Merge pull request #1819 from FlyBase/imaginal-disc-cells

Add terms for some cells of imaginal discs

src/ontology/fbbt-edit.obo

@@ -55448,6 +55448,7 @@ id: FBbt:00006032
 name: mesothoracic tergum primordium
 def: "Region of the dorsal mesothoracic disc that will develop into the mesothoracic tergum." [FlyBase:FBrf0027793, https://orcid.org/0000-0002-7073-9172]
 subset: cur
+synonym: "presumptive notum" EXACT []
 is_a: FBbt:00007027 ! cuboidal/columnar epithelium
 relationship: BFO:0000050 FBbt:00001778 ! part_of wing disc
 
@@ -146159,6 +146160,76 @@ intersection_of: RO:0002100 FBbt:00111082 ! has soma location adult ventral nerv
 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6095-8718
 property_value: http://purl.org/dc/terms/date "2024-04-12T15:31:58Z" xsd:dateTime
 
+[Term]
+id: FBbt:00059290 ! epithelial cell of mesothoracic tergum primordium
+synonym: "epithelial cell of presumptive notum" EXACT []
+property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6095-8718
+property_value: http://purl.org/dc/terms/date "2024-04-18T15:40:35Z" xsd:dateTime
+
+[Term]
+id: FBbt:00059291 ! epithelial cell of wing hinge primordium
+property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6095-8718
+property_value: http://purl.org/dc/terms/date "2024-04-18T15:40:41Z" xsd:dateTime
+
+[Term]
+id: FBbt:00059292 ! epithelial cell of wing pouch
+property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6095-8718
+property_value: http://purl.org/dc/terms/date "2024-04-18T15:40:47Z" xsd:dateTime
+
+[Term]
+id: FBbt:00059293 ! epithelial cell of presumptive wing margin
+property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6095-8718
+property_value: http://purl.org/dc/terms/date "2024-04-18T15:44:17Z" xsd:dateTime
+
+[Term]
+id: FBbt:00059294 ! epithelial cell of presumptive first segment of antenna
+property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6095-8718
+property_value: http://purl.org/dc/terms/date "2024-04-18T15:45:35Z" xsd:dateTime
+
+[Term]
+id: FBbt:00059295 ! epithelial cell of presumptive second segment of antenna
+property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6095-8718
+property_value: http://purl.org/dc/terms/date "2024-04-18T15:46:35Z" xsd:dateTime
+
+[Term]
+id: FBbt:00059296 ! epithelial cell of presumptive third segment of antenna
+property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6095-8718
+property_value: http://purl.org/dc/terms/date "2024-04-18T15:47:17Z" xsd:dateTime
+
+[Term]
+id: FBbt:00059297 ! epithelial cell of presumptive arista
+property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6095-8718
+property_value: http://purl.org/dc/terms/date "2024-04-18T15:48:04Z" xsd:dateTime
+
+[Term]
+id: FBbt:00059298
+name: hemocyte of wing disc
+def: "Larval sessile hemocyte that is attached to a wing disc (Floc'hlay et al., 2023)." [FlyBase:FBrf0256653]
+intersection_of: FBbt:00005496 ! larval sessile hemocyte
+intersection_of: RO:0002371 FBbt:00001778 ! attached to wing disc
+property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6095-8718
+property_value: http://purl.org/dc/terms/date "2024-04-18T16:34:45Z" xsd:dateTime
+
+[Term]
+id: FBbt:00059299
+name: glial cell of eye-antennal disc
+def: "Any glial cell that is found in an eye-antennal disc (Gonzalez-Blas et al., 2020)." [FlyBase:FBrf0245749]
+intersection_of: FBbt:00005144 ! glial cell
+intersection_of: RO:0002131 FBbt:00001766 ! overlaps eye-antennal disc
+property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6095-8718
+property_value: http://purl.org/dc/terms/date "2024-04-18T16:40:39Z" xsd:dateTime
+
+[Term]
+id: FBbt:00059300
+name: eye disc visual progenitor cell
+def: "A cell of the eye disc that is located anteriorly to the morphogenetic furrow, and that will become either a photoreceptor precursor cell or an interommatidial precursor cell after the morphogenetic wave (Gonzalez-Blas et al., 2020)." [FlyBase:FBrf0245749]
+synonym: "eye disc PRPre cell" NARROW [FlyBase:FBrf0245749]
+synonym: "eye disc PRPro cell" NARROW [FlyBase:FBrf0245749]
+is_a: FBbt:00007008 ! somatic precursor cell
+relationship: BFO:0000050 FBbt:00007142 ! part_of eye disc anterior to the morphogenetic furrow
+property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6095-8718
+property_value: http://purl.org/dc/terms/date "2024-04-18T16:43:49Z" xsd:dateTime
+
 [Term]
 id: FBbt:00067000
 name: antennal intermediate sensillum ai3

src/patterns/data/all-axioms/cellByAnatomicalEntity.tsv

@@ -0,0 +1,9 @@
+defined_class	cell_type	cell_type_label	location	location_label
+FBbt:00059290	FBbt:00000124	epithelial cell	FBbt:00006032	mesothoracic tergum primordium
+FBbt:00059291	FBbt:00000124	epithelial cell	FBbt:00006033	wing hinge primordium
+FBbt:00059292	FBbt:00000124	epithelial cell	FBbt:00006029	wing pouch
+FBbt:00059293	FBbt:00000124	epithelial cell	FBbt:00046034	presumptive wing margin
+FBbt:00059294	FBbt:00000124	epithelial cell	FBbt:00110812	presumptive first segment of the antenna
+FBbt:00059295	FBbt:00000124	epithelial cell	FBbt:00110813	presumptive second segment of the antenna
+FBbt:00059296	FBbt:00000124	epithelial cell	FBbt:00110814	presumptive third segment of the antenna
+FBbt:00059297	FBbt:00000124	epithelial cell	FBbt:00110811	presumptive arista

src/patterns/definitions.owl

@@ -7,8 +7,8 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
 
 
 Ontology(<http://purl.obolibrary.org/obo/fbbt/patterns/definitions.owl>
-<http://purl.obolibrary.org/obo/fbbt/releases/2024-04-12/patterns/definitions.owl>
-Annotation(owl:versionInfo "2024-04-12")
+<http://purl.obolibrary.org/obo/fbbt/releases/2024-04-18/patterns/definitions.owl>
+Annotation(owl:versionInfo "2024-04-18")
 
 Declaration(Class(<http://flybase.org/reports/FBgn0004652>))
 Declaration(Class(<http://purl.obolibrary.org/obo/FBbt_00000000>))
@@ -47,6 +47,7 @@ Declaration(Class(<http://purl.obolibrary.org/obo/FBbt_00000112>))
 Declaration(Class(<http://purl.obolibrary.org/obo/FBbt_00000119>))
 Declaration(Class(<http://purl.obolibrary.org/obo/FBbt_00000121>))
 Declaration(Class(<http://purl.obolibrary.org/obo/FBbt_00000122>))
+Declaration(Class(<http://purl.obolibrary.org/obo/FBbt_00000124>))
 Declaration(Class(<http://purl.obolibrary.org/obo/FBbt_00000125>))
 Declaration(Class(<http://purl.obolibrary.org/obo/FBbt_00000126>))
 Declaration(Class(<http://purl.obolibrary.org/obo/FBbt_00000127>))
@@ -5505,6 +5506,14 @@ Declaration(Class(<http://purl.obolibrary.org/obo/FBbt_00059284>))
 Declaration(Class(<http://purl.obolibrary.org/obo/FBbt_00059285>))
 Declaration(Class(<http://purl.obolibrary.org/obo/FBbt_00059286>))
 Declaration(Class(<http://purl.obolibrary.org/obo/FBbt_00059287>))
+Declaration(Class(<http://purl.obolibrary.org/obo/FBbt_00059290>))
+Declaration(Class(<http://purl.obolibrary.org/obo/FBbt_00059291>))
+Declaration(Class(<http://purl.obolibrary.org/obo/FBbt_00059292>))
+Declaration(Class(<http://purl.obolibrary.org/obo/FBbt_00059293>))
+Declaration(Class(<http://purl.obolibrary.org/obo/FBbt_00059294>))
+Declaration(Class(<http://purl.obolibrary.org/obo/FBbt_00059295>))
+Declaration(Class(<http://purl.obolibrary.org/obo/FBbt_00059296>))
+Declaration(Class(<http://purl.obolibrary.org/obo/FBbt_00059297>))
 Declaration(Class(<http://purl.obolibrary.org/obo/FBbt_00067001>))
 Declaration(Class(<http://purl.obolibrary.org/obo/FBbt_00067003>))
 Declaration(Class(<http://purl.obolibrary.org/obo/FBbt_00067005>))
@@ -31157,6 +31166,54 @@ EquivalentClasses(<http://purl.obolibrary.org/obo/FBbt_00059286> ObjectIntersect
 
 EquivalentClasses(<http://purl.obolibrary.org/obo/FBbt_00059287> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/FBbt_00007383> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0013005> <http://purl.obolibrary.org/obo/FBbt_00003957>)))
 
+# Class: <http://purl.obolibrary.org/obo/FBbt_00059290> (epithelial cell of mesothoracic tergum primordium)
+
+AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "FBC:Autogenerated") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/FBbt_00059290> "A(n) epithelial cell that is part of a(n) mesothoracic tergum primordium.")
+AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/FBbt_00059290> "epithelial cell of mesothoracic tergum primordium")
+EquivalentClasses(<http://purl.obolibrary.org/obo/FBbt_00059290> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/FBbt_00000124> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/FBbt_00006032>)))
+
+# Class: <http://purl.obolibrary.org/obo/FBbt_00059291> (epithelial cell of wing hinge primordium)
+
+AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "FBC:Autogenerated") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/FBbt_00059291> "A(n) epithelial cell that is part of a(n) wing hinge primordium.")
+AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/FBbt_00059291> "epithelial cell of wing hinge primordium")
+EquivalentClasses(<http://purl.obolibrary.org/obo/FBbt_00059291> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/FBbt_00000124> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/FBbt_00006033>)))
+
+# Class: <http://purl.obolibrary.org/obo/FBbt_00059292> (epithelial cell of wing pouch)
+
+AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "FBC:Autogenerated") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/FBbt_00059292> "A(n) epithelial cell that is part of a(n) wing pouch.")
+AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/FBbt_00059292> "epithelial cell of wing pouch")
+EquivalentClasses(<http://purl.obolibrary.org/obo/FBbt_00059292> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/FBbt_00000124> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/FBbt_00006029>)))
+
+# Class: <http://purl.obolibrary.org/obo/FBbt_00059293> (epithelial cell of presumptive wing margin)
+
+AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "FBC:Autogenerated") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/FBbt_00059293> "A(n) epithelial cell that is part of a(n) presumptive wing margin.")
+AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/FBbt_00059293> "epithelial cell of presumptive wing margin")
+EquivalentClasses(<http://purl.obolibrary.org/obo/FBbt_00059293> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/FBbt_00000124> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/FBbt_00046034>)))
+
+# Class: <http://purl.obolibrary.org/obo/FBbt_00059294> (epithelial cell of presumptive first segment of antenna)
+
+AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "FBC:Autogenerated") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/FBbt_00059294> "A(n) epithelial cell that is part of a(n) presumptive first segment of antenna.")
+AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/FBbt_00059294> "epithelial cell of presumptive first segment of antenna")
+EquivalentClasses(<http://purl.obolibrary.org/obo/FBbt_00059294> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/FBbt_00000124> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/FBbt_00110812>)))
+
+# Class: <http://purl.obolibrary.org/obo/FBbt_00059295> (epithelial cell of presumptive second segment of antenna)
+
+AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "FBC:Autogenerated") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/FBbt_00059295> "A(n) epithelial cell that is part of a(n) presumptive second segment of antenna.")
+AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/FBbt_00059295> "epithelial cell of presumptive second segment of antenna")
+EquivalentClasses(<http://purl.obolibrary.org/obo/FBbt_00059295> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/FBbt_00000124> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/FBbt_00110813>)))
+
+# Class: <http://purl.obolibrary.org/obo/FBbt_00059296> (epithelial cell of presumptive third segment of antenna)
+
+AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "FBC:Autogenerated") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/FBbt_00059296> "A(n) epithelial cell that is part of a(n) presumptive third segment of antenna.")
+AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/FBbt_00059296> "epithelial cell of presumptive third segment of antenna")
+EquivalentClasses(<http://purl.obolibrary.org/obo/FBbt_00059296> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/FBbt_00000124> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/FBbt_00110814>)))
+
+# Class: <http://purl.obolibrary.org/obo/FBbt_00059297> (epithelial cell of presumptive arista)
+
+AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "FBC:Autogenerated") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/FBbt_00059297> "A(n) epithelial cell that is part of a(n) presumptive arista.")
+AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/FBbt_00059297> "epithelial cell of presumptive arista")
+EquivalentClasses(<http://purl.obolibrary.org/obo/FBbt_00059297> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/FBbt_00000124> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/FBbt_00110811>)))
+
 # Class: <http://purl.obolibrary.org/obo/FBbt_00067014> (<http://purl.obolibrary.org/obo/FBbt_00067014>)
 
 EquivalentClasses(<http://purl.obolibrary.org/obo/FBbt_00067014> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/FBbt_00007383> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002202> <http://purl.obolibrary.org/obo/FBbt_00067346>) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0013005> <http://purl.obolibrary.org/obo/FBbt_00003961>)))

src/patterns/dosdp-patterns/cellByAnatomicalEntity.yaml

@@ -0,0 +1,42 @@
+pattern_name: cellByAnatomicalEntity
+pattern_iri: http://purl.obolibrary.org/obo/fbbt/src/patterns/dosdp-patterns/cellByAnatomicalEntity.yaml
+description: "Pattern for generating terms for cells that are part of an anatomical entity."
+
+contributors:
+  - https://orcid.org/0000-0002-6095-8718
+  - https://orcid.org/0000-0002-1373-1705
+
+classes:
+  cell: FBbt:00007002
+  anatomical_entity: FBbt:00007016
+
+relations:
+  part_of: BFO:0000050
+
+vars:
+  cell_type: cell
+  location: anatomical_entity
+
+annotationProperties:
+  database_cross_reference: oboInOwl:hasDbXref
+
+equivalentTo:
+  text: "%s that 'part_of' some %s"
+  vars:
+    - cell_type
+    - location
+
+name:
+  text: "%s of %s"
+  vars:
+     - cell_type
+     - location
+
+def:
+  text: "A(n) %s that is part of a(n) %s."
+  vars:
+     - cell_type
+     - location
+  annotations:
+     - annotationProperty: database_cross_reference
+       text: "FBC:Autogenerated"

src/patterns/pattern.owl

@@ -23,6 +23,7 @@ Declaration(Class(<http://purl.obolibrary.org/obo/FBbt_00005386>))
 Declaration(Class(<http://purl.obolibrary.org/obo/FBbt_00007002>))
 Declaration(Class(<http://purl.obolibrary.org/obo/FBbt_00007006>))
 Declaration(Class(<http://purl.obolibrary.org/obo/FBbt_00007008>))
+Declaration(Class(<http://purl.obolibrary.org/obo/FBbt_00007016>))
 Declaration(Class(<http://purl.obolibrary.org/obo/FBbt_00007316>))
 Declaration(Class(<http://purl.obolibrary.org/obo/FBbt_00007683>))
 Declaration(Class(<http://purl.obolibrary.org/obo/FBbt_00040005>))
@@ -40,6 +41,7 @@ Declaration(Class(<http://purl.obolibrary.org/obo/fbbt/src/patterns/dosdp-patter
 Declaration(Class(<http://purl.obolibrary.org/obo/fbbt/src/patterns/dosdp-patterns/ALNeuronSubClass.yaml>))
 Declaration(Class(<http://purl.obolibrary.org/obo/fbbt/src/patterns/dosdp-patterns/anatomicalEntityBySegment.yaml>))
 Declaration(Class(<http://purl.obolibrary.org/obo/fbbt/src/patterns/dosdp-patterns/anatomicalEntityBySex.yaml>))
+Declaration(Class(<http://purl.obolibrary.org/obo/fbbt/src/patterns/dosdp-patterns/cellByAnatomicalEntity.yaml>))
 Declaration(Class(<http://purl.obolibrary.org/obo/fbbt/src/patterns/dosdp-patterns/cellTypeFromNeuroblast.yaml>))
 Declaration(Class(<http://purl.obolibrary.org/obo/fbbt/src/patterns/dosdp-patterns/developingEntityWithEarlierAndLaterStructures.yaml>))
 Declaration(Class(<http://purl.obolibrary.org/obo/fbbt/src/patterns/dosdp-patterns/fbTangentialNeuronByLayerAndLineage.yaml>))
@@ -114,6 +116,13 @@ SubClassOf(<http://purl.obolibrary.org/obo/fbbt/src/patterns/dosdp-patterns/anat
 AnnotationAssertion(<http://purl.org/dc/terms/title> <http://purl.obolibrary.org/obo/fbbt/src/patterns/dosdp-patterns/anatomicalEntityBySex.yaml> "anatomicalEntityBySex"^^xsd:string)
 EquivalentClasses(<http://purl.obolibrary.org/obo/fbbt/src/patterns/dosdp-patterns/anatomicalEntityBySex.yaml> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/FBbt_10000000> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/FBbt_00000001>)))
 
+# Class: <http://purl.obolibrary.org/obo/fbbt/src/patterns/dosdp-patterns/cellByAnatomicalEntity.yaml> (cell of anatomical_entity)
+
+AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "FBC:Autogenerated"^^xsd:string) <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/fbbt/src/patterns/dosdp-patterns/cellByAnatomicalEntity.yaml> "A(n) cell that is part of a(n) anatomical_entity."^^xsd:string)
+AnnotationAssertion(<http://purl.org/dc/terms/title> <http://purl.obolibrary.org/obo/fbbt/src/patterns/dosdp-patterns/cellByAnatomicalEntity.yaml> "cellByAnatomicalEntity"^^xsd:string)
+AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/fbbt/src/patterns/dosdp-patterns/cellByAnatomicalEntity.yaml> "cell of anatomical_entity"^^xsd:string)
+EquivalentClasses(<http://purl.obolibrary.org/obo/fbbt/src/patterns/dosdp-patterns/cellByAnatomicalEntity.yaml> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/FBbt_00007002> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/FBbt_00007016>)))
+
 # Class: <http://purl.obolibrary.org/obo/fbbt/src/patterns/dosdp-patterns/cellTypeFromNeuroblast.yaml> (<http://purl.obolibrary.org/obo/fbbt/src/patterns/dosdp-patterns/cellTypeFromNeuroblast.yaml>)
 
 AnnotationAssertion(<http://purl.org/dc/terms/title> <http://purl.obolibrary.org/obo/fbbt/src/patterns/dosdp-patterns/cellTypeFromNeuroblast.yaml> "cellTypeFromNeuroblast"^^xsd:string)