diff --git a/configs/datasource_configs/ols_impc_x_gwas.yaml b/configs/datasource_configs/ols_impc_x_gwas.yaml new file mode 100644 index 0000000..485c05d --- /dev/null +++ b/configs/datasource_configs/ols_impc_x_gwas.yaml @@ -0,0 +1,9 @@ +name: OLS +enabled: true +ingests: + - globs: ["/nfs/production/parkinso/spot/ols4/prod/slurm_pipeline/ontologies.json.gz"] + command: ' + grebi_ingest_ols + --datasource-name $GREBI_INGEST_DATASOURCE_NAME + --ontologies efo,mp,hp,ro,iao,uberon,pato,oba,bspo,iao,obi,bfo,cob,oio,iao,biolink,mondo,doid,dc,dcterms,ncit,edam,upheno + --skip-obsolete' diff --git a/configs/subgraph_configs/Makefile b/configs/subgraph_configs/Makefile index 0c0738d..90e799d 100644 --- a/configs/subgraph_configs/Makefile +++ b/configs/subgraph_configs/Makefile @@ -1,6 +1,6 @@ -all: ebi_monarch_xspecies.json ebi_monarch.json hett.json hra_kg.json impc.json monarch.json +all: ebi_monarch_xspecies.json ebi_monarch.json hett.json hra_kg.json impc.json monarch.json impc_x_gwas.json %.json: src/%.py python3 $< > $@ diff --git a/configs/subgraph_configs/impc_x_gwas.json b/configs/subgraph_configs/impc_x_gwas.json new file mode 100644 index 0000000..dd0ff11 --- /dev/null +++ b/configs/subgraph_configs/impc_x_gwas.json @@ -0,0 +1,145 @@ +{ + "id": "IMPC x GWAS", + "name": "IMPC and the GWAS Catalog", + "bytes_per_merged_file": 1073741824, + "identifier_props": [ + "id", + "owl:equivalentClass", + "owl:equivalentProperty", + "owl:sameAs", + "grebi:hashId", + "grebi:equivalentTo", + "ols:iri", + "ols:shortForm", + "hgnc:ensembl_gene_id", + "obo:chebi/inchi", + "obo:chebi/inchikey", + "obo:chebi/smiles", + "impc:pmId", + "impc:humanGeneAccId", + "monarch:iri", + "skos:exactMatch", + "ncit:P368", + "ncit:C98965", + "dcterms:identifier", + "oboinowl:hasAlternativeId", + "robokop:equivalent_identifiers", + "mesh.vocab:identifier" + ], + "type_superclasses": [ + "mondo:0000001", + "efo:0000408", + "chebi:36080", + "chebi:24431" + ], + "additional_equivalence_groups": [ + [ + "grebi:name", + "ols:label", + "rdfs:label", + "monarch:name", + "impc:name", + "reactome:displayName", + "dcterms:title", + "ncit:Preferred_Name", + "robokop:name" + ], + [ + "grebi:description", + "iao:definition", + "monarch:description", + "ols:definition", + "robokop:description" + ], + [ + "grebi:synonym", + "monarch:synonym", + "iao:alternative_label", + "ols:synonym", + "oboinowl:hasExactSynonym", + "dcterms:alternative" + ], + [ + "mondo:0000001", + "ogms:0000031" + ], + [ + "biolink:broad_match", + "skos:broader", + "skos:broadMatch", + "ols:directAncestor" + ], + [ + "biolink:subclass_of", + "ols:directParent", + "rdfs:subClassOf", + "rdfs:subPropertyOf" + ], + [ + "rdfs:isDefinedBy", + "ols:ontologyIri", + "ols:ontologyId" + ] + ], + "exclude_props": [ + "ols:hierarchicalProperty", + "ols:synonymProperty", + "ols:curie", + "ols:shortForm", + "ols:ontologyPreferredPrefix", + "ols:iri", + "ols:uri", + "ols:imported", + "ols:hasHierarchicalParents", + "ols:hasHierarchicalChildren", + "ols:hasDirectParents", + "ols:hasDirectChildren", + "ols:numDescendants", + "ols:numHierarchicalDescendants", + "oboinowl:id", + "oboinowl:url", + "monarch:iri", + "cco:hasDocument", + "cco:hasMolecule" + ], + "exclude_edges": [], + "exclude_self_referential_edges": [ + "foaf:page", + "rdfs:seeAlso", + "oboinowl:hasDbXref", + "biolink:subclass_of", + "biolink:broad_match", + "ols:ontology_purl", + "ols:ontologyId", + "cheminf:000407", + "cheminf:InChIKey", + "biolink:interacts_with", + "reactome:url", + "dc:Identifier", + "hgnc:agr", + "hgnc:gencc", + "monarch:xref", + "hgnc:uniprot_ids", + "hgnc:omim_id", + "hgnc:entrez_id", + "reactome:referenceGene", + "reactome:identifier", + "reactome:crossReference", + "edam:Ensembl_gene_id", + "obo:pr#has_gene_template", + "ols:relatedTo", + "ols:relatedFrom", + "robokop:smiles", + "ctd:ChemicalURL", + "ctd:UniProtIDs" + ], + "datasource_configs": [ + "./configs/datasource_configs/impc.yaml", + "./configs/datasource_configs/gwas.yaml", + "./configs/datasource_configs/ols.yaml", + "./configs/datasource_configs/mondo_efo.yaml", + "./configs/datasource_configs/monarch.yaml", + "./configs/datasource_configs/sssom.yaml", + "./configs/datasource_configs/mondo_efo.yaml" + ] +} diff --git a/configs/subgraph_configs/src/impc_x_gwas.py b/configs/subgraph_configs/src/impc_x_gwas.py new file mode 100644 index 0000000..ce48e94 --- /dev/null +++ b/configs/subgraph_configs/src/impc_x_gwas.py @@ -0,0 +1,27 @@ + + +from shared import config + +config['id'] = 'IMPC x GWAS' +config['name'] = 'IMPC and the GWAS Catalog' +config['datasource_configs'] = [ + "./configs/datasource_configs/impc.yaml", + "./configs/datasource_configs/gwas.yaml", + "./configs/datasource_configs/ols.yaml", + "./configs/datasource_configs/mondo_efo.yaml", + "./configs/datasource_configs/monarch.yaml", + "./configs/datasource_configs/sssom.yaml", + "./configs/datasource_configs/mondo_efo.yaml" +] +config['identifier_props'] = [ + "id", + "monarch:iri", + "ols:iri", + "ols:shortForm", + "impc:pmId", + "impc:humanGeneAccId" +] + +if __name__ == '__main__': + import json + print(json.dumps(config, indent=2))