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Record W2951825561 · doi:10.1038/s41579-019-0214-5

Whole genome sequencing of Mycobacterium tuberculosis: current standards and open issues

2019· review· en· W2951825561 on OpenAlexaff
Conor J. Meehan, Galo A. Goig, Thomas A. Kohl, Lennert Verboven, Anzaan Dippenaar, Matthew Ezewudo, Maha Farhat, Jennifer L. Guthrie, Kris Laukens, Paolo Miotto, Boatema Ofori-Anyinam, Viola Dreyer, Philip Supply, Anita Suresh, Christian Utpatel, Dick van Soolingen, Yang Zhou, Philip Ashton, Daniela Brites, Andrea Maurizio Cabibbe, Bouke C. de Jong, Margaretha de Vos, Fabrizio Menardo, Sébastien Gagneux, Qian Gao, Tim H. Heupink, Qingyun Liu, Chloé Loiseau, Leen Rigouts, Timothy C. Rodwell, Elisa Tagliani, A Sarah Walker, Robin M. Warren, Yanlin Zhao, Matteo Zignol, Marco Schito, Jennifer L. Gardy, Daniela María Cirillo, Stefan Niemann, Iñaki Comas, Annelies Van Rie

Bibliographic record

VenueNature Reviews Microbiology · 2019
Typereview
Languageen
FieldMedicine
TopicTuberculosis Research and Epidemiology
Canadian institutionsGlobal Institute for Water SecurityCentre for Global Health ResearchOkanagan University CollegeUniversity of British Columbia, Okanagan CampusUniversity of British Columbia
FundersAgence Nationale de la RechercheNational Institute for Health and Care ResearchWorld Health Organization
KeywordsMycobacterium tuberculosisWhole genome sequencingBiologyTuberculosisGenomeComputational biologyGeneticsMedicineGene

Abstract

fetched live from OpenAlex
No abstract in any covered source. Its absence is recorded, not treated as a negative.

No abstract. This is not a gap in this database; OpenAlex has none either. 23.3% of the frame is in this state, and the screen finds HALF as much metaresearch here, so the absence is a measured bias rather than a missing field.

How this classification was reachedexpand

Full frame machine prediction

Teacher imitation

Not calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.

metaresearch head score (Codex)0.006
metaresearch head score (Gemma)0.009
Version: metacan-v3-hybrid-931329e0061cValidation status: machine_predicted_unvalidated
Candidate categoriesnone
Consensus categoriesnone
DomainCandidate signal: none · Consensus signal: none
Study designCandidate signal: Not applicable · Consensus signal: none
GenreCandidate signal: Review · Consensus signal: Review
Teacher disagreement score0.006
Threshold uncertainty score0.032

Distilled classifier scores by category (both heads)

CategoryCodexGemma
Metaresearch0.0060.009
Meta-epidemiology (narrow)0.0010.001
Meta-epidemiology (broad)0.0030.001
Bibliometrics0.0030.003
Science and technology studies0.0000.002
Scholarly communication0.0030.004
Open science0.0020.002
Research integrity0.0040.005
Insufficient payload (model declined to judge)0.0030.002

Machine scores (provisional)

The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.

Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.

Opus teacher head0.087
GPT teacher head0.451
Teacher spread0.364 · how far apart the two teachers sit on this one work
Validation statusscore_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from it

Classification

machine, unvalidated

Machine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.

The models applied no category: nothing in the taxonomy fit this work.
Study designNot applicable
Domainnot available
GenreReview

How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".

Quick stats

Citations429
Published2019
Admission routes1
Has abstractno

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