Fixes #2725

clm-cl.owl component edits

.github/workflows/qc.yml

@@ -27,37 +27,7 @@ jobs:
       - uses: actions/checkout@v3
 
       - name: Run ontology QC checks
-        id: check
-        continue-on-error: true
         env:
           DEFAULT_BRANCH: master
         run: cd src/ontology && make ROBOT_ENV='ROBOT_JAVA_ARGS=-Xmx6G' test IMP=false PAT=false MIR=false
 
-      - name: Reason over taxon constraints
-        id: explaintc
-        continue-on-error: true
-        if: steps.check.outcome == 'failure'
-        run: |
-          if [ -s src/ontology/reports/taxon-constraint-check.txt ]; then
-            robot explain -i src/ontology/tmp/cl-plus-taxon-disjoints.ofn -M unsatisfiability -u all -r ELK -e taxon-unsats.md
-            echo "<details>\n<summary>This PR violates some taxon constraints. Here is what the reasoner has to say:</summary>\n" > comments.md
-            cat taxon-unsats.md >> comment.md
-            echo "</details>" >> comment.md
-            exit 1
-          fi
-
-      - name: Post explanation for taxon constraint violations
-        if: steps.explaintc.outcome == 'failure'
-        uses: NejcZdovc/comment-pr@v2
-        with:
-          github_token: ${{secrets.GITHUB_TOKEN}}
-          file: "../../comment.md"
-          identifier: "TAXON_CONSTRAINTS_REASONING"
-
-      # If the check failed, then the entire job should fail, even if we
-      # allowed it to continue so that we could post the message with
-      # the explanations.
-      - name: Fail on error
-        if: steps.check.outcome == 'failure'
-        run: exit 1
-

docs/odk-workflows/RepositoryFileStructure.md

@@ -22,6 +22,7 @@ These are the current imports in CL
 | ro | http://purl.obolibrary.org/obo/ro.owl | None |
 | pato | http://purl.obolibrary.org/obo/pato.owl | None |
 | ncbitaxon | http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.owl | None |
+| ncbitaxondisjoints | http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim-disjoint-over-in-taxon.owl | None |
 | omo | http://purl.obolibrary.org/obo/omo.owl | mirror |
 
 ## Components
@@ -42,3 +43,4 @@ These are the components in CL
 | general_cell_types_upper_slim.owl | None |
 | kidney_upper_slim.owl | None |
 | cellxgene_subset.owl | None |
+| clm-cl.owl | None |

src/ontology/Makefile

@@ -1,7 +1,7 @@
 # ----------------------------------------
 # Makefile for cl
 # Generated using ontology-development-kit
-# ODK Version: v1.5.3
+# ODK Version: v1.5.2
 # ----------------------------------------
 # 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=                54146b660b46ab72c0abd98ae67a46d194ff618c90da889ded7ed1b99fd74ae2
+CONFIG_HASH=                24177bc2f4b321bf573ab9044ad6a53705855a9bca8bf93a02bb653ac04136b5
 
 
 # ----------------------------------------
@@ -46,14 +46,14 @@ 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 
 SPARQL_EXPORTS =            cl_terms cl-edges cl-synonyms cl-xrefs cl-def-xrefs 
-ODK_VERSION_MAKEFILE =      v1.5.3
+ODK_VERSION_MAKEFILE =      v1.5.2
 
 TODAY ?=                    $(shell date +%Y-%m-%d)
 OBODATE ?=                  $(shell date +'%d:%m:%Y %H:%M')
 VERSION=                    $(TODAY)
 ANNOTATE_ONTOLOGY_VERSION = annotate -V $(ONTBASE)/releases/$(VERSION)/$@ --annotation owl:versionInfo $(VERSION)
 ANNOTATE_CONVERT_FILE =     annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) convert -f ofn --output $@.tmp.owl && mv $@.tmp.owl $@
-OTHER_SRC =                 $(PATTERNDIR)/definitions.owl $(COMPONENTSDIR)/hra_subset.owl $(COMPONENTSDIR)/mappings.owl $(COMPONENTSDIR)/blood_and_immune_upper_slim.owl $(COMPONENTSDIR)/eye_upper_slim.owl $(COMPONENTSDIR)/general_cell_types_upper_slim.owl $(COMPONENTSDIR)/kidney_upper_slim.owl $(COMPONENTSDIR)/cellxgene_subset.owl 
+OTHER_SRC =                 $(PATTERNDIR)/definitions.owl $(COMPONENTSDIR)/hra_subset.owl $(COMPONENTSDIR)/mappings.owl $(COMPONENTSDIR)/blood_and_immune_upper_slim.owl $(COMPONENTSDIR)/eye_upper_slim.owl $(COMPONENTSDIR)/general_cell_types_upper_slim.owl $(COMPONENTSDIR)/kidney_upper_slim.owl $(COMPONENTSDIR)/cellxgene_subset.owl $(COMPONENTSDIR)/clm-cl.owl 
 ONTOLOGYTERMS =             $(TMPDIR)/ontologyterms.txt
 EDIT_PREPROCESSED =         $(TMPDIR)/$(ONT)-preprocess.owl
 PATTERNDIR=                 ../patterns
@@ -510,6 +510,7 @@ $(COMPONENTSDIR)/cellxgene_subset.owl: $(TEMPLATEDIR)/cellxgene_subset.tsv
 		$(ANNOTATE_CONVERT_FILE); fi
 
 .PRECIOUS: $(COMPONENTSDIR)/cellxgene_subset.owl
+
 # ----------------------------------------
 # Mirroring upstream ontologies
 # ----------------------------------------

src/ontology/catalog-v001.xml

@@ -16,6 +16,7 @@
     <uri id="User Entered Import Resolution" name="http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Cell.owl" uri="mirror/NIF-Cell.owl"/>
     <uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/cl/patterns/definitions.owl" uri="../patterns/definitions.owl"/>
     <uri name="http://purl.obolibrary.org/obo/cl/components/hra_subset.owl" uri="components/hra_subset.owl"/>
+    <uri name="http://purl.obolibrary.org/obo/cl/components/clm-cl.owl" uri="components/clm-cl.owl"/>
     <uri name="http://purl.obolibrary.org/obo/cl/components/mappings.owl" uri="components/mappings.owl"/>
     <uri name="http://purl.obolibrary.org/obo/cl/components/blood_and_immune_upper_slim.owl" uri="components/blood_and_immune_upper_slim.owl"/>
     <uri name="http://purl.obolibrary.org/obo/cl/components/eye_upper_slim.owl" uri="components/eye_upper_slim.owl"/>

src/ontology/cl-edit.owl

@@ -31,6 +31,8 @@ Import(<http://purl.obolibrary.org/obo/cl/components/kidney_upper_slim.owl>)
 Import(<http://purl.obolibrary.org/obo/cl/components/mappings.owl>)
 Import(<http://purl.obolibrary.org/obo/cl/imports/merged_import.owl>)
 Import(<http://purl.obolibrary.org/obo/cl/patterns/definitions.owl>)
+Import(<http://purl.obolibrary.org/obo/cl/components/clm-cl.owl>)
+
 Annotation(obo:IAO_0000700 obo:CL_0000000)
 Annotation(dc:description "An ontology of cell types.")
 Annotation(dc:title "Cell Ontology")

src/ontology/cl-odk.yaml

@@ -149,4 +149,5 @@ components:
       use_template: True
       templates:
         - cellxgene_subset.tsv
+    - filename: clm-cl.owl
 

src/ontology/cl.Makefile

@@ -313,6 +313,14 @@ CELLXGENE_SUBSET_URL="https://raw.githubusercontent.com/hkir-dev/cellxgene-cell-
 $(TEMPLATEDIR)/cellxgene_subset.tsv:
 	wget $(CELLXGENE_SUBSET_URL) -O $@
 
+# CellMark reference subset
+CLM_CL_URL="https://raw.githubusercontent.com/Cellular-Semantics/CellMark/main/clm-cl.owl"
+$(TMPDIR)/clm-cl.owl:
+	wget $(CLM_CL_URL) -O $@
+
+$(COMPONENTSDIR)/clm-cl.owl: $(TMPDIR)/clm-cl.owl
+	$(ROBOT) merge -i $< annotate --ontology-iri $(ONTBASE)/$@ --output $@
+
 
 # ----------------------------------------
 # RELEASE DEPLOYMENT

src/ontology/components/clm-cl.owl

@@ -0,0 +1,14 @@
+<?xml version="1.0"?>
+<rdf:RDF 
+     xml:base="http://purl.obolibrary.org/obo/"
+     xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+     xmlns:owl="http://www.w3.org/2002/07/owl#"
+     xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"
+     xmlns:xml="http://www.w3.org/XML/1998/namespace"
+     xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
+     xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
+     xmlns:obo="http://purl.obolibrary.org/obo/">
+    <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/cl/components/clm-cl.owl"/>
+
+    <!-- This is a placeholder, it will be regenerated when makefile is first executed -->
+</rdf:RDF>

src/sparql/class-count-by-prefix.sparql

@@ -7,4 +7,4 @@ SELECT ?prefix (COUNT(DISTINCT ?cls) AS ?numberOfClasses) WHERE
   FILTER (!isBlank(?cls))
   BIND( STRBEFORE(STRAFTER(str(?cls),"http://purl.obolibrary.org/obo/"), "_") AS ?prefix)
 }
-GROUP BY ?prefix
+GROUP BY ?prefix