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Record W4388448853 · doi:10.1021/acs.jnatprod.3c00795

A Data Deposition Platform for Sharing Nuclear Magnetic Resonance Data

2023· article· en· W4388448853 on OpenAlexaff
Matthew Pin, Ella F Poynton, Tamara Jordan, Jonghyeok Kim, Benjamin Ledingham, Jeffrey A. van Santen, Vera Yang, Andrew Maras, Pegah Tavangar, Vasuk Gautam, Harrison Peters, Tanvir Sajed, Brian L. Lee, Hailey A. Shreffler, James T. Koller, Zachary M. Tretter, John Cort, Lloyd W. Sumner, David S. Wishart, Roger G. Linington

Bibliographic record

VenueJournal of Natural Products · 2023
Typearticle
Languageen
FieldBiochemistry, Genetics and Molecular Biology
TopicMetabolomics and Mass Spectrometry Studies
Canadian institutionsUniversity of AlbertaSimon Fraser University
FundersNational Center for Complementary and Integrative HealthNational Institutes of Health
KeywordsRaw dataInteroperabilityComputer scienceData sharingDeposition (geology)Process (computing)World Wide WebGeology

Abstract

fetched live from OpenAlex

Nuclear magnetic resonance (NMR) data are rarely deposited in open databases, leading to loss of critical scientific knowledge. Existing data reporting methods (images, tables, lists of values) contain less information than raw data and are poorly standardized. Together, these issues limit FAIR (findable, accessible, interoperable, reusable) access to these data, which in turn creates barriers for compound dereplication and the development of new data-driven discovery tools. Existing NMR databases either are not designed for natural products data or employ complex deposition interfaces that disincentivize deposition. Journals, including the Journal of Natural Products (JNP), are now requiring data submission as part of the publication process, creating the need for a streamlined, user-friendly mechanism to deposit and distribute NMR data.

Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.

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)0.027
metaresearch head score (Gemma)0.052
Version: metacan-v3-hybrid-931329e0061cValidation status: machine_predicted_unvalidated
Candidate categoriesOpen science
Consensus categoriesnone
DomainCandidate signal: none · Consensus signal: none
Study designCandidate signal: Not applicable · Consensus signal: Not applicable
GenreCandidate signal: Software · Consensus signal: none
Teacher disagreement score0.992
Threshold uncertainty score0.405

Distilled classifier scores by category (both heads)

CategoryCodexGemma
Metaresearch0.0270.052
Meta-epidemiology (narrow)0.0030.003
Meta-epidemiology (broad)0.0030.003
Bibliometrics0.0070.008
Science and technology studies0.0040.002
Scholarly communication0.0130.010
Open science0.0080.018
Research integrity0.0050.007
Insufficient payload (model declined to judge)0.1210.130

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 head0.057
GPT teacher head0.305
Teacher spread0.248 · 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.

Study designNot applicable
Domainnot available
GenreSoftware

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

Citations3
Published2023
Admission routes1
Has abstractyes

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