AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture

Lisa Harper¹, Jacqueline Campbell², Ethalinda K S Cannon^{1

2}, Sook Jung³, Monica Poelchau⁴, Ramona Walls⁵, Carson Andorf^{1

2}, Elizabeth Arnaud⁶, Tanya Z Berardini⁷, Clayton Birkett⁸, Steve Cannon¹, James Carson⁹, Bradford Condon¹⁰, Laurel Cooper¹¹, Nathan Dunn¹², Christine G Elsik¹³, Andrew Farmer¹⁴, Stephen P Ficklin³, David Grant¹, Emily Grau¹⁴, Nic Herndon¹⁵, Zhi-Liang Hu¹⁶, Jodi Humann³, Pankaj Jaiswal¹¹, Clement Jonquet¹⁷, Marie-Angélique Laporte⁶, Pierre Larmande¹⁸, Gerard Lazo¹⁹, Fiona McCarthy²⁰, Naama Menda²¹, Christopher J Mungall²², Monica C Munoz-Torres²², Sushma Naithani¹¹, Rex Nelson¹, Daureen Nesdill²³, Carissa Park¹⁶, James Reecy¹⁶, Leonore Reiser⁷, Lacey-Anne Sanderson²⁴, Taner Z Sen¹⁹, Margaret Staton¹⁰, Sabarinath Subramaniam⁷, Marcela Karey Tello-Ruiz²⁵, Victor Unda³, Deepak Unni¹², Liya Wang²⁵, Doreen Ware^{8

25}, Jill Wegrzyn¹⁵, Jason Williams²⁶, Margaret Woodhouse²⁷, Jing Yu³, Doreen Main³

Affiliations

¹ Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA, USA.
² Computer Science, Iowa State University, Ames, IA, USA.
³ Horticulture, Washington State University, Pullman, WA, USA.
⁴ National Agricultural Library, USDA Agricultural Research Service, Beltsville, MD, USA.
⁵ Cyverse, University of Arizona, Tucson, AZ, USA.
⁶ Bioversity International, Informatics Unit, Conservation and Availability Programme, Parc Scientifique Agropolis II, Montpellier, France.
⁷ The Arabidopsis Information Resource, Phoenix Bioinformatics, Fremont, CA, USA.
⁸ USDA, Plant, Soil and Nutrition Research, Ithaca, NY, USA.
⁹ Texas Advanced Computing Center, The University of Texas at Austin, Austin, TX, USA.
¹⁰ Entomology and Plant Pathology, University of Tennessee Knoxville, Knoxville, TN, USA.
¹¹ Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA.
¹² Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
¹³ Division of Animal Sciences and Division of Plant Sciences, University of Missouri, Columbia, MO, USA.
¹⁴ National Center for Genome Resources, Santa Fe, NM, USA.
¹⁵ Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA.
¹⁶ Animal Science, Iowa State University, Ames, USA.
¹⁷ Laboratory of Informatics, Robotics, Microelectronics of Montpellier, University of Montpellier & CNRS, Montpellier, France.
¹⁸ DIADE, University of Montpellier, IRD, Montpellier, France.
¹⁹ Crop Improvement and Genetics Research Unit, USDA-ARS, Albany, CA, USA.
²⁰ School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ, USA.
²¹ Boyce Thompson Institute, Ithaca, NY, USA.
²² Genomics Division, Lawrence Berkeley National Laboratories, Berkeley, CA, USA.
²³ Marriott Library, University of Utah, Salt Lake City, UT, USA.
²⁴ Department of Plant Sciences, University of Saskatchewan, Saskatoon, Canada.
²⁵ Plant Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
²⁶ Cold Spring Harbor Laboratory, DNA Learning Center, Cold Spring Harbor, NY, USA.
²⁷ Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA.

PMID: 30239679
PMCID: PMC6146126
DOI: 10.1093/database/bay088

AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture

Lisa Harper et al. Database (Oxford). 2018.

. 2018 Jan 1:2018:bay088.

doi: 10.1093/database/bay088.

Authors

Affiliations

¹ Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA, USA.
² Computer Science, Iowa State University, Ames, IA, USA.
³ Horticulture, Washington State University, Pullman, WA, USA.
⁴ National Agricultural Library, USDA Agricultural Research Service, Beltsville, MD, USA.
⁵ Cyverse, University of Arizona, Tucson, AZ, USA.
⁶ Bioversity International, Informatics Unit, Conservation and Availability Programme, Parc Scientifique Agropolis II, Montpellier, France.
⁷ The Arabidopsis Information Resource, Phoenix Bioinformatics, Fremont, CA, USA.
⁸ USDA, Plant, Soil and Nutrition Research, Ithaca, NY, USA.
⁹ Texas Advanced Computing Center, The University of Texas at Austin, Austin, TX, USA.
¹⁰ Entomology and Plant Pathology, University of Tennessee Knoxville, Knoxville, TN, USA.
¹¹ Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA.
¹² Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
¹³ Division of Animal Sciences and Division of Plant Sciences, University of Missouri, Columbia, MO, USA.
¹⁴ National Center for Genome Resources, Santa Fe, NM, USA.
¹⁵ Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA.
¹⁶ Animal Science, Iowa State University, Ames, USA.
¹⁷ Laboratory of Informatics, Robotics, Microelectronics of Montpellier, University of Montpellier & CNRS, Montpellier, France.
¹⁸ DIADE, University of Montpellier, IRD, Montpellier, France.
¹⁹ Crop Improvement and Genetics Research Unit, USDA-ARS, Albany, CA, USA.
²⁰ School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ, USA.
²¹ Boyce Thompson Institute, Ithaca, NY, USA.
²² Genomics Division, Lawrence Berkeley National Laboratories, Berkeley, CA, USA.
²³ Marriott Library, University of Utah, Salt Lake City, UT, USA.
²⁴ Department of Plant Sciences, University of Saskatchewan, Saskatoon, Canada.
²⁵ Plant Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
²⁶ Cold Spring Harbor Laboratory, DNA Learning Center, Cold Spring Harbor, NY, USA.
²⁷ Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA.

PMID: 30239679
PMCID: PMC6146126
DOI: 10.1093/database/bay088

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 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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AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture

Affiliations

AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture

Authors

Affiliations

Abstract

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