ArticleGigaScience2024
PEPhub: a database, web interface, and API for editing, sharing, and validating biological sample metadata.
Article in GigaScience, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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.
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.
Who cites it
4 citing papers in PubMed.
- Using semantic search to find publicly available gene-expression datasets.Bioinformatics (Oxford, England) · 2026Article
- SCSEQ: A web tool for analyzing single-cell RNA-seq data.GigaScience · 2026Article
- EHItk: a toolkit for accessing Earth Hologenome Initiative data resources.Bioinformatics advances · 2026Article
- PEPhub: a database, web interface, and API for editing, sharing, and validating biological sample metadata.GigaScience · 2024Article
Corrections and comments
- Update of
Authors and funding
6 authors.
Funding
Abstract
backgroundAs biological data increase, we need additional infrastructure to share them and promote interoperability. While major effort has been put into sharing data, relatively less emphasis is placed on sharing metadata. Yet, sharing metadata is also important and in some ways has a wider scope than sharing data themselves.
resultsHere, we present PEPhub, an approach to improve sharing and interoperability of biological metadata. PEPhub provides an API, natural-language search, and user-friendly web-based sharing and editing of sample metadata tables. We used PEPhub to process more than 100,000 published biological research projects and index them with fast semantic natural-language search. PEPhub thus provides a fast and user-friendly way to finding existing biological research data or to share new data. AVAILABILITY: https://pephub.databio.org.
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What OpenQuestion holds
Registered trials
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.