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Schema Playground: a tool for authoring, extending, and using metadata schemas to improve FAIRness of biomedical data

BACKGROUND: Biomedical researchers are strongly encouraged to make their research outputs more Findable, Accessible, Interoperable, and Reusable (FAIR). While many biomedical research outputs are more readily accessible through open data efforts, finding relevant outputs remains a significant challe...

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Autores principales: Cano, Marco A., Tsueng, Ginger, Zhou, Xinghua, Xin, Jiwen, Hughes, Laura D., Mullen, Julia L., Su, Andrew I., Wu, Chunlei
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10116472/
https://www.ncbi.nlm.nih.gov/pubmed/37081398
http://dx.doi.org/10.1186/s12859-023-05258-4
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author Cano, Marco A.
Tsueng, Ginger
Zhou, Xinghua
Xin, Jiwen
Hughes, Laura D.
Mullen, Julia L.
Su, Andrew I.
Wu, Chunlei
author_facet Cano, Marco A.
Tsueng, Ginger
Zhou, Xinghua
Xin, Jiwen
Hughes, Laura D.
Mullen, Julia L.
Su, Andrew I.
Wu, Chunlei
author_sort Cano, Marco A.
collection PubMed
description BACKGROUND: Biomedical researchers are strongly encouraged to make their research outputs more Findable, Accessible, Interoperable, and Reusable (FAIR). While many biomedical research outputs are more readily accessible through open data efforts, finding relevant outputs remains a significant challenge. Schema.org is a metadata vocabulary standardization project that enables web content creators to make their content more FAIR. Leveraging Schema.org could benefit biomedical research resource providers, but it can be challenging to apply Schema.org standards to biomedical research outputs. We created an online browser-based tool that empowers researchers and repository developers to utilize Schema.org or other biomedical schema projects. RESULTS: Our browser-based tool includes features which can help address many of the barriers towards Schema.org-compliance such as: The ability to easily browse for relevant Schema.org classes, the ability to extend and customize a class to be more suitable for biomedical research outputs, the ability to create data validation to ensure adherence of a research output to a customized class, and the ability to register a custom class to our schema registry enabling others to search and re-use it. We demonstrate the use of our tool with the creation of the Outbreak.info schema—a large multi-class schema for harmonizing various COVID-19 related resources. CONCLUSIONS: We have created a browser-based tool to empower biomedical research resource providers to leverage Schema.org classes to make their research outputs more FAIR. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12859-023-05258-4.
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spelling pubmed-101164722023-04-21 Schema Playground: a tool for authoring, extending, and using metadata schemas to improve FAIRness of biomedical data Cano, Marco A. Tsueng, Ginger Zhou, Xinghua Xin, Jiwen Hughes, Laura D. Mullen, Julia L. Su, Andrew I. Wu, Chunlei BMC Bioinformatics Software BACKGROUND: Biomedical researchers are strongly encouraged to make their research outputs more Findable, Accessible, Interoperable, and Reusable (FAIR). While many biomedical research outputs are more readily accessible through open data efforts, finding relevant outputs remains a significant challenge. Schema.org is a metadata vocabulary standardization project that enables web content creators to make their content more FAIR. Leveraging Schema.org could benefit biomedical research resource providers, but it can be challenging to apply Schema.org standards to biomedical research outputs. We created an online browser-based tool that empowers researchers and repository developers to utilize Schema.org or other biomedical schema projects. RESULTS: Our browser-based tool includes features which can help address many of the barriers towards Schema.org-compliance such as: The ability to easily browse for relevant Schema.org classes, the ability to extend and customize a class to be more suitable for biomedical research outputs, the ability to create data validation to ensure adherence of a research output to a customized class, and the ability to register a custom class to our schema registry enabling others to search and re-use it. We demonstrate the use of our tool with the creation of the Outbreak.info schema—a large multi-class schema for harmonizing various COVID-19 related resources. CONCLUSIONS: We have created a browser-based tool to empower biomedical research resource providers to leverage Schema.org classes to make their research outputs more FAIR. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12859-023-05258-4. BioMed Central 2023-04-20 /pmc/articles/PMC10116472/ /pubmed/37081398 http://dx.doi.org/10.1186/s12859-023-05258-4 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Software
Cano, Marco A.
Tsueng, Ginger
Zhou, Xinghua
Xin, Jiwen
Hughes, Laura D.
Mullen, Julia L.
Su, Andrew I.
Wu, Chunlei
Schema Playground: a tool for authoring, extending, and using metadata schemas to improve FAIRness of biomedical data
title Schema Playground: a tool for authoring, extending, and using metadata schemas to improve FAIRness of biomedical data
title_full Schema Playground: a tool for authoring, extending, and using metadata schemas to improve FAIRness of biomedical data
title_fullStr Schema Playground: a tool for authoring, extending, and using metadata schemas to improve FAIRness of biomedical data
title_full_unstemmed Schema Playground: a tool for authoring, extending, and using metadata schemas to improve FAIRness of biomedical data
title_short Schema Playground: a tool for authoring, extending, and using metadata schemas to improve FAIRness of biomedical data
title_sort schema playground: a tool for authoring, extending, and using metadata schemas to improve fairness of biomedical data
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10116472/
https://www.ncbi.nlm.nih.gov/pubmed/37081398
http://dx.doi.org/10.1186/s12859-023-05258-4
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