<div class="notebook"> <div class="nb-cell markdown"> # Bio DB: Access, use and manage big, biological datasets This notebook provides example queries for all the predicates of the [bio_db package](http://www.swi-prolog.org/pack/list?p=bio_db), created by [Nicos Angelopoulos](http://stoics.org.uk/~nicos/). The API is documented [here](http://www.swi-prolog.org/pack/file_details/bio_db/prolog/bio_db.pl). Predicates and their signatures are available for **auto completion** when writing SWISH programs and queries: type a partial predicate name and then <control>SPACE. This SWISH instance uses the =Prolog= interface of the bio_db package, which implies that all databases are loaded into Prolog's memory. Please be aware that a first query on a specific predicate with a specific instantiation pattern can be slow because predicates are loaded lazily and indexes are created lazily. Subsequent calls should be instantanious. </div> <div class="nb-cell query" data-tabled="true"> go_term_symbols('GO:0000375', Symbols, []). </div> <div class="nb-cell query" data-tabled="true"> Gont = 'GO:0043552', findall( Symb, map_gont_gont_symb(Gont,Symb), Symbs ), symbols_string_graph( Symbs, Graph, [] ), length( Graph, Len ). </div> <div class="nb-cell query" data-tabled="true"> bio_db_version(Vers, Date). </div> <div class="nb-cell query" data-tabled="true"> once(map_hgnc_hgnc_symb(_,_)), bio_db_info(map_hgnc_hgnc_symb/2, Key, Value). </div> <div class="nb-cell markdown"> ## Map and edge predicates </div> <div class="nb-cell query" data-tabled="true"> edge_string_hs(EnsP1, EnsP2, W). </div> <div class="nb-cell query" data-tabled="true"> edge_string_hs_symb(Symb1, Symb2, W). </div> <div class="nb-cell query" data-tabled="true"> edge_gont_includes(Pa, Ch). </div> <div class="nb-cell query" data-tabled="true"> edge_gont_is_a(Ch, Pa). </div> <div class="nb-cell query" data-tabled="true"> edge_gont_regulates(Pa, Ch). </div> <div class="nb-cell query" data-tabled="true"> edge_gont_positively_regulates(Pa, Ch). </div> <div class="nb-cell query" data-tabled="true"> edge_gont_negatively_regulates(Pa, Ch). </div> <div class="nb-cell query" data-tabled="true"> edge_gont_part_of(Part, Whole). </div> <div class="nb-cell query" data-tabled="true"> edge_gont_consists_of(Whole, Part). </div> <div class="nb-cell query" data-tabled="true"> map_hgnc_hgnc_symb(Hgnc, Symb). </div> <div class="nb-cell query" data-tabled="true"> map_hgnc_hgnc_name(Hgnc, Symb). </div> <div class="nb-cell query" data-tabled="true"> map_hgnc_symb_hgnc(Symb, Hgnc). </div> <div class="nb-cell query" data-tabled="true"> map_hgnc_syno_symb(Syno, Symb). </div> <div class="nb-cell query" data-tabled="true"> map_hgnc_prev_symb(Prev, Symb). </div> <div class="nb-cell query" data-tabled="true"> map_hgnc_ensg_hgnc(Ensg, Symb). </div> <div class="nb-cell query" data-tabled="true"> map_hgnc_symb_entz(Symb, Entz). </div> <div class="nb-cell query" data-tabled="true"> map_hgnc_entz_hgnc(Entz, Symb). </div> <div class="nb-cell query" data-tabled="true"> map_hgnc_entz_symb(Entz, Symb). </div> <div class="nb-cell query" data-tabled="true"> 'map_hgnc_entz-appv_symb'(Entz, Symb). </div> <div class="nb-cell query" data-tabled="true"> map_hgnc_hgnc_chrb(Hgnc, ChrB). </div> <div class="nb-cell query" data-tabled="true"> map_hgnc_hgnc_ensg(Hgnc, EnsG). </div> <div class="nb-cell query" data-tabled="true"> 'map_hgnc_hgnc_entz-appv'(Hgnc, EntzAppv). </div> <div class="nb-cell query" data-tabled="true"> 'map_hgnc_hgnc_entz-ncbi'(Hgnc, EntzNcbi). </div> <div class="nb-cell query" data-tabled="true"> 'map_hgnc_hgnc_entz-ncbi'(Hgnc, EntzNcbi). </div> <div class="nb-cell query" data-tabled="true"> map_hgnc_hgnc_entz(Hgnc, Entz). </div> <div class="nb-cell query" data-tabled="true"> map_pros_pros_prsn(Pros, Prsn). </div> <div class="nb-cell query" data-tabled="true"> map_pros_pros_sprt(Pros, Prsn, Sprt, Symb, Start, End, Seq). </div> <div class="nb-cell query" data-tabled="true"> map_ncbi_ensp_entz(EnsP, Entz). </div> <div class="nb-cell query" data-tabled="true"> map_ncbi_ensg_entz(EnsG, Entz). </div> <div class="nb-cell query" data-tabled="true"> map_ncbi_entz_ensp(Entz, EnsP). </div> <div class="nb-cell query" data-tabled="true"> map_ncbi_rnuc_symb(RnaNucl, Symb). </div> <div class="nb-cell query" data-tabled="true"> map_ncbi_unig_entz(UniG, Entz). </div> <div class="nb-cell query" data-tabled="true"> map_ncbi_entz_ensg(Entz, EnsG). </div> <div class="nb-cell query" data-tabled="true"> map_unip_hgnc_unip(Hgnc, UniP). </div> <div class="nb-cell query" data-tabled="true"> map_unip_unip_hgnc(UniP, Hgnc). </div> <div class="nb-cell query" data-tabled="true"> map_unip_unip_unig(UniP, UniG). </div> <div class="nb-cell query" data-tabled="true"> map_unip_sprt_seqn(Swissprot, Seqn). </div> <div class="nb-cell query" data-tabled="true"> map_unip_trem_seqn(Trem, Seqn). </div> <div class="nb-cell query" data-tabled="true"> map_unip_ensp_unip(EnsP, UniP). </div> <div class="nb-cell query" data-tabled="true"> map_unip_trem_nucs(Trem, Nucs). </div> <div class="nb-cell query" data-tabled="true"> map_unip_unip_entz(UniP, Entz). </div> <div class="nb-cell query" data-tabled="true"> map_gont_gont_symb(Gont, Symb). </div> <div class="nb-cell query" data-tabled="true"> map_gont_gont_gonm(Gont, Gonm). </div> <div class="nb-cell query" data-tabled="true"> map_gont_symb_gont(Symb, Gont). </div> <div class="nb-cell query" data-tabled="true"> map_ense_ensg_hgnc(EnsG, Hgnc). </div> <div class="nb-cell query" data-tabled="true"> map_ense_ensg_symb(EnsG, Hgnc). </div> <div class="nb-cell query" data-tabled="true"> map_ense_enst_chrl(EnsT, Chr, Start, End, Dir). </div> <div class="nb-cell query" data-tabled="true"> map_ense_ensg_chrl(EnsG, Chr, Start, End, Dir). </div> <div class="nb-cell query" data-tabled="true"> map_ense_enst_ensg(EnsT, EnsG). </div> <div class="nb-cell query" data-tabled="true"> hgnc_symbol(Symbol). </div> </div>