1:- module(uniprot,
    2          [
    3           protein/1,
    4           disease_annotation/1,
    5           has_disease_annotation/2,
    6           natural_variant_annotation/1,
    7           has_natural_variant_annotation/2,
    8           protein_natural_variant_disease/3,
    9           protein_natural_variant_disease_xref/4,
   10           protein_natural_variant_disease_dbsnp/4,
   11           is_dbsnp/1,
   12           
   13           transmembrane_annotation/1,
   14           has_transmembrane_annotation/2,
   15
   16           mnemonic/2,
   17           encoded_by/2,
   18
   19           annotation_range/4,
   20           protein_annotation_range/5,
   21           protein_begin/3,
   22
   23           in_taxon/2,
   24           in_human/1,
   25
   26           reviewed/1,
   27           annotation/2,
   28           database/2,
   29
   30           substitution/2,
   31
   32           xref/2,
   33           xref_interpro/2,
   34           xref_panther/2,
   35           xref_pro/2,
   36           is_interpro/1,
   37           is_panther/1,
   38           is_pro/1,
   39           has_full_name/2,
   40
   41           pref_label/2,
   42           recommended_name/2
   43           ]).   44
   45:- use_module(library(sparqlprog/ontologies/faldo)).   46:- use_module(library(sparqlprog)).   47
   48:- use_module(library(sparqlprog/owl_types)).   49:- use_module(library(typedef)).   50
   51:- rdf_register_prefix(up,'http://purl.uniprot.org/core/').   52:- rdf_register_prefix(updb,'http://purl.uniprot.org/database/').   53:- rdf_register_prefix(uniprot,'http://purl.uniprot.org/uniprot/').   54:- rdf_register_prefix(uptaxon,'http://purl.uniprot.org/taxonomy/').   55:- rdf_register_prefix(skos, 'http://www.w3.org/2004/02/skos/core#').   56:- rdf_register_prefix(embl_csd, 'http://purl.uniprot.org/embl-cds/').   57
   58:- sparql_endpoint( uniprot, 'http://sparql.uniprot.org/sparql').   59
   60
   61:- type uniprot_protein ---> atomic_iri.
   62:- type uniprot_annotation ---> atomic_iri.
   63:- type uniprot_disease_annotation ---> uniprot_annotation.
   64:- type uniprot_xref ---> atomic_iri.
   65:- type uniprot_term ---> atomic_iri.
   66:- type uniprot_sequence_string ---> string ^^ xsd_type.

 protein(?P:uniprot_protein) is nondet

true if P is a protein entry in uniprot

   72protein(C) :- rdf(C,rdf:type,up:'Protein').

 disease_annotation(?A:uniprot_disease_annotation) is nondet

true if A is a disease annotation in uniprot

   79disease_annotation(A) :- rdf(A,rdf:type,up:'Disease_Annotation').

 has_disease_annotation(?P:uniprot_protein, ?A:uniprot_disease_annotation) is nondet

protein P links to disease annotation A

   85has_disease_annotation(P,A) :- annotation(P,A),rdf(A,rdf:type,up:'Disease_Annotation').

 natural_variant_annotation(?A:uniprot_annotation) is nondet

A is a natural variant annotation

   92natural_variant_annotation(A) :- rdf(A,rdf:type,up:'Natural_Variant_Annotation').

 has_natural_variant_annotation(?P:uniprot_protein, ?A:uniprot_annotation) is nondet

protein P links to natural variant annotation A

   98has_natural_variant_annotation(P,A) :- annotation(P,A),rdf(A,rdf:type,up:'Natural_Variant_Annotation').

 protein_natural_variant_disease(?P:uniprot_protein, ?A:uniprot_annotation, ?D) is nondet

protein P links to disease D via natural variant annotation A

  105protein_natural_variant_disease(P,A,D) :- annotation(P,A),rdf(A,rdf:type,up:'Natural_Variant_Annotation'),rdf(A,skos:related,D).

 protein_natural_variant_disease_xref(?P:uniprot_protein, ?A:uniprot_annotation, ?D, ?X:uniprot_xref) is nondet

protein P links to disease D via natural variant annotation A with xref (e.g. dbSNP) X

  112protein_natural_variant_disease_xref(P,A,D,X) :- annotation(P,A),rdf(A,rdf:type,up:'Natural_Variant_Annotation'),rdf(A,skos:related,D),rdf(A,rdfs:seeAlso,X).

 protein_natural_variant_disease_dbsnp(?P:uniprot_protein, ?A:uniprot_annotation, ?D, ?X:uniprot_xref) is nondet

protein P links to disease D via natural variant annotation A with dbSNP xref X

  118protein_natural_variant_disease_dbsnp(P,A,D,X) :- protein_natural_variant_disease_xref(P,A,D,X), is_dbsnp(X).

 is_dbsnp(?X:uniprot_xref) is nondet

  122is_dbsnp(X) :- rdf(X,up:database,updb:dbSNP).

 transmembrane_annotation(?A:uniprot_annotation) is nondet

  127transmembrane_annotation(A) :- rdf(A,rdf:type,up:'Transmembrane_Annotation').

 has_transmembrane_annotation(?P:uniprot_protein, ?A:uniprot_annotation) is nondet

  130has_transmembrane_annotation(P,A) :- annotation(P,A),rdf(A,rdf:type,up:'Transmembrane_Annotation').

 mnemonic(?C, ?N) is nondet

  135mnemonic(C,N) :- rdf(C,up:mnemonic,N).

 encoded_by(?P:uniprot_protein, ?G) is nondet

  138encoded_by(P,G) :- rdf(P,up:encodedBy,G).

 recommended_name(?P:uniprot_protein, ?N) is nondet

  142recommended_name(P,N) :- rdf(P,up:recommendedName,N).

 has_full_name(?P:uniprot_protein, ?X) is nondet

  145has_full_name(P,X) :- rdf(P,up:recommendedName,N), rdf(N,up:fullName,X).
  146
  147% for genes only

 pref_label(?E, ?N) is nondet

  150pref_label(E,N) :- rdf(E,skos:prefLabel,N).

 in_taxon(?P:uniprot_protein, ?T) is nondet

  154in_taxon(P,T) :- rdf(P,up:organism,T).

 annotation(?P:uniprot_protein, ?A:uniprot_annotation) is nondet

  158annotation(P,A) :- rdf(P,up:annotation,A).

 database(?X:uniprot_xref, ?D) is nondet

  161database(X,D) :- rdf(X,up:database,D).

 protein_annotation_range(?P:uniprot_protein, ?A, ?B, ?E, ?R) is nondet

  168protein_annotation_range(P,A,B,E,R) :-
  169        protein_annotation(P,A),
  170        annotation_range(P,B,E,R).

 annotation_range(?P:uniprot_annotation, ?B, ?E, ?R) is nondet

  174annotation_range(P,B,E,R) :-
  175        rdf(P,up:range,I),
  176        begin_coord(I,B,R),
  177        end_coord(I,E,R).

 protein_begin(?P:uniprot_protein, ?B, ?R) is nondet

  180protein_begin(P,B,R) :-
  181        rdf(P,up:range,I),
  182        begin_coord(I,B,R).

 classified_with(P:uniprot_protein, T:uniprot_term) is nondet

  187classified_with(P,T) :- rdf(P,up:classifiedWith,T).

 substitution(?A:uniprot_annotation, ?S:uniprot_sequence_string) is nondet

annotation A is associated with a substitution S

  194substitution(A,S) :- rdf(A,up:substitution,S).

 xref(?P:uniprot_protein, ?X:uniprot_xref) is nondet

P has xref X

  202xref(P,X) :- rdf(P,rdfs:seeAlso,X).

 xref_interpro(?P:uniprot_protein, ?X) is nondet

P has xref X where X is in interpro

  208xref_interpro(P,X) :- xref(P,X),is_interpro(X).

 xref_panther(?P:uniprot_protein, ?X) is nondet

P has xref X is in panther

  214xref_panther(P,X) :- xref(P,X),is_panther(X).

 xref_pro(?P:uniprot_protein, ?X:uniprot_xref) is nondet

P has xref X where X is in uniprot

  220xref_pro(P,X) :- xref(P,X),is_pro(X).

 is_interpro(?X:uniprot_xref) is nondet

X is an xref in the UniProt database

  229is_interpro(X) :- database(X,updb:'InterPro').

 is_panther(?X:uniprot_xref) is nondet

X is an xref in the PANTHER database

  235is_panther(X) :- database(X,updb:'PANTHER').

 is_pro(?X:uniprot_xref) is nondet

X is an xref in the PRO database

  241is_pro(X) :- database(X,updb:'PRO').

 in_human(?P:uniprot_protein) is nondet

convenience predicate, true if P is a human protein

  250in_human(P) :- rdf(P,up:organism,uptaxon:'9606').
  251
  252
  253%! reviewed(?P : uniprot_protein) is nondet.
  254%
  255%  P is a protein with review status of true
  256%
  257reviewed(P) :- rdf(P,up:reviewed,true^^xsd:boolean).
  258
  259
  260/*
  261
  262  in_human(P),annotation(P,A),ann_begin(A,B,R),substitution(A,\"F\")
  263
  264  
  265  */