diff options
Diffstat (limited to 'gn3')
| -rw-r--r-- | gn3/api/metadata.py | 128 | ||||
| -rw-r--r-- | gn3/db/constants.py | 150 | ||||
| -rw-r--r-- | gn3/db/rdf.py | 33 |
3 files changed, 159 insertions, 152 deletions
diff --git a/gn3/api/metadata.py b/gn3/api/metadata.py index 8c900df..2e26489 100644 --- a/gn3/api/metadata.py +++ b/gn3/api/metadata.py @@ -17,132 +17,16 @@ from gn3.db.datasets import (retrieve_metadata, from gn3.db.rdf import RDF_PREFIXES from gn3.db.rdf import (query_frame_and_compact, query_and_compact) +from gn3.db.constants import ( + RDF_PREFIXES, BASE_CONTEXT, + DATASET_CONTEXT, SEARCH_CONTEXT, + DATASET_SEARCH_CONTEXT, PUBLICATION_CONTEXT, + PHENOTYPE_CONTEXT +) from gn3.api.metadata_api import wiki -BASE_CONTEXT = { - "data": "@graph", - "id": "@id", - "type": "@type", - "gnc": "http://genenetwork.org/category/", - "gnt": "http://genenetwork.org/term/", - "rdfs": "http://www.w3.org/2000/01/rdf-schema#", - "rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#>", -} - -DATASET_CONTEXT = { - "accessRights": "dct:accessRights", - "accessionId": "dct:identifier", - "acknowledgement": "gnt:hasAcknowledgement", - "altLabel": "skos:altLabel", - "caseInfo": "gnt:hasCaseInfo", - "classifiedUnder": "xkos:classifiedUnder", - "contributors": "dct:creator", - "contactPoint": "dcat:contactPoint", - "created": "dct:created", - "dcat": "http://www.w3.org/ns/dcat#", - "dct": "http://purl.org/dc/terms/", - "description": "dct:description", - "ex": "http://example.org/stuff/1.0/", - "experimentDesignInfo": "gnt:hasExperimentDesignInfo", - "experimentType": "gnt:hasExperimentType", - "foaf": "http://xmlns.com/foaf/0.1/", - "geoSeriesId": "gnt:hasGeoSeriesId", - "gnt": "http://genenetwork.org/term/", - "inbredSet": "gnt:belongsToGroup", - "label": "rdfs:label", - "normalization": "gnt:usesNormalization", - "platformInfo": "gnt:hasPlatformInfo", - "notes": "gnt:hasNotes", - "organization": "foaf:Organization", - "prefLabel": "skos:prefLabel", - "citation": "dct:isReferencedBy", - "GoTree": "gnt:hasGOTreeValue", - "platform": "gnt:usesPlatform", - "processingInfo": "gnt:hasDataProcessingInfo", - "rdfs": "http://www.w3.org/2000/01/rdf-schema#", - "skos": "http://www.w3.org/2004/02/skos/core#", - "specifics": "gnt:hasContentInfo", - "title": "dct:title", - "xkos": "http://rdf-vocabulary.ddialliance.org/xkos#", - "tissueInfo": "gnt:hasTissueInfo", - "tissue": "gnt:hasTissue", - "contactWebUrl": "foaf:homepage", - "contactName": "foaf:name", -} - -SEARCH_CONTEXT = { - "pages": "ex:pages", - "hits": "ex:hits", - "result": "ex:result", - "results": "ex:items", - "resultItem": "ex:resultType", - "currentPage": "ex:currentPage", -} - -DATASET_SEARCH_CONTEXT = SEARCH_CONTEXT | { - "classifiedUnder": "xkos:classifiedUnder", - "created": "dct:created", - "dct": "http://purl.org/dc/terms/", - "ex": "http://example.org/stuff/1.0/", - "inbredSet": "ex:belongsToInbredSet", - "title": "dct:title", - "name": "rdfs:label", - "rdfs": "http://www.w3.org/2000/01/rdf-schema#", - "type": "@type", - "xkos": "http://rdf-vocabulary.ddialliance.org/xkos#", -} - -PUBLICATION_CONTEXT = { - "dct": "http://purl.org/dc/terms/", - "fabio": "http://purl.org/spar/fabio/", - "prism": "http://prismstandard.org/namespaces/basic/2.0/", - "xsd": "http://www.w3.org/2001/XMLSchema#", - "title": "dct:title", - "journal": "fabio:Journal", - "volume": "prism:volume", - "page": "fabio:page", - "creator": "dct:creator", - "abstract": "dct:abstract", - "year": { - "@id": "fabio:hasPublicationYear", - "@type": "xsd:gYear", - }, - "month": { - "@id": "prism:publicationDate", - "@type": "xsd:gMonth" - }, -} - -PHENOTYPE_CONTEXT = BASE_CONTEXT | PUBLICATION_CONTEXT | { - "skos": "http://www.w3.org/2004/02/skos/core#", - "dcat": "http://www.w3.org/ns/dcat#", - "prism": "http://prismstandard.org/namespaces/basic/2.0/", - "traitName": "skos:altLabel", - "trait": "rdfs:label", - "altName": "rdfs:altLabel", - "description": "dct:description", - "abbreviation": "gnt:abbreviation", - "labCode": "gnt:labCode", - "submitter": "gnt:submitter", - "dataset": "dcat:Distribution", - "contributor": "dct:contributor", - "mean": "gnt:mean", - "locus": "gnt:locus", - "lodScore": "gnt:lodScore", - "references": "dct:isReferencedBy", - "additive": "gnt:additive", - "sequence": "gnt:sequence", - "prefLabel": "skos:prefLabel", - "identifier": "dct:identifier", - "chromosome": "gnt:chr", - "mb": "gnt:mb", - "peakLocation": "gnt:locus", - "species": "gnt:belongsToSpecies", - "group": "gnt:belongsToGroup", -} - metadata = Blueprint("metadata", __name__) metadata.register_blueprint(wiki.wiki_blueprint) diff --git a/gn3/db/constants.py b/gn3/db/constants.py new file mode 100644 index 0000000..231dc8b --- /dev/null +++ b/gn3/db/constants.py @@ -0,0 +1,150 @@ +PREFIXES = { + "dcat": "http://www.w3.org/ns/dcat#", + "dct": "http://purl.org/dc/terms/", + "ex": "http://example.org/stuff/1.0/", + "fabio": "http://purl.org/spar/fabio/", + "foaf": "http://xmlns.com/foaf/0.1/", + "generif": "http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=Graphics&list_uids=", + "genotype": "http://genenetwork.org/genotype/", + "gn": "http://genenetwork.org/id/", + "gnc": "http://genenetwork.org/category/", + "gnt": "http://genenetwork.org/term/", + "owl": "http://www.w3.org/2002/07/owl#", + "phenotype": "http://genenetwork.org/phenotype/", + "prism": "http://prismstandard.org/namespaces/basic/2.0/", + "publication": "http://genenetwork.org/publication/", + "pubmed": "http://rdf.ncbi.nlm.nih.gov/pubmed/", + "rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#", + "rdfs": "http://www.w3.org/2000/01/rdf-schema#", + "skos": "http://www.w3.org/2004/02/skos/core#", + "taxon": "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=", + "up": "http://purl.uniprot.org/core/", + "xkos": "http://rdf-vocabulary.ddialliance.org/xkos#", + "xsd": "http://www.w3.org/2001/XMLSchema#", +} + +RDF_PREFIXES = "\n".join([f"PREFIX {key}: <{value}>" + for key, value in PREFIXES.items()]) + +BASE_CONTEXT = { + "data": "@graph", + "id": "@id", + "type": "@type", + "gn": "http://genenetwork.org/id/", + "gnc": "http://genenetwork.org/category/", + "gnt": "http://genenetwork.org/term/", + "rdfs": "http://www.w3.org/2000/01/rdf-schema#", + "rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#>", +} + +DATASET_CONTEXT = { + "accessRights": "dct:accessRights", + "accessionId": "dct:identifier", + "acknowledgement": "gnt:hasAcknowledgement", + "altLabel": "skos:altLabel", + "caseInfo": "gnt:hasCaseInfo", + "classifiedUnder": "xkos:classifiedUnder", + "contributors": "dct:creator", + "contactPoint": "dcat:contactPoint", + "created": "dct:created", + "dcat": "http://www.w3.org/ns/dcat#", + "dct": "http://purl.org/dc/terms/", + "description": "dct:description", + "ex": "http://example.org/stuff/1.0/", + "experimentDesignInfo": "gnt:hasExperimentDesignInfo", + "experimentType": "gnt:hasExperimentType", + "foaf": "http://xmlns.com/foaf/0.1/", + "geoSeriesId": "gnt:hasGeoSeriesId", + "gnt": "http://genenetwork.org/term/", + "inbredSet": "gnt:belongsToGroup", + "label": "rdfs:label", + "normalization": "gnt:usesNormalization", + "platformInfo": "gnt:hasPlatformInfo", + "notes": "gnt:hasNotes", + "organization": "foaf:Organization", + "prefLabel": "skos:prefLabel", + "citation": "dct:isReferencedBy", + "GoTree": "gnt:hasGOTreeValue", + "platform": "gnt:usesPlatform", + "processingInfo": "gnt:hasDataProcessingInfo", + "rdfs": "http://www.w3.org/2000/01/rdf-schema#", + "skos": "http://www.w3.org/2004/02/skos/core#", + "specifics": "gnt:hasContentInfo", + "title": "dct:title", + "xkos": "http://rdf-vocabulary.ddialliance.org/xkos#", + "tissueInfo": "gnt:hasTissueInfo", + "tissue": "gnt:hasTissue", + "contactWebUrl": "foaf:homepage", + "contactName": "foaf:name", +} + +SEARCH_CONTEXT = { + "pages": "ex:pages", + "hits": "ex:hits", + "result": "ex:result", + "results": "ex:items", + "resultItem": "ex:resultType", + "currentPage": "ex:currentPage", +} + +DATASET_SEARCH_CONTEXT = SEARCH_CONTEXT | { + "classifiedUnder": "xkos:classifiedUnder", + "created": "dct:created", + "dct": "http://purl.org/dc/terms/", + "ex": "http://example.org/stuff/1.0/", + "inbredSet": "ex:belongsToInbredSet", + "title": "dct:title", + "name": "rdfs:label", + "rdfs": "http://www.w3.org/2000/01/rdf-schema#", + "type": "@type", + "xkos": "http://rdf-vocabulary.ddialliance.org/xkos#", +} + +PUBLICATION_CONTEXT = { + "dct": "http://purl.org/dc/terms/", + "fabio": "http://purl.org/spar/fabio/", + "prism": "http://prismstandard.org/namespaces/basic/2.0/", + "xsd": "http://www.w3.org/2001/XMLSchema#", + "title": "dct:title", + "journal": "fabio:Journal", + "volume": "prism:volume", + "page": "fabio:page", + "creator": "dct:creator", + "abstract": "dct:abstract", + "year": { + "@id": "fabio:hasPublicationYear", + "@type": "xsd:gYear", + }, + "month": { + "@id": "prism:publicationDate", + "@type": "xsd:gMonth" + }, +} + +PHENOTYPE_CONTEXT = BASE_CONTEXT | PUBLICATION_CONTEXT | { + "skos": "http://www.w3.org/2004/02/skos/core#", + "dcat": "http://www.w3.org/ns/dcat#", + "prism": "http://prismstandard.org/namespaces/basic/2.0/", + "traitName": "skos:altLabel", + "trait": "rdfs:label", + "altName": "rdfs:altLabel", + "description": "dct:description", + "abbreviation": "gnt:abbreviation", + "labCode": "gnt:labCode", + "submitter": "gnt:submitter", + "dataset": "dcat:Distribution", + "contributor": "dct:contributor", + "mean": "gnt:mean", + "locus": "gnt:locus", + "lodScore": "gnt:lodScore", + "references": "dct:isReferencedBy", + "additive": "gnt:additive", + "sequence": "gnt:sequence", + "prefLabel": "skos:prefLabel", + "identifier": "dct:identifier", + "chromosome": "gnt:chr", + "mb": "gnt:mb", + "peakLocation": "gnt:locus", + "species": "gnt:belongsToSpecies", + "group": "gnt:belongsToGroup", +} diff --git a/gn3/db/rdf.py b/gn3/db/rdf.py index eb4014a..c5a8d7f 100644 --- a/gn3/db/rdf.py +++ b/gn3/db/rdf.py @@ -7,36 +7,9 @@ import json from SPARQLWrapper import SPARQLWrapper from pyld import jsonld # type: ignore - - -PREFIXES = { - "dcat": "http://www.w3.org/ns/dcat#", - "dct": "http://purl.org/dc/terms/", - "ex": "http://example.org/stuff/1.0/", - "fabio": "http://purl.org/spar/fabio/", - "foaf": "http://xmlns.com/foaf/0.1/", - "generif": "http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=Graphics&list_uids=", - "genotype": "http://genenetwork.org/genotype/", - "gn": "http://genenetwork.org/id/", - "gnc": "http://genenetwork.org/category/", - "gnt": "http://genenetwork.org/term/", - "owl": "http://www.w3.org/2002/07/owl#", - "phenotype": "http://genenetwork.org/phenotype/", - "prism": "http://prismstandard.org/namespaces/basic/2.0/", - "publication": "http://genenetwork.org/publication/", - "pubmed": "http://rdf.ncbi.nlm.nih.gov/pubmed/", - "rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#", - "rdfs": "http://www.w3.org/2000/01/rdf-schema#", - "skos": "http://www.w3.org/2004/02/skos/core#", - "taxon": "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=", - "up": "http://purl.uniprot.org/core/", - "xkos": "http://rdf-vocabulary.ddialliance.org/xkos#", - "xsd": "http://www.w3.org/2001/XMLSchema#", -} - - -RDF_PREFIXES = "\n".join([f"PREFIX {key}: <{value}>" - for key, value in PREFIXES.items()]) +from gn3.db.constants import ( + RDF_PREFIXES +) def sparql_construct_query(query: str, endpoint: str) -> dict: |