7:- module(disgenet,
8 [
9 gene/1,
10 disease/1,
11
12 refers_to/2,
13 has_evidence/2,
14
15 association/1,
16 gene_disease_association/1,
17 gene_disease_association/3,
18 gene_disease_association/4,
19
20 disease_pair_by_shared_gene/3
21 ]). 22
23:- use_module(library(sparqlprog)). 24:- use_module(library(semweb/rdf11)). 25
26:- use_module(library(sparqlprog/owl_types)). 27:- use_module(library(sparqlprog/ontologies/sio),[has_evidence/2, has_source/2, refers_to/2, has_measurement_value/2]). 28:- use_module(library(typedef)). 29
30:- type disgenet_protein ---> atomic_iri.
31:- type disgenet_annotation ---> atomic_iri.
32:- type disgenet_gene ---> atomic_iri.
33:- type disgenet_publication ---> atomic_iri.
34
35:- sparql_endpoint( disgenet, 'http://rdf.disgenet.org/sparql/'). 36
37:- rdf_register_prefix(disgenet,'http://rdf.disgenet.org/'). 38:- rdf_register_prefix(disgenet_gene_disease_association,'http://rdf.disgenet.org/resource/gene_disease_association/'). 39:- rdf_register_prefix(sio, 'http://semanticscience.org/resource/SIO_'). 40:- rdf_register_prefix(ncitevs, 'http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#'). 41:- rdf_register_prefix(umls, 'http://linkedlifedata.com/resource/umls/id/'). 42:- rdf_register_prefix(ncbigene, 'http://identifiers.org/ncbigene/').
47disease(D) :- rdf(D,rdf:type,ncitevs:'C7057').
50gene(G) :- rdf(G,rdf:type,ncitevs:'C16612').
53association(A) :- rdfs_individual_of(A,sio:'000897').
60gene_disease_association(A) :- rdfs_individual_of(A,sio:'001121').
61gene_disease_association(A,G,D) :- gene_disease_association(A),refers_to(A,G),gene(G),refers_to(A,D),disease(D).
62gene_disease_association(A,G,D,P) :- gene_disease_association(A),refers_to(A,G),gene(G),refers_to(A,D),disease(D),has_evidence(A,P).
67disease_pair_by_shared_gene(D1,D2,G) :- gene_disease_association(_,G,D1),gene_disease_association(_,G,D2).
68
wrapper for disgenet endpoint
See http://www.disgenet.org/rdf
*/