:- module( bio_db_mouse_mgim, [ bio_db_mouse_mgim/0, % + MGI database: fixme: url map_mgim_mouse_mgim_chrl/5, map_mgim_mouse_mgim_entz/2, map_mgim_mouse_mgim_genb/2, map_mgim_mouse_mgim_symb/2, map_mgim_mouse_mgim_unip/2, map_mgim_mouse_symb_wdra/2, map_mgim_mouse_syno_mgim/2 ] ). :- use_module( library(lib) ). :- lib(bio_db). % :- dynamic( map_mgim_mouse_mgim_symb/2 ). /** bio_db_mouse_mgim. Documentation predicate for mouse data from MGI database. DNA fragments are referred to as markers in the database, thus mgim is the 4 letter code for the database and its unique ids. == ?- lib( &bio_db(mouse(mgim)) ). ?- [pack('bio_db/cell/mouse/mgim')]. == @author nicos angelopoulos @version 0.1 2018/11/3 */ bio_db_mouse_mgim. /** map_mgim_mouse_mgim_chrl( +Mgim, -Chr, -Start, -End, -Strand ). MGI marker to chromosomal location. == ?- map_mgim_mouse_mgim_symb(Mgim,'Lmtk3'), map_mgim_mouse_mgim_chrl( Mgim, Chr, Start, End, Strand ). Mgim = 3039582, Chr = 7, Start = 45783738, End = 45804144, Strand = (+). == */ map_mgim_mouse_mgim_chrl( Mgi, Chr, Sta, End, Sgn ) :- bio_db:bio_db_serve( map_mgim_mouse_mgim_chrl(Mgi,Chr,Sta,End,Sgn) ). /** map_mgim_mouse_mgim_genb( +Mgim, -GenB ). Map predicate from MGI marker to Gene Bank ids. == ?- map_mgim_mouse_mgim_symb( Mgim, 'Lmtk3' ), map_mgim_mouse_mgim_genb( Mgim, GenB ), write( GenB ), nl, fail. AB288873 AI413247 AK029204 AW046037 BC057032 BC059845 BC083185 BC094377 BE981921 false. ?- == */ map_mgim_mouse_mgim_genb( X, Y ) :- bio_db:bio_db_serve( map_mgim_mouse_mgim_genb(X,Y) ). /** map_mgim_mouse_mgim_entz( +Mgim, -Entz ). Map predicate from MGI marker to NCBI, Entrez ids. == ?- map_mgim_mouse_mgim_symb( Mgim, 'Lmtk3' ), map_mgim_mouse_mgim_entz( Mgim, Entz ). Entz = 381983, Mgim = 3039582. == */ map_mgim_mouse_mgim_entz( X, Y ) :- bio_db:bio_db_serve( map_mgim_mouse_mgim_entz(X,Y) ). /** map_mgim_mouse_mgim_symb( +Mgim, -Symb ). Map predicate between MGI marker and (MGI) symbols. == ?- map_mgim_mouse_mgim_symb( Mgim, 'Lmtk3' ). Mgim = 3039582. == */ map_mgim_mouse_mgim_symb( X, Y ) :- bio_db:bio_db_serve( map_mgim_mouse_mgim_symb(X,Y) ). /** map_mgim_mouse_mgim_unip( +Mgim, -Unip ). Map predicate from MGI markder ids to Uniprot ids. == ?- map_mgim_mouse_mgim_symb( Mgim, 'Lmtk3' ), map_mgim_mouse_mgim_unip( Mgim, Unip ). Mgim = 3039582, Unip = 'Q5XJV6'. == */ map_mgim_mouse_mgim_unip( Sprt, Seqn ) :- bio_db:bio_db_serve( map_mgim_mouse_mgim_unip(Sprt,Seqn) ). /** map_mgim_mouse_symb_wdra( +Symb, -Wdra ). Map predicate from MGI symbols to withdrawn names. == ?- map_mgim_mouse_symb_wdra( S, W ). S = 15006, W = 'H2-Q1' ; ... == */ map_mgim_mouse_symb_wdra( Symb, Wdra ) :- bio_db:bio_db_serve( map_mgim_mouse_symb_wdra(Symb,Wdra) ). /* map_mgim_mouse_syno_mgim( +Syno, -Mgim ). Map predicate from Synonym to MGI marker ID. == ?- map_mgim_mouse_mgim_symb( Mgim, 'Lmtk3' ), | map_mgim_mouse_syno_mgim( Syno, Mgim ). Mgim = 3039582, Syno = 'AATYK3' ; Mgim = 3039582, Syno = 'Aatyk3'. == */ map_mgim_mouse_syno_mgim( X, Y ) :- bio_db:bio_db_serve( map_mgim_mouse_syno_mgim(X,Y) ).