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Tripal, a community update after 10 years of supporting open source, standards-based genetic, genomic and breeding databases
Online, open access databases for biological knowledge serve as central repositories for research communities to store, find and analyze integrated, multi-disciplinary datasets. With increasing volumes, complexity and the need to integrate genomic, transcriptomic, metabolomic, proteomic, phenomic an...
Autores principales: | , , , , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8574961/ https://www.ncbi.nlm.nih.gov/pubmed/34251419 http://dx.doi.org/10.1093/bib/bbab238 |
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author | Staton, Margaret Cannon, Ethalinda Sanderson, Lacey-Anne Wegrzyn, Jill Anderson, Tavis Buehler, Sean Cobo-Simón, Irene Faaberg, Kay Grau, Emily Guignon, Valentin Gunoskey, Jessica Inderski, Blake Jung, Sook Lager, Kelly Main, Dorrie Poelchau, Monica Ramnath, Risharde Richter, Peter West, Joe Ficklin, Stephen |
author_facet | Staton, Margaret Cannon, Ethalinda Sanderson, Lacey-Anne Wegrzyn, Jill Anderson, Tavis Buehler, Sean Cobo-Simón, Irene Faaberg, Kay Grau, Emily Guignon, Valentin Gunoskey, Jessica Inderski, Blake Jung, Sook Lager, Kelly Main, Dorrie Poelchau, Monica Ramnath, Risharde Richter, Peter West, Joe Ficklin, Stephen |
author_sort | Staton, Margaret |
collection | PubMed |
description | Online, open access databases for biological knowledge serve as central repositories for research communities to store, find and analyze integrated, multi-disciplinary datasets. With increasing volumes, complexity and the need to integrate genomic, transcriptomic, metabolomic, proteomic, phenomic and environmental data, community databases face tremendous challenges in ongoing maintenance, expansion and upgrades. A common infrastructure framework using community standards shared by many databases can reduce development burden, provide interoperability, ensure use of common standards and support long-term sustainability. Tripal is a mature, open source platform built to meet this need. With ongoing improvement since its first release in 2009, Tripal provides full functionality for searching, browsing, loading and curating numerous types of data and is a primary technology powering at least 31 publicly available databases spanning plants, animals and human data, primarily storing genomics, genetics and breeding data. Tripal software development is managed by a shared, inclusive governance structure including both project management and advisory teams. Here, we report on the most important and innovative aspects of Tripal after 11 years development, including integration of diverse types of biological data, successful collaborative projects across member databases, and support for implementing FAIR principles. |
format | Online Article Text |
id | pubmed-8574961 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-85749612021-11-09 Tripal, a community update after 10 years of supporting open source, standards-based genetic, genomic and breeding databases Staton, Margaret Cannon, Ethalinda Sanderson, Lacey-Anne Wegrzyn, Jill Anderson, Tavis Buehler, Sean Cobo-Simón, Irene Faaberg, Kay Grau, Emily Guignon, Valentin Gunoskey, Jessica Inderski, Blake Jung, Sook Lager, Kelly Main, Dorrie Poelchau, Monica Ramnath, Risharde Richter, Peter West, Joe Ficklin, Stephen Brief Bioinform Review Online, open access databases for biological knowledge serve as central repositories for research communities to store, find and analyze integrated, multi-disciplinary datasets. With increasing volumes, complexity and the need to integrate genomic, transcriptomic, metabolomic, proteomic, phenomic and environmental data, community databases face tremendous challenges in ongoing maintenance, expansion and upgrades. A common infrastructure framework using community standards shared by many databases can reduce development burden, provide interoperability, ensure use of common standards and support long-term sustainability. Tripal is a mature, open source platform built to meet this need. With ongoing improvement since its first release in 2009, Tripal provides full functionality for searching, browsing, loading and curating numerous types of data and is a primary technology powering at least 31 publicly available databases spanning plants, animals and human data, primarily storing genomics, genetics and breeding data. Tripal software development is managed by a shared, inclusive governance structure including both project management and advisory teams. Here, we report on the most important and innovative aspects of Tripal after 11 years development, including integration of diverse types of biological data, successful collaborative projects across member databases, and support for implementing FAIR principles. Oxford University Press 2021-07-12 /pmc/articles/PMC8574961/ /pubmed/34251419 http://dx.doi.org/10.1093/bib/bbab238 Text en © The Author(s) 2021. Published by Oxford University Press. https://creativecommons.org/licenses/by-nc/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com |
spellingShingle | Review Staton, Margaret Cannon, Ethalinda Sanderson, Lacey-Anne Wegrzyn, Jill Anderson, Tavis Buehler, Sean Cobo-Simón, Irene Faaberg, Kay Grau, Emily Guignon, Valentin Gunoskey, Jessica Inderski, Blake Jung, Sook Lager, Kelly Main, Dorrie Poelchau, Monica Ramnath, Risharde Richter, Peter West, Joe Ficklin, Stephen Tripal, a community update after 10 years of supporting open source, standards-based genetic, genomic and breeding databases |
title | Tripal, a community update after 10 years of supporting open source, standards-based genetic, genomic and breeding databases |
title_full | Tripal, a community update after 10 years of supporting open source, standards-based genetic, genomic and breeding databases |
title_fullStr | Tripal, a community update after 10 years of supporting open source, standards-based genetic, genomic and breeding databases |
title_full_unstemmed | Tripal, a community update after 10 years of supporting open source, standards-based genetic, genomic and breeding databases |
title_short | Tripal, a community update after 10 years of supporting open source, standards-based genetic, genomic and breeding databases |
title_sort | tripal, a community update after 10 years of supporting open source, standards-based genetic, genomic and breeding databases |
topic | Review |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8574961/ https://www.ncbi.nlm.nih.gov/pubmed/34251419 http://dx.doi.org/10.1093/bib/bbab238 |
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