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Record W2754579667 · doi:10.1038/nbt.3935

Shotgun metagenomics, from sampling to analysis

2017· review· en· W2754579667 on OpenAlexafffund
Christopher Quince, Alan W. Walker, Jared T. Simpson, Nicholas J. Loman, Nicola Segata

Bibliographic record

VenueNature Biotechnology · 2017
Typereview
Languageen
FieldEnvironmental Science
TopicMicrobial Community Ecology and Physiology
Canadian institutionsUniversity of TorontoOntario Institute for Cancer Research
FundersBiotechnology and Biological Sciences Research CouncilMedical Research CouncilMinistero dell’Istruzione, dell’Università e della RicercaEuropean CommissionGovernment of OntarioUniversity of AberdeenFondazione Cassa Di Risparmio Di Trento E RoveretoRural and Environment Science and Analytical Services Division
KeywordsMetagenomicsShotgunComputational biologySampling (signal processing)Shotgun sequencingBiologyComputer scienceGeneticsGenomeGeneComputer vision

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)0.003
metaresearch head score (Gemma)0.003
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 score0.004
Threshold uncertainty score0.016

Distilled classifier scores by category (both heads)

CategoryCodexGemma
Metaresearch0.0030.003
Meta-epidemiology (narrow)0.0020.001
Meta-epidemiology (broad)0.0030.001
Bibliometrics0.0040.005
Science and technology studies0.0000.001
Scholarly communication0.0020.003
Open science0.0030.002
Research integrity0.0020.003
Insufficient payload (model declined to judge)0.0020.001

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 head0.083
GPT teacher head0.387
Teacher spread0.304 · 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

Citations2,155
Published2017
Admission routes2
Has abstractno

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