CellXGene referred cells tagged (#2267)

* CellXGene cited cells subset added * CellXGene subset robot template added
obophenotype · Jan 16, 2024 · 1866963 · 1866963
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commit 1866963
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diff --git a/docs/odk-workflows/RepositoryFileStructure.md b/docs/odk-workflows/RepositoryFileStructure.md
@@ -41,3 +41,4 @@ These are the components in CL
 | eye_upper_slim.owl | None |
 | general_cell_types_upper_slim.owl | None |
 | kidney_upper_slim.owl | None |
+| cellxgene_subset.owl | None |
diff --git a/src/ontology/Makefile b/src/ontology/Makefile
@@ -50,7 +50,7 @@ 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 
+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 
 ONTOLOGYTERMS =             $(TMPDIR)/ontologyterms.txt
 EDIT_PREPROCESSED =         $(TMPDIR)/$(ONT)-preprocess.owl
 PATTERNDIR=                 ../patterns
@@ -437,6 +437,14 @@ $(COMPONENTSDIR)/kidney_upper_slim.owl: $(TEMPLATEDIR)/kidney_upper_slim.csv
 		$(ANNOTATE_CONVERT_FILE); fi
 
 .PRECIOUS: $(COMPONENTSDIR)/kidney_upper_slim.owl
+
+
+$(COMPONENTSDIR)/cellxgene_subset.owl: $(TEMPLATEDIR)/cellxgene_subset.tsv
+	if [ $(COMP) = true ] ; then $(ROBOT) template  \
+		$(patsubst %, --template %, $^) \
+		$(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
@@ -19,5 +19,6 @@
     <uri name="http://purl.obolibrary.org/obo/cl/components/eye_upper_slim.owl" uri="components/eye_upper_slim.owl"/>
     <uri name="http://purl.obolibrary.org/obo/cl/components/general_cell_types_upper_slim.owl" uri="components/general_cell_types_upper_slim.owl"/>
     <uri name="http://purl.obolibrary.org/obo/cl/components/kidney_upper_slim.owl" uri="components/kidney_upper_slim.owl"/>
+    <uri name="http://purl.obolibrary.org/obo/cl/components/cellxgene_subset.owl" uri="components/cellxgene_subset.owl"/>
     <group id="Folder Repository, directory=, recursive=false, Auto-Update=false, version=2" prefer="public" xml:base=""/>
 </catalog>
diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl
@@ -10,6 +10,7 @@ Prefix(oboInOwl:=<http://www.geneontology.org/formats/oboInOwl#>)
 
 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/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
@@ -114,4 +114,8 @@ components:
       use_template: True
       templates:
         - kidney_upper_slim.csv
+    - filename: cellxgene_subset.owl
+      use_template: True
+      templates:
+        - cellxgene_subset.tsv
 
diff --git a/src/ontology/cl.Makefile b/src/ontology/cl.Makefile
@@ -233,7 +233,12 @@ $(TMPDIR)/hra_subset.owl:
 
 $(COMPONENTSDIR)/hra_subset.owl: $(TMPDIR)/hra_subset.owl
 	$(ROBOT) merge -i $< annotate --ontology-iri $(ONTBASE)/$@ --output $@
-
+
+## Download CellXGene reference subset
+
+CELLXGENE_SUBSET_URL="https://raw.githubusercontent.com/hkir-dev/cellxgene-cell-reporter/main/templates/cellxgene_subset.tsv"
+$(TEMPLATEDIR)/cellxgene_subset.tsv:
+	wget $(CELLXGENE_SUBSET_URL) -O $@
 
 # Make CL-plus (CL + PCL product)
 

diff --git a/src/ontology/components/cellxgene_subset.owl b/src/ontology/components/cellxgene_subset.owl
diff --git a/src/templates/cellxgene_subset.tsv b/src/templates/cellxgene_subset.tsv