1:- module(togovar,
    2          [
    3           snv/1,
    4           reference_allele/2,
    5           alternative_allele/2,
    6           snv_interpreted_condition/2,
    7           snv_with_clinvar/5,
    8           frequency/1,
    9           dataset/2,
   10           snv_frequency/3,
   11           snv_japanese_frequency/5
   12          ]).   13
   14:- use_module(library(semweb/rdf11)).   15
   16:- use_module(library(sparqlprog/ontologies/faldo)).   17
   18%:- sparql_endpoint(togovar, 'https://togovar.biosciencedbc.jp/sparql').
   19:- sparql_endpoint(togovar, 'https://togovar.l5dev.jp/sparql').   20
   21:- rdf_register_prefix(rdfs, 'http://www.w3.org/2000/01/rdf-schema#').   22:- rdf_register_prefix(togovar, 'http://togovar.biosciencedbc.jp/variant/').   23:- rdf_register_prefix(tgvo, 'http://togovar.biosciencedbc.jp/ontology/').   24:- rdf_register_prefix(obo, 'http://purl.obolibrary.org/obo/').   25:- rdf_register_prefix(m2r, 'http://med2rdf.org/ontology/med2rdf#').   26:- rdf_register_prefix(hco, 'http://identifiers.org/hco/').

 snv(?V) is nondet

V is a single nucleotide variant (SNV)

   31snv(V) :- rdf(V,rdf:type,obo:'SO_0001483').

 reference_allele(?V, ?A) is nondet

single nucleotide variant V has reference allele A

   36reference_allele(V,A) :- snv(V),rdf(V,m2r:reference_allele,A).

 alternative_allele(?V, ?A) is nondet

single nucleotide variant V has alternative allele A

   41alternative_allele(V,A) :- snv(V),rdf(V,m2r:alternative_allele,A).

 snv_interpreted_condition(?V, ?C) is nondet

single nucleotide variant V has ClinVar's interpreted condition C

   46snv_interpreted_condition(V,C) :- rdf(V,tgvo:hasInterpretedCondition,C).

 snv_with_clinvar(?V, ?C) is nondet

single nucleotide variant V located in genomic region between B and E of reference sequence R has ClinVar's interpreted condition C

(example) pl2sparql -u sparqlprog/ontologies/togovar -u sparqlprog/ontologies/faldo -s togovar "snv_with_clinvar(V,198000000,199000000,'http://identifiers.org/hco/1#GRCh37',CL)" "h(V,CL)"

   57snv_with_clinvar(V,B,E,R,CL) :- snv(V),location(V,P),position(P,C),reference(P,R),C >= B,C =< E,snv_interpreted_condition(V,CL).

 frequency(F) is nondet

F is instance of tgvo:Frequency

   62frequency(F) :- rdf(F,rdf:type,tgvo:'Frequency').

 dataset(D) is nondet

single nucleotide variant V is included in dataset D

   67dataset(V,D) :- rdf(V,tgvo:hasFrequency,N),rdf(N,rdfs:label,D).

 snv_frequency(?V, ?D, ?F) is nondet

single nucleotide variant V in dataset D has frequency F

   72snv_frequency(V,D,F) :- rdf(V,tgvo:hasFrequency,N),frequency(N),rdf(N,rdfs:label,D),rdf(N,tgvo:frequency,F).

 snv_japanese_frequency(?V, ?RA, ?AA, ?D, ?F) is nondet

single nucleotide variant V with reference allele RA and alternative allele AA in dataset D has frequency F (example) pl2sparql -u sparqlprog/ontologies/togovar -s togovar "snv_japanese_frequency(togovar:tgv1006196,"T","C",D,F)" "h(D,F)"

   81snv_japanese_frequency(V,RA,AA,D,F) :- snv(V),reference_allele(V,RA),alternative_allele(V,AA),snv_frequency(V,D,F)