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CellXGene referred cells tagged #2267

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Jan 16, 2024
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CellXGene referred cells tagged #2267

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c9ac734
CellXGene cited cells subset added
hkir-dev Jan 16, 2024
6b0a7ed
CellXGene subset robot template added
hkir-dev Jan 16, 2024
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1 change: 1 addition & 0 deletions docs/odk-workflows/RepositoryFileStructure.md
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Expand Up @@ -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 |
10 changes: 9 additions & 1 deletion src/ontology/Makefile
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Expand Up @@ -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 [email protected] && mv [email protected] $@
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
Expand Down Expand Up @@ -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
# ----------------------------------------
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1 change: 1 addition & 0 deletions src/ontology/catalog-v001.xml
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Expand Up @@ -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>
1 change: 1 addition & 0 deletions src/ontology/cl-edit.owl
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Expand Up @@ -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>)
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4 changes: 4 additions & 0 deletions src/ontology/cl-odk.yaml
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Expand Up @@ -114,4 +114,8 @@ components:
use_template: True
templates:
- kidney_upper_slim.csv
- filename: cellxgene_subset.owl
use_template: True
templates:
- cellxgene_subset.tsv

7 changes: 6 additions & 1 deletion src/ontology/cl.Makefile
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Expand Up @@ -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)

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3,451 changes: 3,451 additions & 0 deletions src/ontology/components/cellxgene_subset.owl
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688 changes: 688 additions & 0 deletions src/templates/cellxgene_subset.tsv
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