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ARS Home » Midwest Area » Ames, Iowa » Corn Insects and Crop Genetics Research » Research » Publications at this Location » Publication #352286
Title: AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture

Author
item Harper, Elisabeth
item CAMPBELL, JACQUELINE - Iowa State University
item Cannon, Ethalinda
item JUNG, SOOK - Washington State University
item MAIN, DOREEN - Washington State University
item Poelchau, Monica
item WALLS, RAMONA - University Of Arizona
item Andorf, Carson
item ARNAUD, ELIZABETH - Bioversity International
item BERARDINI, TANYA - Phoenix Bioinformatics
item Birkett, Clayton
item Cannon, Steven
item CARSON, JAMES - University Of Texas
item CONDON, BRADFORD - University Of Tennessee
item COOPER, LAUREL - Oregon State University
item DUNN, NATHAN - Berkeley National Laboratory
item ELSIK, CHRIS - University Of Missouri
item FARMER, ANDREW - National Center For Genome Resources
item FICKLIN, STEPHEN - Washington State University
item Grant, David
item GRAU, EMILY - University Of Connecticut
item HENDON, NICK - University Of Connecticut
item HU, ZHILIANG - Iowa State University
item HUMANN, JODI - Washington State University
item JAISWAL, PANKAJ - Oregon State University
item JONQUET, CLEMENT - University Of Montpellier
item LAPORTE, MARIE-ANGELIQUE - Bioversity International
item LARMANDE, PIERRE - Herbier De Guyane, Institut De Recherche Pour Le Développement (IRD)
item Lazo, Gerard
item MCCARTHY, FIONA - University Of Arizona
item MENDA, NAAMA - Boyce Thompson Institute
item MUNGALL, CHRISTOPHER - Lawrence Berkeley National Laboratory
item MUNOZ-TORRES, MONICA - Lawrence Berkeley National Laboratory
item NAITHANI, SUSHMA - Oregon State University
item Nelson, Rex
item NESDILL, DAUREEN - University Of Utah
item PARK, CARISSA - Iowa State University
item REECY, JAMES - Iowa State University
item REISER, LEONORE - Phoenix Bioinformatics
item SANDERSON, LACEY-ANNE - University Of Saskatchewan
item Sen, Taner
item STATON, MARGARET - University Of Tennessee
item SUBRAMANIAM, SABARINATH - Phoenix Bioinformatics
item KAREY, TELLO-RUIZ - Cold Spring Harbor Laboratory
item UNDA, VICTOR - Washington State University
item UNNI, DEEPAK - Lawrence Berkeley National Laboratory
item WANG, LIYA - Cold Spring Harbor Laboratory
item Ware, Doreen
item WEGRZYN, JILL - University Of Connecticut
item WILLIAMS, JASON - Cold Spring Harbor Laboratory
item WOODHOUSE, MARGARET - Iowa State University

Submitted to: Database: The Journal of Biological Databases and Curation
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/30/2018
Publication Date: 9/18/2018
Citation: Harper, E.C., Campbell, J., Cannon, E.K., Jung, S., Main, D., Poelchau, M.F., Walls, R.L., Andorf, C.M., Arnaud, E., Berardini, T.Z., Birkett, C.L., Cannon, S.B., Carson, J., Condon, B., Cooper, L., Dunn, N., Elsik, C., Farmer, A., Ficklin, S., Grant, D.M., Grau, E., Hendon, N., Hu, Z., Humann, J., Jaiswal, P., Jonquet, C., Laporte, M., Larmande, P., Lazo, G.R., McCarthy, F., Menda, N., Mungall, C., Munoz-Torres, M., Naithani, S., Nelson, R., Nesdill, D., Park, C., Reecy, J., Reiser, L., Sanderson, L., Sen, T.Z., Staton, M., Subramaniam, S., Karey, T., Unda, V., Unni, D., Wang, L., Ware, D., Wegrzyn, J., Williams, J., Woodhouse, M. 2018. AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture. Database: The Journal of Biological Databases and Curation. 2018(1):1-32. https://doi.org/10.1093/database/bay088.
DOI: https://doi.org/10.1093/database/bay088

Interpretive Summary: At a time of ever increasing volume and complexity of biological data, new paradigms for data management both in the lab, and at the database level are urgently needed to reach the goal of having public biological data available to researchers from easy to find and well-organized resources. In 2015, data curators, bioinformaticists, and computational biologist representing over 25 agriculturally oriented genetic and genomic databases and resources formed the AgBioData consortium to further enhance genomics, genetics, and breeding research outcomes through standardization of practices across agricultural databases. Over the last three years we have established recommendations and best practices in six areas: Biocuration, Ontologies, Metadata and Persistence, GGB (Genomic, Genetic and Breeding) Database Platforms, Programmatic (machine) Access to Data, and Communication.

Technical Abstract: The future of agricultural research depends on data. The sheer volume of agricultural biological data being produced today makes excellent data management essential. Governmental agencies, publishers, and science funders require data management plans for publicly funded research. Furthermore, the value of data increases exponentially when they are properly stored, described, integrated, and shared, so that they can be easily utilized in future analyses. AgBioData (https://www.agbiodata.org) is a consortium of people working at agricultural biological databases, data archives and knowledgebase who strives to identify common issues in database development, curation, and management, with the goal of creating database products that are more findable, accessible, interoperable, and reusable (FAIR). We strive to promote authentic, detailed, accurate, and explicit communication between all parties involved in scientific data. As a step towards this goal, we present the current state of biocuration, ontologies, metadata and persistence, database platforms, programmatic (machine) access to data, communication, and sustainability with regard to data curation. Each section describes challenges and opportunities for these topics, along with recommendations and best practices.