Merge branch 'master' into harmonising-respiratory-tract-and-MCC-names

obophenotype · Nov 28, 2024 · 9b4f378 · 9b4f378
2 parents b995d0d + 1ca7174
commit 9b4f378
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diff --git a/docs/odk-workflows/RepositoryFileStructure.md b/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 |
diff --git a/src/ontology/Makefile b/src/ontology/Makefile
@@ -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=                d4e868f8bbec3ce7b0d7656c824520ab0b96d8901a8c2b9cf400c27c3fb3dac2
+CONFIG_HASH=                fe26dd231ab531dab5609c794de598d2a28083168916941a3276fe672cfe8be2
 
 
 # ----------------------------------------
@@ -53,7 +53,7 @@ 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
@@ -513,6 +513,7 @@ $(COMPONENTSDIR)/cellxgene_subset.owl: $(TEMPLATEDIR)/cellxgene_subset.tsv
 		$(ANNOTATE_CONVERT_FILE); fi
 
 .PRECIOUS: $(COMPONENTSDIR)/cellxgene_subset.owl
+
 # ----------------------------------------
 # Mirroring upstream ontologies
 # ----------------------------------------

diff --git a/src/ontology/catalog-v001.xml b/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"/>

diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl
@@ -24,6 +24,7 @@ Prefix(ncbitaxon:=<http://purl.obolibrary.org/obo/ncbitaxon#>)
 Ontology(<http://purl.obolibrary.org/obo/cl.owl>
 Import(<http://purl.obolibrary.org/obo/cl/components/blood_and_immune_upper_slim.owl>)
 Import(<http://purl.obolibrary.org/obo/cl/components/cellxgene_subset.owl>)
+Import(<http://purl.obolibrary.org/obo/cl/components/clm-cl.owl>)
 Import(<http://purl.obolibrary.org/obo/cl/components/eye_upper_slim.owl>)
 Import(<http://purl.obolibrary.org/obo/cl/components/general_cell_types_upper_slim.owl>)
 Import(<http://purl.obolibrary.org/obo/cl/components/hra_subset.owl>)

diff --git a/src/ontology/cl-odk.yaml b/src/ontology/cl-odk.yaml
@@ -9,6 +9,8 @@ use_dosdps: TRUE
 use_mappings: True
 use_edit_file_imports: FALSE
 release_diff: TRUE
+workflows:
+  - docs
 export_formats:
   - owl
   - obo
@@ -154,4 +156,5 @@ components:
       use_template: True
       templates:
         - cellxgene_subset.tsv
+    - filename: clm-cl.owl
 
diff --git a/src/ontology/cl.Makefile b/src/ontology/cl.Makefile
@@ -95,8 +95,8 @@ $(MAPPINGDIR)/cl.sssom.tsv: $(MAPPINGDIR)/cl-local.sssom.tsv \
 EXTERNAL_SSSOM_PROVIDERS = fbbt zfa
 EXTERNAL_SSSOM_SETS = $(foreach provider, $(EXTERNAL_SSSOM_PROVIDERS), $(MAPPINGDIR)/$(provider).sssom.tsv)
 
-# We only refresh external resources under IMP=true
-ifeq ($(strip $(IMP)),true)
+# We only refresh external resources under MIR=true
+ifeq ($(strip $(MIR)),true)
 
 # FBbt mapping set
 $(MAPPINGDIR)/fbbt.sssom.tsv: .FORCE
@@ -344,10 +344,9 @@ add-replacedby:
 # EXTERNAL RESOURCES
 # ----------------------------------------
 
+ifeq ($(strip $(MIR)),true)
+
 # Human reference atlas subset
-# FIXME: Refreshing of this resource should be uncoupled from the
-# release/QC pipelines.
-# See <https://github.com/obophenotype/cell-ontology/issues/2644>
 HRA_SUBSET_URL="https://raw.githubusercontent.com/hubmapconsortium/ccf-validation-tools/master/owl/CL_ASCTB_subset.owl"
 $(TMPDIR)/hra_subset.owl:
 	wget $(HRA_SUBSET_URL) -O $@
@@ -356,14 +355,20 @@ $(COMPONENTSDIR)/hra_subset.owl: $(TMPDIR)/hra_subset.owl
 	$(ROBOT) merge -i $< annotate --ontology-iri $(ONTBASE)/$@ --output $@
 
 # CellXGene reference subset
-# FIXME: Never actually downloaded again, unless the
-# $(TEMPLATEDIR)/cellxgene_subset.tsv file is manually removed; probably
-# not what was intended.
-# See <https://github.com/obophenotype/cell-ontology/issues/2644>
 CELLXGENE_SUBSET_URL="https://raw.githubusercontent.com/hkir-dev/cellxgene-cell-reporter/main/templates/cellxgene_subset.tsv"
-$(TEMPLATEDIR)/cellxgene_subset.tsv:
+$(TEMPLATEDIR)/cellxgene_subset.tsv: .FORCE
 	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 $@
+
+endif
+
 
 # ----------------------------------------
 # RELEASE DEPLOYMENT

diff --git a/src/ontology/components/clm-cl.owl b/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>
diff --git a/src/scripts/update_repo.sh b/src/scripts/update_repo.sh
@@ -26,7 +26,7 @@ cp target/$OID/src/ontology/run.sh $SRCDIR/ontology/
 cp -r target/$OID/src/sparql/* $SRCDIR/sparql/
 mkdir -p $ROOTDIR/.github
 mkdir -p $ROOTDIR/.github/workflows
-cp target/$OID/.github/workflows/qc.yml $ROOTDIR/.github/workflows/qc.yml
+
 
 
 
@@ -36,5 +36,5 @@ cp target/$OID/.github/workflows/docs.yml $ROOTDIR/.github/workflows/docs.yml
 cp -n target/$OID/mkdocs.yaml $ROOTDIR/
 
 echo "WARNING: These files should be manually migrated: mkdocs.yaml, .gitignore, src/ontology/catalog.xml (if you added a new import or component)"
-
+echo "WARNING: Your QC workflows have not been updated automatically. Please update the ODK version number(s) in .github/workflows/qc.yml."
 echo "Ontology repository update successfully completed."
diff --git a/src/sparql/class-count-by-prefix.sparql b/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