TY - JOUR
T1 - AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture
AU - Harper, Lisa
AU - Campbell, Jacqueline
AU - Cannon, Ethalinda K.S.
AU - Jung, Sook
AU - Poelchau, Monica
AU - Walls, Ramona
AU - Andorf, Carson
AU - Arnaud, Elizabeth
AU - Berardini, Tanya Z.
AU - Birkett, Clayton
AU - Cannon, Steve
AU - Carson, James
AU - Condon, Bradford
AU - Cooper, Laurel
AU - Dunn, Nathan
AU - Elsik, Christine G.
AU - Farmer, Andrew
AU - Ficklin, Stephen P.
AU - Grant, David
AU - Grau, Emily
AU - Herndon, Nic
AU - Hu, Zhi Liang
AU - Humann, Jodi
AU - Jaiswal, Pankaj
AU - Jonquet, Clement
AU - Laporte, Marie Angélique
AU - Larmande, Pierre
AU - Lazo, Gerard
AU - McCarthy, Fiona
AU - Menda, Naama
AU - Mungall, Christopher J.
AU - Munoz-Torres, Monica C.
AU - Naithani, Sushma
AU - Nelson, Rex
AU - Nesdill, Daureen
AU - Park, Carissa
AU - Reecy, James
AU - Reiser, Leonore
AU - Sanderson, Lacey Anne
AU - Sen, Taner Z.
AU - Staton, Margaret
AU - Subramaniam, Sabarinath
AU - Tello-Ruiz, Marcela Karey
AU - Unda, Victor
AU - Unni, Deepak
AU - Wang, Liya
AU - Ware, Doreen
AU - Wegrzyn, Jill
AU - Williams, Jason
AU - Woodhouse, Margaret
AU - Yu, Jing
AU - Main, Doreen
N1 - Funding Information:
The RDA. (https://www.rd-alliance.org) was started in 2013 by the European Commission (EC), the NSF, the National Institute of Standards and Technology and the Australian Government’s Department of Innovation to encourage and enable open sharing of research data in all scientific disciplines and the humanities. Several RDA working groups are focused on metadata. The RDA Metadata Standards Directory and the Metadata Catalog of metadata standards that have been submitted to the RDA is in progress and can be seen at http://rd-alliance.github.io/metadata-directory.
Funding Information:
Proper data management is a critical aspect of research and publication. Scientists working on federally funded research projects are expected to make research findings publicly available. Data are the lifeblood of research, and their value often do not end with the original study, as they can be reused for further investigation if properly handled. Data become much more valuable when integrated with other data and information (1, 2). For example, traits, images, seed/sample sources, sequencing data and high-throughput phenotyping results become much more informative when integrated with germplasm accessions and pedigree data. Access to low-cost, high-throughput sequencing, large-scale phenotyping and advanced computational algorithms, combined with significant funding by the National Science Foundation (NSF), the US Department of Agriculture (USDA) and the US Department of Energy (DOE) for cyberinfrastructure and agricultural-related research have fueled the growth of databases to manage, store, integrate, analyse and serve these data and tools to scientists and other stakeholders.
Funding Information:
US Department of Agriculture (5030-21000-068-00D, 2030-21000-021-00D, 3625-21000-062-00D, 5030-21000-061-00D, 2014-2014-07898, 2014-51181-22376, 2015-70016-23028, 2016-67015-24767, 8062-21000-041-00D, AFRI-005515, NRSP-10 and NRSP-8); The National Science Foundation (1443040, 0735191, 1265383, 1444806, 1127112, 1340112, 1444573, 1564366); The National Institutes of Health (5R01HG004483, 5R01GM080203); The US Department of Energy (Contract No. DE-AC02-05CH11231); The Bill and Melinda Gates Foundation (OP1052983, OPP1048542); The Computational Biology Institute of Montpellier (ANR-11-BINF-0002); The Consultative Group for International Agricultural Research (CGIAR) Platform for Big Data in Agriculture, The Cotton Incorporated and Cotton Industry, Fondazione Edmund Mach (FEM) Research and Innovation Center, The International Institute of Tropical Agriculture, The Northern Pulse Growers, The US Dry Pea and Lentil Council, The US Land Grant Universities; and The Washington Tree Fruit Research Commission.
Funding Information:
We acknowledge with thanks The National Science Foundation Plant Genome Research Program Award # 1444573 for funding the AgBioData Workshop and development and hosting of the AgBio-Data website. For their helpful suggestions and lively discussion, we enthusiastically thank Victoria Carollo Blake, Jean Luc Jannink, Sarah Odell, Nathan Weeks and Richard Westerman.
Funding Information:
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Publisher Copyright:
© The Author(s) 2018. Published by Oxford University Press.
PY - 2018/1/1
Y1 - 2018/1/1
N2 - 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 knowledgbases who strive 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. We strive to promote authentic, detailed, accurate and explicit communication between all parties involved in scientific data. As a step toward 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.
AB - 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 knowledgbases who strive 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. We strive to promote authentic, detailed, accurate and explicit communication between all parties involved in scientific data. As a step toward 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.
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U2 - 10.1093/database/bay088
DO - 10.1093/database/bay088
M3 - Article
C2 - 30239679
AN - SCOPUS:85057262680
SN - 1758-0463
VL - 2018
JO - Database : the journal of biological databases and curation
JF - Database : the journal of biological databases and curation
IS - 2018
ER -