From 45fe6a336e9b4740ef3d610879d953e3f8ce9a6b Mon Sep 17 00:00:00 2001 From: Caroline Eastwood Date: Fri, 15 Nov 2024 09:43:44 +0000 Subject: [PATCH] Fixes #2725 clm-cl.owl component edits --- .github/workflows/qc.yml | 30 ------------------- docs/odk-workflows/RepositoryFileStructure.md | 2 ++ src/ontology/Makefile | 9 +++--- src/ontology/catalog-v001.xml | 1 + src/ontology/cl-edit.owl | 2 ++ src/ontology/cl-odk.yaml | 1 + src/ontology/cl.Makefile | 8 +++++ src/ontology/components/clm-cl.owl | 14 +++++++++ src/sparql/class-count-by-prefix.sparql | 2 +- 9 files changed, 34 insertions(+), 35 deletions(-) create mode 100644 src/ontology/components/clm-cl.owl diff --git a/.github/workflows/qc.yml b/.github/workflows/qc.yml index eb791ff4e..ec0efec47 100644 --- a/.github/workflows/qc.yml +++ b/.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 "
\nThis PR violates some taxon constraints. Here is what the reasoner has to say:\n" > comments.md - cat taxon-unsats.md >> comment.md - echo "
" >> 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 - diff --git a/docs/odk-workflows/RepositoryFileStructure.md b/docs/odk-workflows/RepositoryFileStructure.md index 7f982ace0..bdd66560d 100644 --- 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 index 6b89f1df3..7f3d2ac67 100644 --- a/src/ontology/Makefile +++ b/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 # ---------------------------------------- diff --git a/src/ontology/catalog-v001.xml b/src/ontology/catalog-v001.xml index 373a213f6..7f235c60d 100644 --- a/src/ontology/catalog-v001.xml +++ b/src/ontology/catalog-v001.xml @@ -16,6 +16,7 @@ + diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index 0ef42f204..2fe9facb8 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -31,6 +31,8 @@ Import() Import() Import() Import() +Import() + Annotation(obo:IAO_0000700 obo:CL_0000000) Annotation(dc:description "An ontology of cell types.") Annotation(dc:title "Cell Ontology") diff --git a/src/ontology/cl-odk.yaml b/src/ontology/cl-odk.yaml index 67f79e321..d26e5de4e 100644 --- a/src/ontology/cl-odk.yaml +++ b/src/ontology/cl-odk.yaml @@ -149,4 +149,5 @@ components: use_template: True templates: - cellxgene_subset.tsv + - filename: clm-cl.owl diff --git a/src/ontology/cl.Makefile b/src/ontology/cl.Makefile index c4e7a6d7d..f1f68c4b9 100644 --- a/src/ontology/cl.Makefile +++ b/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 diff --git a/src/ontology/components/clm-cl.owl b/src/ontology/components/clm-cl.owl new file mode 100644 index 000000000..902854fff --- /dev/null +++ b/src/ontology/components/clm-cl.owl @@ -0,0 +1,14 @@ + + + + + + diff --git a/src/sparql/class-count-by-prefix.sparql b/src/sparql/class-count-by-prefix.sparql index 0c4d28446..a6a4851ed 100644 --- 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 \ No newline at end of file