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

BACKGROUND: As biological data increases, we need additional infrastructure to share it 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...

Descripción completa

Detalles Bibliográficos
Autores principales: LeRoy, Nathan J., Khoroshevskyi, Oleksandr, O’Brien, Aaron, Stepień, Rafał, Arslan, Alip, Sheffield, Nathan C.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory 2023
Materias:
Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10462087/
https://www.ncbi.nlm.nih.gov/pubmed/37645717
http://dx.doi.org/10.1101/2023.08.15.551388
_version_ 1785097986919890944
author LeRoy, Nathan J.
Khoroshevskyi, Oleksandr
O’Brien, Aaron
Stepień, Rafał
Arslan, Alip
Sheffield, Nathan C.
author_facet LeRoy, Nathan J.
Khoroshevskyi, Oleksandr
O’Brien, Aaron
Stepień, Rafał
Arslan, Alip
Sheffield, Nathan C.
author_sort LeRoy, Nathan J.
collection PubMed
description BACKGROUND: As biological data increases, we need additional infrastructure to share it 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 itself. 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
format Online
Article
Text
id pubmed-10462087
institution National Center for Biotechnology Information
language English
publishDate 2023
publisher Cold Spring Harbor Laboratory
record_format MEDLINE/PubMed
spelling pubmed-104620872023-08-29 PEPhub: a database, web interface, and API for editing, sharing, and validating biological sample metadata LeRoy, Nathan J. Khoroshevskyi, Oleksandr O’Brien, Aaron Stepień, Rafał Arslan, Alip Sheffield, Nathan C. bioRxiv Article BACKGROUND: As biological data increases, we need additional infrastructure to share it 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 itself. 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 Cold Spring Harbor Laboratory 2023-08-18 /pmc/articles/PMC10462087/ /pubmed/37645717 http://dx.doi.org/10.1101/2023.08.15.551388 Text en https://creativecommons.org/licenses/by/4.0/This work is licensed under a Creative Commons Attribution 4.0 International License (https://creativecommons.org/licenses/by/4.0/) , which allows reusers to distribute, remix, adapt, and build upon the material in any medium or format, so long as attribution is given to the creator. The license allows for commercial use.
spellingShingle Article
LeRoy, Nathan J.
Khoroshevskyi, Oleksandr
O’Brien, Aaron
Stepień, Rafał
Arslan, Alip
Sheffield, Nathan C.
PEPhub: a database, web interface, and API for editing, sharing, and validating biological sample metadata
title PEPhub: a database, web interface, and API for editing, sharing, and validating biological sample metadata
title_full PEPhub: a database, web interface, and API for editing, sharing, and validating biological sample metadata
title_fullStr PEPhub: a database, web interface, and API for editing, sharing, and validating biological sample metadata
title_full_unstemmed PEPhub: a database, web interface, and API for editing, sharing, and validating biological sample metadata
title_short PEPhub: a database, web interface, and API for editing, sharing, and validating biological sample metadata
title_sort pephub: a database, web interface, and api for editing, sharing, and validating biological sample metadata
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10462087/
https://www.ncbi.nlm.nih.gov/pubmed/37645717
http://dx.doi.org/10.1101/2023.08.15.551388
work_keys_str_mv AT leroynathanj pephubadatabasewebinterfaceandapiforeditingsharingandvalidatingbiologicalsamplemetadata
AT khoroshevskyioleksandr pephubadatabasewebinterfaceandapiforeditingsharingandvalidatingbiologicalsamplemetadata
AT obrienaaron pephubadatabasewebinterfaceandapiforeditingsharingandvalidatingbiologicalsamplemetadata
AT stepienrafał pephubadatabasewebinterfaceandapiforeditingsharingandvalidatingbiologicalsamplemetadata
AT arslanalip pephubadatabasewebinterfaceandapiforeditingsharingandvalidatingbiologicalsamplemetadata
AT sheffieldnathanc pephubadatabasewebinterfaceandapiforeditingsharingandvalidatingbiologicalsamplemetadata

Ejemplares similares