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Title: AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture

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.

Authors:
 [1];  [2];  [3];  [4];  [5];  [6];  [3];  [7];  [8];  [9];  [1];  [10];  [11];  [12];  [13];  [14];  [15];  [4];  [1];  [15] more »;  [16];  [17];  [4];  [12];  [18];  [7];  [19];  [20];  [21];  [22];  [23];  [23];  [12];  [1];  [24];  [17];  [17];  [8];  [25];  [20];  [11];  [8];  [26];  [4];  [13];  [26];  [27];  [16];  [28];  [29];  [4];  [4] « less
+ Show Author Affiliations
  1. Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA, USA
  2. Computer Science, Iowa State University, Ames, IA, USA
  3. Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA, USA, Computer Science, Iowa State University, Ames, IA, USA
  4. Horticulture, Washington State University, Pullman, WA, USA
  5. National Agricultural Library, USDA Agricultural Research Service, Beltsville, MD, USA
  6. Cyverse, University of Arizona, Tucson, AZ, USA
  7. Bioversity International, Informatics Unit, Conservation and Availability Programme, Parc Scientifique Agropolis II, Montpellier, France
  8. The Arabidopsis Information Resource, Phoenix Bioinformatics, Fremont, CA, USA
  9. USDA, Plant, Soil and Nutrition Research, Ithaca, NY, USA
  10. Texas Advanced Computing Center, The University of Texas at Austin, Austin, TX, USA
  11. Entomology and Plant Pathology, University of Tennessee Knoxville, Knoxville, TN, USA
  12. Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
  13. Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
  14. Division of Animal Sciences and Division of Plant Sciences, University of Missouri, Columbia, MO, USA
  15. National Center for Genome Resources, Santa Fe, NM, USA
  16. Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
  17. Animal Science, Iowa State University, Ames, USA
  18. Laboratory of Informatics, Robotics, Microelectronics of Montpellier, University of Montpellier & CNRS, Montpellier, France
  19. DIADE, University of Montpellier, IRD, Montpellier, France
  20. Crop Improvement and Genetics Research Unit, USDA-ARS, Albany, CA, USA
  21. School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ, USA
  22. Boyce Thompson Institute, Ithaca, NY, USA
  23. Genomics Division, Lawrence Berkeley National Laboratories, Berkeley, CA, USA
  24. Marriott Library, University of Utah, Salt Lake City, UT, USA
  25. Department of Plant Sciences, University of Saskatchewan, Saskatoon, Canada
  26. Plant Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
  27. USDA, Plant, Soil and Nutrition Research, Ithaca, NY, USA, Plant Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
  28. Cold Spring Harbor Laboratory, DNA Learning Center, Cold Spring Harbor, NY, USA
  29. Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
Publication Date:
Research Org.:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE
Contributing Org.:
AgBioData consortium
OSTI Identifier:
1471253
Alternate Identifier(s):
OSTI ID: 1490698
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Published Article
Journal Name:
Database
Additional Journal Information:
Journal Name: Database Journal Volume: 2018; Journal ID: ISSN 1758-0463
Publisher:
Oxford University Press
Country of Publication:
United Kingdom
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Harper, Lisa, Campbell, Jacqueline, Cannon, Ethalinda K. S., Jung, Sook, Poelchau, Monica, Walls, Ramona, Andorf, Carson, Arnaud, Elizabeth, Berardini, Tanya Z., Birkett, Clayton, Cannon, Steve, Carson, James, Condon, Bradford, Cooper, Laurel, Dunn, Nathan, Elsik, Christine G., Farmer, Andrew, Ficklin, Stephen P., Grant, David, Grau, Emily, Herndon, Nic, Hu, Zhi-Liang, Humann, Jodi, Jaiswal, Pankaj, Jonquet, Clement, Laporte, Marie-Angélique, Larmande, Pierre, Lazo, Gerard, McCarthy, Fiona, Menda, Naama, Mungall, Christopher J., Munoz-Torres, Monica C., Naithani, Sushma, Nelson, Rex, Nesdill, Daureen, Park, Carissa, Reecy, James, Reiser, Leonore, Sanderson, Lacey-Anne, Sen, Taner Z., Staton, Margaret, Subramaniam, Sabarinath, Tello-Ruiz, Marcela Karey, Unda, Victor, Unni, Deepak, Wang, Liya, Ware, Doreen, Wegrzyn, Jill, Williams, Jason, Woodhouse, Margaret, Yu, Jing, and Main, Doreen. AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture. United Kingdom: N. p., 2018. Web. doi:10.1093/database/bay088.
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Harper, Lisa, Campbell, Jacqueline, Cannon, Ethalinda K. S., Jung, Sook, Poelchau, Monica, Walls, Ramona, Andorf, Carson, Arnaud, Elizabeth, Berardini, Tanya Z., Birkett, Clayton, Cannon, Steve, Carson, James, Condon, Bradford, Cooper, Laurel, Dunn, Nathan, Elsik, Christine G., Farmer, Andrew, Ficklin, Stephen P., Grant, David, Grau, Emily, Herndon, Nic, Hu, Zhi-Liang, Humann, Jodi, Jaiswal, Pankaj, Jonquet, Clement, Laporte, Marie-Angélique, Larmande, Pierre, Lazo, Gerard, McCarthy, Fiona, Menda, Naama, Mungall, Christopher J., Munoz-Torres, Monica C., Naithani, Sushma, Nelson, Rex, Nesdill, Daureen, Park, Carissa, Reecy, James, Reiser, Leonore, Sanderson, Lacey-Anne, Sen, Taner Z., Staton, Margaret, Subramaniam, Sabarinath, Tello-Ruiz, Marcela Karey, Unda, Victor, Unni, Deepak, Wang, Liya, Ware, Doreen, Wegrzyn, Jill, Williams, Jason, Woodhouse, Margaret, Yu, Jing, & Main, Doreen. AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture. United Kingdom. https://doi.org/10.1093/database/bay088
Copy to clipboard
Harper, Lisa, Campbell, Jacqueline, Cannon, Ethalinda K. S., Jung, Sook, Poelchau, Monica, Walls, Ramona, Andorf, Carson, Arnaud, Elizabeth, Berardini, Tanya Z., Birkett, Clayton, Cannon, Steve, Carson, James, Condon, Bradford, Cooper, Laurel, Dunn, Nathan, Elsik, Christine G., Farmer, Andrew, Ficklin, Stephen P., Grant, David, Grau, Emily, Herndon, Nic, Hu, Zhi-Liang, Humann, Jodi, Jaiswal, Pankaj, Jonquet, Clement, Laporte, Marie-Angélique, Larmande, Pierre, Lazo, Gerard, McCarthy, Fiona, Menda, Naama, Mungall, Christopher J., Munoz-Torres, Monica C., Naithani, Sushma, Nelson, Rex, Nesdill, Daureen, Park, Carissa, Reecy, James, Reiser, Leonore, Sanderson, Lacey-Anne, Sen, Taner Z., Staton, Margaret, Subramaniam, Sabarinath, Tello-Ruiz, Marcela Karey, Unda, Victor, Unni, Deepak, Wang, Liya, Ware, Doreen, Wegrzyn, Jill, Williams, Jason, Woodhouse, Margaret, Yu, Jing, and Main, Doreen. Tue . "AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture". United Kingdom. https://doi.org/10.1093/database/bay088.
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@article{osti_1471253,
title = {AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture},
author = {Harper, Lisa and Campbell, Jacqueline and Cannon, Ethalinda K. S. and Jung, Sook and Poelchau, Monica and Walls, Ramona and Andorf, Carson and Arnaud, Elizabeth and Berardini, Tanya Z. and Birkett, Clayton and Cannon, Steve and Carson, James and Condon, Bradford and Cooper, Laurel and Dunn, Nathan and Elsik, Christine G. and Farmer, Andrew and Ficklin, Stephen P. and Grant, David and Grau, Emily and Herndon, Nic and Hu, Zhi-Liang and Humann, Jodi and Jaiswal, Pankaj and Jonquet, Clement and Laporte, Marie-Angélique and Larmande, Pierre and Lazo, Gerard and McCarthy, Fiona and Menda, Naama and Mungall, Christopher J. and Munoz-Torres, Monica C. and Naithani, Sushma and Nelson, Rex and Nesdill, Daureen and Park, Carissa and Reecy, James and Reiser, Leonore and Sanderson, Lacey-Anne and Sen, Taner Z. and Staton, Margaret and Subramaniam, Sabarinath and Tello-Ruiz, Marcela Karey and Unda, Victor and Unni, Deepak and Wang, Liya and Ware, Doreen and Wegrzyn, Jill and Williams, Jason and Woodhouse, Margaret and Yu, Jing and Main, Doreen},
abstractNote = {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.},
doi = {10.1093/database/bay088},
journal = {Database},
number = ,
volume = 2018,
place = {United Kingdom},
year = {Tue Sep 18 00:00:00 EDT 2018},
month = {Tue Sep 18 00:00:00 EDT 2018}
}
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https://doi.org/10.1093/database/bay088
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Cited by: 23 works
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Figures / Tables:

Table 1 Table 1: Survey results for ontology use in databases for each data type (from 29 respondents)
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    Works referencing / citing this record:

    The BioMart community portal: an innovative alternative to large, centralized data repositories
    journal, April 2015

    • Smedley, Damian; Haider, Syed; Durinck, Steffen
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