uniprot.pl

    1:- module(uniprot,
    2          [
    3           protein/1,
    4           in_reference_proteome/1,
    5           has_annotation_type/3,
    6           disease_annotation/1,
    7           has_disease_annotation/2,
    8           natural_variant_annotation/1,
    9           has_natural_variant_annotation/2,
   10           protein_natural_variant_disease/3,
   11           protein_natural_variant_disease_xref/4,
   12           protein_natural_variant_disease_dbsnp/4,
   13           is_dbsnp/1,
   14
   15           has_ptm_annotation/2,
   16
   17           modification_annotation/1,
   18           peptide_annotation/1,
   19           transmembrane_annotation/1,
   20           has_transmembrane_annotation/2,
   21
   22           classified_with/2,
   23           classified_with_go/2,
   24           classified_with_go_mf/2,
   25           classified_with_go_catalysis/2,
   26           has_catalytic_activity/2,
   27           protein_has_enzyme_class/2,
   28           protein_has_catalyzed_reaction/2,
   29           enzyme_class/2,
   30           catalyzed_reaction/2,
   31
   32           mnemonic/2,
   33           encoded_by/2,
   34
   35           annotation_range/4,
   36           protein_annotation_range/5,
   37           protein_begin/3,
   38
   39           in_taxon/2,
   40           in_human/1,
   41
   42           reviewed/1,
   43           annotation/2,
   44           database/2,
   45
   46           substitution/2,
   47
   48           xref/2,
   49           xref_intersection_count/3,
   50           xref_union_count/3,
   51           xref_in/3,
   52           xref_interpro/2,
   53           xref_panther/2,
   54           xref_pro/2,
   55           xref_araport/2,
   56           xref_tair/2,
   57           is_interpro/1,
   58           is_panther/1,
   59           is_pro/1,
   60           is_organism_database/1,
   61           is_organism_database/2,
   62           is_xenbase/1,
   63           is_wormbase/1,
   64           has_full_name/2,
   65
   66           pref_label/2,
   67           recommended_name/2,
   68
   69           rhea_count/2,
   70
   71           uniprot_class/1,
   72           predicate_summary/5
   73           ]).   74
   75:- use_module(library(sparqlprog/ontologies/faldo)).   76:- use_module(library(sparqlprog)).   77
   78:- use_module(library(sparqlprog/owl_types)).   79:- use_module(library(typedef)).   80
   81:- rdf_register_prefix(up,'http://purl.uniprot.org/core/').   82:- rdf_register_prefix(updb,'http://purl.uniprot.org/database/').   83:- rdf_register_prefix(uniprot,'http://purl.uniprot.org/uniprot/').   84:- rdf_register_prefix(uniprotkw,'http://purl.uniprot.org/keywords/').   85:- rdf_register_prefix(uniprot_annotation,'http://purl.uniprot.org/annotation/').   86:- rdf_register_prefix(uptaxon,'http://purl.uniprot.org/taxonomy/').   87:- rdf_register_prefix(interpro,'http://purl.uniprot.org/interpro/').   88:- rdf_register_prefix(skos, 'http://www.w3.org/2004/02/skos/core#').   89:- rdf_register_prefix(embl_cds, 'http://purl.uniprot.org/embl-cds/').   90:- rdf_register_prefix(rhea, 'http://rdf.rhea-db.org/').   91:- rdf_register_prefix(enzyme, 'http://purl.uniprot.org/enzyme/').   92:- rdf_register_prefix('GO', 'http://purl.obolibrary.org/obo/GO_').   93
   94:- sparql_endpoint( uniprot, 'http://sparql.uniprot.org/sparql').   95
   96:- type uniprot_protein ---> atomic_iri.
   97:- type uniprot_annotation ---> atomic_iri.
   98:- type uniprot_disease_annotation ---> uniprot_annotation.
   99:- type uniprot_variant_annotation ---> uniprot_annotation.
  100:- type uniprot_xref ---> atomic_iri.
  101:- type uniprot_term ---> atomic_iri.
  102:- type uniprot_sequence_string ---> string ^^ xsd_type.
  103
  104uniprot_class(C) :-
  105        rdf(C,rdf:type,owl:'Class'),
  106        str_starts(str(C),'http://purl.uniprot.org/core/').
  107
  108predicate_summary(P,ST,OT,Num,1) :-
  109        ??(uniprot,
  110           rdf(P,rdf:type,owl:'ObjectProperty')),
  111        format('# ~w',[P]),
  112        ??(uniprot,
  113           uniprot_class(ST)),
  114        ??(uniprot,
  115           exists(rdf(_,rdf:type,ST))),
  116        format('# ~w',[ST]),
  117        ??(uniprot,
  118           exists( (rdf(X,rdf:type,ST),rdf(X,P,_)))),
  119        format('#f ~w',[P]),
  120        ??(uniprot,
  121           aggregate_group(count(O),
  122                           [OT],
  123                           (   rdf(S,rdf:type,ST),rdf(S,P,O),rdf(O,rdf:type,OT)),
  124                           Num)),
  125        format('# ~w',[P/Num]).

protein(?P:uniprot_protein) is nondet: true if P is a protein entry in uniprot

  134protein(C) :- rdf(C,rdf:type,up:'Protein').
  135
  136in_reference_proteome(C) :- rdf(C,up:classifiedWith,uniprotkw:'1185').

has_annotation_type(?P:uniprot_protein, ?A:uniprot_annotation, ?T:owl_class) is nondet

  140has_annotation_type(P,A,T) :- annotation(P,A),rdf(A,rdf:type,T).

disease_annotation(?A:uniprot_disease_annotation) is nondet: true if A is a disease annotation in uniprot

  146disease_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

  152has_disease_annotation(P,A) :- annotation(P,A),rdf(A,rdf:type,up:'Disease_Annotation').
  153
  154
  155has_ptm_annotation(P,A) :-
  156        annotation(P,A),
  157        rdf(A,rdf:type,up:'PTM_Annotation').

natural_variant_annotation(?A:uniprot_annotation) is nondet: A is a natural variant annotation

  164natural_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

  170has_natural_variant_annotation(P,A) :- annotation(P,A),rdf(A,rdf:type,up:'Natural_Variant_Annotation').

protein_natural_variant_disease(?P:uniprot_protein, ?V:uniprot_variant_annotation, ?D) is nondet: protein P links to disease D via natural variant annotation A

  177protein_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

  184protein_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

  190protein_natural_variant_disease_dbsnp(P,A,D,X) :- protein_natural_variant_disease_xref(P,A,D,X), is_dbsnp(X).

modification_annotation(?A:uniprot_annotation) is nondet

  194modification_annotation(A) :- rdfs_individual_of(A,up:'Modification_Annotation').

peptid_annotation(?A:peptide_annotation) is nondet

  198peptide_annotation(A) :- rdfs_individual_of(A,up:'Peptide_Annotation').

transmembrane_annotation(?A:uniprot_annotation) is nondet

  202transmembrane_annotation(A) :- rdf(A,rdf:type,up:'Transmembrane_Annotation').

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

  205has_transmembrane_annotation(P,A) :- annotation(P,A),rdf(A,rdf:type,up:'Transmembrane_Annotation').

has_catalytic_activity(?P:uniprot_protein, ?CA:catalytic_activity) is nondet

  208has_catalytic_activity(P,CA) :- annotation(P,Ann),rdf(Ann,up:catalyticActivity,CA).
  209
  210
  211catalyzed_reaction(CA,R) :- rdf(CA,up:catalyzedReaction,R).
  212enzyme_class(CA,R) :- rdf(CA,up:enzymeClass,R).
  213
  214% rhea
  215protein_has_catalyzed_reaction(P,R) :- has_catalytic_activity(P,A),catalyzed_reaction(A,R).
  216protein_has_enzyme_class(P,R) :- has_catalytic_activity(P,A),enzyme_class(A,R).

mnemonic(?C, ?N) is nondet

  221mnemonic(C,N) :- rdf(C,up:mnemonic,N).

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

  224encoded_by(P,G) :- rdf(P,up:encodedBy,G).

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

  228recommended_name(P,N) :- rdf(P,up:recommendedName,N).

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

  231has_full_name(P,X) :- rdf(P,up:recommendedName,N), rdf(N,up:fullName,X).
  232
  233% for genes only

pref_label(?E, ?N) is nondet

  236pref_label(E,N) :- rdf(E,skos:prefLabel,N).

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

  240in_taxon(P,T) :- rdf(P,up:organism,T).

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

  244annotation(P,A) :- rdf(P,up:annotation,A).

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

  247database(X,D) :- rdf(X,up:database,D).

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

  254protein_annotation_range(P,A,B,E,R) :-
  255        annotation(P,A),
  256        annotation_range(A,B,E,R).

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

  260annotation_range(P,B,E,R) :-
  261        rdf(P,up:range,I),
  262        begin_coord(I,B,R),
  263        end_coord(I,E,R).

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

  266protein_begin(P,B,R) :-
  267        rdf(P,up:range,I),
  268        begin_coord(I,B,R).

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

  273classified_with(P,T) :- rdf(P,up:classifiedWith,T).
  274
  275classified_with_go(P,T) :- rdf(P,up:classifiedWith,T),str_starts(str(T),"http://purl.obolibrary.org/obo/GO_").
  276
  277% slow/timeouts
  278classified_with_go_mf(P,T) :- rdf(P,up:classifiedWith,T),rdf(T,zeroOrMore(rdfs:subClassOf),'GO':'0003674').
  279
  280% move to other module? bit of a hack
  281classified_with_go_catalysis(P,T) :- rdf(P,up:classifiedWith,T),rdf(T,'http://purl.obolibrary.org/obo/IAO_0000115',Def),str_starts(Def,'Catalysis of the reaction:').
  282
  283
  284% R is a faldo range
  285alt_sequence_annotation(PF,A) :-
  286        rdf(PF,up:modification,A),
  287        rdf(A,rdf:type,up:'Alternative_Sequence_Annotation').
  288isoform_region(PF,R) :-
  289        alt_sequence_annotation(PF,A),
  290        rdf(A,up:range,R).

substitution(?A:uniprot_annotation, ?S:uniprot_sequence_string) is nondet: annotation A is associated with a substitution S

  300substitution(A,S) :- rdf(A,up:substitution,S).

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

  308xref(P,X) :- rdf(P,rdfs:seeAlso,X).
  309
  310
  311
  312xref_in(P,X,DB) :- xref(P,X),database(X,updb:DB).
  313
  314
  315xref_intersection_count(X1,X2,N) :-
  316        aggregate(count(distinct(P)),(xref(P,X1),xref(P,X2)),N).
  317xref_union_count(X1,X2,N) :-
  318        aggregate(count(distinct(P)),(xref(P,X1);xref(P,X2)),N).

in_human(?P:uniprot_protein) is nondet: convenience predicate, true if P is a human protein

  329in_human(P) :- rdf(P,up:organism,uptaxon:'9606').
  330
  331
  332%! reviewed(?P : uniprot_protein) is nondet.
  333%
  334%  P is a protein with review status of true
  335%
  336reviewed(P) :- rdf(P,up:reviewed,true^^xsd:boolean).
  337
  338
  339rhea_count(R,Num) :-
  340        aggregate(count(P),protein_has_catalyzed_reaction(P,R),Num).
  341
  342
  343/*
  344
  345  in_human(P),annotation(P,A),ann_begin(A,B,R),substitution(A,\"F\")
  346
  347  
  348  */
  349
  350xref_organism_database(P,X) :-
  351        xref(P,X),database(X,D), is_organism_database(D).
  352is_organism_database(X) :-
  353        is_organism_database(X,_).
  354is_organism_database(X,D) :-
  355        database(X,D),
  356        member(D,
  357               [
  358                updb:'HGNC',
  359                updb:'BioCyc',
  360                updb:'MGI',
  361                updb:'RGD',
  362                updb:'SGD',
  363                updb:'FlyBase',
  364                updb:'PomBase',
  365                updb:'dictyBase',
  366                updb:'TAIR',
  367                updb:'ZFIN',
  368                updb:'WormBase',
  369                updb:'Xenbase'
  370               ]).
  371
  372
  373
  374
  375is_ensembl(X) :- database(X,updb:'Ensembl').
  376is_ensemblbacteria(X) :- database(X,updb:'EnsemblBacteria').
  377is_ensemblfungi(X) :- database(X,updb:'EnsemblFungi').
  378is_ensemblplants(X) :- database(X,updb:'EnsemblPlants').
  379is_pdb(X) :- database(X,updb:'PDB').
  380is_abcd(X) :- database(X,updb:'ABCD').
  381is_allergome(X) :- database(X,updb:'Allergome').
  382is_antibodypedia(X) :- database(X,updb:'Antibodypedia').
  383is_arachnoserver(X) :- database(X,updb:'ArachnoServer').
  384is_araport(X) :- database(X,updb:'Araport').
  385is_bmrb(X) :- database(X,updb:'BMRB').
  386is_brenda(X) :- database(X,updb:'BRENDA').
  387is_bgee(X) :- database(X,updb:'Bgee').
  388is_bindingdb(X) :- database(X,updb:'BindingDB').
  389is_biocyc(X) :- database(X,updb:'BioCyc').
  390is_biogrid(X) :- database(X,updb:'BioGRID').
  391is_biogridorcs(X) :- database(X,updb:'BioGRID-ORCS').
  392is_biomuta(X) :- database(X,updb:'BioMuta').
  393is_cazy(X) :- database(X,updb:'CAZy').
  394is_ccds(X) :- database(X,updb:'CCDS').
  395is_cdd(X) :- database(X,updb:'CDD').
  396is_cgd(X) :- database(X,updb:'CGD').
  397is_clae(X) :- database(X,updb:'CLAE').
  398is_compluyeast2dpage(X) :- database(X,updb:'COMPLUYEAST-2DPAGE').
  399is_corum(X) :- database(X,updb:'CORUM').
  400is_cptac(X) :- database(X,updb:'CPTAC').
  401is_cptc(X) :- database(X,updb:'CPTC').
  402is_ctd(X) :- database(X,updb:'CTD').
  403is_carbonyldb(X) :- database(X,updb:'CarbonylDB').
  404is_chembl(X) :- database(X,updb:'ChEMBL').
  405is_chitars(X) :- database(X,updb:'ChiTaRS').
  406is_collectf(X) :- database(X,updb:'CollecTF').
  407is_complexportal(X) :- database(X,updb:'ComplexPortal').
  408is_conoserver(X) :- database(X,updb:'ConoServer').
  409is_depod(X) :- database(X,updb:'DEPOD').
  410is_dip(X) :- database(X,updb:'DIP').
  411is_dmdm(X) :- database(X,updb:'DMDM').
  412is_dnasu(X) :- database(X,updb:'DNASU').
  413is_dosaccobs2dpage(X) :- database(X,updb:'DOSAC-COBS-2DPAGE').
  414is_disgenet(X) :- database(X,updb:'DisGeNET').
  415is_disprot(X) :- database(X,updb:'DisProt').
  416is_drugbank(X) :- database(X,updb:'DrugBank').
  417is_drugcentral(X) :- database(X,updb:'DrugCentral').
  418is_elm(X) :- database(X,updb:'ELM').
  419is_embl(X) :- database(X,updb:'EMBL').
  420is_epd(X) :- database(X,updb:'EPD').
  421is_esther(X) :- database(X,updb:'ESTHER').
  422is_echobase(X) :- database(X,updb:'EchoBASE').
  423is_ensemblmetazoa(X) :- database(X,updb:'EnsemblMetazoa').
  424is_ensemblprotists(X) :- database(X,updb:'EnsemblProtists').
  425is_evolutionarytrace(X) :- database(X,updb:'EvolutionaryTrace').
  426is_expressionatlas(X) :- database(X,updb:'ExpressionAtlas').
  427is_flybase(X) :- database(X,updb:'FlyBase').
  428is_gene3d(X) :- database(X,updb:'Gene3D').
  429is_genecards(X) :- database(X,updb:'GeneCards').
  430is_genedb(X) :- database(X,updb:'GeneDB').
  431is_geneid(X) :- database(X,updb:'GeneID').
  432is_genereviews(X) :- database(X,updb:'GeneReviews').
  433is_genetree(X) :- database(X,updb:'GeneTree').
  434is_genewiki(X) :- database(X,updb:'GeneWiki').
  435is_genevisible(X) :- database(X,updb:'Genevisible').
  436is_genomernai(X) :- database(X,updb:'GenomeRNAi').
  437is_glyconnect(X) :- database(X,updb:'GlyConnect').
  438is_glygen(X) :- database(X,updb:'GlyGen').
  439is_gramene(X) :- database(X,updb:'Gramene').
  440is_guidetopharmacology(X) :- database(X,updb:'GuidetoPHARMACOLOGY').
  441is_hamap(X) :- database(X,updb:'HAMAP').
  442is_hgnc(X) :- database(X,updb:'HGNC').
  443is_hogenom(X) :- database(X,updb:'HOGENOM').
  444is_hpa(X) :- database(X,updb:'HPA').
  445is_ideal(X) :- database(X,updb:'IDEAL').
  446is_imgt_genedb(X) :- database(X,updb:'IMGT_GENE-DB').
  447is_inparanoid(X) :- database(X,updb:'InParanoid').
  448is_intact(X) :- database(X,updb:'IntAct').
  449is_interpro(X) :- database(X,updb:'InterPro').
  450is_kegg(X) :- database(X,updb:'KEGG').
  451is_legiolist(X) :- database(X,updb:'LegioList').
  452is_leproma(X) :- database(X,updb:'Leproma').
  453is_merops(X) :- database(X,updb:'MEROPS').
  454is_mgi(X) :- database(X,updb:'MGI').
  455is_mim(X) :- database(X,updb:'MIM').
  456is_mint(X) :- database(X,updb:'MINT').
  457is_maizegdb(X) :- database(X,updb:'MaizeGDB').
  458is_malacards(X) :- database(X,updb:'MalaCards').
  459is_massive(X) :- database(X,updb:'MassIVE').
  460is_maxqb(X) :- database(X,updb:'MaxQB').
  461is_metosite(X) :- database(X,updb:'MetOSite').
  462is_moondb(X) :- database(X,updb:'MoonDB').
  463is_moonprot(X) :- database(X,updb:'MoonProt').
  464is_niagads(X) :- database(X,updb:'NIAGADS').
  465is_ogp(X) :- database(X,updb:'OGP').
  466is_oma(X) :- database(X,updb:'OMA').
  467is_opentargets(X) :- database(X,updb:'OpenTargets').
  468is_orphanet(X) :- database(X,updb:'Orphanet').
  469is_orthodb(X) :- database(X,updb:'OrthoDB').
  470is_panther(X) :- database(X,updb:'PANTHER').
  471is_patric(X) :- database(X,updb:'PATRIC').
  472is_pcddb(X) :- database(X,updb:'PCDDB').
  473is_pdbsum(X) :- database(X,updb:'PDBsum').
  474is_phibase(X) :- database(X,updb:'PHI-base').
  475is_pir(X) :- database(X,updb:'PIR').
  476is_pirsf(X) :- database(X,updb:'PIRSF').
  477is_pride(X) :- database(X,updb:'PRIDE').
  478is_prints(X) :- database(X,updb:'PRINTS').
  479is_pro(X) :- database(X,updb:'PRO').
  480is_prosite(X) :- database(X,updb:'PROSITE').
  481is_pathwaycommons(X) :- database(X,updb:'PathwayCommons').
  482is_paxdb(X) :- database(X,updb:'PaxDb').
  483is_peptideatlas(X) :- database(X,updb:'PeptideAtlas').
  484is_peroxibase(X) :- database(X,updb:'PeroxiBase').
  485is_pfam(X) :- database(X,updb:'Pfam').
  486is_pharmgkb(X) :- database(X,updb:'PharmGKB').
  487is_pharos(X) :- database(X,updb:'Pharos').
  488is_phosphositeplus(X) :- database(X,updb:'PhosphoSitePlus').
  489is_phylomedb(X) :- database(X,updb:'PhylomeDB').
  490is_plantreactome(X) :- database(X,updb:'PlantReactome').
  491is_pombase(X) :- database(X,updb:'PomBase').
  492is_promex(X) :- database(X,updb:'ProMEX').
  493is_proteomicsdb(X) :- database(X,updb:'ProteomicsDB').
  494is_pseudocap(X) :- database(X,updb:'PseudoCAP').
  495is_rebase(X) :- database(X,updb:'REBASE').
  496is_reproduction2dpage(X) :- database(X,updb:'REPRODUCTION-2DPAGE').
  497is_rgd(X) :- database(X,updb:'RGD').
  498is_rnact(X) :- database(X,updb:'RNAct').
  499is_reactome(X) :- database(X,updb:'Reactome').
  500is_refseq(X) :- database(X,updb:'RefSeq').
  501is_sabiork(X) :- database(X,updb:'SABIO-RK').
  502is_sasbdb(X) :- database(X,updb:'SASBDB').
  503is_sfld(X) :- database(X,updb:'SFLD').
  504is_sgd(X) :- database(X,updb:'SGD').
  505is_signor(X) :- database(X,updb:'SIGNOR').
  506is_smart(X) :- database(X,updb:'SMART').
  507is_smr(X) :- database(X,updb:'SMR').
  508is_string(X) :- database(X,updb:'STRING').
  509is_supfam(X) :- database(X,updb:'SUPFAM').
  510is_swiss2dpage(X) :- database(X,updb:'SWISS-2DPAGE').
  511is_signalink(X) :- database(X,updb:'SignaLink').
  512is_swisslipids(X) :- database(X,updb:'SwissLipids').
  513is_swisspalm(X) :- database(X,updb:'SwissPalm').
  514is_tair(X) :- database(X,updb:'TAIR').
  515is_tcdb(X) :- database(X,updb:'TCDB').
  516is_tigrfams(X) :- database(X,updb:'TIGRFAMs').
  517is_topdownproteomics(X) :- database(X,updb:'TopDownProteomics').
  518is_treefam(X) :- database(X,updb:'TreeFam').
  519is_tuberculist(X) :- database(X,updb:'TubercuList').
  520is_ucd2dpage(X) :- database(X,updb:'UCD-2DPAGE').
  521is_ucsc(X) :- database(X,updb:'UCSC').
  522is_unilectin(X) :- database(X,updb:'UniLectin').
  523is_veupathdb(X) :- database(X,updb:'VEuPathDB').
  524is_vgnc(X) :- database(X,updb:'VGNC').
  525is_wbparasite(X) :- database(X,updb:'WBParaSite').
  526is_world2dpage(X) :- database(X,updb:'World-2DPAGE').
  527is_wormbase(X) :- database(X,updb:'WormBase').
  528is_xenbase(X) :- database(X,updb:'Xenbase').
  529is_zfin(X) :- database(X,updb:'ZFIN').
  530is_dbsnp(X) :- database(X,updb:'dbSNP').
  531is_dictybase(X) :- database(X,updb:'dictyBase').
  532is_eggnog(X) :- database(X,updb:'eggNOG').
  533is_euhcvdb(X) :- database(X,updb:'euHCVdb').
  534is_iptmnet(X) :- database(X,updb:'iPTMnet').
  535is_jpost(X) :- database(X,updb:'jPOST').
  536is_nextprot(X) :- database(X,updb:'neXtProt').
  537is_po(X) :- database(X,updb:'PO').
  538is_mesh(X) :- database(X,updb:'MeSH').
  539is_medgen(X) :- database(X,updb:'MedGen').
  540is_go(X) :- database(X,updb:'go').
  541
  542%%%%
  543
  544xref_ensembl(P,X) :- xref(P,X),database(X,updb:'Ensembl').
  545xref_ensemblbacteria(P,X) :- xref(P,X),database(X,updb:'EnsemblBacteria').
  546xref_ensemblfungi(P,X) :- xref(P,X),database(X,updb:'EnsemblFungi').
  547xref_ensemblplants(P,X) :- xref(P,X),database(X,updb:'EnsemblPlants').
  548xref_pdb(P,X) :- xref(P,X),database(X,updb:'PDB').
  549xref_abcd(P,X) :- xref(P,X),database(X,updb:'ABCD').
  550xref_allergome(P,X) :- xref(P,X),database(X,updb:'Allergome').
  551xref_antibodypedia(P,X) :- xref(P,X),database(X,updb:'Antibodypedia').
  552xref_arachnoserver(P,X) :- xref(P,X),database(X,updb:'ArachnoServer').
  553xref_araport(P,X) :- xref(P,X),database(X,updb:'Araport').
  554xref_bmrb(P,X) :- xref(P,X),database(X,updb:'BMRB').
  555xref_brenda(P,X) :- xref(P,X),database(X,updb:'BRENDA').
  556xref_bgee(P,X) :- xref(P,X),database(X,updb:'Bgee').
  557xref_bindingdb(P,X) :- xref(P,X),database(X,updb:'BindingDB').
  558xref_biocyc(P,X) :- xref(P,X),database(X,updb:'BioCyc').
  559xref_biogrid(P,X) :- xref(P,X),database(X,updb:'BioGRID').
  560xref_biogridorcs(P,X) :- xref(P,X),database(X,updb:'BioGRID-ORCS').
  561xref_biomuta(P,X) :- xref(P,X),database(X,updb:'BioMuta').
  562xref_cazy(P,X) :- xref(P,X),database(X,updb:'CAZy').
  563xref_ccds(P,X) :- xref(P,X),database(X,updb:'CCDS').
  564xref_cdd(P,X) :- xref(P,X),database(X,updb:'CDD').
  565xref_cgd(P,X) :- xref(P,X),database(X,updb:'CGD').
  566xref_clae(P,X) :- xref(P,X),database(X,updb:'CLAE').
  567xref_compluyeast2dpage(P,X) :- xref(P,X),database(X,updb:'COMPLUYEAST-2DPAGE').
  568xref_corum(P,X) :- xref(P,X),database(X,updb:'CORUM').
  569xref_cptac(P,X) :- xref(P,X),database(X,updb:'CPTAC').
  570xref_cptc(P,X) :- xref(P,X),database(X,updb:'CPTC').
  571xref_ctd(P,X) :- xref(P,X),database(X,updb:'CTD').
  572xref_carbonyldb(P,X) :- xref(P,X),database(X,updb:'CarbonylDB').
  573xref_chembl(P,X) :- xref(P,X),database(X,updb:'ChEMBL').
  574xref_chitars(P,X) :- xref(P,X),database(X,updb:'ChiTaRS').
  575xref_collectf(P,X) :- xref(P,X),database(X,updb:'CollecTF').
  576xref_complexportal(P,X) :- xref(P,X),database(X,updb:'ComplexPortal').
  577xref_conoserver(P,X) :- xref(P,X),database(X,updb:'ConoServer').
  578xref_depod(P,X) :- xref(P,X),database(X,updb:'DEPOD').
  579xref_dip(P,X) :- xref(P,X),database(X,updb:'DIP').
  580xref_dmdm(P,X) :- xref(P,X),database(X,updb:'DMDM').
  581xref_dnasu(P,X) :- xref(P,X),database(X,updb:'DNASU').
  582xref_dosaccobs2dpage(P,X) :- xref(P,X),database(X,updb:'DOSAC-COBS-2DPAGE').
  583xref_disgenet(P,X) :- xref(P,X),database(X,updb:'DisGeNET').
  584xref_disprot(P,X) :- xref(P,X),database(X,updb:'DisProt').
  585xref_drugbank(P,X) :- xref(P,X),database(X,updb:'DrugBank').
  586xref_drugcentral(P,X) :- xref(P,X),database(X,updb:'DrugCentral').
  587xref_elm(P,X) :- xref(P,X),database(X,updb:'ELM').
  588xref_embl(P,X) :- xref(P,X),database(X,updb:'EMBL').
  589xref_epd(P,X) :- xref(P,X),database(X,updb:'EPD').
  590xref_esther(P,X) :- xref(P,X),database(X,updb:'ESTHER').
  591xref_echobase(P,X) :- xref(P,X),database(X,updb:'EchoBASE').
  592xref_ensemblmetazoa(P,X) :- xref(P,X),database(X,updb:'EnsemblMetazoa').
  593xref_ensemblprotists(P,X) :- xref(P,X),database(X,updb:'EnsemblProtists').
  594xref_evolutionarytrace(P,X) :- xref(P,X),database(X,updb:'EvolutionaryTrace').
  595xref_expressionatlas(P,X) :- xref(P,X),database(X,updb:'ExpressionAtlas').
  596xref_flybase(P,X) :- xref(P,X),database(X,updb:'FlyBase').
  597xref_gene3d(P,X) :- xref(P,X),database(X,updb:'Gene3D').
  598xref_genecards(P,X) :- xref(P,X),database(X,updb:'GeneCards').
  599xref_genedb(P,X) :- xref(P,X),database(X,updb:'GeneDB').
  600xref_geneid(P,X) :- xref(P,X),database(X,updb:'GeneID').
  601xref_genereviews(P,X) :- xref(P,X),database(X,updb:'GeneReviews').
  602xref_genetree(P,X) :- xref(P,X),database(X,updb:'GeneTree').
  603xref_genewiki(P,X) :- xref(P,X),database(X,updb:'GeneWiki').
  604xref_genevisible(P,X) :- xref(P,X),database(X,updb:'Genevisible').
  605xref_genomernai(P,X) :- xref(P,X),database(X,updb:'GenomeRNAi').
  606xref_glyconnect(P,X) :- xref(P,X),database(X,updb:'GlyConnect').
  607xref_glygen(P,X) :- xref(P,X),database(X,updb:'GlyGen').
  608xref_gramene(P,X) :- xref(P,X),database(X,updb:'Gramene').
  609xref_guidetopharmacology(P,X) :- xref(P,X),database(X,updb:'GuidetoPHARMACOLOGY').
  610xref_hamap(P,X) :- xref(P,X),database(X,updb:'HAMAP').
  611xref_hgnc(P,X) :- xref(P,X),database(X,updb:'HGNC').
  612xref_hogenom(P,X) :- xref(P,X),database(X,updb:'HOGENOM').
  613xref_hpa(P,X) :- xref(P,X),database(X,updb:'HPA').
  614xref_ideal(P,X) :- xref(P,X),database(X,updb:'IDEAL').
  615xref_imgt_genedb(P,X) :- xref(P,X),database(X,updb:'IMGT_GENE-DB').
  616xref_inparanoid(P,X) :- xref(P,X),database(X,updb:'InParanoid').
  617xref_intact(P,X) :- xref(P,X),database(X,updb:'IntAct').
  618xref_interpro(P,X) :- xref(P,X),database(X,updb:'InterPro').
  619xref_kegg(P,X) :- xref(P,X),database(X,updb:'KEGG').
  620xref_legiolist(P,X) :- xref(P,X),database(X,updb:'LegioList').
  621xref_leproma(P,X) :- xref(P,X),database(X,updb:'Leproma').
  622xref_merops(P,X) :- xref(P,X),database(X,updb:'MEROPS').
  623xref_mgi(P,X) :- xref(P,X),database(X,updb:'MGI').
  624xref_mim(P,X) :- xref(P,X),database(X,updb:'MIM').
  625xref_mint(P,X) :- xref(P,X),database(X,updb:'MINT').
  626xref_maizegdb(P,X) :- xref(P,X),database(X,updb:'MaizeGDB').
  627xref_malacards(P,X) :- xref(P,X),database(X,updb:'MalaCards').
  628xref_massive(P,X) :- xref(P,X),database(X,updb:'MassIVE').
  629xref_maxqb(P,X) :- xref(P,X),database(X,updb:'MaxQB').
  630xref_metosite(P,X) :- xref(P,X),database(X,updb:'MetOSite').
  631xref_moondb(P,X) :- xref(P,X),database(X,updb:'MoonDB').
  632xref_moonprot(P,X) :- xref(P,X),database(X,updb:'MoonProt').
  633xref_niagads(P,X) :- xref(P,X),database(X,updb:'NIAGADS').
  634xref_ogp(P,X) :- xref(P,X),database(X,updb:'OGP').
  635xref_oma(P,X) :- xref(P,X),database(X,updb:'OMA').
  636xref_opentargets(P,X) :- xref(P,X),database(X,updb:'OpenTargets').
  637xref_orphanet(P,X) :- xref(P,X),database(X,updb:'Orphanet').
  638xref_orthodb(P,X) :- xref(P,X),database(X,updb:'OrthoDB').
  639xref_panther(P,X) :- xref(P,X),database(X,updb:'PANTHER').
  640xref_patric(P,X) :- xref(P,X),database(X,updb:'PATRIC').
  641xref_pcddb(P,X) :- xref(P,X),database(X,updb:'PCDDB').
  642xref_pdbsum(P,X) :- xref(P,X),database(X,updb:'PDBsum').
  643xref_phibase(P,X) :- xref(P,X),database(X,updb:'PHI-base').
  644xref_pir(P,X) :- xref(P,X),database(X,updb:'PIR').
  645xref_pirsf(P,X) :- xref(P,X),database(X,updb:'PIRSF').
  646xref_pride(P,X) :- xref(P,X),database(X,updb:'PRIDE').
  647xref_prints(P,X) :- xref(P,X),database(X,updb:'PRINTS').
  648xref_pro(P,X) :- xref(P,X),database(X,updb:'PRO').
  649xref_prosite(P,X) :- xref(P,X),database(X,updb:'PROSITE').
  650xref_pathwaycommons(P,X) :- xref(P,X),database(X,updb:'PathwayCommons').
  651xref_paxdb(P,X) :- xref(P,X),database(X,updb:'PaxDb').
  652xref_peptideatlas(P,X) :- xref(P,X),database(X,updb:'PeptideAtlas').
  653xref_peroxibase(P,X) :- xref(P,X),database(X,updb:'PeroxiBase').
  654xref_pfam(P,X) :- xref(P,X),database(X,updb:'Pfam').
  655xref_pharmgkb(P,X) :- xref(P,X),database(X,updb:'PharmGKB').
  656xref_pharos(P,X) :- xref(P,X),database(X,updb:'Pharos').
  657xref_phosphositeplus(P,X) :- xref(P,X),database(X,updb:'PhosphoSitePlus').
  658xref_phylomedb(P,X) :- xref(P,X),database(X,updb:'PhylomeDB').
  659xref_plantreactome(P,X) :- xref(P,X),database(X,updb:'PlantReactome').
  660xref_pombase(P,X) :- xref(P,X),database(X,updb:'PomBase').
  661xref_promex(P,X) :- xref(P,X),database(X,updb:'ProMEX').
  662xref_proteomicsdb(P,X) :- xref(P,X),database(X,updb:'ProteomicsDB').
  663xref_pseudocap(P,X) :- xref(P,X),database(X,updb:'PseudoCAP').
  664xref_rebase(P,X) :- xref(P,X),database(X,updb:'REBASE').
  665xref_reproduction2dpage(P,X) :- xref(P,X),database(X,updb:'REPRODUCTION-2DPAGE').
  666xref_rgd(P,X) :- xref(P,X),database(X,updb:'RGD').
  667xref_rnact(P,X) :- xref(P,X),database(X,updb:'RNAct').
  668xref_reactome(P,X) :- xref(P,X),database(X,updb:'Reactome').
  669xref_refseq(P,X) :- xref(P,X),database(X,updb:'RefSeq').
  670xref_sabiork(P,X) :- xref(P,X),database(X,updb:'SABIO-RK').
  671xref_sasbdb(P,X) :- xref(P,X),database(X,updb:'SASBDB').
  672xref_sfld(P,X) :- xref(P,X),database(X,updb:'SFLD').
  673xref_sgd(P,X) :- xref(P,X),database(X,updb:'SGD').
  674xref_signor(P,X) :- xref(P,X),database(X,updb:'SIGNOR').
  675xref_smart(P,X) :- xref(P,X),database(X,updb:'SMART').
  676xref_smr(P,X) :- xref(P,X),database(X,updb:'SMR').
  677xref_string(P,X) :- xref(P,X),database(X,updb:'STRING').
  678xref_supfam(P,X) :- xref(P,X),database(X,updb:'SUPFAM').
  679xref_swiss2dpage(P,X) :- xref(P,X),database(X,updb:'SWISS-2DPAGE').
  680xref_signalink(P,X) :- xref(P,X),database(X,updb:'SignaLink').
  681xref_swisslipids(P,X) :- xref(P,X),database(X,updb:'SwissLipids').
  682xref_swisspalm(P,X) :- xref(P,X),database(X,updb:'SwissPalm').
  683xref_tair(P,X) :- xref(P,X),database(X,updb:'TAIR').
  684xref_tcdb(P,X) :- xref(P,X),database(X,updb:'TCDB').
  685xref_tigrfams(P,X) :- xref(P,X),database(X,updb:'TIGRFAMs').
  686xref_topdownproteomics(P,X) :- xref(P,X),database(X,updb:'TopDownProteomics').
  687xref_treefam(P,X) :- xref(P,X),database(X,updb:'TreeFam').
  688xref_tuberculist(P,X) :- xref(P,X),database(X,updb:'TubercuList').
  689xref_ucd2dpage(P,X) :- xref(P,X),database(X,updb:'UCD-2DPAGE').
  690xref_ucsc(P,X) :- xref(P,X),database(X,updb:'UCSC').
  691xref_unilectin(P,X) :- xref(P,X),database(X,updb:'UniLectin').
  692xref_veupathdb(P,X) :- xref(P,X),database(X,updb:'VEuPathDB').
  693xref_vgnc(P,X) :- xref(P,X),database(X,updb:'VGNC').
  694xref_wbparasite(P,X) :- xref(P,X),database(X,updb:'WBParaSite').
  695xref_world2dpage(P,X) :- xref(P,X),database(X,updb:'World-2DPAGE').
  696xref_wormbase(P,X) :- xref(P,X),database(X,updb:'WormBase').
  697xref_xenbase(P,X) :- xref(P,X),database(X,updb:'Xenbase').
  698xref_zfin(P,X) :- xref(P,X),database(X,updb:'ZFIN').
  699xref_dbsnp(P,X) :- xref(P,X),database(X,updb:'dbSNP').
  700xref_dictybase(P,X) :- xref(P,X),database(X,updb:'dictyBase').
  701xref_eggnog(P,X) :- xref(P,X),database(X,updb:'eggNOG').
  702xref_euhcvdb(P,X) :- xref(P,X),database(X,updb:'euHCVdb').
  703xref_iptmnet(P,X) :- xref(P,X),database(X,updb:'iPTMnet').
  704xref_jpost(P,X) :- xref(P,X),database(X,updb:'jPOST').
  705xref_nextprot(P,X) :- xref(P,X),database(X,updb:'neXtProt').
  706xref_po(P,X) :- xref(P,X),database(X,updb:'PO').
  707xref_mesh(P,X) :- xref(P,X),database(X,updb:'MeSH').
  708xref_medgen(P,X) :- xref(P,X),database(X,updb:'MedGen').
  709xref_go(P,X) :- xref(P,X),database(X,updb:'go')