1/*
    2
    3  @Deprecated
    4
    5  now in its own pack
    6  
    7expose a subclass of dbpedia for demo purposes
    8
    9See examples/wikidata-examples.sh
   10
   11  For complete ontology use rdfs2pl
   12
   13Note: this module uses macros to generate predicates. For every pname_wid/2 and cname_wid/2, predicates will be generated 
   14  
   15*/
   16
   17:- module(wikidata,
   18          [
   19
   20           property_constraint_pv/4,
   21           
   22           var_drug_condition/4,
   23           
   24           enlabel/2,
   25           enlabelp/2,
   26           enlabel_any/2,
   27           exact_match/2
   28
   29           ]).   30
   31:- use_module(library(sparqlprog)).   32:- use_module(library(semweb/rdf11)).   33
   34:- sparql_endpoint( wd, 'http://query.wikidata.org/sparql').   35
   36:- rdf_register_prefix(foaf,'http://xmlns.com/foaf/0.1/').   37:- rdf_register_prefix(dbont,'http://dbpedia.org/ontology/').   38%:- rdf_register_prefix(dcterms,'http://purl.org/dc/terms').
   39:- rdf_register_prefix(wikipathways,'http://vocabularies.wikipathways.org/wp#').   40:- rdf_register_prefix(obo,'http://purl.obolibrary.org/obo/').   41:- rdf_register_prefix(so,'http://purl.obolibrary.org/obo/SO_').   42
   43% https://www.mediawiki.org/wiki/Wikibase/Indexing/RDF_Dump_Format#Prefixes_used
   44:- rdf_register_prefix(wd,'http://www.wikidata.org/entity/').   45:- rdf_register_prefix(wdt,'http://www.wikidata.org/prop/direct/').   46:- rdf_register_prefix(wbont,'http://wikiba.se/ontology#').   47
   48:- rdf_register_prefix(instance_of,'http://www.wikidata.org/prop/direct/P31').   49
   50user:term_expansion(pname_wid(P,Id),
   51                    [(   Head :- Body),
   52                     (   Head_trans :- Body_trans),
   53                     (   Head_s :- Body_s),
   54                     (   Head_ps :- Body_ps),
   55                     (   Head_q :- Body_q),
   56                     (   Head_iri :- true),
   57                     (   Head_eiri :- true),
   58                     (   :- initialization(export(P_trans/2), now)),
   59                     (   :- initialization(export(P_s/2), now)),
   60                     (   :- initialization(export(P_ps/2), now)),
   61                     (   :- initialization(export(P_q/2), now)),
   62                     (   :- initialization(export(P_iri/1), now)),
   63                     (   :- initialization(export(P_eiri/1), now)),
   64                     (   :- initialization(export(P/2), now))
   65                    ]) :-
   66
   67        % e.g. p9 ==> P9
   68        upcase_atom(Id,Frag),
   69        
   70        
   71        % Truthy assertions about the data, links entity to value directly
   72        % wd:Q2  wdt:P9 <http://acme.com/> ==> P9(Q2,"...")
   73        Head =.. [P,S,O],
   74        atom_concat('http://www.wikidata.org/prop/direct/',Frag,Px),
   75        Body = rdf(S,Px,O),
   76
   77        atom_concat(P,'_transitive',P_trans),
   78        Head_trans =.. [P_trans,S,O],
   79        Body_trans = rdf_path(S,zeroOrMore(Px),O),
   80        
   81        
   82        % p: Links entity to statement
   83        % wd:Q2 p:P9 wds:Q2-82a6e009 ==> P9_statement(Q2,wds:....)
   84        atom_concat(P,'_e2s',P_s),
   85        Head_s =.. [P_s,S,O],
   86        atom_concat('http://www.wikidata.org/prop/',Frag,Px_s),
   87        Body_s = rdf(S,Px_s,O),
   88
   89        atom_concat(P,'_iri',P_iri),
   90        Head_iri =.. [P_iri,Px],
   91
   92        atom_concat('http://www.wikidata.org/entity/',Frag,Pe),        
   93        atom_concat(P,'_eiri',P_eiri),
   94        Head_eiri =.. [P_eiri,Pe],
   95        
   96        % ps: Links value from statement
   97        % wds:Q3-24bf3704-4c5d-083a-9b59-1881f82b6b37 ps:P8 "-13000000000-01-01T00:00:00Z"^^xsd:dateTime
   98        atom_concat(P,'_s2v',P_ps),
   99        Head_ps =.. [P_ps,S,O],
  100        atom_concat('http://www.wikidata.org/prop/statement/',Frag,Px_ps),
  101        Body_ps = rdf(S,Px_ps,O),
  102        
  103        % pq: Links qualifier from statement node
  104        % wds:Q3-24bf3704-4c5d-083a-9b59-1881f82b6b37 pq:P8 "-13000000000-01-01T00:00:00Z"^^xsd:dateTime
  105        % => P8_q(wds:..., "..."^^...)
  106        atom_concat(P,'_s2q',P_q),
  107        Head_q =.. [P_q,S,O],
  108        atom_concat('http://www.wikidata.org/prop/qualifier/',Frag,Px_q),
  109        Body_q = rdf(S,Px_q,O).
  110
  111        
  112
  113user:term_expansion(cname_wid(C,Id),
  114                    [Rule,
  115                     RuleInf,
  116                     RuleIsa,
  117                     (   Head_iri :- true),
  118                     (:- initialization(export(InfC/1), now)),
  119                     (:- initialization(export(SubC/1), now)),
  120                     (:- initialization(export(C_iri/1), now)),
  121                     (:- initialization(export(C/1), now))
  122                     ]) :-
  123        upcase_atom(Id,Frag),
  124        atom_concat('http://www.wikidata.org/entity/',Frag,Cx),
  125        
  126        Head =.. [C,I],
  127        Body = rdf(I,'http://www.wikidata.org/prop/direct/P31',Cx),
  128        Rule = (Head :- Body),
  129
  130        atom_concat(C,'_iri',C_iri),
  131        Head_iri =.. [C_iri,Cx],
  132        
  133        atom_concat(C,'_inf',InfC),
  134        Head2 =.. [InfC,I],
  135        Body2 = rdf(I,('http://www.wikidata.org/prop/direct/P31'/zeroOrMore('http://www.wikidata.org/prop/direct/P279')),Cx),
  136        RuleInf = (Head2 :- Body2),
  137        
  138        atom_concat('isa_',C,SubC),
  139        Head3 =.. [SubC,I],
  140        Body3 = rdf(I,zeroOrMore('http://www.wikidata.org/prop/direct/P279'),Cx),
  141        RuleIsa = (Head3 :- Body3).
  142
  143
  144enlabel(E,N) :- label(E,N),lang(N)="en".
  145enlabelp(E,N) :- rdf(X,wbont:directClaim,E),enlabel(X,N).
  146enlabel_any(E,N) :- enlabel(E,N).
  147enlabel_any(E,N) :- enlabelp(E,N).
  148
  149
  150
  151% --------------------
  152% classes
  153% --------------------
  154
  155% geography
  156
  157% disease
  158%cancer(I) :- rdf(I,instance_of:'',wd:'Q12078').
  159%:- initialization(export(cancer/1), now).
  160
  161% --------------------
  162% predicates
  163% --------------------
  164
  165% meta
  166subproperty_of(S,O) :- rdf(S,'http://www.wikidata.org/prop/direct/P1647',O).
  167%exact_match(S,O) :- rdf(S,'http://www.wikidata.org/prop/direct/P2888',O).
  168
  169% info
  170%author(S,O) :- rdf(S,'http://www.wikidata.org/prop/direct/P50',O).
  171
  172% geo
  173%coordinate_location(S,O) :- rdf(S,'http://www.wikidata.org/prop/direct/P625',O).
  174
  175
  176
  177% PROPS
  178
  179% meta
  180pname_wid(instance_of, p31).
  181pname_wid(subclass_of, p279).
  182pname_wid(equivalent_property, p1628).
  183pname_wid(property_constraint, p2302).
  184
  185property_constraint_pv(P,C,PP,V) :-
  186        property_constraint_e2s(P,S),
  187        rdf(S,PP,V),
  188        property_constraint_s2v(S,C).
  189
  190% general
  191pname_wid(author, p50).
  192pname_wid(exact_match, p2888).
  193
  194% geo
  195pname_wid(coordinate_location, p625).
  196
  197% bio
  198% IDs
  199pname_wid(hp_id, p3841).
  200pname_wid(envo_id, p3859).
  201pname_wid(doid_id, p699).
  202pname_wid(chebi_id, p683).
  203pname_wid(uniprot_id, p352).
  204pname_wid(ncbigene_id, p351).
  205pname_wid(ipr_id, p2926).
  206pname_wid(civic_id, p3329).
  207pname_wid(ro_id, p3590).
  208pname_wid(mesh_id, p486).
  209pname_wid(go_id, p686).
  210pname_wid(ncbitaxon_id, p685).
  211pname_wid(uberon_id, p1554).
  212pname_wid(umls_id, p2892).
  213
  214% rels
  215pname_wid(encodes, p688).
  216pname_wid(genetic_association, p2293).
  217pname_wid(treated_by_drug, p2176).
  218pname_wid(symptoms, p780).
  219pname_wid(pathogen_transmission_process, p1060).
  220pname_wid(has_cause, p828).
  221pname_wid(biological_variant_of, p3433).
  222pname_wid(has_part, p527).
  223
  224% https://www.wikidata.org/wiki/Wikidata:SPARQL_query_service/queries/examples#Get_known_variants_reported_in_CIViC_database_(Q27612411)_of_genes_reported_in_a_Wikipathways_pathway:_Bladder_Cancer_(Q30230812)
  225pname_wid(positive_therapeutic_predictor, p3354).
  226pname_wid(negative_therapeutic_predictor, p3355).
  227pname_wid(positive_diagnostic_predictor, p3356).
  228pname_wid(negative_diagnostic_predictor, p3357).
  229pname_wid(positive_prognostic_predictor, p3358).
  230pname_wid(negative_prognostic_predictor, p3359).
  231pname_wid(medical_condition_treated, p2175).
  232
  233% beacon
  234pname_wid(physically_interacts_with, p129).
  235pname_wid(location, p276).
  236pname_wid(manifestation_of, p1557).
  237pname_wid(part_of, p361).
  238pname_wid(followed_by, p156).
  239pname_wid(product_or_material_produced, p1056).
  240pname_wid(uses, p2283).
  241pname_wid(has_effect, p1542).
  242pname_wid(drug_used_for_treatment, p2176).
  243pname_wid(found_in_taxon, p703).
  244pname_wid(ortholog, p684).
  245pname_wid(biological_process, p682).
  246pname_wid(cell_component, p681).
  247pname_wid(molecular_function, p680).
  248pname_wid(has_quality, p1552).
  249pname_wid(regulates, p128).
  250
  251
  252    
  253% CLASSES
  254
  255% geo
  256cname_wid(geographic_entity, q27096213).
  257cname_wid(continent, q5107).
  258cname_wid(country, q6256).
  259cname_wid(city, q515).
  260pname_wid(population, p1082).
  261pname_wid(part_of_continent, p30).
  262
  263
  264% bio
  265cname_wid(cancer, q12078).
  266cname_wid(disease, q12136).
  267cname_wid(infectious_disease, q18123741).
  268
  269cname_wid(chemical_compound, q11173).
  270cname_wid(chemical_element, q11344).
  271cname_wid(drug, q12140).
  272
  273cname_wid(symptom, q169872).
  274cname_wid(medical_finding, q639907).
  275cname_wid(trait, q1211967).
  276cname_wid(pathway, q4915012).
  277cname_wid(macromolecular_complex, qQ22325163).
  278cname_wid(gene, qQ7187).
  279cname_wid(gene_product, qQ424689).
  280cname_wid(sequence_variant, qQ15304597).
  281
  282cname_wid(therapy, q179661).
  283cname_wid(medical_procedure, qQ796194).
  284
  285
  286% random
  287cname_wid(power_station, q159719).
  288
  289% TODO
  290nary(ptp_var_drug_condition, positive_therapeutic_predictor, medical_condition_treated).
  291
  292
  293
  294var_drug_condition(V,D,C,positive_therapeutic_predictor) :-
  295        positive_therapeutic_predictor_e2s(V,S),
  296        medical_condition_treated_s2q(S,C),
  297        positive_therapeutic_predictor_s2v(S,D)