diff --git a/.github/workflows/qc.yml b/.github/workflows/qc.yml index 6d132aa50..6f5dd3eb8 100644 --- a/.github/workflows/qc.yml +++ b/.github/workflows/qc.yml @@ -24,6 +24,10 @@ jobs: DEFAULT_BRANCH: main run: pip install --upgrade pip && pip install -U sssom - uses: actions/checkout@v2 + - name: Prepare mappings + env: + DEFAULT_BRANCH: main + run: make RUN="" mappings - name: Run Mapping QC checks env: DEFAULT_BRANCH: main diff --git a/metadata/gene_mappings.sssom.yml b/metadata/gene_mappings.sssom.yml new file mode 100644 index 000000000..ca0850923 --- /dev/null +++ b/metadata/gene_mappings.sssom.yml @@ -0,0 +1,14 @@ +curie_map: + owl: http://www.w3.org/2002/07/owl# + Xenbase: https://www.xenbase.org/entry/ + FB: https://flybase.org/reports/ + RGD: http://rgd.mcw.edu/rgdweb/report/gene/main.html?id= + HGNC: http://identifiers.org/hgnc/ + WB: https://www.wormbase.org/get?name= + OMIM: "https://omim.org/MIM:" + UniProtKB: http://purl.uniprot.org/uniprot/ + ZFIN: http://zfin.org/ +license: https://creativecommons.org/licenses/by/4.0/ +mapping_set_description: The monarch gene mappings, based on HGNC and ENSEMBL base mappings. +mapping_set_id: https://data.monarchinitiative.org/mappings/gene_mappings.sssom.tsv +mapping_set_source: https://w3id.org/biopragmatics/biomappings/sssom/biomappings.sssom.tsv diff --git a/metadata/mesh_chebi_biomappings.sssom.yml b/metadata/mesh_chebi_biomappings.sssom.yml new file mode 100644 index 000000000..13e5790e8 --- /dev/null +++ b/metadata/mesh_chebi_biomappings.sssom.yml @@ -0,0 +1,6 @@ +curie_map: + MESH: http://id.nlm.nih.gov/mesh/ +license: https://creativecommons.org/licenses/by/4.0/ +mapping_set_description: A subset of the biomappings containing mesh to chebi associations. +mapping_set_id: https://data.monarchinitiative.org/mappings/mesh_chebi_biomappings.sssom.tsv +mapping_set_source: https://w3id.org/biopragmatics/biomappings/sssom/biomappings.sssom.tsv diff --git a/monarch_mapping_commons.Makefile b/monarch_mapping_commons.Makefile index c3c2b59b3..0d18d3687 100644 --- a/monarch_mapping_commons.Makefile +++ b/monarch_mapping_commons.Makefile @@ -8,18 +8,27 @@ MAPPING_DIR = mappings SCRIPT_DIR = scripts SRC_DIR = sources TMP_DIR = tmp +METADATA_DIR = metadata RUN = poetry run $(MAPPING_DIR)/ $(SCRIPT_DIR)/ $(SRC_DIR)/ $(TMP_DIR)/: mkdir -p $@ -$(MAPPING_DIR)/mondo.sssom.tsv: | $(MAPPING_DIR)/ +$(MAPPING_DIR)/mondo.sssom.tsv: + mkdir -p $(MAPPING_DIR) $(TMP_DIR) wget http://purl.obolibrary.org/obo/mondo/mappings/mondo.sssom.tsv -O $@ -$(MAPPING_DIR)/biomappings.sssom.tsv: | $(MAPPING_DIR)/ $(SCRIPT_DIR)/ $(TMP_DIR)/ +$(MAPPING_DIR)/mesh_chebi_biomappings.sssom.tsv: + mkdir -p $(MAPPING_DIR) $(TMP_DIR) wget https://raw.githubusercontent.com/biopragmatics/biomappings/master/docs/_data/sssom/biomappings.sssom.tsv -O $(TMP_DIR)/biomappings.sssom.tsv - $(RUN) python3 $(SCRIPT_DIR)/process_biomappings.py --input $(TMP_DIR)/biomappings.sssom.tsv --output $(MAPPING_DIR)/mesh_chebi_biomappings.sssom.tsv + $(RUN) python3 $(SCRIPT_DIR)/process_biomappings.py --input $(TMP_DIR)/biomappings.sssom.tsv --output $(TMP_DIR)/mesh_chebi_biomappings.sssom.tsv + sssom parse $(TMP_DIR)/mesh_chebi_biomappings.sssom.tsv -m $(METADATA_DIR)/mesh_chebi_biomappings.sssom.yml --prefix-map-mode merged -o $@ $(MAPPING_DIR)/gene_mappings.sssom.tsv: - wget http://data.monarchinitiative.org/monarch-gene-mapping/latest/gene_mappings.tsv -O $@ + mkdir -p $(MAPPING_DIR) $(TMP_DIR) + wget http://data.monarchinitiative.org/monarch-gene-mapping/latest/gene_mappings.tsv -O $(TMP_DIR)/gene_mappings.sssom.tsv + # see https://github.com/monarch-initiative/monarch-mapping-commons/issues/33 + grep -v "" $(TMP_DIR)/gene_mappings.sssom.tsv > $@.tmp && mv $@.tmp $(TMP_DIR)/gene_mappings.sssom.tsv + grep -v ";" $(TMP_DIR)/gene_mappings.sssom.tsv > $@.tmp && mv $@.tmp $(TMP_DIR)/gene_mappings.sssom.tsv + sssom parse $(TMP_DIR)/gene_mappings.sssom.tsv -m $(METADATA_DIR)/gene_mappings.sssom.yml --prefix-map-mode merged -o $@ diff --git a/poetry.lock b/poetry.lock index d14bd308c..1863a7ecc 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.7.0 and should not be changed by hand. 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