{"id":"W4378651302","doi":"10.3390/plants12112139","title":"Looking beyond Virus Detection in RNA Sequencing Data: Lessons Learned from a Community-Based Effort to Detect Cellular Plant Pathogens and Pests","year":2023,"lang":"en","type":"article","venue":"Plants","topic":"Plant Virus Research Studies","field":"Agricultural and Biological Sciences","cited_by":10,"is_retracted":false,"has_abstract":true,"ca_institutions":"Canadian Food Inspection Agency","funders":"FOD Volksgezondheid, Veiligheid van de Voedselketen en Leefmilieu; Javna Agencija za Raziskovalno Dejavnost RS","keywords":"Biology; RNA; Virus; Plant virus; Computational biology; RNA-Seq; DNA sequencing; Plant species; Virology; Gene; Genetics; Botany; Transcriptome; Gene expression","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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00090842,0.0001595011,0.0002326857,0.0000734726,0.0005220858,0.00008708463,0.0004101041,0.0000848605,0.000009308367],"category_scores_gemma":[0.0002108183,0.00007770736,0.00002335797,0.0004222289,0.00004066114,0.0001193182,0.0005040533,0.0003735548,0.00006317369],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00006291625,"about_ca_system_score_gemma":0.00001557383,"about_ca_topic_candidate":true,"about_ca_topic_consensus":true,"about_ca_topic_score_codex":0.01388934,"about_ca_topic_score_gemma":0.1420894,"domain_scores_codex":[0.9984398,0.0002611611,0.0001864329,0.0003676079,0.0002933123,0.0004516285],"domain_scores_gemma":[0.9986204,0.001033759,0.0000494693,0.0001508304,0.00001628046,0.0001292843],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.00008272019,0.00001366296,0.002611901,0.00001092879,0.00001489841,0.0001612869,0.0002961534,0.00007350798,0.9595119,4.587253e-7,0.0001003303,0.0371222],"study_design_scores_gemma":[0.0006031889,0.0003440653,0.3707334,0.0003047101,0.00002615829,0.00001513641,0.002100587,0.009929973,0.6089675,0.0007641406,0.005580407,0.0006307474],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9912256,0.00008684812,0.00001137251,0.0003276913,0.00006419681,0.0002215143,0.007911446,0.0001128189,0.00003849931],"genre_scores_gemma":[0.9974262,0.0002985487,0.00004886895,0.0001340241,0.00006833598,0.00001702726,0.001993186,0.00000203042,0.00001176458],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.3681215,"threshold_uncertainty_score":0.9926773,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.1807535767501763,"score_gpt":0.3144540838734149,"score_spread":0.1337005071232387,"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."}}