From aaaa83ddca4e8fbc0b46c07d779dceafa97278bd Mon Sep 17 00:00:00 2001 From: Aleix Puig <94959119+aleixpuigb@users.noreply.github.com> Date: Tue, 9 Jul 2024 16:05:04 +0100 Subject: [PATCH] Lung hackathon - epithelial cells (#2402) * Changes in respiratory epithelial cell Create equivalentTo in endo-epithelial cell and fix 'respiratory epithelial cell' * Partial refactor of epithelial cells * Changing lung epithelial cells to follow standard pattern 'epitihelial cell' part_of some { subclass of 'resipratory epithelium' } - Important to look for non-local effects on classification * Moved tb goblet cell to be part of membrane Moved * Fix bronchioalveolar cell part_of two different locations - Import bronchoalveolar duct junction * lung goblet cell part of some lung epithelium --------- Co-authored-by: dosumis --- src/mappings/zfa.sssom.tsv | 1 - src/ontology/cl-edit.owl | 51 ++++++++++++-------------- src/ontology/components/mappings.owl | 2 +- src/ontology/imports/merged_import.owl | 18 ++++++++- src/ontology/imports/uberon_terms.txt | 3 +- src/patterns/definitions.owl | 4 +- 6 files changed, 44 insertions(+), 35 deletions(-) diff --git a/src/mappings/zfa.sssom.tsv b/src/mappings/zfa.sssom.tsv index 6c8f79183..932d1b132 100644 --- a/src/mappings/zfa.sssom.tsv +++ b/src/mappings/zfa.sssom.tsv @@ -3,7 +3,6 @@ # ZFA: "http://purl.obolibrary.org/obo/ZFA_" #mapping_set_id: "http://purl.obolibrary.org/obo/zfa/zfa.sssom.tsv" #license: "https://creativecommons.org/licenses/by/3.0/" -#subject_source: "http://purl.obolibrary.org/obo/zfa.owl" subject_id subject_label predicate_id object_id mapping_justification mapping_cardinality ZFA:0000003 adaxial cell semapv:crossSpeciesExactMatch CL:0007016 semapv:UnspecifiedMatching 1:1 ZFA:0000084 yolk semapv:crossSpeciesExactMatch CL:0000428 semapv:UnspecifiedMatching 1:1 diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index 1d33b43d3..90dbec24e 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -3141,6 +3141,7 @@ Declaration(Class(obo:UBERON_0004024)) Declaration(Class(obo:UBERON_0004026)) Declaration(Class(obo:UBERON_0004196)) Declaration(Class(obo:UBERON_0004197)) +Declaration(Class(obo:UBERON_0004903)) Declaration(Class(obo:UBERON_0005101)) Declaration(Class(obo:UBERON_0005102)) Declaration(Class(obo:UBERON_0005378)) @@ -3257,7 +3258,7 @@ 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") @@ -3351,11 +3352,11 @@ 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") @@ -4247,8 +4248,7 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "https://orcid.org/0000-0001-5 AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000082 "BTO:0004299") AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0000082 "lung epithelial cell") AnnotationAssertion(rdfs:label obo:CL_0000082 "epithelial cell of lung") -EquivalentClasses(obo:CL_0000082 ObjectIntersectionOf(obo:CL_0000066 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0002048))) -SubClassOf(obo:CL_0000082 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0000115)) +EquivalentClasses(obo:CL_0000082 ObjectIntersectionOf(obo:CL_0000066 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0000115))) # Class: obo:CL_0000083 (epithelial cell of pancreas) @@ -14389,7 +14389,7 @@ AnnotationAssertion(terms:contributor obo:CL_0002075 ) AnnotationAssertion(oboInOwl:creation_date obo:CL_0002631 "2011-06-21T12:28:55Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label obo:CL_0002631 "epithelial cell of upper respiratory tract") -EquivalentClasses(obo:CL_0002631 ObjectIntersectionOf(obo:CL_0002368 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0001557))) -SubClassOf(Annotation(oboInOwl:is_inferred "true") obo:CL_0002631 obo:CL_0002368) +EquivalentClasses(obo:CL_0002631 ObjectIntersectionOf(obo:CL_0000066 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0004814))) # Class: obo:CL_0002632 (epithelial cell of lower respiratory tract) AnnotationAssertion(terms:contributor obo:CL_0002632 ) AnnotationAssertion(oboInOwl:creation_date obo:CL_0002632 "2011-06-21T12:29:31Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label obo:CL_0002632 "epithelial cell of lower respiratory tract") -EquivalentClasses(obo:CL_0002632 ObjectIntersectionOf(obo:CL_0002368 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0001558))) -SubClassOf(Annotation(oboInOwl:is_inferred "true") obo:CL_0002632 obo:CL_0002368) +EquivalentClasses(obo:CL_0002632 ObjectIntersectionOf(obo:CL_0000066 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0004815))) # Class: obo:CL_0002633 (respiratory basal cell) @@ -20103,8 +20099,7 @@ AnnotationAssertion(oboInOwl:creation_date obo:CL_0002633 "2011-06-21T03:11:10Z" AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0002633 "airway basal cell") AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0002633 "airway basal stem cell") AnnotationAssertion(rdfs:label obo:CL_0002633 "respiratory basal cell") -SubClassOf(obo:CL_0002633 obo:CL_0000646) -SubClassOf(obo:CL_0002633 obo:CL_0002368) +EquivalentClasses(obo:CL_0002633 ObjectIntersectionOf(obo:CL_0000646 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0004802))) # Class: obo:CL_0002634 (epithelial cell of anal column) @@ -20152,8 +20147,9 @@ AnnotationAssertion(oboInOwl:creation_date obo:CL_0002638 "2011-06-21T03:26:08Z" AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0002638 "BASC") AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0002638 "basal epithelial cell of bronchioalveolar duct junction") AnnotationAssertion(rdfs:label obo:CL_0002638 "bronchioalveolar stem cell") -EquivalentClasses(obo:CL_0002638 ObjectIntersectionOf(obo:CL_0002633 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0001955) ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0001958))) SubClassOf(Annotation(oboInOwl:is_inferred "true") obo:CL_0002638 obo:CL_0002633) +SubClassOf(obo:CL_0002638 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0002051)) +SubClassOf(obo:CL_0002638 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0004903)) # Class: obo:CL_0002639 (amniotic stem cell) @@ -24442,7 +24438,7 @@ SubClassOf(obo:CL_0015000 obo:CL_0000100) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:30069044") Annotation(oboInOwl:hasDbXref "PMID:30069046") obo:IAO_0000115 obo:CL_0017000 "An ionocyte that is part of the lung epithelium. The cells from this type are major sources of the CFTR protein in human and mice.") AnnotationAssertion(terms:contributor obo:CL_0017000 ) AnnotationAssertion(rdfs:label obo:CL_0017000 "pulmonary ionocyte") -SubClassOf(obo:CL_0017000 obo:CL_0000082) +EquivalentClasses(obo:CL_0017000 ObjectIntersectionOf(obo:CL_0005006 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0000115))) SubClassOf(obo:CL_0017000 obo:CL_0005006) # Class: obo:CL_0017001 (splanchnic mesodermal cell) @@ -24649,7 +24645,7 @@ AnnotationAssertion(terms:date obo:CL_0019003 "2020-05-07T18:14:52Z"^^xsd:dateTi AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0019003 "goblet cell of tracheobronchial tree") AnnotationAssertion(oboInOwl:inSubset obo:CL_0019003 cl:added_for_HCA) AnnotationAssertion(rdfs:label obo:CL_0019003 "tracheobronchial goblet cell"@en) -EquivalentClasses(obo:CL_0019003 ObjectIntersectionOf(obo:CL_0000160 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0007196))) +EquivalentClasses(obo:CL_0019003 ObjectIntersectionOf(obo:CL_0000160 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0008397))) # Class: obo:CL_0019015 (lung parenchyma resident eosinophil) @@ -24834,7 +24830,7 @@ EquivalentClasses(obo:CL_1000123 ObjectIntersectionOf(obo:CL_0000066 ObjectSomeV # Class: obo:CL_1000143 (lung goblet cell) AnnotationAssertion(rdfs:label obo:CL_1000143 "lung goblet cell") -EquivalentClasses(obo:CL_1000143 ObjectIntersectionOf(obo:CL_0000160 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0002048))) +EquivalentClasses(obo:CL_1000143 ObjectIntersectionOf(obo:CL_0000160 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0000115))) # Class: obo:CL_1000147 (cardiac valve cell) @@ -30795,8 +30791,7 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref ) ObjectIntersectionOf(obo:CL_0000540 ObjectSomeValuesFrom(obo:RO_0002162 obo:NCBITaxon_7742)) ObjectSomeValuesFrom(obo:RO_0002202 obo:CL_0000031)) -) +) \ No newline at end of file diff --git a/src/ontology/components/mappings.owl b/src/ontology/components/mappings.owl index cfb6e4cbc..56e87ec7d 100644 --- a/src/ontology/components/mappings.owl +++ b/src/ontology/components/mappings.owl @@ -4572,5 +4572,5 @@ - + diff --git a/src/ontology/imports/merged_import.owl b/src/ontology/imports/merged_import.owl index 0e1603c34..71931fffb 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 "2024-07-04") + +Annotation(owl:versionInfo "2024-07-09") Declaration(Class()) Declaration(Class()) @@ -11153,6 +11153,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -186158,6 +186159,19 @@ SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) +# Class: (bronchoalveolar duct junction) + +AnnotationAssertion(Annotation( "MP:0004390") "A branch point connecting the respiratory bronchioles to the alveolar ducts[MP].") +AnnotationAssertion(Annotation( "MA:th") "EMAPA:37448") +AnnotationAssertion( "uberon") +AnnotationAssertion( "UBERON:0004903") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "bronchoalveolar duct junction") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (neuron projection bundle connecting eye with brain) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "A neuron projection bundle that connects the retina or its analog in the eye with the brain. This includes the vertebrate optic nerve (not truly a nerve) as well as analogous structures such as the Bolwig nerve in Drosophila.") diff --git a/src/ontology/imports/uberon_terms.txt b/src/ontology/imports/uberon_terms.txt index 3e366d6ac..6993def5d 100644 --- a/src/ontology/imports/uberon_terms.txt +++ b/src/ontology/imports/uberon_terms.txt @@ -48,4 +48,5 @@ UBERON:0001058 UBERON:0001038 UBERON:0000371 UBERON:0008198 -UBERON:0004025 \ No newline at end of file +UBERON:0004025 +UBERON:0004903 \ No newline at end of file diff --git a/src/patterns/definitions.owl b/src/patterns/definitions.owl index d91a69371..ccbcd836b 100644 --- a/src/patterns/definitions.owl +++ b/src/patterns/definitions.owl @@ -7,8 +7,8 @@ Prefix(rdfs:=) Ontology( - -Annotation(owl:versionInfo "2024-07-04") + +Annotation(owl:versionInfo "2024-07-09")