{"id":"W1986365650","doi":"10.1371/journal.pcbi.1003194","title":"Using Biological Pathway Data with Paxtools","year":2013,"lang":"en","type":"article","venue":"PLoS Computational Biology","topic":"Bioinformatics and Genomic Networks","field":"Biochemistry, Genetics and Molecular Biology","cited_by":67,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Toronto","funders":"National Human Genome Research Institute; National Institutes of Health","keywords":"Computer science; Java; Source code; Software; Software engineering; License; Code (set theory); Software system; Programming language; Operating system; Set (abstract data type)","routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.001731022,0.001417554,0.0008960641,0.0046278,0.001188783,0.003773936,0.002340296,0.001073275,0.04065342],"category_scores_gemma":[0.006504133,0.00116714,0.002326487,0.004339906,0.0007298736,0.003816886,0.002804804,0.002192807,0.01246029],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.001004682,"about_ca_system_score_gemma":0.002574346,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.004829855,"about_ca_topic_score_gemma":0.00578956,"domain_scores_codex":[0.9991072,0.0001444869,0.0001020953,0.0003079374,0.0002595765,0.00007874185],"domain_scores_gemma":[0.9976888,0.001174975,0.0001627434,0.0006088279,0.0002645731,0.0001000644],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"not_applicable","study_design_gemma":"not_applicable","study_design_scores_codex":[0.002856592,0.0003131092,0.01324165,0.007450737,0.001113598,0.001230682,0.001905875,0.04760313,0.04241399,0.143424,0.4087547,0.3296919],"study_design_scores_gemma":[0.0004095864,0.0001027426,0.004317123,0.0005910911,0.0002250801,0.0007860396,0.0004622538,0.1006385,0.04954721,0.1725125,0.6701184,0.000289367],"study_design_candidate":"not_applicable","study_design_consensus":"not_applicable","genre_codex":"methods","genre_gemma":"software","genre_scores_codex":[0.01156109,0.0006851346,0.5150467,0.0007061487,0.000392848,0.0002972856,0.1605156,0.2966922,0.01410315],"genre_scores_gemma":[0.08622503,0.001637817,0.556215,0.0008421454,0.0001188015,0.001931791,0.3048824,0.03970955,0.008437394],"genre_candidate":"software","genre_consensus":null,"teacher_disagreement_score":0.04065342,"threshold_uncertainty_score":0.1359992,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.07401512202566655,"score_gpt":0.2774376329437105,"score_spread":0.203422510918044,"validation_status":"score_only:v0-immature-baseline","note":"Baseline scores from an immature model (maturity gate not passed). Scores rank; they never assert a category."}}