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Developing data interoperability using standards: A wheat community use case
In this article, we present a joint effort of the wheat research community, along with data and ontology experts, to develop wheat data interoperability guidelines. Interoperability is the ability of two or more systems and devices to cooperate and exchange data, and interpret that shared informatio...
Autores principales: | , , , , , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
F1000 Research Limited
2017
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5747345/ https://www.ncbi.nlm.nih.gov/pubmed/29333241 http://dx.doi.org/10.12688/f1000research.12234.2 |
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author | Dzale Yeumo, Esther Alaux, Michael Arnaud, Elizabeth Aubin, Sophie Baumann, Ute Buche, Patrice Cooper, Laurel Ćwiek-Kupczyńska, Hanna Davey, Robert P. Fulss, Richard Allan Jonquet, Clement Laporte, Marie-Angélique Larmande, Pierre Pommier, Cyril Protonotarios, Vassilis Reverte, Carmen Shrestha, Rosemary Subirats, Imma Venkatesan, Aravind Whan, Alex Quesneville, Hadi |
author_facet | Dzale Yeumo, Esther Alaux, Michael Arnaud, Elizabeth Aubin, Sophie Baumann, Ute Buche, Patrice Cooper, Laurel Ćwiek-Kupczyńska, Hanna Davey, Robert P. Fulss, Richard Allan Jonquet, Clement Laporte, Marie-Angélique Larmande, Pierre Pommier, Cyril Protonotarios, Vassilis Reverte, Carmen Shrestha, Rosemary Subirats, Imma Venkatesan, Aravind Whan, Alex Quesneville, Hadi |
author_sort | Dzale Yeumo, Esther |
collection | PubMed |
description | In this article, we present a joint effort of the wheat research community, along with data and ontology experts, to develop wheat data interoperability guidelines. Interoperability is the ability of two or more systems and devices to cooperate and exchange data, and interpret that shared information. Interoperability is a growing concern to the wheat scientific community, and agriculture in general, as the need to interpret the deluge of data obtained through high-throughput technologies grows. Agreeing on common data formats, metadata, and vocabulary standards is an important step to obtain the required data interoperability level in order to add value by encouraging data sharing, and subsequently facilitate the extraction of new information from existing and new datasets. During a period of more than 18 months, the RDA Wheat Data Interoperability Working Group (WDI-WG) surveyed the wheat research community about the use of data standards, then discussed and selected a set of recommendations based on consensual criteria. The recommendations promote standards for data types identified by the wheat research community as the most important for the coming years: nucleotide sequence variants, genome annotations, phenotypes, germplasm data, gene expression experiments, and physical maps. For each of these data types, the guidelines recommend best practices in terms of use of data formats, metadata standards and ontologies. In addition to the best practices, the guidelines provide examples of tools and implementations that are likely to facilitate the adoption of the recommendations. To maximize the adoption of the recommendations, the WDI-WG used a community-driven approach that involved the wheat research community from the start, took into account their needs and practices, and provided them with a framework to keep the recommendations up to date. We also report this approach’s potential to be generalizable to other (agricultural) domains. |
format | Online Article Text |
id | pubmed-5747345 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | F1000 Research Limited |
record_format | MEDLINE/PubMed |
spelling | pubmed-57473452018-01-11 Developing data interoperability using standards: A wheat community use case Dzale Yeumo, Esther Alaux, Michael Arnaud, Elizabeth Aubin, Sophie Baumann, Ute Buche, Patrice Cooper, Laurel Ćwiek-Kupczyńska, Hanna Davey, Robert P. Fulss, Richard Allan Jonquet, Clement Laporte, Marie-Angélique Larmande, Pierre Pommier, Cyril Protonotarios, Vassilis Reverte, Carmen Shrestha, Rosemary Subirats, Imma Venkatesan, Aravind Whan, Alex Quesneville, Hadi F1000Res Opinion Article In this article, we present a joint effort of the wheat research community, along with data and ontology experts, to develop wheat data interoperability guidelines. Interoperability is the ability of two or more systems and devices to cooperate and exchange data, and interpret that shared information. Interoperability is a growing concern to the wheat scientific community, and agriculture in general, as the need to interpret the deluge of data obtained through high-throughput technologies grows. Agreeing on common data formats, metadata, and vocabulary standards is an important step to obtain the required data interoperability level in order to add value by encouraging data sharing, and subsequently facilitate the extraction of new information from existing and new datasets. During a period of more than 18 months, the RDA Wheat Data Interoperability Working Group (WDI-WG) surveyed the wheat research community about the use of data standards, then discussed and selected a set of recommendations based on consensual criteria. The recommendations promote standards for data types identified by the wheat research community as the most important for the coming years: nucleotide sequence variants, genome annotations, phenotypes, germplasm data, gene expression experiments, and physical maps. For each of these data types, the guidelines recommend best practices in terms of use of data formats, metadata standards and ontologies. In addition to the best practices, the guidelines provide examples of tools and implementations that are likely to facilitate the adoption of the recommendations. To maximize the adoption of the recommendations, the WDI-WG used a community-driven approach that involved the wheat research community from the start, took into account their needs and practices, and provided them with a framework to keep the recommendations up to date. We also report this approach’s potential to be generalizable to other (agricultural) domains. F1000 Research Limited 2017-12-06 /pmc/articles/PMC5747345/ /pubmed/29333241 http://dx.doi.org/10.12688/f1000research.12234.2 Text en Copyright: © 2017 Dzale Yeumo E et al. http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Opinion Article Dzale Yeumo, Esther Alaux, Michael Arnaud, Elizabeth Aubin, Sophie Baumann, Ute Buche, Patrice Cooper, Laurel Ćwiek-Kupczyńska, Hanna Davey, Robert P. Fulss, Richard Allan Jonquet, Clement Laporte, Marie-Angélique Larmande, Pierre Pommier, Cyril Protonotarios, Vassilis Reverte, Carmen Shrestha, Rosemary Subirats, Imma Venkatesan, Aravind Whan, Alex Quesneville, Hadi Developing data interoperability using standards: A wheat community use case |
title | Developing data interoperability using standards: A wheat community use case |
title_full | Developing data interoperability using standards: A wheat community use case |
title_fullStr | Developing data interoperability using standards: A wheat community use case |
title_full_unstemmed | Developing data interoperability using standards: A wheat community use case |
title_short | Developing data interoperability using standards: A wheat community use case |
title_sort | developing data interoperability using standards: a wheat community use case |
topic | Opinion Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5747345/ https://www.ncbi.nlm.nih.gov/pubmed/29333241 http://dx.doi.org/10.12688/f1000research.12234.2 |
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