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-rw-r--r--gn3/api/metadata.py128
-rw-r--r--gn3/db/constants.py150
-rw-r--r--gn3/db/rdf.py33
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:
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-29 02:18:48 +0000