Record W3010629926 · doi:10.1038/s41587-020-0446-y

MEMOTE for standardized genome-scale metabolic model testing

2020· letter· en· W3010629926 on OpenAlexafffund

Christian Lieven, Moritz E. Beber, Brett G. Olivier, Frank Bergmann, Meriç Ataman, Parizad Babaei, Jennifer Bartell, Lars M. Blank, Siddharth Chauhan, Kevin Correia, Christian Diener, Andreas Dräger, Birgitta E. Ebert, Janaka N. Edirisinghe, José P. Faria, Adam M. Feist, Georgios Fengos, Ronan M. T. Fleming, Beatriz García-Jiménez, Vassily Hatzimanikatis, Wout van Helvoirt, Christopher S. Henry, Henning Hermjakob, Markus J. Herrgård, Ali Kaafarani, Hyun Uk Kim, Zachary A. King, Steffen Klamt, Edda Klipp, Jasper J. Koehorst, Matthias König, Meiyappan Lakshmanan, Dong‐Yup Lee, Sang Yup Lee, Sunjae Lee, Nathan E. Lewis, Filipe Liu, Hongwu Ma, Daniel Machado, Radhakrishnan Mahadevan, Paulo Maia, Adil Mardinoğlu, Gregory L. Medlock, Jonathan M. Monk, Jens Nielsen, Lars K. Nielsen, Juan Nogales, Intawat Nookaew, Bernhard Ø. Palsson, Jason A. Papin, Kiran Raosaheb Patil, Mark G. Poolman, Nathan D. Price, Osbaldo Reséndis-Antonio, Anne Richelle, Isabel Rocha, Benjamín J. Sánchez, Peter J. Schaap, Rahuman S. Malik‐Sheriff, Saeed Shoaie, Nikolaus Sonnenschein, Bas Teusink, Paulo Vilaça, Jon Olav Vik, Judith A. H. Wodke, Joana C. Xavier, Qianqian Yuan, Maksim Zakhartsev, Cheng Zhang

Bibliographic record

VenueNature Biotechnology · 2020

Typeletter

Languageen

FieldBiochemistry, Genetics and Molecular Biology

TopicMicrobial Metabolic Engineering and Bioproduction

Canadian institutionsUniversity of Toronto

FundersArgonne National LaboratoryCentro Nacional de BiotecnologíaBiological and Environmental ResearchNational Institute of General Medical SciencesNational Cancer InstituteInstituto de Tecnologia Química e Biológica, Universidade Nova de LisboaMax Planck Institute for Dynamics of Complex Technical Systems MagdeburgBiotechnology and Biological Sciences Research CouncilDirectorate for Biological SciencesNational Institutes of HealthAdvanced Scientific Computing ResearchGerman Network for Bioinformatics InfrastructureNovo Nordisk FondenUniversity of California, San DiegoNorges Miljø- og Biovitenskapelige UniversitetEli Lilly and CompanyDanmarks Tekniske UniversitetRWTH Aachen UniversityKorea Advanced Institute of Science and TechnologyHumboldt-Universität zu BerlinKnut och Alice Wallenbergs StiftelseUniversidad Politécnica de MadridRural Development AdministrationU.S. National Library of MedicineChalmers Tekniska HögskolaHanzehogeschool GroningenSungkyunkwan UniversityUniversiteit LeidenSchweizerischer Nationalfonds zur Förderung der Wissenschaftlichen ForschungEberhard Karls Universität TübingenSchool of Medicine, University of California, San DiegoUniversidade Nova de LisboaNorges ForskningsrådKungliga Tekniska HögskolanNational Center for Complementary and Integrative HealthVrije Universiteit AmsterdamUniversity of TorontoChinese Academy of SciencesOxford Brookes UniversityDeutsche ForschungsgemeinschaftNational Research FoundationInnovationsfondenBundesministerium für Bildung und ForschungWellcome TrustMinistry of Science and ICT, South KoreaCoordinación de la Investigación CientíficaEuropean Molecular Biology LaboratoryNovo NordiskConsejo Superior de Investigaciones CientíficasAgency for Science, Technology and ResearchDeutsches Zentrum für InfektionsforschungWageningen University and ResearchCommonwealth Scientific and Industrial Research OrganisationUniversity of Arkansas for Medical SciencesBill and Melinda Gates FoundationInstituto Nacional de Investigación y Tecnología Agraria y AlimentariaUniversidade do MinhoW. M. Keck FoundationKing's College LondonEuropean Bioinformatics InstituteWashington Research FoundationEuropean CommissionU.S. Department of EnergyUniversity of QueenslandScience for Life LaboratoryNational Science Foundation

KeywordsEuropean unionExcellencePolitical scienceLibrary scienceEuropean commissionBasic researchResearch councilPublic administrationManagementBusinessEconomicsInternational tradeComputer scienceGovernment (linguistics)LawPhilosophy

DOI10.1038/s41587-020-0446-y

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)0.007

metaresearch head score (Gemma)0.009

Version: metacan-v3-hybrid-931329e0061cValidation status: machine_predicted_unvalidated

Candidate categoriesMetaresearch

Consensus categoriesnone

DomainCandidate signal: Methods · Consensus signal: none

Study designCandidate signal: Not applicable · Consensus signal: Not applicable

GenreCandidate signal: Methods · Consensus signal: none

Teacher disagreement score0.993

Threshold uncertainty score0.126

Distilled classifier scores by category (both heads)

Category	Codex	Gemma
Metaresearch	0.007	0.009
Meta-epidemiology (narrow)	0.001	0.001
Meta-epidemiology (broad)	0.001	0.001
Bibliometrics	0.001	0.001
Science and technology studies	0.001	0.001
Scholarly communication	0.002	0.003
Open science	0.003	0.003
Research integrity	0.008	0.009
Insufficient payload (model declined to judge)	0.038	0.027

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 head0.010

GPT teacher head0.230

Teacher spread0.220 · 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