%%%% %%%% abductive prism from probabilistic examples with failure --- inhibition_psm.psm %%%% contact: jz.chen@imperial.ac.uk %%%% Copyright (C) 2008 %%------------------------------------- %% Declarations: target(concentration,2). % Observations are of the form concentration(a,down). target(failure,0). data(user). values(inhibited,[ [e2_6_1_39,l-2-aminoadipate,2-oxo-glutarate,t], [e2_6_1_39,2-oxo-glutarate,l-2-aminoadipate,t], [e1_1_1_42,2-oxo-glutarate,isocitrate,t], [e1_1_1_42,isocitrate,2-oxo-glutarate,t], [e2_3_1_61,2-oxo-glutarate,succinate,t], [e2_3_1_61,succinate,2-oxo-glutarate,t], [e4_2_1_3,isocitrate,citrate,t], [e4_2_1_3,citrate,isocitrate,t], [e4_2_1_3,isocitrate,trans-aconitate,t], [e4_2_1_3,trans-aconitate,isocitrate,t], [e4_2_1_2,citrate,fumarate,t], [e4_2_1_2,fumarate,citrate,t], [e1_3_99_1,succinate,fumarate,t], [e1_3_99_1,fumarate,succinate,t], [e1_13_11_16,succinate,hippurate,t], [e1_13_11_16,hippurate,succinate,t], [e2_6_1,citrate,taurine,t], [e2_6_1,taurine,citrate,t], [e4_3_2_1,arginine,l-as,t], [e4_3_2_1,l-as,arginine,t], [e4_3_2_1,fumarate,l-as,t], [e4_3_2_1,l-as,fumarate,t], [e2_1_1_1,nmnd,fumarate,t], [e2_1_1_1,fumarate,nmnd,t], [e2_1_1_7,nmna,fumarate,t], [e2_1_1_7,fumarate,nmna,t], [e6_3_4_5,l-as,citruline,t], [e6_3_4_5,citruline,l-as,t], [e2_1_3_3,citruline,ornithine,t], [e2_1_3_3,ornithine,citruline,t], [e3_5_3_1,arginine,urea,t], [e3_5_3_1,arginine,ornithine,t], [e3_5_3_1,urea,arginine,t], [e3_5_3_1,ornithine,arginine,t], [e2_1_1_2,ornithine,creatine,t], [e2_1_1_2,creatine,ornithine,t], [e3_5_3_3,creatine,urea,t], [e3_5_3_3,creatine,sarcosine,t], [e3_5_3_3,urea,creatine,t], [e3_5_3_3,sarcosine,creatine,t], [e3_5_2_10,creatinine,creatine,t], [e3_5_2_10,creatine,creatinine,t], [e3_5_1_59,creatinine,sarcosine,t], [e3_5_1_59,sarcosine,creatinine,t], [e1_5_99_1,formaldehyde,sarcosine,t], [e1_5_99_1,sarcosine,formaldehyde,t], [e1_1_99_8,formaldehyde,formate,t], [e1_1_99_8,formate,formaldehyde,t], [e1_4_99_3,formaldehyde,methylamine,t], [e1_4_99_3,methylamine,formaldehyde,t], [e4_1_2_32,tmao,formaldehyde,t], [e4_1_2_32,tmao,methylamine,t], [e4_1_2_32,formaldehyde,tmao,t], [e4_1_2_32,methylamine,tmao,t], [e4_2_1_54,lactate,acryloyl-coA,t], [e4_2_1_54,acryloyl-coA,lactate,t], [e4_3_1_6,beta-alanine,acryloyl-coA,t], [e4_3_1_6,acryloyl-coA,beta-alanine,t], [e2_1_3_1,acryloyl-coA,succinate,t], [e2_1_3_1,succinate,acryloyl-coA,t], [e4_1_1_20,beta-alanine,l-lysine,t], [e4_1_1_20,l-lysine,beta-alanine,t], [e2_6_1_14,beta-alanine,citrate,t], [e2_6_1_14,citrate,beta-alanine,t], [e1_2_1_31,l-2-aminoadipate,l-lysine,t], [e1_2_1_31,l-lysine,l-2-aminoadipate,t], [e2_7_1_69,glucose,pyruvate,t], [e2_7_1_69,pyruvate,glucose,t], [e1_1_1_27,pyruvate,lactate,t], [e1_1_1_27,lactate,pyruvate,t], [e1_2_4_1,pyruvate,acetylCoA,t], [e1_2_4_1,acetylCoA,pyruvate,t], [e2_3_3_1,acetylCoA,citrate,t], [e2_3_3_1,citrate,acetylCoA,t], [e6_2_1_1,acetylCoA,acetate,t], [e6_2_1_1,acetate,acetylCoA,t], [e2_6_1_39,l-2-aminoadipate,2-oxo-glutarate,f], [e2_6_1_39,2-oxo-glutarate,l-2-aminoadipate,f], [e1_1_1_42,2-oxo-glutarate,isocitrate,f], [e1_1_1_42,isocitrate,2-oxo-glutarate,f], [e2_3_1_61,2-oxo-glutarate,succinate,f], [e2_3_1_61,succinate,2-oxo-glutarate,f], [e4_2_1_3,isocitrate,citrate,f], [e4_2_1_3,citrate,isocitrate,f], [e4_2_1_3,isocitrate,trans-aconitate,f], [e4_2_1_3,trans-aconitate,isocitrate,f], [e4_2_1_2,citrate,fumarate,f], [e4_2_1_2,fumarate,citrate,f], [e1_3_99_1,succinate,fumarate,f], [e1_3_99_1,fumarate,succinate,f], [e1_13_11_16,succinate,hippurate,f], [e1_13_11_16,hippurate,succinate,f], [e2_6_1,citrate,taurine,f], [e2_6_1,taurine,citrate,f], [e4_3_2_1,arginine,l-as,f], [e4_3_2_1,l-as,arginine,f], [e4_3_2_1,fumarate,l-as,f], [e4_3_2_1,l-as,fumarate,f], [e2_1_1_1,nmnd,fumarate,f], [e2_1_1_1,fumarate,nmnd,f], [e2_1_1_7,nmna,fumarate,f], [e2_1_1_7,fumarate,nmna,f], [e6_3_4_5,l-as,citruline,f], [e6_3_4_5,citruline,l-as,f], [e2_1_3_3,citruline,ornithine,f], [e2_1_3_3,ornithine,citruline,f], [e3_5_3_1,arginine,urea,f], [e3_5_3_1,arginine,ornithine,f], [e3_5_3_1,urea,arginine,f], [e3_5_3_1,ornithine,arginine,f], [e2_1_1_2,ornithine,creatine,f], [e2_1_1_2,creatine,ornithine,f], [e3_5_3_3,creatine,urea,f], [e3_5_3_3,creatine,sarcosine,f], [e3_5_3_3,urea,creatine,f], [e3_5_3_3,sarcosine,creatine,f], [e3_5_2_10,creatinine,creatine,f], [e3_5_2_10,creatine,creatinine,f], [e3_5_1_59,creatinine,sarcosine,f], [e3_5_1_59,sarcosine,creatinine,f], [e1_5_99_1,formaldehyde,sarcosine,f], [e1_5_99_1,sarcosine,formaldehyde,f], [e1_1_99_8,formaldehyde,formate,f], [e1_1_99_8,formate,formaldehyde,f], [e1_4_99_3,formaldehyde,methylamine,f], [e1_4_99_3,methylamine,formaldehyde,f], [e4_1_2_32,tmao,formaldehyde,f], [e4_1_2_32,tmao,methylamine,f], [e4_1_2_32,formaldehyde,tmao,f], [e4_1_2_32,methylamine,tmao,f], [e4_2_1_54,lactate,acryloyl-coA,f], [e4_2_1_54,acryloyl-coA,lactate,f], [e4_3_1_6,beta-alanine,acryloyl-coA,f], [e4_3_1_6,acryloyl-coA,beta-alanine,f], [e2_1_3_1,acryloyl-coA,succinate,f], [e2_1_3_1,succinate,acryloyl-coA,f], [e4_1_1_20,beta-alanine,l-lysine,f], [e4_1_1_20,l-lysine,beta-alanine,f], [e2_6_1_14,beta-alanine,citrate,f], [e2_6_1_14,citrate,beta-alanine,f], [e1_2_1_31,l-2-aminoadipate,l-lysine,f], [e1_2_1_31,l-lysine,l-2-aminoadipate,f], [e2_7_1_69,glucose,pyruvate,f], [e2_7_1_69,pyruvate,glucose,f], [e1_1_1_27,pyruvate,lactate,f], [e1_1_1_27,lactate,pyruvate,f], [e1_2_4_1,pyruvate,acetylCoA,f], [e1_2_4_1,acetylCoA,pyruvate,f], [e2_3_3_1,acetylCoA,citrate,f], [e2_3_3_1,citrate,acetylCoA,f], [e6_2_1_1,acetylCoA,acetate,f], [e6_2_1_1,acetate,acetylCoA,f] ]). %%------------------------------------ %% Modeling part: prism_main([A1,A2]):- parse_atom(A1,Nfailure), parse_atom(A2,Metabolite), Gs=[ count(concentration(citrate,down),98), count(concentration(citrate,up),2), count(concentration(2-oxo-glutarate,down),100), count(concentration(2-oxo-glutarate,up),0), count(concentration(succinate,down),94), count(concentration(succinate,up),6), count(concentration(l-2-aminoadipate,up),100), count(concentration(l-2-aminoadipate,down),0), count(concentration(creatine,down),51), count(concentration(creatine,up),49), count(concentration(creatinine,down),58), count(concentration(creatinine,up),42), count(concentration(hippurate,down),71), count(concentration(hippurate,up),29), count(concentration(beta-alanine,up),97), count(concentration(beta-alanine,down),3), count(concentration(lactate,up),95), count(concentration(lactate,down),5), count(concentration(methylamine,up),100), count(concentration(methylamine,down),0), count(concentration(trans-aconitate,down),65), count(concentration(trans-aconitate,up),35), count(concentration(formate,down),94), count(concentration(formate,up),6), count(concentration(taurine,up),74), count(concentration(taurine,down),26), count(concentration(acetate,up),67), count(concentration(acetate,down),33), count(concentration(nmna,up),52), count(concentration(nmna,down),48), count(concentration(nmnd,up),64), count(concentration(nmnd,down),36), count(concentration(tmao,up),52), count(concentration(tmao,down),48), count(concentration(fumarate,up),70), count(concentration(fumarate,down),30), count(concentration(l-as,up),67), count(concentration(l-as,down),33), count(concentration(glucose,up),81), count(concentration(glucose,down),19), count(failure,Nfailure) ], learn(Gs), show_sw, % show_goals, prob(failure), prob(success), prob(concentration(Metabolite,down),X),prob(concentration(Metabolite,up),Y),Xdown is X/(X+Y),Yup is Y/(X+Y), format("P("),write(Metabolite),format(",down)= ~6f~n",[Xdown]), format("P("),write(Metabolite),format(",up)= ~6f~n",[Yup]). failure :- not(success). success :- concentration(_,_). concentration(X,down) :- reactionnode(X,Enz,Y), msw(inhibited,[Enz,Y,X,t]). concentration(X, down) :- reactionnode(X,Enz,Y), msw(inhibited,[Enz,Y,X,f]), observed(Y, down). concentration(X,up) :- reactionnode(X,Enz,Y), msw(inhibited,[Enz,X,Y,t]). concentration(X,up) :- reactionnode(X,Enz,Y), msw(inhibited,[Enz,Y,X,f]), observed(Y,up). %%------------------------------------ %% Utility part: reactionnode(l-2-aminoadipate,e2_6_1_39,2-oxo-glutarate). reactionnode(2-oxo-glutarate,e2_6_1_39,l-2-aminoadipate). reactionnode(2-oxo-glutarate,e1_1_1_42,isocitrate). reactionnode(isocitrate,e1_1_1_42,2-oxo-glutarate). reactionnode(2-oxo-glutarate,e2_3_1_61,succinate). reactionnode(succinate,e2_3_1_61,2-oxo-glutarate). reactionnode(isocitrate,e4_2_1_3,citrate). reactionnode(citrate,e4_2_1_3,isocitrate). reactionnode(isocitrate,e4_2_1_3,trans-aconitate). reactionnode(trans-aconitate,e4_2_1_3,isocitrate). reactionnode(citrate,e4_2_1_2,fumarate). reactionnode(fumarate,e4_2_1_2,citrate). reactionnode(succinate,e1_3_99_1,fumarate). reactionnode(fumarate,e1_3_99_1,succinate). reactionnode(succinate,e1_13_11_16,hippurate). reactionnode(hippurate,e1_13_11_16,succinate). reactionnode(citrate,e2_6_1,taurine). reactionnode(taurine,e2_6_1,citrate). reactionnode(arginine,e4_3_2_1,l-as). reactionnode(l-as,e4_3_2_1,arginine). reactionnode(fumarate,e4_3_2_1,l-as). reactionnode(l-as,e4_3_2_1,fumarate). reactionnode(nmnd,e2_1_1_1,fumarate). reactionnode(fumarate,e2_1_1_1,nmnd). reactionnode(nmna,e2_1_1_7,fumarate). reactionnode(fumarate,e2_1_1_7,nmna). reactionnode(l-as,e6_3_4_5,citruline). reactionnode(citruline,e6_3_4_5,l-as). reactionnode(citruline,e2_1_3_3,ornithine). reactionnode(ornithine,e2_1_3_3,citruline). reactionnode(arginine,e3_5_3_1,urea). reactionnode(arginine,e3_5_3_1,ornithine). reactionnode(urea,e3_5_3_1,arginine). reactionnode(ornithine,e3_5_3_1,arginine). reactionnode(ornithine,e2_1_1_2,creatine). reactionnode(creatine,e2_1_1_2,ornithine). reactionnode(creatine,e3_5_3_3,urea). reactionnode(creatine,e3_5_3_3,sarcosine). reactionnode(urea,e3_5_3_3,creatine). reactionnode(sarcosine,e3_5_3_3,creatine). reactionnode(creatinine,e3_5_2_10,creatine). reactionnode(creatine,e3_5_2_10,creatinine). reactionnode(creatinine,e3_5_1_59,sarcosine). reactionnode(sarcosine,e3_5_1_59,creatinine). reactionnode(formaldehyde,e1_5_99_1,sarcosine). reactionnode(sarcosine,e1_5_99_1,formaldehyde). reactionnode(formaldehyde,e1_1_99_8,formate). reactionnode(formate,e1_1_99_8,formaldehyde). reactionnode(formaldehyde,e1_4_99_3,methylamine). reactionnode(methylamine,e1_4_99_3,formaldehyde). reactionnode(tmao,e4_1_2_32,formaldehyde). reactionnode(tmao,e4_1_2_32,methylamine). reactionnode(formaldehyde,e4_1_2_32,tmao). reactionnode(methylamine,e4_1_2_32,tmao). reactionnode(lactate,e4_2_1_54,acryloyl-coA). reactionnode(acryloyl-coA,e4_2_1_54,lactate). reactionnode(beta-alanine,e4_3_1_6,acryloyl-coA). reactionnode(acryloyl-coA,e4_3_1_6,beta-alanine). reactionnode(acryloyl-coA,e2_1_3_1,succinate). reactionnode(succinate,e2_1_3_1,acryloyl-coA). reactionnode(beta-alanine,e4_1_1_20,l-lysine). reactionnode(l-lysine,e4_1_1_20,beta-alanine). reactionnode(beta-alanine,e2_6_1_14,citrate). reactionnode(citrate,e2_6_1_14,beta-alanine). reactionnode(l-2-aminoadipate,e1_2_1_31,l-lysine). reactionnode(l-lysine,e1_2_1_31,l-2-aminoadipate). reactionnode(glucose,e2_7_1_69,pyruvate). reactionnode(pyruvate,e2_7_1_69,glucose). reactionnode(pyruvate,e1_1_1_27,lactate). reactionnode(lactate,e1_1_1_27,pyruvate). reactionnode(pyruvate,e1_2_4_1,acetylCoA). reactionnode(acetylCoA,e1_2_4_1,pyruvate). reactionnode(acetylCoA,e2_3_3_1,citrate). reactionnode(citrate,e2_3_3_1,acetylCoA). reactionnode(acetylCoA,e6_2_1_1,acetate). reactionnode(acetate,e6_2_1_1,acetylCoA). observed(citrate,down). observed(2-oxo-glutarate,down). observed(succinate,down). observed(l-2-aminoadipate,up). observed(creatine,down). observed(creatinine,down). observed(hippurate,down). observed(beta-alanine,up). observed(lactate,up). observed(methylamine,up). observed(trans-aconitate,down). observed(formate,down). observed(taurine,up). observed(acetate,up). observed(nmna,up). observed(nmnd,up). observed(tmao,up). observed(fumarate,up). observed(l-as,up). observed(glucose,up).