAA2:0000143") AnnotationAssertion( "EHDAA:396") @@ -184793,7 +184903,6 @@ AnnotationAssertion( "VHOG:0000273") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0004572") -AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "arterial system") SubClassOf(Annotation( "MA") ) @@ -184831,7 +184940,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (venous system) AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "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.") -AnnotationAssertion( ) AnnotationAssertion( "BTO:0004692") AnnotationAssertion( "EHDAA2:0002171") AnnotationAssertion( "EHDAA:486") @@ -184844,7 +184952,6 @@ AnnotationAssertion( "vein system") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0004582") -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "venous system") SubClassOf(Annotation( "MA") ) SubClassOf( ObjectSomeValuesFrom( )) @@ -185511,10 +185618,10 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (Peyer's patch epithelium) -AnnotationAssertion(Annotation( "ISBN:0-8153-1691-7") Annotation( "MGI:cwg") Annotation( "MP:0002388") "The specialized epithelium of the Peyer's patch.") +AnnotationAssertion(Annotation( "ISBN:0-8153-1691-7") Annotation( "MGI:cwg") Annotation( "MP:0002388") "The specialized epithelial layer covering the entire Peyer's patch, including both the follicular and interfollicular areas and forming part of the gut-associated lymphoid tissue.") AnnotationAssertion( "EMAPA:36506") AnnotationAssertion( "MA:0000731") -AnnotationAssertion(Annotation( "MA:0000731") "Peyer's patch epithelium") +AnnotationAssertion(Annotation( "MA:0000731") Annotation( "PMID:31813624") "Peyer's patch epithelium") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0004693") AnnotationAssertion( ) @@ -185997,24 +186104,21 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (vasa recta) -AnnotationAssertion(Annotation( "Wikipedia:Vasa_recta") "In the blood supply of the kidney, the vasa recta renis (or straight arteries of kidney, or straight arterioles of kidney) form a series of straight capillaries in the medulla. They lie parallel to the loop of Henle. These vessels branch off the efferent arterioles of juxtamedullary nephrons (those nephrons closest to the medulla), enter the medulla, and surround the loop of Henle.") -AnnotationAssertion( "TODO - is this a vein or set of veins? in MA it is a venous blood vessel") +AnnotationAssertion(Annotation( "PMID:23126245") Annotation( "Wikipedia:Vasa_recta") "A group of microvessels that are part of the kidney. A vasa recta has a hairpin-like shape, entering the renal medulla as the straight arterioles and surrounds the loop of Henle, forming a capillary network. Finally it leaves the renal medulla to ascend to the cortex as the straight venules. The primary function of the vasa recta is to facilitate countercurrent exchange, which is essential for the kidney's ability to concentrate urine") AnnotationAssertion( ) AnnotationAssertion( "EMAPA:30043") AnnotationAssertion( "FMA:72006") AnnotationAssertion( "MA:0002595") AnnotationAssertion( "Wikipedia:Vasa_recta") AnnotationAssertion( "galen:ArteriaeRectae") -AnnotationAssertion(Annotation( "FMA:72006") Annotation( "FMA:TA") Annotation( ) "arteriolae rectae renis") AnnotationAssertion(Annotation( "MP:0011324") "kidney vasa recta") -AnnotationAssertion(Annotation( "EMAPA:30043") "renal medullary capillary") -AnnotationAssertion(Annotation( "FMA:72006") "set of straight arterioles of kidney") -AnnotationAssertion(Annotation( "FMA:72006") "straight arterioles of kidney") AnnotationAssertion(Annotation( "FMA:72006") "vasa recta of kidney") AnnotationAssertion(Annotation( "FMA:72006") Annotation( "FMA:TA") Annotation( ) "vasa recta renis") +AnnotationAssertion(Annotation( "FMA:72006") Annotation( "FMA:TA") Annotation( ) "arteriolae rectae renis") +AnnotationAssertion(Annotation( "EMAPA:30043") "renal medullary capillary") +AnnotationAssertion(Annotation( "FMA:72006") "set of straight arterioles of kidney") +AnnotationAssertion(Annotation( "FMA:72006") "straight arterioles of kidney") AnnotationAssertion( "uberon") -AnnotationAssertion(Annotation( "Wikipedia:Vasa_recta") "arteria recta") -AnnotationAssertion(Annotation( "Wikipedia:Vasa_recta") "arteriae rectae") AnnotationAssertion(Annotation( "Wikipedia:Vasa_recta") Annotation( ) "arteriolae rectae renis") AnnotationAssertion(Annotation( "Wikipedia:Vasa_recta") "arteriolae recti") AnnotationAssertion(Annotation( "Wikipedia:Vasa_recta") "vasa rectae") @@ -186023,7 +186127,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "vasa recta") AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/2/21/Kidney_nephron.png"^^xsd:anyURI) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (cochlear nerve) @@ -186574,8 +186678,6 @@ AnnotationAssertion( "outer renal medulla vasa recta") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -186599,8 +186701,6 @@ AnnotationAssertion( "inner renal medulla vasa recta") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -189176,6 +189276,7 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (mucosa of ascending colon) AnnotationAssertion(Annotation( "OBOL:automatic") "A mucosa that is part of an ascending colon [Automatically generated definition].") +AnnotationAssertion( ) AnnotationAssertion( "FMA:15005") AnnotationAssertion(Annotation( "OBOL:automatic") "ascending colon mucosa") AnnotationAssertion(Annotation( "OBOL:automatic") "ascending colon mucosa of organ") @@ -189186,6 +189287,7 @@ AnnotationAssertion(Annotation( "OBOL:automatic") "organ mucosa of ascending colon") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0004990") +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "mucosa of ascending colon") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -189194,6 +189296,7 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (mucosa of transverse colon) AnnotationAssertion(Annotation( "OBOL:automatic") "A mucosa that is part of a transverse colon [Automatically generated definition].") +AnnotationAssertion( ) AnnotationAssertion( "FMA:15012") AnnotationAssertion(Annotation( "OBOL:automatic") "mucosa of organ of transverse colon") AnnotationAssertion(Annotation( "OBOL:automatic") "mucous membrane of transverse colon") @@ -189204,6 +189307,7 @@ AnnotationAssertion(Annotation( "OBOL:automatic") "transverse colon organ mucosa") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0004991") +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "mucosa of transverse colon") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -189212,6 +189316,7 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (mucosa of descending colon) AnnotationAssertion(Annotation( "OBOL:automatic") "A mucosa that is part of a descending colon [Automatically generated definition].") +AnnotationAssertion( ) AnnotationAssertion( "FMA:15019") AnnotationAssertion(Annotation( "OBOL:automatic") "descending colon mucosa") AnnotationAssertion(Annotation( "OBOL:automatic") "descending colon mucosa of organ") @@ -189222,6 +189327,7 @@ AnnotationAssertion(Annotation( "OBOL:automatic") "organ mucosa of descending colon") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0004992") +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "mucosa of descending colon") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -189230,6 +189336,7 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (mucosa of sigmoid colon) AnnotationAssertion(Annotation( "OBOL:automatic") "A mucosa that is part of a sigmoid colon [Automatically generated definition].") +AnnotationAssertion( ) AnnotationAssertion( "FMA:15026") AnnotationAssertion(Annotation( "OBOL:automatic") "mucosa of organ of sigmoid colon") AnnotationAssertion(Annotation( "OBOL:automatic") "mucous membrane of sigmoid colon") @@ -189240,6 +189347,7 @@ AnnotationAssertion(Annotation( "OBOL:automatic") "sigmoid colon organ mucosa") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0004993") +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "mucosa of sigmoid colon") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -199177,6 +199285,23 @@ AnnotationAssertion( "annulus fibrosus") SubClassOf( ) +# Class: (pallidum) + +AnnotationAssertion(Annotation( "http://www.medterms.com/script/main/art.asp?articlekey=11614") "Part of what are called the basal ganglia of the brain which consist of the globus pallidus and the ventral pallidum.") +AnnotationAssertion( "BAMS:PAL") +AnnotationAssertion( "EMAPA:32780") +AnnotationAssertion( "FMA:83684") +AnnotationAssertion( "MA:0000889") +AnnotationAssertion( "MBA:803") +AnnotationAssertion( "neuronames:2673") +AnnotationAssertion(Annotation( "FMA:83684") "neuraxis pallidum") +AnnotationAssertion(Annotation( "FMA:83684") "pallidum of neuraxis") +AnnotationAssertion( "uberon") +AnnotationAssertion( "UBERON:0006514") +AnnotationAssertion(rdfs:label "pallidum") +SubClassOf( ) +SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) + # Class: (right lung lobe) AnnotationAssertion(Annotation( "OBOL:automatic") "A lobe of lung that is part of a right lung.") @@ -199422,6 +199547,7 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "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.") AnnotationAssertion( "consider merging with lymph vasculature") +AnnotationAssertion( ) AnnotationAssertion( "AAO:0010522") AnnotationAssertion( "CALOHA:TS-2024") AnnotationAssertion( "EFO:0000870") @@ -199438,6 +199564,7 @@ AnnotationAssertion( "VHOG:0001761") "lymporeticular system") AnnotationAssertion( "UBERON:0006558") AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "lymphatic part of lymphoid system") SubClassOf( ) @@ -204152,6 +204279,7 @@ AnnotationAssertion( "SCTID:361355005") AnnotationAssertion(Annotation( "ncithesaurus:Head_and_Neck") "UMLS:C0460004") AnnotationAssertion( "WikipediaCategory:Head_and_neck") +AnnotationAssertion( "ZFA:0001114") AnnotationAssertion( "galen:HeadAndNeck") AnnotationAssertion( "uberon") AnnotationAssertion(Annotation( "https://github.com/obophenotype/uberon/issues/379") "cephalic area") @@ -206371,56 +206499,51 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (inner medulla vasa recta descending limb) +# Class: (inner medulla descending vasa recta) AnnotationAssertion( "KUPO:0001003") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0009089") -AnnotationAssertion(rdfs:label "inner medulla vasa recta descending limb") +AnnotationAssertion(rdfs:label "inner medulla descending vasa recta") SubClassOf( ) -SubClassOf( ) SubClassOf(Annotation( "KUPO") ObjectSomeValuesFrom( )) -# Class: (outer medulla vasa recta descending limb) +# Class: (outer medulla descending vasa recta) AnnotationAssertion( "KUPO:0001004") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0009090") -AnnotationAssertion(rdfs:label "outer medulla vasa recta descending limb") +AnnotationAssertion(rdfs:label "outer medulla descending vasa recta") SubClassOf( ) -SubClassOf( ) SubClassOf(Annotation( "KUPO") ObjectSomeValuesFrom( )) -# Class: (vasa recta ascending limb) +# Class: (ascending vasa recta) AnnotationAssertion( ) AnnotationAssertion( "KUPO:0001005") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0009091") AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "vasa recta ascending limb") +AnnotationAssertion(rdfs:label "ascending vasa recta") SubClassOf( ) -SubClassOf( ) SubClassOf(Annotation( "KUPO") ObjectSomeValuesFrom( )) -# Class: (inner medulla vasa recta ascending limb) +# Class: (inner medulla ascending vasa recta) AnnotationAssertion( "KUPO:0001006") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0009092") -AnnotationAssertion(rdfs:label "inner medulla vasa recta ascending limb") +AnnotationAssertion(rdfs:label "inner medulla ascending vasa recta") SubClassOf( ) -SubClassOf( ) SubClassOf(Annotation( "KUPO") ObjectSomeValuesFrom( )) -# Class: (outer medulla vasa recta ascending limb) +# Class: (outer medulla ascending vasa recta) AnnotationAssertion( "KUPO:0001007") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0009093") -AnnotationAssertion(rdfs:label "outer medulla vasa recta ascending limb") +AnnotationAssertion(rdfs:label "outer medulla ascending vasa recta") SubClassOf( ) -SubClassOf( ) SubClassOf(Annotation( "KUPO") ObjectSomeValuesFrom( )) # Class: (tip of renal papilla) @@ -206775,16 +206898,15 @@ SubClassOf( ) SubClassOf( ) -# Class: (vasa recta descending limb) +# Class: (descending vasa recta) AnnotationAssertion( ) AnnotationAssertion( "KUPO:0001002") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0009202") AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "vasa recta descending limb") +AnnotationAssertion(rdfs:label "descending vasa recta") SubClassOf( ) -SubClassOf( ) SubClassOf(Annotation( "KUPO") ObjectSomeValuesFrom( )) # Class: (medial nasal process mesenchyme) @@ -207028,7 +207150,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "pharyngeal arch mesenchymal region") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -211167,7 +211289,6 @@ AnnotationAssertion( "UBERON:0010341") AnnotationAssertion(rdfs:label "1st arch mesenchyme from head mesenchyme") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf(Annotation( "EMAPA") ObjectSomeValuesFrom( )) @@ -211186,7 +211307,6 @@ AnnotationAssertion( "2nd arch mesenchyme from head mesenchyme") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) @@ -211204,7 +211324,6 @@ AnnotationAssertion( "3rd arch mesenchyme from head mesenchyme") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) @@ -211222,7 +211341,6 @@ AnnotationAssertion( "4th arch mesenchyme from head mesenchyme") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) @@ -211237,7 +211355,6 @@ AnnotationAssertion( "UBERON:0010347") AnnotationAssertion(rdfs:label "6th arch mesenchyme from head mesenchyme") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) @@ -215681,6 +215798,7 @@ AnnotationAssertion( "Wikipedia:Acoelomorpha") ) AnnotationAssertion( "EHDAA2:0004731") AnnotationAssertion( "Wikipedia:Coelom") +AnnotationAssertion( "ZFA:0001438") AnnotationAssertion(Annotation( "NCBITaxon:33511") "enterocoelom") AnnotationAssertion( "haemocoelom") AnnotationAssertion( "schizocoelom") @@ -228758,6 +228876,18 @@ EquivalentClasses( ObjectIntersec SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (embryonic craniocervical region) + +AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6095-8718") "A craniocervical region that is part of an embryo.") +AnnotationAssertion( ) +AnnotationAssertion( "2024-09-12T14:40:00Z"^^xsd:dateTime) +AnnotationAssertion( "uberon") +AnnotationAssertion( "UBERON:8450003") +AnnotationAssertion(rdfs:label "embryonic craniocervical region") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (placental blood) AnnotationAssertion(Annotation( "http://orcid.org/0000-0001-6595-0902") Annotation( "https://www.ncbi.nlm.nih.gov/books/NBK53254/") "Blood located in the placenta.") @@ -229506,6 +229636,7 @@ SubClassOf(ObjectIntersectionOf( SubClassOf(Annotation( "FMA") ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) SubClassOf(ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) +SubClassOf(ObjectIntersectionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) SubClassOf(ObjectSomeValuesFrom( ) ) SubClassOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) SubClassOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) diff --git a/src/ontology/imports/uberon_terms.txt b/src/ontology/imports/uberon_terms.txt index ac467ed38..314db955c 100644 --- a/src/ontology/imports/uberon_terms.txt +++ b/src/ontology/imports/uberon_terms.txt @@ -59,4 +59,5 @@ UBERON:0013740 UBERON:0012186 UBERON:0000156 UBERON:0000157 -UBERON:0003884 \ No newline at end of file +UBERON:0003884 +UBERON:0001875 \ No newline at end of file diff --git a/src/patterns/definitions.owl b/src/patterns/definitions.owl index a1ab1c29f..8453abae1 100644 --- a/src/patterns/definitions.owl +++ b/src/patterns/definitions.owl @@ -7,8 +7,8 @@ Prefix(rdfs:=) Ontology( - -Annotation(owl:versionInfo "2024-11-21") + +Annotation(owl:versionInfo "2024-12-04") Declaration(Class()) Declaration(Class()) diff --git a/src/templates/cellxgene_subset.tsv b/src/templates/cellxgene_subset.tsv index 0cf80642c..05eb7ab12 100644 --- a/src/templates/cellxgene_subset.tsv +++ b/src/templates/cellxgene_subset.tsv @@ -1,688 +1,806 @@ ID subset ID AI oboInOwl:inSubset -CL:4023015 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:0002322 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:0002324 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:0008001 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0002362 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:1000768 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:1001567 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0000451 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:4033036 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0005022 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0000030 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0000815 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0000790 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0019028 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0000135 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0000317 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0000453 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0002632 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:4033034 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0000813 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:4030026 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0000667 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:2000055 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:1000326 http://purl.obolibrary.org/obo/cl#cellxgene_subset CL:4023181 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:0008036 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:0000878 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:0005026 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:0013000 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:0000897 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:0002092 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0002355 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0000905 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0002063 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0002275 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0002046 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:1001568 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:4033033 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0002207 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0011012 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0000449 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