investigation(investigation_into_flux_balance_analysis_model). domain_of_study(systems_biology). has_proposition(investigation_into_flux_balance_analysis_model,systems_biology). has_specified_input(investigation_into_flux_balance_analysis_model,reuse_data_reuse). objective(reuse_data_reuse). has_proposition(investigation_into_flux_balance_analysis_model,test_suitability_goal). has_proposition(investigation_into_flux_balance_analysis_model,test_accuracy_goal). has_representation(test_suitability_goal, 'to test suitability of flux balance analysis models'). text_representation('to test suitability of flux balance analysis models'). has_representation(test_accuracy_goal, 'to test accuracy of flux balance analysis models'). text_representation('to test accuracy of flux balance analysis models'). role(investigator). investigator(chuan_lu). has_agent(investigation_into_flux_balance_analysis_model,chuan_lu). link('http://systemsbiology.ucsd.edu/In_Silico_Organisms/Yeast'). has_proposition(sb_model,'http://systemsbiology.ucsd.edu/In_Silico_Organisms/Yeast'). role(object_of_study). object_of_study(fba_model). has_object(investigation_into_flux_balance_analysis_model,fba_model). has_specified_input(investigation_into_flux_balance_analysis_model,fba_model). has_part(investigation_into_flux_balance_analysis_model,study_of_iIN750_systems_biology_model). has_specified_input(investigation_into_flux_balance_analysis_model,stoichiometric_matrix_s). has_specified_input(investigation_into_flux_balance_analysis_model,'not_match(model_iND750_prediction,data_reuse_results_rich_media)'). has_specified_input(investigation_into_flux_balance_analysis_model,'not_match(model_iND750_prediction,data_reuse_results_minimal_media)'). has_specified_output(investigation_into_flux_balance_analysis_model,'flux balance analysis models are not accurate'). text_representation('flux balance analysis models are not accurate'). conclusion('flux balance analysis models are not accurate'). has_specified_output(investigation_into_flux_balance_analysis_model,'flux balance analysis models are not suitable'). text_representation('flux balance analysis models are not suitable'). conclusion('flux balance analysis models are not suitable'). %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% study(study_of_iIN750_systems_biology_model). has_specified_input(study_of_iIN750_systems_biology_model,iIN750_model). object_of_study(iIN750_model). link('http://gcrg.ucsd.edu/In_Silico_Organisms/Yeast?action=AttachFile&do=get&target=Sc_iND750.xml'). has_proposition(iIN750_model,'http://gcrg.ucsd.edu/In_Silico_Organisms/Yeast?action=AttachFile&do=get&target=Sc_iND750.xml'). parameter(maximum_uptake_rate). parameter(set_knock-outs). parameter(set_upper_bound_fluxes). parameter(set_lower_bound_fluxes). parameter(growth_rate_maximisation). objective_function(growth_rate_maximisation). has_proposition(iIN750_model,maximum_uptake_rate). has_proposition(iIN750_model,set_knock-outs). has_proposition(iIN750_model,set_upper_bound_fluxes). has_proposition(iIN750_model,set_lower_bound_fluxes). has_proposition(iIN750_model,growth_rate_maximisation). has_proposition(study_of_iIN750_systems_biology_model,test_accuracy_goal_iIN750). text_representation('to test the accuracy of iND750 model for the study of relative growth of the knock-out and wild-type yeast strains'). has_representation(test_accuracy_goal_iIN750,'to test the accuracy of iND750 model for the study of relative growth of the knock-out and wild-type yeast strains'). has_proposition(study_of_iIN750_systems_biology_model,compare_goal). text_representation('to compare growth rate from the investigation into the data reuse with the growth rate predicted by iND750 model'). has_representation(compare_goal,'to compare growth rate from the investigation into the data reuse with the growth rate predicted by iND750 model'). has_part(test_accuracy_goal_iIN750,compare_goal). biological_object(saccharomyces_cerevisiae). role(object_of_study). object_of_study(saccharomyces_cerevisiae). has_object(study_of_iIN750_systems_biology_model,saccharomyces_cerevisiae). has_specified_input(study_of_iIN750_systems_biology_model,saccharomyces_cerevisiae). has_proposition(saccharomyces_cerevisiae,'http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=4932&lvl=3&p=mapview&p=has_linkout&p=blast_url&p=genome_blast&lin=f&keep=1&srchmode=1&unlock'). link('http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=4932&lvl=3&p=mapview&p=has_linkout&p=blast_url&p=genome_blast&lin=f&keep=1&srchmode=1&unlock'). goal(compare_on_rich_media_goal). has_proposition(study_of_iIN750_systems_biology_model,compare_on_rich_media_goal). has_representation(compare_on_rich_media_goal,'to compare growth rate from the investigation into the data reuse with the growth rate predicted by iND750 model in rich media'). text_representation('to compare growth rate from the investigation into the data reuse with the growth rate predicted by iND750 model in rich media'). hypothesis(research_hypothesis). research_hypothesis(h_1_1). logical_representation('not_match(model_iND750_prediction,data_reuse_results_rich_media)'). text_representation('iND750 systems biology model prediction does not match to the results of the data reuse investigation for rich media'). has_representation(h_1_1,'not_match(model_iND750_prediction,data_reuse_results_rich_media)'). has_representation(h_1_1,'iND750 systems biology model prediction does not match to the results of the data reuse investigation for rich media'). hypothesis(negative_hypothesis). negative_hypothesis(h_2_1). logical_representation('match(model_iND750_prediction,data_reuse_results_rich_media)'). text_representation('iND750 systems biology model prediction matches to the results of the data reuse investigation for rich media'). has_representation(h_2_1,'match(model_iND750_prediction,data_reuse_results_rich_media)'). has_representation(h_2_1,'iND750 systems biology model prediction matches to the results of the data reuse investigation for rich media'). goal(compare_on_minimal_media_goal). has_proposition(study_of_iIN750_systems_biology_model,compare_on_minimal_media_goal). has_representation(compare_on_minimal_media_goal,'to compare growth rate from the investigation into the data reuse with the growth rate predicted by iND750 model in minimal media'). text_representation('to compare growth rate from the investigation into the data reuse with the growth rate predicted by iND750 model in minimal media'). research_hypothesis(h_1_2). logical_representation('not_match(model_iND750_prediction,data_reuse_results_minimal_media)'). text_representation('iND750 systems biology model prediction does not match to the results of the data reuse investigation for minimal media'). has_representation(h_1_2,'not_match(model_iND750_prediction,data_reuse_results_minimal_media)'). has_representation(h_1_2,'iND750 systems biology model prediction does not match to the results of the data reuse investigation for minimal media'). negative_hypothesis(h_2_2). logical_representation('match(model_iND750_prediction,data_reuse_results_minimal_media)'). text_representation('iND750 systems biology model prediction matches to the results of the data reuse investigation for rich media'). has_representation(h_2_2,'match(model_iND750_prediction,data_reuse_results_minimal_media)'). has_representation(h_2_2,'iND750 systems biology model prediction matches to the results of the data reuse investigation for minimal media'). has_specified_input(study_of_iIN750_systems_biology_model,h_1_1). has_specified_input(study_of_iIN750_systems_biology_model,h_1_2). has_specified_input(study_of_iIN750_systems_biology_model,h_2_1). has_specified_input(study_of_iIN750_systems_biology_model,h_2_2). classification_of_study(classification_of_study_by_organism). classification_of_study_by_organism(study_of_iIN750_systems_biology_model,saccharomyces_cerevisiae_study). classification_of_study(classification_of_study_by_hypothesis). classification_of_study_by_hypothesis(study_of_iIN750_systems_biology_model,hypothesis_driven_study). has_specified_output(study_of_iIN750_systems_biology_model,h_1_1_has_been_confirmed). conclusion(h_1_1_has_been_confirmed). has_specified_output(study_of_iIN750_systems_biology_model,h_1_2_has_been_confirmed). conclusion(h_1_2_has_been_confirmed). %%%%%%%%%%%%%%%%%%%%%% has_part(study_of_iIN750_systems_biology_model,study_on_rich). %study_on_rich is defined in the data_reuse.pl has_part(study_of_iIN750_systems_biology_model,study_on_minimal). %study_on_rich is defined in the data_reuse.pl %%%%%%%%%%%%%%%%%%%%%%%%% procedure(model_modification_procedure). has_part(study_of_iIN750_systems_biology_model,model_modification_procedure). goal(add_absent_gene). has_proposition(model_modification_procedure,add_absent_gene). link('http://www.aber.ac.uk/~dcswww/Research/bio/unicellsys/DataReuse/'). has_proposition(model_modification_procedure,'http://www.aber.ac.uk/~dcswww/Research/bio/unicellsys/DataReuse/'). has_specified_input(model_modification_procedure,iIN750_model). has_specified_output(model_modification_procedure,modified_iIN750_model). result(modified_iIN750_model). %%%%%%%%%%%%%%%%%%%%%%%%% procedure(model_solving_procedure). has_part(study_of_iIN750_systems_biology_model,model_solving_procedure). link('http://www.aber.ac.uk/~dcswww/Research/bio/unicellsys/DataReuse/'). has_proposition(model_solving_procedure,'http://www.aber.ac.uk/~dcswww/Research/bio/unicellsys/DataReuse/'). has_specified_input(model_solving_procedure,modified_iIN750_model). has_specified_output(model_solving_procedure,estimation_growth_rate_knock_out_minimal_media). has_specified_output(model_solving_procedure,estimation_growth_rate_wild_type_minimal_media). has_specified_output(model_solving_procedure,estimation_growth_rate_knock_out_rich_media). has_specified_output(model_solving_procedure,estimation_growth_rate_wild_type_rich_media). has_specified_output(model_solving_procedure,estimation_growth_rate_for_knock_out_minimal_media). has_specified_output(model_solving_procedure,estimation_growth_rate_for_wild_type_minimal_media). has_specified_output(model_solving_procedure,estimation_growth_rate_for_knock_out_rich_media). has_specified_output(model_solving_procedure,estimation_growth_rate_for_wild_type_rich_media). data(flux_balance_analysis_investigation_data). flux_balance_analysis_investigation_data(estimation_growth_rate_knock_out_minimal_media). flux_balance_analysis_investigation_data(estimation_growth_rate_wild_type_minimal_media). flux_balance_analysis_investigation_data(estimation_growth_rate_knock_out_rich_media). flux_balance_analysis_investigation_data(estimation_growth_rate_wild_type_rich_media). link('http://www.aber.ac.uk/~dcswww/Research/bio/unicellsys/DataReuse/'). has_proposition(flux_balance_analysis_investigation_data,'http://www.aber.ac.uk/~dcswww/Research/bio/unicellsys/DataReuse/'). % this procedure can be detailed into procedures for each deletant, i.e. YR152C. %%%%%%%%%%%%%%%% procedure(comparison_of_results_procedure). has_part(study_of_iIN750_systems_biology_model,comparison_of_results_procedure). has_proposition(comparison_of_results_procedure,'http://www.aber.ac.uk/~dcswww/Research/bio/unicellsys/DataReuse/'). link('http://www.aber.ac.uk/~dcswww/Research/bio/unicellsys/DataReuse/'). has_specified_input(comparison_of_results_procedure,growth_rate_knock_out_minimal_media). has_specified_input(comparison_of_results_procedure,growth_rate_wild_type_minimal_media). has_specified_input(comparison_of_results_procedure,growth_rate_knock_out_rich_media). has_specified_input(comparison_of_results_procedure,growth_rate_wild_type_rich_media). data(automated_investigation_data). automated_investigation_data(growth_rate_knock_out_minimal_media). automated_investigation_data(growth_rate_wild_type_minimal_media). automated_investigation_data(growth_rate_knock_out_rich_media). automated_investigation_data(growth_rate_wild_type_rich_media). link('http://www.aber.ac.uk/compsci/Research/bio/robotsci/data/data_reuse/results/'). has_proposition(automated_investigation_data,'http://www.aber.ac.uk/compsci/Research/bio/robotsci/data/data_reuse/results/'). has_specified_input(comparison_of_results_procedure,estimation_growth_rate_knock_out_minimal_media). has_specified_input(comparison_of_results_procedure,estimation_growth_rate_wild_type_minimal_media). has_specified_input(comparison_of_results_procedure,estimation_growth_rate_knock_out_rich_media). has_specified_input(comparison_of_results_procedure,estimation_growth_rate_wild_type_rich_media). has_specified_output(comparison_of_results_procedure,'not_match(model_iND750_prediction,data_reuse_results_rich_media)'). has_specified_output(comparison_of_results_procedure,'not_match(model_iND750_prediction,data_reuse_results_minimal_media)'). %%%%%%%%%%% % A-box % has_transitive_part(X,Y):-has_part(X,Y). has_transitive_part(X,Z):-has_part(X,Y),has_transitive_part(Y,Z). goal(test_suitability_goal). goal(test_accuracy_goal). goal(test_accuracy_goal_iIN750). goal(compare_goal). representation(text_representation). representation(logical_representation).