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)').







