1 files changed, 152 insertions, 0 deletions
diff --git a/gn3/db/constants.py b/gn3/db/constants.py
new file mode 100644
index 0000000..45e3bfc
--- /dev/null
+++ b/gn3/db/constants.py
@@ -0,0 +1,152 @@
+"""
+This module contains some constants used in other modules.
+"""
+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",
+    "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",
+}