Evidence map›Paper›PMID 41377518›Full record

ArticlebioRxiv : the preprint server for biology2025

Large-scale Manual Curation and Harmonization of Metadata from Metagenomic and Cancer Genomic Repositories: Challenges and Solutions.

Kaelyn Long, Kai Gravel-Pucillo, Levi Waldron, Sean Davis, Sehyun Oh

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

5 authors.

Kaelyn LongInstitute for Implementation Science in Population Health, City University of New York School of Public Health, New York, NY.
Kai Gravel-PucilloInstitute for Implementation Science in Population Health, City University of New York School of Public Health, New York, NY.
Levi WaldronInstitute for Implementation Science in Population Health, City University of New York School of Public Health, New York, NY.ORCID 0000-0003-2725-0694
Sean DavisDepartments of Biomedical Informatics and Medicine, University of Colorado Anschutz School of Medicine, Denver, CO.ORCID 0000-0002-8991-6458
Sehyun OhInstitute for Implementation Science in Population Health, City University of New York School of Public Health, New York, NY.ORCID 0000-0002-9490-3061

Funding

Cancer Genomics:Integrative and Scalable Solutions in R / BioconductorU24CA180996 · NCI · ROSWELL PARK CANCER INSTITUTE CORP · PI MORGAN, MARTIN T, WALDRON, LEVI · 2014 to 2023
$6.9M
Cancer Genomics: Integrative and Scalable Solutions in R/BioconductorU24CA289073 · NCI · GRADUATE SCHOOL OF PUBLIC HEALTH AND HEALTH POLICY · PI Sean Davis, Levi Waldron · 2024 to 2026
$3.2M
NCI NIH HHS U24 CA180996NCI NIH HHS U24 CA289073
6 · The paper itself

Abstract

Public omics repositories contain vast amounts of valuable data, but their metadata suffers from extreme heterogeneity, unstandardized terminologies, and quality issues that severely limit data reusability and cross-study integration. While prospective metadata standards exist, the majority of published omics data remain in non-standardized formats requiring retrospective curation. We performed comprehensive manual curation and harmonization of clinical metadata from 212,027 samples across 468 studies in two major repositories:

Indexed as

AI/ML-readycBioPortalClinical DatacuratedMetagenomicDataFAIR PrinciplesMetadata HarmonizationOmicsMLRepo

Identifiers

PMID41377518
PMCPMC12687785

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.