{"id":"W3199394352","doi":"10.1186/s12864-021-07982-8","title":"PathFams: statistical detection of pathogen-associated protein domains","year":2021,"lang":"en","type":"article","venue":"BMC Genomics","topic":"Bacteriophages and microbial interactions","field":"Environmental Science","cited_by":12,"is_retracted":false,"has_abstract":true,"ca_institutions":"Wilfrid Laurier University; University of Waterloo","funders":"Natural Sciences and Engineering Research Council of Canada","keywords":"Virulence; Biology; Genome; Computational biology; Pathogen; Protein domain; Metagenomics; Genetics; Virulence factor; Gene","routes":{"ca_aff":true,"ca_fund":true,"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":[0.004660285,0.001396186,0.001409176,0.007377773,0.0009960614,0.001600852,0.001855296,0.001145935,0.01391645],"category_scores_gemma":[0.01716885,0.0005924253,0.001843616,0.004620992,0.0007512294,0.002010262,0.002746547,0.001257657,0.003669392],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0006738879,"about_ca_system_score_gemma":0.001798005,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001645426,"about_ca_topic_score_gemma":0.00189034,"domain_scores_codex":[0.9975606,0.0006752738,0.0002121521,0.0008944935,0.0004957858,0.0001617173],"domain_scores_gemma":[0.9904808,0.006745176,0.001079532,0.0007957681,0.0004640083,0.0004345863],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"design_other","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.005610755,0.000635523,0.2374471,0.006571916,0.003358126,0.001936792,0.001231722,0.02643669,0.04361873,0.01545507,0.3252451,0.3324524],"study_design_scores_gemma":[0.001214216,0.001331497,0.1196344,0.0006014794,0.0009491444,0.005819187,0.0009601325,0.5084083,0.03750436,0.05129954,0.2718752,0.0004024762],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"dataset","genre_gemma":"methods","genre_scores_codex":[0.3105424,0.004389043,0.2328692,0.001398639,0.0005175906,0.0006616515,0.3128018,0.1305006,0.006319062],"genre_scores_gemma":[0.4966983,0.0009672837,0.2732103,0.0003730132,0.0001872388,0.001659791,0.2182682,0.006562291,0.002073601],"genre_candidate":"methods","genre_consensus":null,"teacher_disagreement_score":0.01391645,"threshold_uncertainty_score":0.0465551,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01063085851951757,"score_gpt":0.2196792303363206,"score_spread":0.209048371816803,"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."}}