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make config more modular, exclude impc observations from default graph
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@@ -19,4 +19,6 @@ graph.db | |
| *.swp | ||
| .nextflow* | ||
| work | ||
| __pycache__ | ||
| *.pyc | ||
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| @@ -0,0 +1,35 @@ | ||
| name: IMPC | ||
| enabled: true | ||
| ingests: | ||
| - globs: ["/nfs/production/parkinso/spot/jmcl/impc-kg/categorical_observation_json/*.json.gz"] | ||
| command: ' | ||
| grebi_transform_jsonl | ||
| --json-rename-field observationId:id | ||
| --json-inject-type impc:CategoricalObservation | ||
| --json-inject-key-prefix impc:' | ||
| - globs: ["/nfs/production/parkinso/spot/jmcl/impc-kg/time_series_observation_json/*.json.gz"] | ||
| command: ' | ||
| grebi_transform_jsonl | ||
| --json-rename-field observationId:id | ||
| --json-inject-type impc:TimeSeriesObservation | ||
| --json-inject-key-prefix impc:' | ||
| - globs: ["/nfs/production/parkinso/spot/jmcl/impc-kg/unidimensional_observation_json/*.json.gz"] | ||
| command: ' | ||
| grebi_transform_jsonl | ||
| --json-rename-field observationId:id | ||
| --json-inject-type impc:UnidimensionalObservation | ||
| --json-inject-key-prefix impc:' | ||
| - globs: ["/nfs/production/parkinso/spot/jmcl/impc-kg/statistical_result_json/*.json.gz"] | ||
| command: ' | ||
| grebi_transform_jsonl | ||
| --json-rename-field statisticalResultId:id | ||
| --json-inject-type impc:StatisticalResult | ||
| --json-inject-key-prefix impc: | ||
| --json-de-nest-field potentialPhenotypes.id | ||
| --json-de-nest-field statisticalMethod.name' | ||
| - globs: ["/nfs/production/parkinso/spot/jmcl/impc-kg/specimen_experiment_json/*.json.gz"] | ||
| command: ' | ||
| grebi_transform_jsonl | ||
| --json-rename-field experimentId:id | ||
| --json-inject-type impc:SpecimenExperiment | ||
| --json-inject-key-prefix impc:' |
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| { | ||
| "subgraphs": [ | ||
| "ebi_full_monarch", | ||
| "ebi_monarch_xspecies", | ||
| "impc", | ||
| "monarch", | ||
| "hra_kg", | ||
| "hett" | ||
| "hra_kg" | ||
| ] | ||
| } |
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| all: ebi_monarch_xspecies.json ebi_monarch.json hett.json hra_kg.json impc.json monarch.json | ||
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| %.json: src/%.py | ||
| python3 $< > $@ | ||
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| .PHONY: all |
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| { | ||
| "id": "EBI_MONARCH", | ||
| "name": "EBI Resources and MONARCH Initiative KG", | ||
| "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/gwas.yaml", | ||
| "./configs/datasource_configs/hgnc.yaml", | ||
| "./configs/datasource_configs/impc.yaml", | ||
| "./configs/datasource_configs/sssom.yaml", | ||
| "./configs/datasource_configs/ols.yaml", | ||
| "./configs/datasource_configs/reactome.yaml", | ||
| "./configs/datasource_configs/ubergraph.yaml", | ||
| "./configs/datasource_configs/otar.yaml", | ||
| "./configs/datasource_configs/monarch.yaml", | ||
| "./configs/datasource_configs/metabolights.yaml", | ||
| "./configs/datasource_configs/mondo_efo.yaml", | ||
| "./configs/datasource_configs/ctd.yaml", | ||
| "./configs/datasource_configs/hett_pesticides_appril.yaml", | ||
| "./configs/datasource_configs/hett_pesticides_eu.yaml", | ||
| "./configs/datasource_configs/hett_pesticides_gb.yaml", | ||
| "./configs/datasource_configs/aopwiki.yaml", | ||
| "./configs/datasource_configs/chembl.yaml", | ||
| "./configs/datasource_configs/robokop_alliance.yaml", | ||
| "./configs/datasource_configs/robokop_binding.yaml", | ||
| "./configs/datasource_configs/robokop_cam.yaml", | ||
| "./configs/datasource_configs/robokop_drugcentral.yaml", | ||
| "./configs/datasource_configs/robokop_gtex.yaml", | ||
| "./configs/datasource_configs/robokop_gtopdb.yaml", | ||
| "./configs/datasource_configs/robokop_hetionet.yaml", | ||
| "./configs/datasource_configs/robokop_hgoa.yaml", | ||
| "./configs/datasource_configs/robokop_hmdb.yaml", | ||
| "./configs/datasource_configs/robokop_icees.yaml", | ||
| "./configs/datasource_configs/robokop_intact.yaml", | ||
| "./configs/datasource_configs/robokop_panther.yaml", | ||
| "./configs/datasource_configs/robokop_pharos.yaml", | ||
| "./configs/datasource_configs/robokop_string.yaml", | ||
| "./configs/datasource_configs/robokop_textmining.yaml", | ||
| "./configs/datasource_configs/robokop_viralproteome.yaml", | ||
| "./configs/datasource_configs/mesh.yaml" | ||
| ] | ||
| } |
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