def to_tccm_rdf(self, see_also_format=''):
cs_uri = URIRef("http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl")
self.graph.add((cs_uri, RDF.type, SKOS.ConceptScheme))
self.graph.add((
cs_uri, DC.description,
Literal(
"A vocabulary for clinical care, translational and basic research, and public information and administrative activities."
)))
self.graph.add(
(cs_uri, RDFS.seeAlso,
Literal("https://ncithesaurus.nci.nih.gov/ncitbrowser/")))
self.graph.add(
(cs_uri, SH.namespace,
URIRef("http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#")))
for line in self.zipfile.open("Thesaurus.txt"):
tokens = line.decode("utf-8").split("\t")
uri = URIRef(tokens[1][1:-1])
self.graph.add((uri, RDF.type, SKOS.Concept))
self.graph.add((uri, SKOS.notation, Literal(tokens[0])))
self.graph.add((uri, SKOS.definition, Literal(tokens[4])))
self.graph.add(
(uri, SKOS.prefLabel, Literal(tokens[3].split("|")[0])))
if tokens[2]:
for code in tokens[2].split("|"):
code = code.strip()
sc_uri = URIRef(curie_to_uri(f"NCIT:{code}", NAMESPACES))
self.graph.add((uri, SKOS.broader, sc_uri))
see_also = f"https://ncit.nci.nih.gov/ncitbrowser/pages/concept_details.jsf?dictionary=NCI%20Thesaurus&code={tokens[0]}"
self.graph.add((uri, RDFS.seeAlso, Literal(see_also)))
self.graph.add((uri, SKOS.inScheme, cs_uri))
with open('ncit-termci.ttl', 'w') as file:
file.write(self.graph.serialize(format='turtle').decode('utf-8'))
def get_concept_reference_by_id(curie: str, request: Request,
response: Response):
graph: TccmGraph = request.app.state.graph
new_value = unquote(curie_to_uri(curie))
records = graph.get_concept_references_by_value(
ConceptReferenceKeyName.curie, new_value, SearchModifier.equals)
if not records:
raise HTTPException(
status_code=404,
detail=f"ConceptReference curie={curie} not found.")
response.headers['Link'] = build_jsonld_link_header(
str(request.base_url) + request.scope.get("root_path"),
'termci_schema')
return records[0]
def get_concept_references(key: ConceptReferenceKeyName, value: str,
modifier: SearchModifier, request: Request,
response: Response):
graph: TccmGraph = request.app.state.graph
new_value = value
if key == ConceptReferenceKeyName.uri:
new_value = unquote(value)
elif key == ConceptReferenceKeyName.curie:
new_value = unquote(curie_to_uri(value))
records = graph.get_concept_references_by_value(key, new_value, modifier)
if not records:
raise HTTPException(
status_code=404,
detail=f"ConceptReference {key}={value}|{modifier} not found.")
response.headers['Link'] = build_jsonld_link_header(
str(request.base_url) + request.scope.get("root_path"),
'termci_schema')
return records
def test_curie_to_uri_ncit():
curie = "NCIT:C7227"
uri = curie_to_uri(curie, NAMESPACES)
assert uri == "http://purl.obolibrary.org/obo/NCIT_C7227"
def test_curie_to_uri_uri():
curie = "https://ontologies-r.us/ontology/ICD-O-3-M/800"
uri = curie_to_uri(curie, NAMESPACES)
assert uri == "https://ontologies-r.us/ontology/ICD-O-3-M/800"