version(10-06-08). % ---------------------------------------------------------- study('manual study of gene functions predicted by Adam'). domain_of_study(domain_1_manual_study). has_proposition('manual study of gene functions predicted by Adam',domain_1_manual_study). has_representation(domain_1_manual_study,'artificial intelligence'). keywords_representation('artificial intelligence'). has_role('manual study of gene functions predicted by Adam','RS team'). investigator('RS team'). has_participant('manual study of gene functions predicted by Adam','robot scientist Adam'). object('robot scientist Adam'). has_proposition('manual study of gene functions predicted by Adam',manual_study_hset). hypotheses_set(manual_study_hset). has_proposition(manual_study_hset,manual_study_hset_hyp1). research_hypothesis(manual_study_hset_hyp1). has_representation(manual_study_hset_hyp1,'hypotheses confirmed by RS Adam are correct'). text_representation('hypotheses confirmed by RS Adam are correct'). has_proposition(manual_study_hset,manual_study_hset_hyp2). negative_hypothesis(manual_study_hset_hyp2). has_representation(manual_study_hset_hyp2,'hypotheses confirmed by RS Adam are incorrect'). text_representation('hypotheses confirmed by RS Adam are incorrect'). hypotheses_set(confirmed_by_adam_hset). has_proposition(confirmed_by_adam_hset,confirmed_hyp_1_1). has_representation(confirmed_hyp_1_1,'encodes(yer152c,ec_2_6_1_39)'). logic_representation('encodes(yer152c,ec_2_6_1_39)'). %has_link(confirmed_hyp_1_1,'XXX'). has_proposition(confirmed_by_adam_hset,confirmed_hyp_1_2). has_representation(confirmed_hyp_1_2,'encodes(ygl202w,ec_2_6_1_39)'). logic_representation('encodes(ygl202w,ec_2_6_1_39)'). %has_link(confirmed_hyp_1_2,'XXX'). has_proposition(confirmed_by_adam_hset,confirmed_hyp_1_3). has_representation(confirmed_hyp_1_3,'encodes(yjl060w,ec_2_6_1_39)'). logic_representation('encodes(yjl060w,ec_2_6_1_39)'). %has_link(confirmed_hyp_1_3,'XXX'). has_proposition('manual study of gene functions predicted by Adam','manual study of yer152cp function'). has_proposition('manual study of gene functions predicted by Adam','manual study of ygl202wp function'). has_proposition('manual study of gene functions predicted by Adam','manual study of yjl060wp function'). study('manual study of yer152cp function'). study('manual study of ygl202wp function'). study('manual study of yjl060wp function'). has_proposition('manual study of gene functions predicted by Adam',manual_study_result_1). has_proposition('manual study of gene functions predicted by Adam',manual_study_result_2). has_proposition('manual study of gene functions predicted by Adam',manual_study_result_3). result(manual_study_result_1). result(manual_study_result_2). result(manual_study_result_3). has_representation(manual_study_result_1,'confirmed(confirmed_hyp_1_1)'). has_representation(manual_study_result_2,'confirmed(confirmed_hyp_1_2)'). has_representation(manual_study_result_3,'confirmed(confirmed_hyp_1_3)'). logic_representation('confirmed(confirmed_hyp_1_1)'). logic_representation('confirmed(confirmed_hyp_1_2)'). logic_representation('confirmed(confirmed_hyp_1_3)'). has_proposition('manual study of gene functions predicted by Adam',manual_study_conclusion). conclusion(manual_study_conclusion). has_representation(manual_study_conclusion,'confirmed(manual_study_hset_hyp1), denied(manual_study_hset_hyp2)'). logic_representation('confirmed(manual_study_hset_hyp1), denied(manual_study_hset_hyp2)'). % ---------------------------------------------------------- % study('manual study of yer152cp function'). domain_of_study(domain_yer152cp_study). has_proposition('manual study of yer152cp function',domain_yer152cp_study). has_representation(domain_yer152cp_study,'systems biology'). keywords_representation('systems biology'). has_role('manual study of yer152cp function','Magdalena Markham'). investigator('Magdalena Markham'). has_proposition('manual study of yer152cp function', goal_study_yer152cp). confirm_goal(goal_study_1). has_representation(goal_study_1,'to manually test hypotheses about gene yer152c function that have been confirmed by Adam'). text_representation('to manually test hypotheses about gene yer152c function that have been confirmed by Adam'). has_participant('manual study of yer152cp function', saccharomyces_cerevisiae). organism_of_study(saccharomyces_cerevisiae). ncbi_taxonomy_id(ncbi_4932). has_representation(saccharomyces_cerevisiae, ncbi_4932). has_link(ncbi_4932, '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'). classification_of_study(classification_study_yer152cp). has_proposition('manual study of yer152cp function', classification_study_yer152cp). has_representation(classification_study_yer152cp, classification_study_yer152cp_repr_1). has_representation(classification_study_yer152cp_repr_1, classification_study_yer152cp_repr_1_c1). classification_code(classification_study_yer152cp_repr_1_c1). has_representation(classification_study_yer152cp_repr_1_c1, 'organism'). text_representation('organism'). has_representation(classification_study_yer152cp_repr_1, classification_study_yer152cp_repr_1_n1). classification_name(classification_study_yer152cp_repr_1_n1). has_representation(classification_study_yer152cp_repr_1_n1, 'saccharomyces cerevisiae'). text_representation('saccharomyces cerevisiae'). has_representation(classification_study_yer152cp, classification_study_yer152cp_repr_2). has_representation(classification_study_yer152cp_repr_2, classification_study_yer152cp_repr_2_c1). classification_code(classification_study_yer152cp_repr_2_c1). has_representation(classification_study_yer152cp_repr_2_c1, 'hypothesis_type'). text_representation('hypothesis_type'). has_representation(classification_study_yer152cp_repr_2, classification_study_yer152cp_repr_2_n1). classification_name(classification_study_yer152cp_repr_2_n1). has_representation(classification_study_yer152cp_repr_2_n1, 'hypothesis driven study'). text_representation('hypothesis driven study'). has_proposition('manual study of yer152cp function',study_yer152cp_cycle_1). cycle_of_study(study_yer152cp_cycle_1). hypotheses_set(study_yer152cp_cycle_1_hset). has_proposition(study_yer152cp_cycle_1,study_yer152cp_cycle_1_hset). research_hypothesis(study_yer152cp_cycle_1_hset_hyp_1_1_1). has_proposition(study_yer152cp_cycle_1_hset,study_yer152cp_cycle_1_hset_hyp_1_1_1). has_representation(study_yer152cp_cycle_1_hset_hyp_1_1_1,'activity(yer152cp,ec_2_6_1_39)'). logic_representation('activity(yer152cp,ec_2_6_1_39)'). has_representation(study_yer152cp_cycle_1_hset_hyp_1_1_1,'protein yer152cp has 2-aminoadipate transaminase activity (enzyme 2_6_1_39)'). text_representation('protein yer152cp has 2-aminoadipate transaminase activity (enzyme 2_6_1_39)'). negative_hypothesis(study_yer152cp_cycle_1_hset_hyp_1_1_2). has_proposition(study_yer152cp_cycle_1_hset,study_yer152cp_cycle_1_hset_hyp_1_1_2). has_representation(study_yer152cp_cycle_1_hset_hyp_1_1_2,'no_activity(yer152cp,ec_2_6_1_39)'). logic_representation('no_activity(yer152cp,ec_2_6_1_39)'). has_representation(study_yer152cp_cycle_1_hset_hyp_1_1_2,'protein yer152cp does not have 2-aminoadipate transaminase activity (enzyme 2_6_1_39)'). text_representation('protein yer152cp does not have 2-aminoadipate transaminase activity (enzyme 2_6_1_39)'). has_proposition(study_yer152cp_cycle_1,protein_preparation). protocol(protein_preparation). has_proposition(protein_preparation,'protein_prep.txt'). link('protein_prep.txt'). has_proposition(study_yer152cp_cycle_1,yeast_cell_disruption). protocol(yeast_cell_disruption). has_proposition(yeast_cell_disruption,'yeast_cell_disruption.txt'). link('yeast_cell_disruption.txt'). has_proposition(study_yer152cp_cycle_1,protein_purification). protocol(protein_purification). has_proposition(protein_purification,'purification.txt'). link('purification.txt'). has_proposition(study_yer152cp_cycle_1,confirmation_of_protein_expression). protocol(confirmation_of_protein_expression). has_proposition(confirmation_of_protein_expression,'confirmation_of_protein_expression.txt'). link('confirmation_of_protein_expression.txt'). result(gel_photo). has_proposition(confirmation_of_protein_expression,gel_photo). has_representation(gel_photo,'photo of SDS-PAGE gel confirming protein'). text_representation('photo of SDS-PAGE gel confirming protein'). has_proposition(gel_photo,'gel_YER152C.jpg'). link('gel_YER152C.jpg'). has_proposition(study_yer152cp_cycle_1,dialysis_of_eluate_containing_protein). protocol(dialysis_of_eluate_containing_protein). has_proposition(dialysis_of_eluate_containing_protein,'dialysis.txt'). link('dialysis.txt'). has_proposition(dialysis_of_eluate_containing_protein,dialysis_result). result(dialysis_result). has_representation(dialysis_result). text_representation('clear protein'). has_proposition(study_yer152cp_cycle_1, assay_protocol). protocol(assay_protocol). has_proposition(assay_protocol,'assay_protocol.txt'). link('assay_protocol.txt'). has_proposition(study_yer152cp_cycle_1,study_yer152cp_cycle_1_aminoadipate). trial(study_yer152cp_cycle_1_aminoadipate). has_proposition(study_yer152cp_cycle_1,study_yer152cp_cycle_1_alanine). trial(study_yer152cp_cycle_1_alanine). has_proposition(study_yer152cp_cycle_1,study_yer152cp_cycle_1_aspartate). trial(study_yer152cp_cycle_1_aspartate). has_proposition(study_yer152cp_cycle_1,study_yer152cp_cycle_1_result). result(study_yer152cp_cycle_1_result). has_representation(study_yer152cp_cycle_1_result,'aminoadipate, alanine, asparate activity curves'). text_representation(study_yer152cp_cycle_1_result,'aminoadipate, alanine, asparate activity curves'). has_representation(study_yer152cp_cycle_1_result,study_yer152cp_cycle_1_result_spreadsheet). spreadsheet(study_yer152cp_cycle_1_result_spreadsheet). has_proposition(study_yer152cp_cycle_1_result_spreadsheet,'xls/YER152C.xls'). link('xls/YER152C.xls'). has_proposition(study_yer152cp_cycle_1_result_spreadsheet,'xls/3_mutants_plus_control.xls'). link('xls/3_mutants_plus_control.xls'). has_proposition(study_yer152cp_cycle_1,study_yer152cp_cycle_1_conclusion). conclusion(study_yer152cp_cycle_1_conclusion). has_representation(study_yer152cp_cycle_1_conclusion,'confirmed(study_yer152cp_cycle_1_hset_hyp_1_1_1),denied(study_yer152cp_cycle_1_hset_hyp_1_1_2)'). text_representation('confirmed(study_yer152cp_cycle_1_hset_hyp_1_1_1),denied(study_yer152cp_cycle_1_hset_hyp_1_1_2)'). % ---------------------------------------------------------- % trial(study_yer152cp_cycle_1_aminoadipate). has_proposition(study_yer152cp_cycle_1_aminoadipate,study_yer152cp_cycle_1_aminoadipate_hset). hypotheses_set(study_yer152cp_cycle_1_aminoadipate_hset). has_proposition(study_yer152cp_cycle_1_aminoadipate_hset,study_yer152cp_cycle_1_aminoadipate_hset_method). inference(study_yer152cp_cycle_1_aminoadipate_hset_method). has_proposition(study_yer152cp_cycle_1_aminoadipate_hset_method, 'coupled_reaction'). inference_base('coupled reaction'). has_proposition(study_yer152cp_cycle_1_aminoadipate_hset,study_yer152cp_cycle_1_aminoadipate_hset_hyp_1_1_1_1). research_hypothesis(study_yer152cp_cycle_1_aminoadipate_hset_hyp_1_1_1_1). has_representation(study_yer152cp_cycle_1_aminoadipate_hset_hyp_1_1_1_1,'NADPH_production(yer152cp, aminoadipate)'). logic_representation('NADPH_production(yer152cp, aminoadipate)'). has_representation(study_yer152cp_cycle_1_aminoadipate_hset_hyp_1_1_1_1,'the addition of aminoadipate and the purified protein yer152cp will result in production of NADPH'). text_representation('the addition of aminoadipate and the purified protein yer152cp will result in production of NADPH'). negative_hypothesis(study_yer152cp_cycle_1_aminoadipate_hset_hyp_1_1_1_2). has_representation(study_yer152cp_cycle_1_aminoadipate_hset_hyp_1_1_1_2,'no_NADPH_production(yer152cp, aminoadipate)'). logic_representation('no_NADPH_production(yer152cp, aminoadipate)'). has_representation(study_yer152cp_cycle_1_aminoadipate_hset_hyp_1_1_1_2,'the addition of aminoadipate and the purified protein yer152cp will not result in production of NADPH'). text_representation('the addition of aminoadipate and the purified protein yer152cp will not result in production of NADPH'). has_role(study_yer152cp_cycle_1_aminoadipate,study_yer152cp_cycle_1_aminoadipate_abs). absorbance_readings(study_yer152cp_cycle_1_aminoadipate_abs). has_proposition(study_yer152cp_cycle_1_aminoadipate_abs,study_yer152cp_cycle_1_result_spreadsheet). has_proposition(study_yer152cp_cycle_1_aminoadipate,study_yer152cp_cycle_1_aminoadipate_result). result(study_yer152cp_cycle_1_aminoadipate_result). has_representation(study_yer152cp_cycle_1_aminoadipate_result,'confirmed(study_yer152cp_cycle_1_aminoadipate_hset_hyp_1_1_1_1),denied(study_yer152cp_cycle_1_aminoadipate_hset_hyp_1_1_1_2)'). logic_representation('confirmed(study_yer152cp_cycle_1_aminoadipate_hset_hyp_1_1_1_1),denied(study_yer152cp_cycle_1_aminoadipate_hset_hyp_1_1_1_2)'). % ---------------------------------------------------------- % trial(study_yer152cp_cycle_1_alanine). has_proposition(study_yer152cp_cycle_1_alanine,study_yer152cp_cycle_1_alanine_hset). hypotheses_set(study_yer152cp_cycle_1_alanine_hset). has_proposition(study_yer152cp_cycle_1_alanine_hset,study_yer152cp_cycle_1_alanine_hset_method). inference(study_yer152cp_cycle_1_alanine_hset_method). has_proposition(study_yer152cp_cycle_1_alanine_hset_method, 'coupled_reaction'). inference_base('coupled reaction'). has_proposition(study_yer152cp_cycle_1_alanine_hset,study_yer152cp_cycle_1_alanine_hset_hyp_1_1_1_1). research_hypothesis(study_yer152cp_cycle_1_alanine_hset_hyp_1_1_1_1). has_representation(study_yer152cp_cycle_1_alanine_hset_hyp_1_1_1_1,'NADPH_production(yer152cp, alanine)'). logic_representation('NADPH_production(yer152cp, alanine)'). has_representation(study_yer152cp_cycle_1_alanine_hset_hyp_1_1_1_1,'the addition of alanine and the purified protein yer152cp will result in production of NADPH'). text_representation('the addition of alanine and the purified protein yer152cp will result in production of NADPH'). negative_hypothesis(study_yer152cp_cycle_1_alanine_hset_hyp_1_1_1_2). has_representation(study_yer152cp_cycle_1_alanine_hset_hyp_1_1_1_2,'no_NADPH_production(yer152cp, alanine)'). logic_representation('no_NADPH_production(yer152cp, alanine)'). has_representation(study_yer152cp_cycle_1_alanine_hset_hyp_1_1_1_2,'the addition of alanine and the purified protein yer152cp will not result in production of NADPH'). text_representation('the addition of alanine and the purified protein yer152cp will not result in production of NADPH'). has_role(study_yer152cp_cycle_1_alanine,study_yer152cp_cycle_1_alanine_abs). absorbance_readings(study_yer152cp_cycle_1_alanine_abs). has_proposition(study_yer152cp_cycle_1_alanine_abs,study_yer152cp_cycle_1_result_spreadsheet). has_proposition(study_yer152cp_cycle_1_alanine,study_yer152cp_cycle_1_alanine_result). result(study_yer152cp_cycle_1_alanine_result). has_representation(study_yer152cp_cycle_1_alanine_result,'confirmed(study_yer152cp_cycle_1_alanine_hset_hyp_1_1_1_1),denied(study_yer152cp_cycle_1_alanine_hset_hyp_1_1_1_2)'). logic_representation('confirmed(study_yer152cp_cycle_1_alanine_hset_hyp_1_1_1_1),denied(study_yer152cp_cycle_1_alanine_hset_hyp_1_1_1_2)'). % ---------------------------------------------------------- % trial(study_yer152cp_cycle_1_aspartate). has_proposition(study_yer152cp_cycle_1_aspartate,study_yer152cp_cycle_1_aspartate_hset). hypotheses_set(study_yer152cp_cycle_1_aspartate_hset). has_proposition(study_yer152cp_cycle_1_aspartate_hset,study_yer152cp_cycle_1_aspartate_hset_method). inference(study_yer152cp_cycle_1_aspartate_hset_method). has_proposition(study_yer152cp_cycle_1_aspartate_hset_method, 'coupled_reaction'). inference_base('coupled reaction'). has_proposition(study_yer152cp_cycle_1_aspartate_hset,study_yer152cp_cycle_1_aspartate_hset_hyp_1_1_1_1). research_hypothesis(study_yer152cp_cycle_1_aspartate_hset_hyp_1_1_1_1). has_representation(study_yer152cp_cycle_1_aspartate_hset_hyp_1_1_1_1,'NADPH_production(yer152cp, aspartate)'). logic_representation('NADPH_production(yer152cp, aspartate)'). has_representation(study_yer152cp_cycle_1_aspartate_hset_hyp_1_1_1_1,'the addition of aspartate and the purified protein yer152cp will result in production of NADPH'). text_representation('the addition of aspartate and the purified protein yer152cp will result in production of NADPH'). negative_hypothesis(study_yer152cp_cycle_1_aspartate_hset_hyp_1_1_1_2). has_representation(study_yer152cp_cycle_1_aspartate_hset_hyp_1_1_1_2,'no_NADPH_production(yer152cp, aspartate)'). logic_representation('no_NADPH_production(yer152cp, aspartate)'). has_representation(study_yer152cp_cycle_1_aspartate_hset_hyp_1_1_1_2,'the addition of aspartate and the purified protein yer152cp will not result in production of NADPH'). text_representation('the addition of aspartate and the purified protein yer152cp will not result in production of NADPH'). has_role(study_yer152cp_cycle_1_aspartate,study_yer152cp_cycle_1_aspartate_abs). absorbance_readings(study_yer152cp_cycle_1_aspartate_abs). has_proposition(study_yer152cp_cycle_1_aspartate_abs,study_yer152cp_cycle_1_result_spreadsheet). has_proposition(study_yer152cp_cycle_1_aspartate,study_yer152cp_cycle_1_aspartate_result). result(study_yer152cp_cycle_1_aspartate_result). has_representation(study_yer152cp_cycle_1_aspartate_result,'confirmed(study_yer152cp_cycle_1_aspartate_hset_hyp_1_1_1_1),denied(study_yer152cp_cycle_1_aspartate_hset_hyp_1_1_1_2)'). logic_representation('confirmed(study_yer152cp_cycle_1_aspartate_hset_hyp_1_1_1_1),denied(study_yer152cp_cycle_1_aspartate_hset_hyp_1_1_1_2)'). % ---------------------------------------------------------- % study('manual study of ygl202wp function'). domain_of_study(domain_ygl202wp_study). has_proposition('manual study of ygl202wp function',domain_ygl202wp_study). has_representation(domain_ygl202wp_study,'systems biology'). keywords_representation('systems biology'). has_role('manual study of ygl202wp function','Magdalena Markham'). investigator('Magdalena Markham'). has_proposition('manual study of ygl202wp function', goal_study_ygl202wp). confirm_goal(goal_study_1). has_representation(goal_study_1,'to manually test hypotheses about gene ygl202w function that have been confirmed by Adam'). text_representation('to manually test hypotheses about gene ygl202w function that have been confirmed by Adam'). has_participant('manual study of ygl202wp function', saccharomyces_cerevisiae). organism_of_study(saccharomyces_cerevisiae). ncbi_taxonomy_id(ncbi_4932). has_representation(saccharomyces_cerevisiae, ncbi_4932). has_link(ncbi_4932, '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'). classification_of_study(classification_study_ygl202wp). has_proposition('manual study of ygl202wp function', classification_study_ygl202wp). has_representation(classification_study_ygl202wp, classification_study_ygl202wp_repr_1). has_representation(classification_study_ygl202wp_repr_1, classification_study_ygl202wp_repr_1_c1). classification_code(classification_study_ygl202wp_repr_1_c1). has_representation(classification_study_ygl202wp_repr_1_c1, 'organism'). text_representation('organism'). has_representation(classification_study_ygl202wp_repr_1, classification_study_ygl202wp_repr_1_n1). classification_name(classification_study_ygl202wp_repr_1_n1). has_representation(classification_study_ygl202wp_repr_1_n1, 'saccharomyces cerevisiae'). text_representation('saccharomyces cerevisiae'). has_representation(classification_study_ygl202wp, classification_study_ygl202wp_repr_2). has_representation(classification_study_ygl202wp_repr_2, classification_study_ygl202wp_repr_2_c1). classification_code(classification_study_ygl202wp_repr_2_c1). has_representation(classification_study_ygl202wp_repr_2_c1, 'hypothesis_type'). text_representation('hypothesis_type'). has_representation(classification_study_ygl202wp_repr_2, classification_study_ygl202wp_repr_2_n1). classification_name(classification_study_ygl202wp_repr_2_n1). has_representation(classification_study_ygl202wp_repr_2_n1, 'hypothesis driven study'). text_representation('hypothesis driven study'). has_proposition('manual study of ygl202wp function',study_ygl202wp_cycle_1). cycle_of_study(study_ygl202wp_cycle_1). hypotheses_set(study_ygl202wp_cycle_1_hset). has_proposition(study_ygl202wp_cycle_1,study_ygl202wp_cycle_1_hset). research_hypothesis(study_ygl202wp_cycle_1_hset_hyp_1_1_1). has_proposition(study_ygl202wp_cycle_1_hset,study_ygl202wp_cycle_1_hset_hyp_1_1_1). has_representation(study_ygl202wp_cycle_1_hset_hyp_1_1_1,'activity(ygl202wp,ec_2_6_1_39)'). logic_representation('activity(ygl202wp,ec_2_6_1_39)'). has_representation(study_ygl202wp_cycle_1_hset_hyp_1_1_1,'protein ygl202wp has 2-aminoadipate transaminase activity (enzyme 2_6_1_39)'). text_representation('protein ygl202wp has 2-aminoadipate transaminase activity (enzyme 2_6_1_39)'). negative_hypothesis(study_ygl202wp_cycle_1_hset_hyp_1_1_2). has_proposition(study_ygl202wp_cycle_1_hset,study_ygl202wp_cycle_1_hset_hyp_1_1_2). has_representation(study_ygl202wp_cycle_1_hset_hyp_1_1_2,'no_activity(ygl202wp,ec_2_6_1_39)'). logic_representation('no_activity(ygl202wp,ec_2_6_1_39)'). has_representation(study_ygl202wp_cycle_1_hset_hyp_1_1_2,'protein ygl202wp does not have 2-aminoadipate transaminase activity (enzyme 2_6_1_39)'). text_representation('protein ygl202wp does not have 2-aminoadipate transaminase activity (enzyme 2_6_1_39)'). has_proposition(study_ygl202wp_cycle_1,protein_preparation). protocol(protein_preparation). has_proposition(protein_preparation,'protein_prep.txt'). link('protein_prep.txt'). has_proposition(study_ygl202wp_cycle_1,yeast_cell_disruption). protocol(yeast_cell_disruption). has_proposition(yeast_cell_disruption,'yeast_cell_disruption.txt'). link('yeast_cell_disruption.txt'). has_proposition(study_ygl202wp_cycle_1,protein_purification). protocol(protein_purification). has_proposition(protein_purification,'purification.txt'). link('purification.txt'). has_proposition(study_ygl202wp_cycle_1,confirmation_of_protein_expression). protocol(confirmation_of_protein_expression). has_proposition(confirmation_of_protein_expression,'confirmation_of_protein_expression.txt'). link('confirmation_of_protein_expression.txt'). result(gel_photo). has_proposition(confirmation_of_protein_expression,gel_photo). has_representation(gel_photo,'photo of SDS-PAGE gel confirming protein'). text_representation('photo of SDS-PAGE gel confirming protein'). has_proposition(gel_photo,'gel_YGL202W.jpg'). link('gel_YGL202W.jpg'). has_proposition(study_ygl202wp_cycle_1,dialysis_of_eluate_containing_protein). protocol(dialysis_of_eluate_containing_protein). has_proposition(dialysis_of_eluate_containing_protein,'dialysis.txt'). link('dialysis.txt'). has_proposition(dialysis_of_eluate_containing_protein,dialysis_result). result(dialysis_result). has_representation(dialysis_result). text_representation('clear protein'). has_proposition(study_ygl202wp_cycle_1, assay_protocol). protocol(assay_protocol). has_proposition(assay_protocol,'assay_protocol.txt'). link('assay_protocol.txt'). has_proposition(study_ygl202wp_cycle_1,study_ygl202wp_cycle_1_aminoadipate). trial(study_ygl202wp_cycle_1_aminoadipate). has_proposition(study_ygl202wp_cycle_1,study_ygl202wp_cycle_1_alanine). trial(study_ygl202wp_cycle_1_alanine). has_proposition(study_ygl202wp_cycle_1,study_ygl202wp_cycle_1_aspartate). trial(study_ygl202wp_cycle_1_aspartate). has_proposition(study_ygl202wp_cycle_1,study_ygl202wp_cycle_1_result). result(study_ygl202wp_cycle_1_result). has_representation(study_ygl202wp_cycle_1_result,'aminoadipate, alanine, asparate activity curves'). text_representation(study_ygl202wp_cycle_1_result,'aminoadipate, alanine, asparate activity curves'). has_representation(study_ygl202wp_cycle_1_result,study_ygl202wp_cycle_1_result_spreadsheet). spreadsheet(study_ygl202wp_cycle_1_result_spreadsheet). has_proposition(study_ygl202wp_cycle_1_result_spreadsheet,'xls/YGL202W.xls'). link('xls/YGL202W.xls'). has_proposition(study_ygl202wp_cycle_1_result_spreadsheet,'xls/3_mutants_plus_control.xls'). link('xls/3_mutants_plus_control.xls'). has_proposition(study_ygl202wp_cycle_1,study_ygl202wp_cycle_1_conclusion). conclusion(study_ygl202wp_cycle_1_conclusion). has_representation(study_ygl202wp_cycle_1_conclusion,'confirmed(study_ygl202wp_cycle_1_hset_hyp_1_1_1),denied(study_ygl202wp_cycle_1_hset_hyp_1_1_2)'). text_representation('confirmed(study_ygl202wp_cycle_1_hset_hyp_1_1_1),denied(study_ygl202wp_cycle_1_hset_hyp_1_1_2)'). % ---------------------------------------------------------- % trial(study_ygl202wp_cycle_1_aminoadipate). has_proposition(study_ygl202wp_cycle_1_aminoadipate,study_ygl202wp_cycle_1_aminoadipate_hset). hypotheses_set(study_ygl202wp_cycle_1_aminoadipate_hset). has_proposition(study_ygl202wp_cycle_1_aminoadipate_hset,study_ygl202wp_cycle_1_aminoadipate_hset_method). inference(study_ygl202wp_cycle_1_aminoadipate_hset_method). has_proposition(study_ygl202wp_cycle_1_aminoadipate_hset_method, 'coupled_reaction'). inference_base('coupled reaction'). has_proposition(study_ygl202wp_cycle_1_aminoadipate_hset,study_ygl202wp_cycle_1_aminoadipate_hset_hyp_1_1_1_1). research_hypothesis(study_ygl202wp_cycle_1_aminoadipate_hset_hyp_1_1_1_1). has_representation(study_ygl202wp_cycle_1_aminoadipate_hset_hyp_1_1_1_1,'NADPH_production(ygl202wp, aminoadipate)'). logic_representation('NADPH_production(ygl202wp, aminoadipate)'). has_representation(study_ygl202wp_cycle_1_aminoadipate_hset_hyp_1_1_1_1,'the addition of aminoadipate and the purified protein ygl202wp will result in production of NADPH'). text_representation('the addition of aminoadipate and the purified protein ygl202wp will result in production of NADPH'). negative_hypothesis(study_ygl202wp_cycle_1_aminoadipate_hset_hyp_1_1_1_2). has_representation(study_ygl202wp_cycle_1_aminoadipate_hset_hyp_1_1_1_2,'no_NADPH_production(ygl202wp, aminoadipate)'). logic_representation('no_NADPH_production(ygl202wp, aminoadipate)'). has_representation(study_ygl202wp_cycle_1_aminoadipate_hset_hyp_1_1_1_2,'the addition of aminoadipate and the purified protein ygl202wp will not result in production of NADPH'). text_representation('the addition of aminoadipate and the purified protein ygl202wp will not result in production of NADPH'). has_role(study_ygl202wp_cycle_1_aminoadipate,study_ygl202wp_cycle_1_aminoadipate_abs). absorbance_readings(study_ygl202wp_cycle_1_aminoadipate_abs). has_proposition(study_ygl202wp_cycle_1_aminoadipate_abs,study_ygl202wp_cycle_1_result_spreadsheet). has_proposition(study_ygl202wp_cycle_1_aminoadipate,study_ygl202wp_cycle_1_aminoadipate_result). result(study_ygl202wp_cycle_1_aminoadipate_result). has_representation(study_ygl202wp_cycle_1_aminoadipate_result,'confirmed(study_ygl202wp_cycle_1_aminoadipate_hset_hyp_1_1_1_1),denied(study_ygl202wp_cycle_1_aminoadipate_hset_hyp_1_1_1_2)'). logic_representation('confirmed(study_ygl202wp_cycle_1_aminoadipate_hset_hyp_1_1_1_1),denied(study_ygl202wp_cycle_1_aminoadipate_hset_hyp_1_1_1_2)'). % ---------------------------------------------------------- % trial(study_ygl202wp_cycle_1_alanine). has_proposition(study_ygl202wp_cycle_1_alanine,study_ygl202wp_cycle_1_alanine_hset). hypotheses_set(study_ygl202wp_cycle_1_alanine_hset). has_proposition(study_ygl202wp_cycle_1_alanine_hset,study_ygl202wp_cycle_1_alanine_hset_method). inference(study_ygl202wp_cycle_1_alanine_hset_method). has_proposition(study_ygl202wp_cycle_1_alanine_hset_method, 'coupled_reaction'). inference_base('coupled reaction'). has_proposition(study_ygl202wp_cycle_1_alanine_hset,study_ygl202wp_cycle_1_alanine_hset_hyp_1_1_1_1). research_hypothesis(study_ygl202wp_cycle_1_alanine_hset_hyp_1_1_1_1). has_representation(study_ygl202wp_cycle_1_alanine_hset_hyp_1_1_1_1,'NADPH_production(ygl202wp, alanine)'). logic_representation('NADPH_production(ygl202wp, alanine)'). has_representation(study_ygl202wp_cycle_1_alanine_hset_hyp_1_1_1_1,'the addition of alanine and the purified protein ygl202wp will result in production of NADPH'). text_representation('the addition of alanine and the purified protein ygl202wp will result in production of NADPH'). negative_hypothesis(study_ygl202wp_cycle_1_alanine_hset_hyp_1_1_1_2). has_representation(study_ygl202wp_cycle_1_alanine_hset_hyp_1_1_1_2,'no_NADPH_production(ygl202wp, alanine)'). logic_representation('no_NADPH_production(ygl202wp, alanine)'). has_representation(study_ygl202wp_cycle_1_alanine_hset_hyp_1_1_1_2,'the addition of alanine and the purified protein ygl202wp will not result in production of NADPH'). text_representation('the addition of alanine and the purified protein ygl202wp will not result in production of NADPH'). has_role(study_ygl202wp_cycle_1_alanine,study_ygl202wp_cycle_1_alanine_abs). absorbance_readings(study_ygl202wp_cycle_1_alanine_abs). has_proposition(study_ygl202wp_cycle_1_alanine_abs,study_ygl202wp_cycle_1_result_spreadsheet). has_proposition(study_ygl202wp_cycle_1_alanine,study_ygl202wp_cycle_1_alanine_result). result(study_ygl202wp_cycle_1_alanine_result). has_representation(study_ygl202wp_cycle_1_alanine_result,'confirmed(study_ygl202wp_cycle_1_alanine_hset_hyp_1_1_1_1),denied(study_ygl202wp_cycle_1_alanine_hset_hyp_1_1_1_2)'). logic_representation('confirmed(study_ygl202wp_cycle_1_alanine_hset_hyp_1_1_1_1),denied(study_ygl202wp_cycle_1_alanine_hset_hyp_1_1_1_2)'). % ---------------------------------------------------------- % trial(study_ygl202wp_cycle_1_aspartate). has_proposition(study_ygl202wp_cycle_1_aspartate,study_ygl202wp_cycle_1_aspartate_hset). hypotheses_set(study_ygl202wp_cycle_1_aspartate_hset). has_proposition(study_ygl202wp_cycle_1_aspartate_hset,study_ygl202wp_cycle_1_aspartate_hset_method). inference(study_ygl202wp_cycle_1_aspartate_hset_method). has_proposition(study_ygl202wp_cycle_1_aspartate_hset_method, 'coupled_reaction'). inference_base('coupled reaction'). has_proposition(study_ygl202wp_cycle_1_aspartate_hset,study_ygl202wp_cycle_1_aspartate_hset_hyp_1_1_1_1). research_hypothesis(study_ygl202wp_cycle_1_aspartate_hset_hyp_1_1_1_1). has_representation(study_ygl202wp_cycle_1_aspartate_hset_hyp_1_1_1_1,'NADPH_production(ygl202wp, aspartate)'). logic_representation('NADPH_production(ygl202wp, aspartate)'). has_representation(study_ygl202wp_cycle_1_aspartate_hset_hyp_1_1_1_1,'the addition of aspartate and the purified protein ygl202wp will result in production of NADPH'). text_representation('the addition of aspartate and the purified protein ygl202wp will result in production of NADPH'). negative_hypothesis(study_ygl202wp_cycle_1_aspartate_hset_hyp_1_1_1_2). has_representation(study_ygl202wp_cycle_1_aspartate_hset_hyp_1_1_1_2,'no_NADPH_production(ygl202wp, aspartate)'). logic_representation('no_NADPH_production(ygl202wp, aspartate)'). has_representation(study_ygl202wp_cycle_1_aspartate_hset_hyp_1_1_1_2,'the addition of aspartate and the purified protein ygl202wp will not result in production of NADPH'). text_representation('the addition of aspartate and the purified protein ygl202wp will not result in production of NADPH'). has_role(study_ygl202wp_cycle_1_aspartate,study_ygl202wp_cycle_1_aspartate_abs). absorbance_readings(study_ygl202wp_cycle_1_aspartate_abs). has_proposition(study_ygl202wp_cycle_1_aspartate_abs,study_ygl202wp_cycle_1_result_spreadsheet). has_proposition(study_ygl202wp_cycle_1_aspartate,study_ygl202wp_cycle_1_aspartate_result). result(study_ygl202wp_cycle_1_aspartate_result). has_representation(study_ygl202wp_cycle_1_aspartate_result,'confirmed(study_ygl202wp_cycle_1_aspartate_hset_hyp_1_1_1_1),denied(study_ygl202wp_cycle_1_aspartate_hset_hyp_1_1_1_2)'). logic_representation('confirmed(study_ygl202wp_cycle_1_aspartate_hset_hyp_1_1_1_1),denied(study_ygl202wp_cycle_1_aspartate_hset_hyp_1_1_1_2)'). % ---------------------------------------------------------- % study('manual study of yjl060wp function'). domain_of_study(domain_yjl060wp_study). has_proposition('manual study of yjl060wp function',domain_yjl060wp_study). has_representation(domain_yjl060wp_study,'systems biology'). keywords_representation('systems biology'). has_role('manual study of yjl060wp function','Magdalena Markham'). investigator('Magdalena Markham'). has_proposition('manual study of yjl060wp function', goal_study_yjl060wp). confirm_goal(goal_study_1). has_representation(goal_study_1,'to manually test hypotheses about gene yjl060w function that have been confirmed by Adam'). text_representation('to manually test hypotheses about gene yjl060w function that have been confirmed by Adam'). has_participant('manual study of yjl060wp function', saccharomyces_cerevisiae). organism_of_study(saccharomyces_cerevisiae). ncbi_taxonomy_id(ncbi_4932). has_representation(saccharomyces_cerevisiae, ncbi_4932). has_link(ncbi_4932, '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'). classification_of_study(classification_study_yjl060wp). has_proposition('manual study of yjl060wp function', classification_study_yjl060wp). has_representation(classification_study_yjl060wp, classification_study_yjl060wp_repr_1). has_representation(classification_study_yjl060wp_repr_1, classification_study_yjl060wp_repr_1_c1). classification_code(classification_study_yjl060wp_repr_1_c1). has_representation(classification_study_yjl060wp_repr_1_c1, 'organism'). text_representation('organism'). has_representation(classification_study_yjl060wp_repr_1, classification_study_yjl060wp_repr_1_n1). classification_name(classification_study_yjl060wp_repr_1_n1). has_representation(classification_study_yjl060wp_repr_1_n1, 'saccharomyces cerevisiae'). text_representation('saccharomyces cerevisiae'). has_representation(classification_study_yjl060wp, classification_study_yjl060wp_repr_2). has_representation(classification_study_yjl060wp_repr_2, classification_study_yjl060wp_repr_2_c1). classification_code(classification_study_yjl060wp_repr_2_c1). has_representation(classification_study_yjl060wp_repr_2_c1, 'hypothesis_type'). text_representation('hypothesis_type'). has_representation(classification_study_yjl060wp_repr_2, classification_study_yjl060wp_repr_2_n1). classification_name(classification_study_yjl060wp_repr_2_n1). has_representation(classification_study_yjl060wp_repr_2_n1, 'hypothesis driven study'). text_representation('hypothesis driven study'). has_proposition('manual study of yjl060wp function',study_yjl060wp_cycle_1). cycle_of_study(study_yjl060wp_cycle_1). hypotheses_set(study_yjl060wp_cycle_1_hset). has_proposition(study_yjl060wp_cycle_1,study_yjl060wp_cycle_1_hset). research_hypothesis(study_yjl060wp_cycle_1_hset_hyp_1_1_1). has_proposition(study_yjl060wp_cycle_1_hset,study_yjl060wp_cycle_1_hset_hyp_1_1_1). has_representation(study_yjl060wp_cycle_1_hset_hyp_1_1_1,'activity(yjl060wp,ec_2_6_1_39)'). logic_representation('activity(yjl060wp,ec_2_6_1_39)'). has_representation(study_yjl060wp_cycle_1_hset_hyp_1_1_1,'protein yjl060wp has 2-aminoadipate transaminase activity (enzyme 2_6_1_39)'). text_representation('protein yjl060wp has 2-aminoadipate transaminase activity (enzyme 2_6_1_39)'). negative_hypothesis(study_yjl060wp_cycle_1_hset_hyp_1_1_2). has_proposition(study_yjl060wp_cycle_1_hset,study_yjl060wp_cycle_1_hset_hyp_1_1_2). has_representation(study_yjl060wp_cycle_1_hset_hyp_1_1_2,'no_activity(yjl060wp,ec_2_6_1_39)'). logic_representation('no_activity(yjl060wp,ec_2_6_1_39)'). has_representation(study_yjl060wp_cycle_1_hset_hyp_1_1_2,'protein yjl060wp does not have 2-aminoadipate transaminase activity (enzyme 2_6_1_39)'). text_representation('protein yjl060wp does not have 2-aminoadipate transaminase activity (enzyme 2_6_1_39)'). has_proposition(study_yjl060wp_cycle_1,protein_preparation). protocol(protein_preparation). has_proposition(protein_preparation,'protein_prep.txt'). link('protein_prep.txt'). has_proposition(study_yjl060wp_cycle_1,yeast_cell_disruption). protocol(yeast_cell_disruption). has_proposition(yeast_cell_disruption,'yeast_cell_disruption.txt'). link('yeast_cell_disruption.txt'). has_proposition(study_yjl060wp_cycle_1,protein_purification). protocol(protein_purification). has_proposition(protein_purification,'purification.txt'). link('purification.txt'). has_proposition(study_yjl060wp_cycle_1,confirmation_of_protein_expression). protocol(confirmation_of_protein_expression). has_proposition(confirmation_of_protein_expression,'confirmation_of_protein_expression.txt'). link('confirmation_of_protein_expression.txt'). result(gel_photo). has_proposition(confirmation_of_protein_expression,gel_photo). has_representation(gel_photo,'photo of SDS-PAGE gel confirming protein'). text_representation('photo of SDS-PAGE gel confirming protein'). has_proposition(gel_photo,'gel_YJL060W.jpg'). link('gel_YJL060W.jpg'). has_proposition(study_yjl060wp_cycle_1,dialysis_of_eluate_containing_protein). protocol(dialysis_of_eluate_containing_protein). has_proposition(dialysis_of_eluate_containing_protein,'dialysis.txt'). link('dialysis.txt'). has_proposition(dialysis_of_eluate_containing_protein,dialysis_result). result(dialysis_result). has_representation(dialysis_result). text_representation('clear protein'). has_proposition(study_yjl060wp_cycle_1, assay_protocol). protocol(assay_protocol). has_proposition(assay_protocol,'assay_protocol.txt'). link('assay_protocol.txt'). has_proposition(study_yjl060wp_cycle_1,study_yjl060wp_cycle_1_aminoadipate). trial(study_yjl060wp_cycle_1_aminoadipate). has_proposition(study_yjl060wp_cycle_1,study_yjl060wp_cycle_1_alanine). trial(study_yjl060wp_cycle_1_alanine). has_proposition(study_yjl060wp_cycle_1,study_yjl060wp_cycle_1_aspartate). trial(study_yjl060wp_cycle_1_aspartate). has_proposition(study_yjl060wp_cycle_1,study_yjl060wp_cycle_1_result). result(study_yjl060wp_cycle_1_result). has_representation(study_yjl060wp_cycle_1_result,'aminoadipate, alanine, asparate activity curves'). text_representation(study_yjl060wp_cycle_1_result,'aminoadipate, alanine, asparate activity curves'). has_representation(study_yjl060wp_cycle_1_result,study_yjl060wp_cycle_1_result_spreadsheet). spreadsheet(study_yjl060wp_cycle_1_result_spreadsheet). has_proposition(study_yjl060wp_cycle_1_result_spreadsheet,'xls/YJL060W.xls'). link('xls/YJL060W.xls'). has_proposition(study_yjl060wp_cycle_1_result_spreadsheet,'xls/3_mutants_plus_control.xls'). link('xls/3_mutants_plus_control.xls'). has_proposition(study_yjl060wp_cycle_1,study_yjl060wp_cycle_1_conclusion). conclusion(study_yjl060wp_cycle_1_conclusion). has_representation(study_yjl060wp_cycle_1_conclusion,'confirmed(study_yjl060wp_cycle_1_hset_hyp_1_1_1),denied(study_yjl060wp_cycle_1_hset_hyp_1_1_2)'). text_representation('confirmed(study_yjl060wp_cycle_1_hset_hyp_1_1_1),denied(study_yjl060wp_cycle_1_hset_hyp_1_1_2)'). % ---------------------------------------------------------- % trial(study_yjl060wp_cycle_1_aminoadipate). has_proposition(study_yjl060wp_cycle_1_aminoadipate,study_yjl060wp_cycle_1_aminoadipate_hset). hypotheses_set(study_yjl060wp_cycle_1_aminoadipate_hset). has_proposition(study_yjl060wp_cycle_1_aminoadipate_hset,study_yjl060wp_cycle_1_aminoadipate_hset_method). inference(study_yjl060wp_cycle_1_aminoadipate_hset_method). has_proposition(study_yjl060wp_cycle_1_aminoadipate_hset_method, 'coupled_reaction'). inference_base('coupled reaction'). has_proposition(study_yjl060wp_cycle_1_aminoadipate_hset,study_yjl060wp_cycle_1_aminoadipate_hset_hyp_1_1_1_1). research_hypothesis(study_yjl060wp_cycle_1_aminoadipate_hset_hyp_1_1_1_1). has_representation(study_yjl060wp_cycle_1_aminoadipate_hset_hyp_1_1_1_1,'NADPH_production(yjl060wp, aminoadipate)'). logic_representation('NADPH_production(yjl060wp, aminoadipate)'). has_representation(study_yjl060wp_cycle_1_aminoadipate_hset_hyp_1_1_1_1,'the addition of aminoadipate and the purified protein yjl060wp will result in production of NADPH'). text_representation('the addition of aminoadipate and the purified protein yjl060wp will result in production of NADPH'). negative_hypothesis(study_yjl060wp_cycle_1_aminoadipate_hset_hyp_1_1_1_2). has_representation(study_yjl060wp_cycle_1_aminoadipate_hset_hyp_1_1_1_2,'no_NADPH_production(yjl060wp, aminoadipate)'). logic_representation('no_NADPH_production(yjl060wp, aminoadipate)'). has_representation(study_yjl060wp_cycle_1_aminoadipate_hset_hyp_1_1_1_2,'the addition of aminoadipate and the purified protein yjl060wp will not result in production of NADPH'). text_representation('the addition of aminoadipate and the purified protein yjl060wp will not result in production of NADPH'). has_role(study_yjl060wp_cycle_1_aminoadipate,study_yjl060wp_cycle_1_aminoadipate_abs). absorbance_readings(study_yjl060wp_cycle_1_aminoadipate_abs). has_proposition(study_yjl060wp_cycle_1_aminoadipate_abs,study_yjl060wp_cycle_1_result_spreadsheet). has_proposition(study_yjl060wp_cycle_1_aminoadipate,study_yjl060wp_cycle_1_aminoadipate_result). result(study_yjl060wp_cycle_1_aminoadipate_result). has_representation(study_yjl060wp_cycle_1_aminoadipate_result,'confirmed(study_yjl060wp_cycle_1_aminoadipate_hset_hyp_1_1_1_1),denied(study_yjl060wp_cycle_1_aminoadipate_hset_hyp_1_1_1_2)'). logic_representation('confirmed(study_yjl060wp_cycle_1_aminoadipate_hset_hyp_1_1_1_1),denied(study_yjl060wp_cycle_1_aminoadipate_hset_hyp_1_1_1_2)'). % ---------------------------------------------------------- % trial(study_yjl060wp_cycle_1_alanine). has_proposition(study_yjl060wp_cycle_1_alanine,study_yjl060wp_cycle_1_alanine_hset). hypotheses_set(study_yjl060wp_cycle_1_alanine_hset). has_proposition(study_yjl060wp_cycle_1_alanine_hset,study_yjl060wp_cycle_1_alanine_hset_method). inference(study_yjl060wp_cycle_1_alanine_hset_method). has_proposition(study_yjl060wp_cycle_1_alanine_hset_method, 'coupled_reaction'). inference_base('coupled reaction'). has_proposition(study_yjl060wp_cycle_1_alanine_hset,study_yjl060wp_cycle_1_alanine_hset_hyp_1_1_1_1). research_hypothesis(study_yjl060wp_cycle_1_alanine_hset_hyp_1_1_1_1). has_representation(study_yjl060wp_cycle_1_alanine_hset_hyp_1_1_1_1,'NADPH_production(yjl060wp, alanine)'). logic_representation('NADPH_production(yjl060wp, alanine)'). has_representation(study_yjl060wp_cycle_1_alanine_hset_hyp_1_1_1_1,'the addition of alanine and the purified protein yjl060wp will result in production of NADPH'). text_representation('the addition of alanine and the purified protein yjl060wp will result in production of NADPH'). negative_hypothesis(study_yjl060wp_cycle_1_alanine_hset_hyp_1_1_1_2). has_representation(study_yjl060wp_cycle_1_alanine_hset_hyp_1_1_1_2,'no_NADPH_production(yjl060wp, alanine)'). logic_representation('no_NADPH_production(yjl060wp, alanine)'). has_representation(study_yjl060wp_cycle_1_alanine_hset_hyp_1_1_1_2,'the addition of alanine and the purified protein yjl060wp will not result in production of NADPH'). text_representation('the addition of alanine and the purified protein yjl060wp will not result in production of NADPH'). has_role(study_yjl060wp_cycle_1_alanine,study_yjl060wp_cycle_1_alanine_abs). absorbance_readings(study_yjl060wp_cycle_1_alanine_abs). has_proposition(study_yjl060wp_cycle_1_alanine_abs,study_yjl060wp_cycle_1_result_spreadsheet). has_proposition(study_yjl060wp_cycle_1_alanine,study_yjl060wp_cycle_1_alanine_result). result(study_yjl060wp_cycle_1_alanine_result). has_representation(study_yjl060wp_cycle_1_alanine_result,'confirmed(study_yjl060wp_cycle_1_alanine_hset_hyp_1_1_1_1),denied(study_yjl060wp_cycle_1_alanine_hset_hyp_1_1_1_2)'). logic_representation('confirmed(study_yjl060wp_cycle_1_alanine_hset_hyp_1_1_1_1),denied(study_yjl060wp_cycle_1_alanine_hset_hyp_1_1_1_2)'). % ---------------------------------------------------------- % trial(study_yjl060wp_cycle_1_aspartate). has_proposition(study_yjl060wp_cycle_1_aspartate,study_yjl060wp_cycle_1_aspartate_hset). hypotheses_set(study_yjl060wp_cycle_1_aspartate_hset). has_proposition(study_yjl060wp_cycle_1_aspartate_hset,study_yjl060wp_cycle_1_aspartate_hset_method). inference(study_yjl060wp_cycle_1_aspartate_hset_method). has_proposition(study_yjl060wp_cycle_1_aspartate_hset_method, 'coupled_reaction'). inference_base('coupled reaction'). has_proposition(study_yjl060wp_cycle_1_aspartate_hset,study_yjl060wp_cycle_1_aspartate_hset_hyp_1_1_1_1). research_hypothesis(study_yjl060wp_cycle_1_aspartate_hset_hyp_1_1_1_1). has_representation(study_yjl060wp_cycle_1_aspartate_hset_hyp_1_1_1_1,'NADPH_production(yjl060wp, aspartate)'). logic_representation('NADPH_production(yjl060wp, aspartate)'). has_representation(study_yjl060wp_cycle_1_aspartate_hset_hyp_1_1_1_1,'the addition of aspartate and the purified protein yjl060wp will result in production of NADPH'). text_representation('the addition of aspartate and the purified protein yjl060wp will result in production of NADPH'). negative_hypothesis(study_yjl060wp_cycle_1_aspartate_hset_hyp_1_1_1_2). has_representation(study_yjl060wp_cycle_1_aspartate_hset_hyp_1_1_1_2,'no_NADPH_production(yjl060wp, aspartate)'). logic_representation('no_NADPH_production(yjl060wp, aspartate)'). has_representation(study_yjl060wp_cycle_1_aspartate_hset_hyp_1_1_1_2,'the addition of aspartate and the purified protein yjl060wp will not result in production of NADPH'). text_representation('the addition of aspartate and the purified protein yjl060wp will not result in production of NADPH'). has_role(study_yjl060wp_cycle_1_aspartate,study_yjl060wp_cycle_1_aspartate_abs). absorbance_readings(study_yjl060wp_cycle_1_aspartate_abs). has_proposition(study_yjl060wp_cycle_1_aspartate_abs,study_yjl060wp_cycle_1_result_spreadsheet). has_proposition(study_yjl060wp_cycle_1_aspartate,study_yjl060wp_cycle_1_aspartate_result). result(study_yjl060wp_cycle_1_aspartate_result). has_representation(study_yjl060wp_cycle_1_aspartate_result,'confirmed(study_yjl060wp_cycle_1_aspartate_hset_hyp_1_1_1_1),denied(study_yjl060wp_cycle_1_aspartate_hset_hyp_1_1_1_2)'). logic_representation('confirmed(study_yjl060wp_cycle_1_aspartate_hset_hyp_1_1_1_1),denied(study_yjl060wp_cycle_1_aspartate_hset_hyp_1_1_1_2)').