study('manual study by wet and dry biology of gene functions predicted by Adam').
has_proposition('manual study by wet and dry biology of gene functions predicted by Adam',domain_man_lit_study).
domain_of_study(domain_man_lit_study).

has_representation(domain_man_lit_study,'artificial intelligence').
keywords_representation('artificial intelligence').

has_role('manual study by wet and dry biology of gene functions predicted by Adam','RS team').
investigator('RS team').
has_participant('manual study by wet and dry biology of gene functions predicted by Adam','robot scientist RS').
object('robot scientist RS').
has_proposition('manual study by wet and dry biology of gene functions predicted by Adam',man_lit_study_hset).
hypotheses_set(man_lit_study_hset).

has_proposition(man_lit_study_hset,man_lit_study_hset_hyp_1).
research_hypothesis(man_lit_study_hset_hyp_1).
has_representation(man_lit_study_hset_hyp_1,'RS hypotheses are correct').
text_representation('RS hypotheses are correct').
has_proposition(man_lit_study_hset,man_lit_study_hset_hyp_2).
negative_hypothesis(man_lit_study_hset_hyp_2).
has_representation(man_lit_study_hset_hyp_2,'RS hypotheses are not correct').
text_representation('RS hypotheses are not correct').
hypotheses_set(rs_hypotheses).
has_input('manual study by wet and dry biology of gene functions predicted by Adam',rs_hypotheses).
has_quality(rs_hypotheses,'confirmed').

has_proposition(rs_hypotheses, rs_hyp_1).
has_representation(rs_hyp_1,'encodes(yhr163w, ec_3_5_99_6)').  
logic_representation('encodes(yhr163w, ec_3_5_99_6)').  

has_proposition(rs_hypotheses, rs_hyp_2).
has_representation(rs_hyp_2,'encodes(yil033c, ec_3_5_1_2)').
logic_representation('encodes(yil033c, ec_3_5_1_2)').

has_proposition(rs_hypotheses, rs_hyp_3).
has_representation(rs_hyp_3,'encodes(ydl168w, ec_1_1_1_103)'). 
logic_representation('encodes(ydl168w, ec_1_1_1_103)'). 

has_proposition(rs_hypotheses, rs_hyp_4). 
has_representation(rs_hyp_4,'encodes(ylr209c, ec_2_4_2_1)').  
logic_representation('encodes(ylr209c, ec_2_4_2_1)').  

has_proposition(rs_hypotheses, rs_hyp_5). 
has_representation(rs_hyp_5,'encodes(ygl202w, ec_2_6_1_39)').  
logic_representation('encodes(ygl202w, ec_2_6_1_39)').  

has_proposition(rs_hypotheses, rs_hyp_6). 
has_representation(rs_hyp_6,'encodes(yer183c, ec_6_3_3_2)'). 
logic_representation('encodes(yer183c, ec_6_3_3_2)'). 

has_proposition(rs_hypotheses, rs_hyp_7). 
has_representation(rs_hyp_7,'encodes(ynr034w, ec_3_5_99_6)').  
logic_representation('encodes(ynr034w, ec_3_5_99_6)').

has_proposition(rs_hypotheses, rs_hyp_8).
has_representation(rs_hyp_8, 'encodes(ypr121w, ec_2_7_1_35)').
logic_representation('encodes(ypr121w, ec_2_7_1_35)').

has_proposition(rs_hypotheses, rs_hyp_9). 
has_representation(rs_hyp_9,'encodes(ynr073c, ec_3_5_99_6)').
logic_representation('encodes(ynr073c, ec_3_5_99_6)').

has_proposition(rs_hypotheses, rs_hyp_10). 
has_representation(rs_hyp_10,'encodes(ydl052c, ec_2_3_1_51)').
logic_representation('encodes(ydl052c, ec_2_3_1_51)').

has_proposition(rs_hypotheses, rs_hyp_11). 
has_representation(rs_hyp_11,'encodes(ygr248w, ec_3_5_99_6)').  
logic_representation('encodes(ygr248w, ec_3_5_99_6)').  

has_proposition(rs_hypotheses,rs_hyp_12).
has_representation(rs_hyp_12,'encodes(yll060c, ec_5_2_1_2)').  
logic_representation('encodes(yll060c, ec_5_2_1_2)').  

has_proposition(rs_hypotheses, rs_hyp_13). 
has_representation(rs_hyp_13,'encodes(yjl218w, ec_2_3_1_30)').
logic_representation('encodes(yjl218w, ec_2_3_1_30)').

has_proposition(rs_hypotheses,rs_hyp_14).
has_representation(rs_hyp_14,'encodes(ylr070c, ec_1_1_1_103)').
logic_representation('encodes(ylr070c, ec_1_1_1_103)').

has_proposition(rs_hypotheses,rs_hyp_15).
has_representation(rs_hyp_15,'encodes(yjl060w, ec_2_6_1_39)').   
logic_representation('encodes(yjl060w, ec_2_6_1_39)').   

has_proposition(rs_hypotheses,rs_hyp_16).
has_representation(rs_hyp_16,'encodes(ynr027w, ec_2_7_1_35)'). 
logic_representation('encodes(ynr027w, ec_2_7_1_35)'). 
 
has_proposition(rs_hypotheses,rs_hyp_17).
has_representation(rs_hyp_17,'encodes(ymr020w, ec_1_5_3_11)').
logic_representation('encodes(ymr020w, ec_1_5_3_11)').

has_proposition(rs_hypotheses,rs_hyp_18).
has_representation(rs_hyp_18,'encodes(yer152c, ec_2_6_1_39)').
logic_representation('encodes(yer152c, ec_2_6_1_39)').

has_proposition(rs_hypotheses,rs_hyp_19).
has_representation(rs_hyp_19,'encodes(yjl045w, ec_1_4_3_16)').
logic_representation('encodes(yjl045w, ec_1_4_3_16)').

has_proposition(rs_hypotheses,rs_hyp_20).
has_representation(rs_hyp_20,'encodes(ylr017w, ec_2_4_2_1)').  
logic_representation('encodes(ylr017w, ec_2_4_2_1)').  
 


has_proposition('manual study by wet and dry biology of gene functions predicted by Adam',proc_literature).
has_representation(proc_literature,'procedure to find gene function in bio-informatics and bibliographic resources').
text_representation('procedure to find gene function in bio-informatics and bibliographic resources').
has_proposition(proc_literature,'protocol_manual_literature_study.txt').
link('protocol_manual_literature_study.txt').

has_output('manual study by wet and dry biology of gene functions predicted by Adam', conclusion_about_evidence).   
conclusion(conclusion_about_evidence).




has_proposition(conclusion_about_evidence,'supports(rs_hyp_1)').
has_proposition(conclusion_about_evidence,'rejects(rs_hyp_2)').
has_proposition(conclusion_about_evidence,'supports(rs_hyp_3)').
has_proposition(conclusion_about_evidence,'supports(rs_hyp_4)').
has_proposition(conclusion_about_evidence,'supports(rs_hyp_5)').
has_proposition(conclusion_about_evidence,'supports(rs_hyp_6)').
has_proposition(conclusion_about_evidence,'supports(rs_hyp_7)').
has_proposition(conclusion_about_evidence,'supports(rs_hyp_8)').
has_proposition(conclusion_about_evidence,'supports(rs_hyp_9)').
has_proposition(conclusion_about_evidence,'supports(rs_hyp_10)').
has_proposition(conclusion_about_evidence,'supports(rs_hyp_11)').
has_proposition(conclusion_about_evidence,'supports(rs_hyp_12)').
has_proposition(conclusion_about_evidence,'neutral(rs_hyp_13)').
has_proposition(conclusion_about_evidence,'neutral(rs_hyp_14)').
has_proposition(conclusion_about_evidence,'supports(rs_hyp_15)').
has_proposition(conclusion_about_evidence,'neutral(rs_hyp_16)').
has_proposition(conclusion_about_evidence,'supports(rs_hyp_17)').
has_proposition(conclusion_about_evidence,'supports(rs_hyp_18)').
has_proposition(conclusion_about_evidence,'neutral(rs_hyp_19)').
has_proposition(conclusion_about_evidence,'supports(rs_hyp_20)').



has_output('manual study by wet and dry biology of gene functions predicted by Adam',study_man_lit_conclusion).
conclusion(study_man_lit_conclusion, 'confirmed(man_lit_study_hset_hyp_1), denied(man_lit_study_hset_hyp_2)').
logic_representation('confirmed(man_lit_study_hset_hyp_1), denied(man_lit_study_hset_hyp_2)').

