From 3f79c0d93f4db07a165e790eaa3a07fd8d7a9453 Mon Sep 17 00:00:00 2001 From: Caroline Eastwood Date: Wed, 12 Feb 2025 12:12:02 +0000 Subject: [PATCH] Fixes #2957 NTR-tuft cell of auditory tube Fixes #2957 NTR-tuft cell of auditory tube --- src/ontology/cl-edit.owl | 21 +- src/ontology/components/cellxgene_subset.owl | 4 +- src/ontology/imports/merged_import.owl | 238 ++- src/ontology/imports/uberon_terms.txt | 3 +- src/patterns/definitions.owl | 4 +- src/templates/cellxgene_subset.tsv | 1502 +++++++++--------- 6 files changed, 1003 insertions(+), 769 deletions(-) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index cc15a429c..1da87b375 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -3158,6 +3158,7 @@ Declaration(Class(obo:CL_4052035)) Declaration(Class(obo:CL_4052036)) Declaration(Class(obo:CL_4052037)) Declaration(Class(obo:CL_4052038)) +Declaration(Class(obo:CL_4052041)) Declaration(Class(obo:CL_4052048)) Declaration(Class(obo:CL_4052049)) Declaration(Class(obo:CP_0000000)) @@ -3297,6 +3298,7 @@ Declaration(Class(obo:UBERON_0009739)) Declaration(Class(obo:UBERON_0009841)) Declaration(Class(obo:UBERON_0009851)) Declaration(Class(obo:UBERON_0009852)) +Declaration(Class(obo:UBERON_0010062)) Declaration(Class(obo:UBERON_0010397)) Declaration(Class(obo:UBERON_0011184)) Declaration(Class(obo:UBERON_0011949)) @@ -3405,7 +3407,7 @@ AnnotationAssertion(rdfs:label obo:IAO_0000115 "definition") AnnotationAssertion(rdfs:label obo:IAO_0000424 "expand expression to") -# Annotation Property: obo:IAO_0000700 (has ontology root term) +# Annotation Property: obo:IAO_0000700 (preferred_root) AnnotationAssertion(rdfs:label obo:IAO_0000700 "preferred_root") @@ -3495,11 +3497,11 @@ AnnotationAssertion(rdfs:label oboInOwl:hasBroadSynonym "has_broad_synonym") AnnotationAssertion(rdfs:label oboInOwl:hasDbXref "database_cross_reference") -# Annotation Property: oboInOwl:hasExactSynonym (has exact synonym) +# Annotation Property: oboInOwl:hasExactSynonym (has_exact_synonym) AnnotationAssertion(rdfs:label oboInOwl:hasExactSynonym "has_exact_synonym") -# Annotation Property: oboInOwl:hasNarrowSynonym (has narrow synonym) +# Annotation Property: oboInOwl:hasNarrowSynonym (has_narrow_synonym) AnnotationAssertion(rdfs:label oboInOwl:hasNarrowSynonym "has_narrow_synonym") @@ -33626,10 +33628,10 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:38306414") Annotation(ob AnnotationAssertion(terms:contributor obo:CL_4052037 ) AnnotationAssertion(terms:date obo:CL_4052037 "2025-02-06T15:03:53Z"^^xsd:dateTime) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:38306414") oboInOwl:hasExactSynonym obo:CL_4052037 "olfactory tuft cell") -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:38306414") oboInOwl:hasRelatedSynonym obo:CL_4052037 "TRPM5+ microvillous cell") -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:38306414") oboInOwl:hasRelatedSynonym obo:CL_4052037 "tuft-microvillous cell") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:38306414") oboInOwl:hasRelatedSynonym obo:CL_4052037 "TPRM5+ tuft-MVC") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:38306414") oboInOwl:hasRelatedSynonym obo:CL_4052037 "TRPM5+ microvillous cell") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "doi:/10.1101/2022.09.26.509561") oboInOwl:hasRelatedSynonym obo:CL_4052037 "TRPM5+ microvillous tuft cell") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:38306414") oboInOwl:hasRelatedSynonym obo:CL_4052037 "tuft-microvillous cell") AnnotationAssertion(rdfs:label obo:CL_4052037 "tuft cell of olfactory epithelium") EquivalentClasses(obo:CL_4052037 ObjectIntersectionOf(obo:CL_0002204 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0001997))) SubClassOf(obo:CL_4052037 ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0072091)) @@ -33645,6 +33647,15 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:38306414") oboInOwl:hasR AnnotationAssertion(rdfs:label obo:CL_4052038 "tuft cell of nasal cavity respiratory epithelium") EquivalentClasses(obo:CL_4052038 ObjectIntersectionOf(obo:CL_0002204 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0005385))) +# Class: obo:CL_4052041 (tuft cell of auditory tube) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:30379593") Annotation(oboInOwl:hasDbXref "PMID:32733896") obo:IAO_0000115 obo:CL_4052041 "A tuft cell that is part of the epithelium of the pharyngotympanic (auditory) tube. This chemosensory cell is often positioned near cholinoreceptive sensory nerve fibers, suggesting a role in neuroimmune communication. It detects chemical signals and releases neuropeptides, such as acetylcholine (ACh) and CGRP, which contribute to inflammatory responses that help protect deeper tissues from harmful substances.") +AnnotationAssertion(terms:contributor obo:CL_4052041 ) +AnnotationAssertion(terms:date obo:CL_4052041 "2025-02-12T12:00:10Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label obo:CL_4052041 "tuft cell of auditory tube") +EquivalentClasses(obo:CL_4052041 ObjectIntersectionOf(obo:CL_0002204 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0010062))) +SubClassOf(obo:CL_4052041 obo:CL_0002491) + # Class: obo:CL_4052048 (intercalated cell of salivary gland) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:30855909") Annotation(oboInOwl:hasDbXref "PMID:35799078") Annotation(oboInOwl:hasDbXref "PMID:36726292") Annotation(oboInOwl:hasDbXref "PMID:37724716") obo:IAO_0000115 obo:CL_4052048 "A cuboidal epithelial cell that is part of the intercalated duct of salivary gland. This cell expresses proteins commonly associated with acinar cells and displays calcium signaling characteristics similar to secretory cells, indicating an active role in the secretory process rather than ion reabsorption.") diff --git a/src/ontology/components/cellxgene_subset.owl b/src/ontology/components/cellxgene_subset.owl index 6fb64ebc6..dfc3652b8 100644 --- a/src/ontology/components/cellxgene_subset.owl +++ b/src/ontology/components/cellxgene_subset.owl @@ -7,8 +7,8 @@ Prefix(rdfs:=) Ontology( - -Annotation(owl:versionInfo "2025-01-17") + +Annotation(owl:versionInfo "2025-02-12") Declaration(Class()) Declaration(Class()) diff --git a/src/ontology/imports/merged_import.owl b/src/ontology/imports/merged_import.owl index e4a5db361..3c6720c79 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 "2025-01-17") + +Annotation(owl:versionInfo "2025-02-12") Declaration(Class()) Declaration(Class()) @@ -3869,6 +3869,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -10285,6 +10286,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -11448,6 +11450,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -12161,6 +12164,8 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -12471,6 +12476,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -12570,6 +12576,9 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -13723,6 +13732,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -17116,12 +17126,6 @@ DisjointClasses( ) DisjointClasses( ) -# Class: (obsolete neuronal brush cell) - -AnnotationAssertion( ) -AnnotationAssertion(rdfs:comment "https://github.com/obophenotype/cell-ontology/issues/2634") -AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) - # Class: (vacuole inheritance) AnnotationAssertion(Annotation( "GOC:mcc") Annotation( "PMID:10873824") Annotation( "PMID:14616069") "The distribution of vacuoles into daughter cells after mitosis or meiosis, mediated by interactions between vacuoles and the cytoskeleton.") @@ -56209,6 +56213,19 @@ AnnotationAssertion(rdfs:label "tran SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (obsolete cellular metabolic process) + +AnnotationAssertion(Annotation( "GOC:go_curators") "OBSOLETE. The chemical reactions and pathways by which individual cells transform chemical substances.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/29021"^^xsd:anyURI) +AnnotationAssertion( "GO:0008152") +AnnotationAssertion( "cellular metabolism") +AnnotationAssertion( "biological_process") +AnnotationAssertion(Annotation( "GOC:mah") "intermediary metabolism") +AnnotationAssertion( "GO:0044237") +AnnotationAssertion(rdfs:comment "The reason for obsoletion is that this term is now redundant with GO:0008152, metabolic process") +AnnotationAssertion(rdfs:label "obsolete cellular metabolic process") +AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) + # Class: (primary metabolic process) AnnotationAssertion(Annotation( "GOC:go_curators") "The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism.") @@ -162150,6 +162167,42 @@ SubClassOf( ObjectSomeValuesFrom( SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (pharyngotympanic tube) + +AnnotationAssertion(Annotation( "FMA:FMA") Annotation( "Wikipedia:Eustachian_tube") "Organ with organ cavity which connects the cavity of the middle ear to the cavity of the pharynx. Examples: There are only two pharyngotympanic tubes, the right and the left pharyngotympanic tubes.[FMA].") +AnnotationAssertion( "AAO:0000146") +AnnotationAssertion( "AAO:0011016") +AnnotationAssertion( "EMAPA:17601") +AnnotationAssertion( "EV:0100359") +AnnotationAssertion( "FMA:9705") +AnnotationAssertion( "GAID:869") +AnnotationAssertion( "MA:0000255") +AnnotationAssertion( "NCIT:C12500") +AnnotationAssertion(Annotation( "ncithesaurus:Eustachian_Tube") "UMLS:C0015183") +AnnotationAssertion( "VHOG:0001145") +AnnotationAssertion( "Wikipedia:Eustachian_tube") +AnnotationAssertion( "XAO:0000213") +AnnotationAssertion(Annotation( "MA:0000255") "auditory tube") +AnnotationAssertion( "internal auditory tube") +AnnotationAssertion(Annotation( "MA:0000255") "pharyngo-tympanic tube") +AnnotationAssertion(Annotation( "FMA:9705") Annotation( "FMA:TA") Annotation( ) "tuba auditiva") +AnnotationAssertion(Annotation( "FMA:9705") Annotation( "FMA:TA") Annotation( ) "tuba auditoria") +AnnotationAssertion( "uberon") +AnnotationAssertion( "eustachian tube") +AnnotationAssertion(Annotation( "Wikipedia:Eustachian_tube") Annotation( ) "tuba auditiva; tuba auditoria; tuba auditivea") +AnnotationAssertion(Annotation( ) "tuba pharyngotympanica") +AnnotationAssertion( "UBERON:0002393") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "EDITOR_NOTE we follow FMA in making this an organ, but include a separate class for the part that is epithelium, which is equivalent to the EHDAA2 structure. From this we infer the developmental relationship") +AnnotationAssertion(rdfs:label "pharyngotympanic tube") +AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/4/40/Ear-anatomy-text-small-en.svg"^^xsd:anyURI) +SubClassOf(Annotation( "FMA") ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf(Annotation( "UBERON:0010062") ObjectSomeValuesFrom( )) + # Class: (bile duct) AnnotationAssertion(Annotation( "Wikipedia:Bile_duct") Annotation( "http://orcid.org/0000-0002-6601-2165") "Any of the ducts that form the biliary tree, carrying bile from the liver to the small intestine.") @@ -187714,6 +187767,44 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (mucosa of pharyngotympanic tube) + +AnnotationAssertion(Annotation( "OBOL:automatic") "A mucosa that is part of a pharyngotympanic tube [Automatically generated definition].") +AnnotationAssertion( "FMA:60109") +AnnotationAssertion(Annotation( "OBOL:automatic") "auditory tube mucosa") +AnnotationAssertion(Annotation( "OBOL:automatic") "auditory tube mucosa of organ") +AnnotationAssertion(Annotation( "OBOL:automatic") "auditory tube mucous membrane") +AnnotationAssertion(Annotation( "OBOL:automatic") "auditory tube organ mucosa") +AnnotationAssertion(Annotation( "OBOL:automatic") "internal auditory tube mucosa") +AnnotationAssertion(Annotation( "OBOL:automatic") "internal auditory tube mucosa of organ") +AnnotationAssertion(Annotation( "OBOL:automatic") "internal auditory tube mucous membrane") +AnnotationAssertion(Annotation( "OBOL:automatic") "internal auditory tube organ mucosa") +AnnotationAssertion(Annotation( "OBOL:automatic") "mucosa of auditory tube") +AnnotationAssertion(Annotation( "OBOL:automatic") "mucosa of internal auditory tube") +AnnotationAssertion(Annotation( "OBOL:automatic") "mucosa of organ of auditory tube") +AnnotationAssertion(Annotation( "OBOL:automatic") "mucosa of organ of internal auditory tube") +AnnotationAssertion(Annotation( "OBOL:automatic") "mucosa of organ of pharyngotympanic tube") +AnnotationAssertion(Annotation( "OBOL:automatic") "mucous membrane of auditory tube") +AnnotationAssertion(Annotation( "OBOL:automatic") "mucous membrane of internal auditory tube") +AnnotationAssertion(Annotation( "OBOL:automatic") "mucous membrane of pharyngotympanic tube") +AnnotationAssertion(Annotation( "FMA:60109") "mucuous membrane of eustachian tube") +AnnotationAssertion(Annotation( "FMA:60109") "mucuous membrane of pharyngotympanic tube") +AnnotationAssertion(Annotation( "OBOL:automatic") "organ mucosa of auditory tube") +AnnotationAssertion(Annotation( "OBOL:automatic") "organ mucosa of internal auditory tube") +AnnotationAssertion(Annotation( "OBOL:automatic") "organ mucosa of pharyngotympanic tube") +AnnotationAssertion(Annotation( "OBOL:automatic") "pharyngotympanic tube mucosa") +AnnotationAssertion(Annotation( "OBOL:automatic") "pharyngotympanic tube mucosa of organ") +AnnotationAssertion(Annotation( "OBOL:automatic") "pharyngotympanic tube mucous membrane") +AnnotationAssertion(Annotation( "OBOL:automatic") "pharyngotympanic tube organ mucosa") +AnnotationAssertion(Annotation( "FMA:60109") "tunica mucosa (tuba auditiva)") +AnnotationAssertion(Annotation( "FMA:60109") "tunica mucosa (tuba auditoria)") +AnnotationAssertion( "uberon") +AnnotationAssertion( "UBERON:0005044") +AnnotationAssertion(rdfs:label "mucosa of pharyngotympanic tube") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (mucosa of fallopian tube) AnnotationAssertion(Annotation( "OBOL:automatic") "A mucosa that is part of a fallopian tube [Automatically generated definition].") @@ -200553,6 +200644,48 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (cartilage of pharyngotympanic tube) + +AnnotationAssertion(Annotation( "Wikipedia:Cartilage_of_pharyngotympanic_tube") Annotation( "http://orcid.org/0000-0002-6601-2165") "A triangular plate of elastic fibrocartilage that forms the cartilage component of the pharyngotympanic tube.") +AnnotationAssertion( "FMA:60096") +AnnotationAssertion( "SCTID:362565000") +AnnotationAssertion( "Wikipedia:Cartilage_of_pharyngotympanic_tube") +AnnotationAssertion(Annotation( "FMA:60096") "cartilage of auditory tube") +AnnotationAssertion(Annotation( "FMA:60096") "cartilage of eustachian tube") +AnnotationAssertion(Annotation( "FMA:60096") Annotation( "FMA:TA") Annotation( ) "cartilago tubae auditivae") +AnnotationAssertion(Annotation( "FMA:60096") Annotation( "FMA:TA") Annotation( ) "cartilago tubae auditoriae") +AnnotationAssertion(Annotation( "FMA:60096") "pharyngotympanic tube cartilage") +AnnotationAssertion( "uberon") +AnnotationAssertion(Annotation( "Wikipedia:Cartilage_of_pharyngotympanic_tube") Annotation( ) "cartilago tubae auditivae; cartilago tubae auditoriae") +AnnotationAssertion( "UBERON:0007354") +AnnotationAssertion(rdfs:label "cartilage of pharyngotympanic tube") +AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/b/b9/Gray915.png"^^xsd:anyURI) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (bony part of pharyngotympanic tube) + +AnnotationAssertion(Annotation( "Wikipedia:Bony_part_of_pharyngotympanic_tube") "The bony part of pharyngotympanic tube is about 12 mm. in length. It begins in the carotid wall of the tympanic cavity, below the septum canalis musculotubarii, and, gradually narrowing, ends at the angle of junction of the squama and the petrous portion of the temporal bone, its extremity presenting a jagged margin which serves for the attachment of the cartilaginous portion.") +AnnotationAssertion( "FMA:60057") +AnnotationAssertion( "SCTID:362563007") +AnnotationAssertion( "Wikipedia:Bony_part_of_pharyngotympanic_tube") +AnnotationAssertion(Annotation( "FMA:60057") "bony part of auditory tube") +AnnotationAssertion(Annotation( "FMA:60057") "bony part of eustachian tube") +AnnotationAssertion(Annotation( "FMA:60057") "osseous portion of eustachian tube") +AnnotationAssertion(Annotation( "FMA:60057") "pars ossea (tuba auditiva)") +AnnotationAssertion(Annotation( "FMA:60057") "pars ossea (tuba auditoria)") +AnnotationAssertion( "uberon") +AnnotationAssertion(Annotation( "Wikipedia:Bony_part_of_pharyngotympanic_tube") "osseous portion") +AnnotationAssertion(Annotation( "Wikipedia:Bony_part_of_pharyngotympanic_tube") Annotation( ) "pars ossea tubae auditivae") +AnnotationAssertion( "UBERON:0007355") +AnnotationAssertion(rdfs:label "bony part of pharyngotympanic tube") +AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/9/9d/Gray911.png"^^xsd:anyURI) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (surface of tongue) AnnotationAssertion(Annotation( "OBOL:automatic") "An anatomical surface that is part of a tongue.") @@ -205648,6 +205781,27 @@ EquivalentClasses( ObjectIntersec SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (lumen of pharyngotympanic tube) + +AnnotationAssertion(Annotation( "OBOL:automatic") "An organ cavity that is part of a pharyngotympanic tube.") +AnnotationAssertion( "Check relationships for conformance with AAO and XAO") +AnnotationAssertion( "EHDAA2:0004118") +AnnotationAssertion( "FMA:60079") +AnnotationAssertion(Annotation( "EHDAA2:0004118") "auditory tube lumen") +AnnotationAssertion(Annotation( "FMA:60079") "lumen of auditory tube") +AnnotationAssertion(Annotation( "FMA:60079") "lumen of eustachian tube") +AnnotationAssertion(Annotation( "FMA:60079") "pharyngotympanic tube lumen") +AnnotationAssertion( "uberon") +AnnotationAssertion( "UBERON:0009692") +AnnotationAssertion(rdfs:label "lumen of pharyngotympanic tube") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf(Annotation( "EHDAA2") ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf(Annotation( "cjm") ObjectSomeValuesFrom( )) +SubClassOf(Annotation( "EHDAA2/Kardong") ObjectSomeValuesFrom( )) + # Class: (epithelium of appendix) AnnotationAssertion(Annotation( "OBOL:automatic") "An epithelium that is part of a vermiform appendix.") @@ -207298,6 +207452,63 @@ AnnotationAssertion(rdfs:label " SubClassOf(Annotation( "EHDAA2") ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) +# Class: (pharyngeal opening of pharyngotympanic tube) + +AnnotationAssertion(Annotation( "Wikipedia:Pharyngeal_opening_of_auditory_tube") "On the lateral wall of the nasal part of the pharynx is the pharyngeal opening of auditory tube (pharyngeal ostium), somewhat triangular in shape, and bounded behind by a firm prominence, the torus or cushion, caused by the medial end of the cartilage of the tube which elevates the mucous membrane.") +AnnotationAssertion( "FMA:54979") +AnnotationAssertion( "SCTID:368945008") +AnnotationAssertion( "Wikipedia:Pharyngeal_opening_of_auditory_tube") +AnnotationAssertion(Annotation( "FMA:TA") Annotation( ) "ostium pharyngeum tubae auditivae") +AnnotationAssertion(Annotation( "FMA:TA") Annotation( ) "ostium pharyngeum tubae auditoriae") +AnnotationAssertion(Annotation( "FMA:54979") "pharyngeal opening of auditory tube") +AnnotationAssertion(Annotation( "FMA:54979") "pharyngeal opening of eustachian tube") +AnnotationAssertion(Annotation( "FMA:54979") "pharyngeal orifice of auditory tube") +AnnotationAssertion(Annotation( "FMA:54979") "pharyngeal orifice of eustachian tube") +AnnotationAssertion(Annotation( "FMA:54979") "pharyngeal orifice of pharyngotympanic tube") +AnnotationAssertion(Annotation( "FMA:54979") "pharyngeal ostium of auditory tube") +AnnotationAssertion(Annotation( "FMA:54979") "pharyngeal ostium of eustachian tube") +AnnotationAssertion(Annotation( "FMA:54979") "pharyngeal ostium of pharyngotympanic tube") +AnnotationAssertion(Annotation( "FMA:54979") "pharyngeal tubal ostium") +AnnotationAssertion( "uberon") +AnnotationAssertion(Annotation( "Wikipedia:Pharyngeal_opening_of_auditory_tube") Annotation( ) "ostium pharyngeum tubae auditivae") +AnnotationAssertion(Annotation( "Wikipedia:Pharyngeal_opening_of_auditory_tube") "pharyngeal ostium") +AnnotationAssertion( "UBERON:0010060") +AnnotationAssertion(rdfs:label "pharyngeal opening of pharyngotympanic tube") +AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/1/1b/Gray1029.png"^^xsd:anyURI) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (lumen of nasopharynx) + +AnnotationAssertion( "FMA:55094") +AnnotationAssertion( "nasopharyngeal luman") +AnnotationAssertion( "nasopharynx cavity") +AnnotationAssertion(Annotation( "FMA:55094") "nasopharynx lumen") +AnnotationAssertion( "uberon") +AnnotationAssertion( "UBERON:0010061") +AnnotationAssertion(rdfs:label "lumen of nasopharynx") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (pharyngotympanic tube epithelium) + +AnnotationAssertion( "EHDAA2:0004117") +AnnotationAssertion( "EMAPA:32801") +AnnotationAssertion( "FMA:285217") +AnnotationAssertion( "MA:0003142") +AnnotationAssertion(Annotation( "EHDAA2:0004117") "auditory tube epithelium") +AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "eustachian tube epithelium") +AnnotationAssertion( "uberon") +AnnotationAssertion( "UBERON:0010062") +AnnotationAssertion(rdfs:label "pharyngotympanic tube epithelium") +SubClassOf(Annotation( "EHDAA2") ) +SubClassOf( ) +SubClassOf( ) +SubClassOf(Annotation( "cjm") ObjectSomeValuesFrom( )) +SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) + # Class: (tympanic cavity epithelium) AnnotationAssertion( "EHDAA2:0004116") @@ -224155,6 +224366,17 @@ SubClassOf(Annotation( "FMA SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) +# Class: (wall of pharyngotympanic tube) + +AnnotationAssertion( "FMA:60069") +AnnotationAssertion(Annotation( "FMA:60069") "pharyngotympanic tube wall") +AnnotationAssertion( "uberon") +AnnotationAssertion( "UBERON:0036990") +AnnotationAssertion(rdfs:label "wall of pharyngotympanic tube") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf(Annotation( "FMA") ) +SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) + # Class: (wall of orbit) AnnotationAssertion( "FMA:63144") diff --git a/src/ontology/imports/uberon_terms.txt b/src/ontology/imports/uberon_terms.txt index 985ee0a96..7a8dfebb0 100644 --- a/src/ontology/imports/uberon_terms.txt +++ b/src/ontology/imports/uberon_terms.txt @@ -60,4 +60,5 @@ UBERON:0012186 UBERON:0000156 UBERON:0000157 UBERON:0003884 -UBERON:0000482 \ No newline at end of file +UBERON:0000482 +UBERON:0010062 \ No newline at end of file diff --git a/src/patterns/definitions.owl b/src/patterns/definitions.owl index cd785fde4..ece291b0a 100644 --- a/src/patterns/definitions.owl +++ b/src/patterns/definitions.owl @@ -7,8 +7,8 @@ Prefix(rdfs:=) Ontology( - -Annotation(owl:versionInfo "2025-02-10") + +Annotation(owl:versionInfo "2025-02-12") Declaration(Class()) Declaration(Class()) diff --git a/src/templates/cellxgene_subset.tsv b/src/templates/cellxgene_subset.tsv index b1fd696f2..6a97018fb 100644 --- a/src/templates/cellxgene_subset.tsv +++ b/src/templates/cellxgene_subset.tsv @@ -1,806 +1,806 @@ ID subset ID AI oboInOwl:inSubset -CL:0000800 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:0002259 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:1000414 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:0008015 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:0009022 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:0011010 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:0002605 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:0000823 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:0002131 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:0001064 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:0000921 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:0000765 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:0002396 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:1000500 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