From 18669633b325bdc603643cd852dac528523a8e5a Mon Sep 17 00:00:00 2001 From: Huseyin Kir <73784267+hkir-dev@users.noreply.github.com> Date: Tue, 16 Jan 2024 12:18:53 +0000 Subject: [PATCH] CellXGene referred cells tagged (#2267) * CellXGene cited cells subset added * CellXGene subset robot template added --- docs/odk-workflows/RepositoryFileStructure.md | 1 + src/ontology/Makefile | 10 +- src/ontology/catalog-v001.xml | 1 + src/ontology/cl-edit.owl | 1 + src/ontology/cl-odk.yaml | 4 + src/ontology/cl.Makefile | 7 +- src/ontology/components/cellxgene_subset.owl | 3451 +++++++++++++++++ src/templates/cellxgene_subset.tsv | 688 ++++ 8 files changed, 4161 insertions(+), 2 deletions(-) create mode 100644 src/ontology/components/cellxgene_subset.owl create mode 100644 src/templates/cellxgene_subset.tsv diff --git a/docs/odk-workflows/RepositoryFileStructure.md b/docs/odk-workflows/RepositoryFileStructure.md index e1cd5f6b8..7f982ace0 100644 --- 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 index 7db2dc393..39e1ff4ac 100644 --- 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 index 558f86f37..67df007a1 100644 --- a/src/ontology/catalog-v001.xml +++ b/src/ontology/catalog-v001.xml @@ -19,5 +19,6 @@ + diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index b18bd1d8d..8d9b79014 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -10,6 +10,7 @@ Prefix(oboInOwl:=) Ontology( Import() +Import() Import() Import() Import() diff --git a/src/ontology/cl-odk.yaml b/src/ontology/cl-odk.yaml index 49777fd3f..17c52bf48 100644 --- 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 index 204af26bd..8544b1521 100644 --- 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 new file mode 100644 index 000000000..384e6b488 --- /dev/null +++ b/src/ontology/components/cellxgene_subset.owl @@ -0,0 +1,3451 @@ +Prefix(:=) +Prefix(owl:=) +Prefix(rdf:=) +Prefix(xml:=) +Prefix(xsd:=) +Prefix(rdfs:=) + + +Ontology( + +Annotation(owl:versionInfo "2024-01-16") + +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) 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+Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(AnnotationProperty()) + + +############################ +# Classes +############################ + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + 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+AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + 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