PEPhub: a database, web interface, and API for editing, sharing, and validating biological sample metadata.

Autor:	LeRoy NJ; Center for Public Health Genomics, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA.; Department of Biomedical Engineering, School of Medicine, University of Virginia, Charlottesville, VA 22904, USA., Khoroshevskyi O; Center for Public Health Genomics, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA., O'Brien A; Center for Public Health Genomics, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA., Stępień R; Center for Public Health Genomics, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA., Arslan A; Department of Computer Science, School of Engineering, University of Virginia, Charlottesville, VA 22908, USA., Sheffield NC; Center for Public Health Genomics, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA.; Department of Biomedical Engineering, School of Medicine, University of Virginia, Charlottesville, VA 22904, USA.; School of Data Science, University of Virginia, Charlottesville, VA 22904, USA.; Department of Public Health Sciences, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA.; Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA.; Child Health Research Center, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA.
Jazyk:	angličtina
Zdroj:	GigaScience [Gigascience] 2024 Jan 02; Vol. 13.
DOI:	10.1093/gigascience/giae033
Abstrakt:	Background: As 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. Results: Here, 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. (© The Author(s) 2024. Published by Oxford University Press GigaScience.)
Databáze:	MEDLINE
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