Merge branch 'master' into Obsolete-neuronal-brush-cell

obophenotype · Jan 16, 2025 · ce98489 · ce98489
2 parents 710ea6b + 58677e7
commit ce98489
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Showing 56 changed files with 47,030 additions and 35,063 deletions.
diff --git a/cl-base.owl b/cl-base.owl
diff --git a/cl.obo b/cl.obo
diff --git a/docs/cl-release.md b/docs/cl-release.md
@@ -44,6 +44,7 @@ The release is done in two parts:
 1. Ensure you are on the master branch and have locally the latest changes from master (`git pull`)
 1. Ensure you have the latest ODK installed by running `docker pull obolibrary/odkfull`
 1. Navigate to the cell-ontology/src/ontology directory (`cd src/ontology`)
+1. Delete all temporary files (e.g., outdated plugins) by running `sh run.sh make clean`
 
 ### Refresh imports and components
 

diff --git a/patterns/definitions.owl b/patterns/definitions.owl
diff --git a/src/mappings/fbbt.sssom.tsv b/src/mappings/fbbt.sssom.tsv
@@ -1,17 +1,17 @@
 #curie_map:
-#  CL: "http://purl.obolibrary.org/obo/CL_"
-#  FBbt: "http://purl.obolibrary.org/obo/FBbt_"
-#  ORCID: "https://orcid.org/"
-#  obo: "http://purl.obolibrary.org/obo/"
-#mapping_set_id: "http://purl.obolibrary.org/obo/fbbt/fbbt-mappings.sssom.tsv"
-#mapping_set_description: "Mappings between the Drosophila Anatomy Ontology and foreign ontologies."
+#  CL: http://purl.obolibrary.org/obo/CL_
+#  FBbt: http://purl.obolibrary.org/obo/FBbt_
+#  ORCID: https://orcid.org/
+#  obo: http://purl.obolibrary.org/obo/
+#mapping_set_id: http://purl.obolibrary.org/obo/fbbt/fbbt-mappings.sssom.tsv
+#mapping_set_description: Mappings between the Drosophila Anatomy Ontology and foreign ontologies.
 #creator_id:
-#  - "ORCID:0000-0002-1373-1705"
-#  - "ORCID:0000-0002-6095-8718"
-#license: "https://creativecommons.org/licenses/by/4.0/"
-#subject_source: "obo:fbbt.owl"
-#object_source: "obo:cl.owl"
-#mapping_date: "2024-07-12"
+#  - ORCID:0000-0002-1373-1705
+#  - ORCID:0000-0002-6095-8718
+#license: https://creativecommons.org/licenses/by/4.0/
+#subject_source: obo:fbbt.owl
+#object_source: obo:cl.owl
+#mapping_date: 2024-07-12
 subject_id	subject_label	predicate_id	object_id	object_label	mapping_justification
 FBbt:00000092	primordial germ cell	semapv:crossSpeciesExactMatch	CL:0000301	pole cell	semapv:ManualMappingCuration
 FBbt:00000124	epithelial cell	semapv:crossSpeciesExactMatch	CL:0000066	epithelial cell	semapv:ManualMappingCuration

diff --git a/src/mappings/zfa.sssom.tsv b/src/mappings/zfa.sssom.tsv
@@ -1,10 +1,10 @@
 #curie_map:
-#  CL: "http://purl.obolibrary.org/obo/CL_"
-#  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"
-#object_source: "http://purl.obolibrary.org/obo/cl.owl"
+#  CL: http://purl.obolibrary.org/obo/CL_
+#  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
+#object_source: http://purl.obolibrary.org/obo/cl.owl
 subject_id	subject_label	predicate_id	object_id	object_label	mapping_justification
 ZFA:0000003	adaxial cell	semapv:crossSpeciesExactMatch	CL:0007016	adaxial cell	semapv:UnspecifiedMatching
 ZFA:0000084	yolk	semapv:crossSpeciesExactMatch	CL:0000428	yolk cell	semapv:UnspecifiedMatching
@@ -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
@@ -235,7 +235,6 @@ ZFA:0009187	nephrogenic mesenchyme stem cell	semapv:crossSpeciesExactMatch	CL:00
 ZFA:0009188	ligament cell	semapv:crossSpeciesExactMatch	CL:0000384	ligament cell	semapv:UnspecifiedMatching
 ZFA:0009189	tendon cell	semapv:crossSpeciesExactMatch	CL:0000388	tendon cell	semapv:UnspecifiedMatching
 ZFA:0009190	electrically responsive cell	semapv:crossSpeciesExactMatch	CL:0000393	electrically responsive cell	semapv:UnspecifiedMatching
-ZFA:0009191	CNS interneuron	semapv:crossSpeciesExactMatch	CL:0000402	CNS interneuron	semapv:UnspecifiedMatching
 ZFA:0009193	electrically signaling cell	semapv:crossSpeciesExactMatch	CL:0000404	electrically signaling cell	semapv:UnspecifiedMatching
 ZFA:0009194	CNS short range interneuron	semapv:crossSpeciesExactMatch	CL:0000406	CNS short range interneuron	semapv:UnspecifiedMatching
 ZFA:0009195	CNS long range interneuron	semapv:crossSpeciesExactMatch	CL:0000410	CNS long range interneuron	semapv:UnspecifiedMatching

diff --git a/src/ontology/Makefile b/src/ontology/Makefile
@@ -1,7 +1,7 @@
 # ----------------------------------------
 # Makefile for cl
 # Generated using ontology-development-kit
-# ODK Version: v1.5.3
+# ODK Version: v1.5.4
 # ----------------------------------------
 # IMPORTANT: DO NOT EDIT THIS FILE. To override default make goals, use cl.Makefile instead
 
@@ -10,7 +10,7 @@
 # More information: https://github.com/INCATools/ontology-development-kit/
 
 # Fingerprint of the configuration file when this Makefile was last generated
-CONFIG_HASH=                fe26dd231ab531dab5609c794de598d2a28083168916941a3276fe672cfe8be2
+CONFIG_HASH=                b8fef012ac2d7e3df8e8871cfa305bf6b9d5b6a56394a042bdf48a83d3d2e019
 
 
 # ----------------------------------------
@@ -46,7 +46,7 @@ REPORT_PROFILE_OPTS =
 OBO_FORMAT_OPTIONS =        
 SPARQL_VALIDATION_CHECKS =  equivalent-classes owldef-self-reference nolabels pmid-not-dbxref obsolete-replaced_by obsolete-alt-id orcid-contributor illegal-annotation-property label-synonym-polysemy illegal-date def-not-only-xref id-format 
 SPARQL_EXPORTS =            cl_terms cl-edges cl-synonyms cl-xrefs cl-def-xrefs 
-ODK_VERSION_MAKEFILE =      v1.5.3
+ODK_VERSION_MAKEFILE =      v1.5.4
 
 TODAY ?=                    $(shell date +%Y-%m-%d)
 OBODATE ?=                  $(shell date +'%d:%m:%Y %H:%M')
@@ -156,7 +156,7 @@ $(ROBOT_PLUGINS_DIRECTORY)/flybase.jar:
 	curl -L -o $@ https://github.com/FlyBase/flybase-robot-plugin/releases/download/flybase-robot-plugin-0.2.2/flybase.jar
 
 $(ROBOT_PLUGINS_DIRECTORY)/uberon.jar:
-	curl -L -o $@ https://github.com/gouttegd/uberon-robot-plugin/releases/download/uberon-robot-plugin-0.3.1/uberon.jar
+	curl -L -o $@ https://github.com/gouttegd/uberon-robot-plugin/releases/download/uberon-robot-plugin-0.3.3/uberon.jar
 
 
 # ----------------------------------------