AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture

Lisa Harper; Jacqueline Campbell; Ethalinda K.S. Cannon; Sook Jung; Monica Poelchau; Ramona Walls; Carson Andorf; Elizabeth Arnaud; Tanya Z. Berardini; Clayton Birkett; Steve Cannon; James Carson; Bradford Condon; Laurel Cooper; Nathan Dunn; Christine G. Elsik; Andrew Farmer; Stephen P. Ficklin; David Grant; Emily Grau; Nic Herndon; Zhi Liang Hu; Jodi Humann; Pankaj Jaiswal; Clement Jonquet; Marie Angélique Laporte; Pierre Larmande; Gerard Lazo; Fiona McCarthy; Naama Menda; Christopher J. Mungall; Monica C. Munoz-Torres; Sushma Naithani; Rex Nelson; Daureen Nesdill; Carissa Park; James Reecy; Leonore Reiser; Lacey Anne Sanderson; Taner Z. Sen; Margaret Staton; Sabarinath Subramaniam; Marcela Karey Tello-Ruiz; Victor Unda; Deepak Unni; Liya Wang; Doreen Ware; Jill Wegrzyn; Jason Williams; Margaret Woodhouse; Jing Yu; Doreen Main

doi:10.1093/database/bay088

AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture

Lisa Harper, Jacqueline Campbell, Ethalinda K.S. Cannon, Sook Jung, Monica Poelchau, Ramona Walls, Carson Andorf, Elizabeth Arnaud, Tanya Z. Berardini, Clayton Birkett, Steve Cannon, James Carson, Bradford Condon, Laurel Cooper, Nathan Dunn, Christine G. Elsik, Andrew Farmer, Stephen P. Ficklin, David Grant, Emily GrauNic Herndon, Zhi Liang Hu, Jodi Humann, Pankaj Jaiswal, Clement Jonquet, Marie Angélique Laporte, Pierre Larmande, Gerard Lazo, Fiona McCarthy, Naama Menda, Christopher J. Mungall, Monica C. Munoz-Torres, Sushma Naithani, Rex Nelson, Daureen Nesdill, Carissa Park, James Reecy, Leonore Reiser, Lacey Anne Sanderson, Taner Z. Sen, Margaret Staton, Sabarinath Subramaniam, Marcela Karey Tello-Ruiz, Victor Unda, Deepak Unni, Liya Wang, Doreen Ware, Jill Wegrzyn, Jason Williams, Margaret Woodhouse, Jing Yu, Doreen Main

Research output: Contribution to journal › Article › peer-review

55 Scopus citations

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.

Original language	English (US)
Journal	Database
Volume	2018
Issue number	2018
DOIs	https://doi.org/10.1093/database/bay088
State	Published - Jan 1 2018

ASJC Scopus subject areas

Information Systems
General Biochemistry, Genetics and Molecular Biology
General Agricultural and Biological Sciences

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10.1093/database/bay088

Cite this

Harper, L., Campbell, J., Cannon, E. K. S., Jung, S., Poelchau, M., Walls, R., Andorf, C., Arnaud, E., Berardini, T. Z., Birkett, C., Cannon, S., Carson, J., Condon, B., Cooper, L., Dunn, N., Elsik, C. G., Farmer, A., Ficklin, S. P., Grant, D., ... Main, D. (2018). AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture. Database, 2018(2018). https://doi.org/10.1093/database/bay088

Harper, L, Campbell, J, Cannon, EKS, Jung, S, Poelchau, M, Walls, R, Andorf, C, Arnaud, E, Berardini, TZ, Birkett, C, Cannon, S, Carson, J, Condon, B, Cooper, L, Dunn, N, Elsik, CG, Farmer, A, Ficklin, SP, Grant, D, Grau, E, Herndon, N, Hu, ZL, Humann, J, Jaiswal, P, Jonquet, C, Laporte, MA, Larmande, P, Lazo, G, McCarthy, F, Menda, N, Mungall, CJ, Munoz-Torres, MC, Naithani, S, Nelson, R, Nesdill, D, Park, C, Reecy, J, Reiser, L, Sanderson, LA, Sen, TZ, Staton, M, Subramaniam, S, Tello-Ruiz, MK, Unda, V, Unni, D, Wang, L, Ware, D, Wegrzyn, J, Williams, J, Woodhouse, M, Yu, J & Main, D 2018, 'AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture', Database, vol. 2018, no. 2018. https://doi.org/10.1093/database/bay088

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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.",

author = "Lisa Harper and Jacqueline Campbell and Cannon, {Ethalinda K.S.} and Sook Jung and Monica Poelchau and Ramona Walls and Carson Andorf and Elizabeth Arnaud and Berardini, {Tanya Z.} and Clayton Birkett and Steve Cannon and James Carson and Bradford Condon and Laurel Cooper and Nathan Dunn and Elsik, {Christine G.} and Andrew Farmer and Ficklin, {Stephen P.} and David Grant and Emily Grau and Nic Herndon and Hu, {Zhi Liang} and Jodi Humann and Pankaj Jaiswal and Clement Jonquet and Laporte, {Marie Ang{\'e}lique} and Pierre Larmande and Gerard Lazo and Fiona McCarthy and Naama Menda and Mungall, {Christopher J.} and Munoz-Torres, {Monica C.} and Sushma Naithani and Rex Nelson and Daureen Nesdill and Carissa Park and James Reecy and Leonore Reiser and Sanderson, {Lacey Anne} and Sen, {Taner Z.} and Margaret Staton and Sabarinath Subramaniam and Tello-Ruiz, {Marcela Karey} and Victor Unda and Deepak Unni and Liya Wang and Doreen Ware and Jill Wegrzyn and Jason Williams and Margaret Woodhouse and Jing Yu and Doreen Main",

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doi = "10.1093/database/bay088",

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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

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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ER -

AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture

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ASJC Scopus subject areas

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