XHTML representation of automated study of YER152C function
This example shows a human-friendly clickable structure of the study
(in contrast with the machine oriented datalog representation).The
XHTML representation contains the most essential properties of the key
concepts defined in the ontology LABORS: hypothesis, experiment
design, cycle, result, conclusion.
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- study: study_YER152C
- has proposition
- domain of study: study_YER152C_domain_1
- has representation
- key words representation: functional genomics
- has representation
- ddc classification code: 575
- ddc classification name: evolution and genetics
- ddc classification code: 576
- ddc classification name: microbiology
- has representation
- lcc classification code: QH426-470
- lcc classification name: genetics
- lcc classification code: QR1-502
- lcc classification name: microbiology
- has role
- investigator: robot scientist adam
- has proposition
- confirm goal: study_YER152C_goal
- has representation
- text representation: 'To test the hypothesis that gene YER152C encodes an enzyme with enzyme class E.C. 2.6.1.39'
- has role
- object: gene functions of saccharomyces cerevisiae
- has participant
- organism of study: saccharomyces cerevisiae
- has proposition
- classification of study: study_YER152C_classfn_1
- has representation
- has representation
- classification code: organism
- classification name: saccharomyces cerevisiae
- has representation
- classification code: hypothesis type
- classification name: hypothesis driven study
- classification name: hypothesis forming study
- has proposition
- hypothesis-set: study_YER152C_hset
- has proposition
- research hypothesis: study_YER152C_hset_hyp_1
- has logic representation: encodes(yer152c,ec_2_6_1_39)
- has text representation: gene YER152C encodes an enzyme with enzyme class E.C. 2.6.1.39
- negative hypothesis: study_YER152C_hset_hyp_2
- has logic representation: not encodes(yer152c,ec_2_6_1_39)
- has text representation: gene YER152C does not encode an enzyme with enzyme class E.C. 2.6.1.39
- inference: study_YER152C_hset_method
- has_proposition
- cycle of study: study_YER152C_cycle_1
- has proposition
- input hypothesis set: study_YER152C_cycle_1_ihset
- has proposition
- research hypothesis: study_YER152C_cycle_1_ihset_hyp_1
- has logic representation: encodes(yer152c, ec_2_6_1_39)
- has text representation: 'gene YER152C encodes an enzyme with enzyme class E.C. 2.6.1.39'
- negative hypothesis: study_YER152C_cycle_1_ihset_hyp_2
- has logic representation: not encodes(yer152c, ec_2_6_1_39)
- has text representation: 'gene YER152C does not encode an enzyme with enzyme class E.C. 2.6.1.39'
- derived hypothesis set: study_YER152C_cycle_1_dhset
- has proposition
- research hypothesis: study_YER152C_cycle_1_dhset_hyp_1_1
- has logic representation: affects_growth(C00047, delta_YER152C)
- has text representation: 'Addition of the metabolite C00047 to a defined growth medium will differentially affect the growth of the yeast strain delta_YER152C compared to the wild type (Mat A, BY4741)'
- negative hypothesis: study_YER152C_cycle_1_dhset_hyp_1_2
- has logic representation: affects_growth(C00047, delta_YER152C)
- has text representation: 'Addition of the metabolite C00047 to a defined growth medium will not differentially affect the growth of the yeast strain delta_YER152C compared to the wild type (Mat A, BY4741)'
- research hypothesis: study_YER152C_cycle_1_dhset_hyp_2_1
- has logic representation: affects_growth(C00449, delta_YER152C)
- has text representation: 'Addition of the metabolite C00449 to a defined growth medium will differentially affect the growth of the yeast strain delta_YER152C compared to the wild type (Mat A, BY4741)'
- negative hypothesis: study_YER152C_cycle_1_dhset_hyp_2_2
- has logic representation: affects_growth(C00449, delta_YER152C)
- has text representation: 'Addition of the metabolite C00449 to a defined growth medium will not differentially affect the growth of the yeast strain delta_YER152C compared to the wild type (Mat A, BY4741)'
- research hypothesis: study_YER152C_cycle_1_dhset_hyp_3_1
- has logic representation: affects_growth(C00956, delta_YER152C)
- has text representation: 'Addition of the metabolite C00047 to a defined growth medium will differentially affect the growth of the yeast strain delta_YER152C compared to the wild type (Mat A, BY4741)'
- negative hypothesis: study_YER152C_cycle_1_dhset_hyp_3_2
- has logic representation: affects_growth(C00956, delta_YER152C)
- has text representation: 'Addition of the metabolite C00956 to a defined growth medium will not differentially affect the growth of the yeast strain delta_YER152C compared to the wild type (Mat A, BY4741)'
- has proposition
- inference: study_YER152C_cycle_1_dhset_method
- has proposition
- has proposition
- trial: trial_10
- has proposition
- hypothesis-set: trial_10_hset
- has proposition
- research hypothesis: trial_10_hset_hyp_1_1
- has logic representation: affects_growth(C00047, delta_YER152C)
- has text representation: 'addition of the metabolite C00047 to a standard growth medium will differentially affect the growth of the yeast strain delta_YER152C compared to the wild type (Mat A, BY4741)'
- negative hypothesis: trial_10_hset_hyp_1_2
- has logic representation: not affects_growth(C00047, delta_YER152C)
- has text representation: 'addition of the metabolite C00047 to a standard growth medium will not differentially affect the growth of the yeast strain delta_YER152C compared to the wild type (Mat A, BY4741)'
- has proposition
- trial design: trial_10_design
- has proposition
- pairwise design strategy: pairwise comparison
- design pair: trial_10_design_1
- has target
- factor-set: yer152c_c00047
- has representation
- text representation: 'yeast strain delta-yer152c with C00047'
- has proposition
- factor level: trial_10_factor_1_level_2
- factor level: trial_10_factor_2_level_1
- has control
- factor-set: yer152c_none
- has representation
- text representation: 'yeast strain yer152c without C00047'
- has proposition
- factor level: trial_10_factor_1_level_2
- factor level: trial_10_factor_2_level_2
- design pair: trial_10_design_2
- has target
- factor-set: wt_c00047
- has representation
- text representation: 'yeast strain wild type with C00047'
- has proposition
- factor level: trial_10_factor_1_level_1
- factor level: trial_10_factor_2_level_1
- has control
- factor-set: wt_none
- has representation
- text representation: 'yeast strain wildtype without C00047'
- has proposition
- factor level: trial_10_factor_1_level_1
- factor level: trial_10_factor_2_level_2
- design pair: trial_10_design_3
- has target
- factor-set: yer152c_c00047
- has representation
- text representation: 'yeast strain yer152c with C00047'
- has proposition
- factor level: trial_10_factor_1_level_2
- factor level: trial_10_factor_2_level_1
- has control
- factor-set: wt_C00047
- has representation
- text representation: 'yeast strain wild type with C00047'
- has proposition
- factor level: trial_10_factor_1_level_1
- factor level: trial_10_factor_2_level_1
- design pair: trial_10_design_4
- has target
- factor-set: yer152c_none
- has representation
- text representation: 'yeast strain yer152c without C00047'
- has proposition
- factor level: trial_10_factor_1_level_2
- factor level: trial_10_factor_2_level_2
- has control
- factor-set: wt_none
- has representation
- text representation: 'yeast strain wildtype without C00047'
- has proposition
- factor level: trial_10_factor_1_level_1
- factor level: trial_10_factor_2_level_2
- has proposition
- plate layout: 'set of 6 latin squares'
- has proposition
- experiment factor 1: trial_10_factor_1
- has representation
- text representation: 'presence or absence of gene YER152C in yeast strain'
- has proposition
- factor level: trial_10_factor_1_level_2
- has representation
- text representation: 'yeast strain delta_YER152C'
- factor level: trial_10_factor_1_level_1
- has representation
- text representation: 'yeast strain wild type (Mat A, BY4741)'
- experiment factor 2: trial_10_factor_2
- has representation
- text representation: 'presence or absence of metabolite C00047'
- has proposition
- factor level: trial_10_factor_2_level_1
- has representation
- text representation: 'presence of C00047'
- factor level: trial_10_factor_2_level_2
- has representation
- text representation: 'absence of C00047'
- has proposition
- expected result: trial_10_exp_res_1
- significance of difference in growth curves: trial_10_exp_res_1
- has part
- factor-set: trial_10_exp_res_1_a
- has part
- factor level: trial_10_factor_1_level_2
- factor level: trial_10_factor_2_level_1
- factor-set: trial_10_exp_res_1_b
- has part
- factor level: trial_10_factor_1_level_2
- factor level: trial_10_factor_2_level_2
- has representation
- text representation: 'The model checks if there will be a significant difference in the difference in growth curves between the knockout with and without C00047. N.B. a difference in growth curve may not change the mean of any of the growth curve parameters.'
- expected result: trial_10_exp_res_2
- significance of difference in growth curves: trial_10_exp_res_2
- has part
- factor-set: trial_10_exp_res_2_a
- has part
- factor level: trial_10_factor_1_level_1
- factor level: trial_10_factor_2_level_1
- factor-set: trial_10_exp_res_2_b
- has part
- factor level: trial_10_factor_1_level_1
- factor level: trial_10_factor_2_level_2
- has representation
- text representation: 'The model checks if there will be a significant difference in the difference in growth curves between the wildtype with and without C00047. N.B. a difference in growth curve may not change the mean of any of the growth curve parameters.'
- expected result: trial_10_exp_res_3
- significance of difference in growth curves: trial_10_exp_res_3
- has part
- factor-set: trial_10_exp_res_3_a
- has part
- factor level: trial_10_factor_1_level_2
- factor level: trial_10_factor_2_level_1
- factor-set: trial_10_exp_res_3_b
- has part
- factor level: trial_10_factor_1_level_1
- factor level: trial_10_factor_2_level_1
- has representation
- text representation: 'The model checks if there will be a significant difference in the difference in growth curves between the knockout and wildtype, each with C00047. N.B. a difference in growth curve may not change the mean of any of the growth curve parameters.'
- expected result: trial_10_exp_res_4
- significance of difference in growth curves: trial_10_exp_res_4
- has part
- factor-set: trial_10_exp_res_4_a
- has part
- factor level: trial_10_factor_1_level_2
- factor level: trial_10_factor_2_level_2
- factor-set: trial_10_exp_res_4_b
- has part
- factor level: trial_10_factor_1_level_1
- factor level: trial_10_factor_2_level_2
- has representation
- text representation: 'The model checks if there will be a significant difference in the difference in growth curves between the knockout and wildtype, each without C00047. N.B. a difference in growth curve may not change the mean of any of the growth curve parameters.'
- expected result: trial_10_exp_res_5
- significance of the differences in growth curves: trial_10_exp_res_5
- has part
- has_part
- minuend: trial_10_exp_res_5_a_minuend
- has part
- factor level: trial_10_factor_1_level_2
- factor level: trial_10_factor_2_level_1
- minuend: trial_10_exp_res_5_a_subtrahend
- has part
- factor level: trial_10_factor_1_level_2
- factor level: trial_10_factor_2_level_2
- has_part
- minuend: trial_10_exp_res_5_b_minuend
- has part
- factor level: trial_10_factor_1_level_1
- factor level: trial_10_factor_2_level_1
- minuend: trial_10_exp_res_5_b_subtrahend
- has part
- factor level: trial_10_factor_1_level_1
- factor level: trial_10_factor_2_level_2
- has representation
- text representation: The model checks if there will be a significant difference in the growth curves between the knockout and the wildtype caused by the metabolite C00065. The difference that the metabolite makes to the wildtype is compared to the difference the metabolite makes to the knockout'
- has expected result: trial_10_exp_res_6
- random forest discrimination of the difference that the addition of metabolite makes to growth curves: trial_10_exp_res_6
- has part
- has_part
- minuend: trial_10_exp_res_6_a_minuend
- has part
- factor level: trial_10_factor_1_level_2
- factor level: trial_10_factor_2_level_1
- minuend: trial_10_exp_res_6_a_subtrahend
- has part
- factor level: trial_10_factor_1_level_2
- factor level: trial_10_factor_2_level_2
- has_part
- minuend: trial_10_exp_res_6_b_minuend
- has part
- factor level: trial_10_factor_1_level_1
- factor level: trial_10_factor_2_level_1
- minuend: trial_10_exp_res_6_b_subtrahend
- has part
- factor level: trial_10_factor_1_level_1
- factor level: trial_10_factor_2_level_2
- has representation
- text representation: 'The random forest checks if discrimination of wildtype and knockout strains is possible by considering the difference that the addition of the metabolite makes to their growth curves.
- expected result: trial_10_exp_res_7
- decision tree discrimination of the difference that the addition of metabolite makes to growth curves: trial_10_exp_res_7
- has part
- has_part
- minuend: trial_10_exp_res_7_a_minuend
- has part
- factor level: trial_10_factor_1_level_2
- factor level: trial_10_factor_2_level_1
- minuend: trial_10_exp_res_7_a_subtrahend
- has part
- factor level: trial_10_factor_1_level_2
- factor level: trial_10_factor_2_level_2
- has_part
- minuend: trial_10_exp_res_7_b_minuend
- has part
- factor level: trial_10_factor_1_level_1
- factor level: trial_10_factor_2_level_1
- minuend: trial_10_exp_res_7_b_subtrahend
- has part
- factor level: trial_10_factor_1_level_1
- factor level: trial_10_factor_2_level_2
- has representation
- text representation: 'The decision tree checks if discrimination of wildtype and knockout strains is possible by considering the difference that the addition of the metabolite makes to their growth curves.
- has proposition
- test: test_37
- has participant
- object of test: test_37_object
- has representation
- text representation: 'wild type'
- has proposition
- ploidy: 'mat a haploid'
- phenotype: 'Wild type strain that is reliant on Leucine Histidine Uracil and Methionine'
- has role
- supplier: Manchester University
- derives from
- has proposition
- replicate: test_37_rep_1
- located in
- pregrowth plate location: 11448
- pregrowth well location: 'A11'
- growth plate location: 15632
- growth plate location: 'A11
- has role
- has role
- pregrowth_parameter: test_37_rep_1_pg_lag_time
- pregrowth_parameter: test_37_rep_1_pg_miy_lag_time
- pregrowth_parameter: test_37_rep_1_pg_start_linear
- pregrowth_parameter: test_37_rep_1_pg_end_linear
- pregrowth_parameter: test_37_rep_1_pg_dur_linear
- pregrowth_parameter: test_37_rep_1_pg_linear_slope
- pregrowth_parameter: test_37_rep_1_pg_max_od_emg
- pregrowth_parameter: test_37_rep_1_pg_max_od_time_emg
- pregrowth_parameter: test_37_rep_1_pg_double_time
- pregrowth_parameter: test_37_rep_1_pg_global_max_od
- pregrowth_parameter: test_37_rep_1_pg_global_max_od_time
- global max od time: 23.9792
- pregrowth_parameter: test_37_rep_1_pg_signal_to_noise_ratio
- signal to noise ratio: 460.335
- pregrowth_parameter: test_37_rep_1_pg_threshold
- growth_parameter: test_37_rep_1_pg_lag_time
- growth_parameter: test_37_rep_1_pg_miy_lag_time
- growth_parameter: test_37_rep_1_pg_start_linear
- growth_parameter: test_37_rep_1_pg_end_linear
- growth_parameter: test_37_rep_1_pg_dur_linear
- growth_parameter: test_37_rep_1_pg_linear_slope
- growth_parameter: test_37_rep_1_pg_max_od_emg
- growth_parameter: test_37_rep_1_pg_max_od_time_emg
- growth_parameter: test_37_rep_1_pg_double_time
- growth_parameter: test_37_rep_1_pg_global_max_od
- growth_parameter: test_37_rep_1_pg_global_max_od_time
- global max od time: 23.9792
- growth_parameter: test_37_rep_1_pg_signal_to_noise_ratio
- signal to noise ratio: 460.335
- growth_parameter: test_37_rep_1_pg_threshold
- has proposition
- replicate: test_37_rep_2
- replicate: test_37_rep_3
- replicate: test_37_rep_4
- replicate: test_37_rep_5
- replicate: test_37_rep_6
- replicate: test_37_rep_7
- replicate: test_37_rep_8
- replicate: test_37_rep_9
- replicate: test_37_rep_10
- replicate: test_37_rep_11
- replicate: test_37_rep_12
- replicate: test_37_rep_13
- replicate: test_37_rep_14
- replicate: test_37_rep_15
- replicate: test_37_rep_16
- replicate: test_37_rep_17
- replicate: test_37_rep_18
- replicate: test_37_rep_19
- replicate: test_37_rep_20
- replicate: test_37_rep_21
- replicate: test_37_rep_22
- replicate: test_37_rep_23
- replicate: test_37_rep_24
- test: test_38
- test: test_39
- test: test_40
- has role
- has role
- trial conclusion: trial_10_conclusion
- has representation
- logic representation: 'confirmed(trial_10_hset_hyp_1_1), denied(trial_10_hset_hyp_1_2)'
- text representation: 'the difference in growth of the yeast strain YER152C with the addition of C00047 to the standard defined medium is different to that of the wild type (Mat A, BY4741) with the addition of C00047 to the standard defined medium.'
- has proposition
- conclusion base: trial_10_conclusion_base
- trial: trial_11
- trial: trial_12
- has role
- result: study_YER152C_cycle_1_result
- output hypotheses set: study_YER152C_cycle_1_result
- has part
- hypothesis: study_YER152C_cycle_1_ihset_hyp_1
- has role
- conclusion: study_YER152C_cycle_1_conclusion
- has representation
- logic representation: 'confirmed(study_YER152C_cycle_1_ihset_hyp_1), denied(study_YER152C_cycle_1_ihset_hyp_2)'
- has role
- result: study_YER152C_result
- has representation
- text representation: 'the strength of evidence that encodes(yer152c,ec_2_6_1_39)'
- has part
- highest accuracy of random forest evidence: 74%
- proportion of random forest evidence >=70%: 2/3
- has proposition
- has role
- conclusion: study_YER152C_conclusion
- has representation
- logic representation: 'confirmed(study_YER152C_hset_hyp_1), denied(study_YER152C_hset_hyp_2)'