{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,8]],"date-time":"2026-02-08T02:15:42Z","timestamp":1770516942735,"version":"3.49.0"},"reference-count":38,"publisher":"Oxford University Press (OUP)","funder":[{"DOI":"10.13039\/100005825","name":"NIFA","doi-asserted-by":"publisher","award":["2021-77039-35992"],"award-info":[{"award-number":["2021-77039-35992"]}],"id":[{"id":"10.13039\/100005825","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["1340112 1940330 2126334"],"award-info":[{"award-number":["1340112 1940330 2126334"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"name":"CGIAR Research Initiative on Digital Innovation"},{"DOI":"10.13039\/100000199","name":"U.S. Department of Agriculture","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000199","id-type":"DOI","asserted-by":"publisher"}]},{"name":"New Zealand\u2019s Ministry of Business Innovation and Employment"},{"DOI":"10.13039\/100005825","name":"NIFA","doi-asserted-by":"publisher","award":["2021-77039-35992"],"award-info":[{"award-number":["2021-77039-35992"]}],"id":[{"id":"10.13039\/100005825","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["1340112 1940330 2126334"],"award-info":[{"award-number":["1340112 1940330 2126334"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"name":"CGIAR Research Initiative on Digital Innovation"},{"DOI":"10.13039\/100000199","name":"U.S. Department of Agriculture","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000199","id-type":"DOI","asserted-by":"publisher"}]},{"name":"New Zealand\u2019s Ministry of Business Innovation and Employment"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,3,29]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Over the last couple of decades, there has been a rapid growth in the number and scope of agricultural genetics, genomics and breeding databases and resources. The AgBioData Consortium (https:\/\/www.agbiodata.org\/) currently represents 44 databases and resources (https:\/\/www.agbiodata.org\/databases) covering model or crop plant and animal GGB data, ontologies, pathways, genetic variation and breeding platforms (referred to as \u2018databases\u2019 throughout). One of the goals of the Consortium is to facilitate FAIR (Findable, Accessible, Interoperable, and Reusable) data management and the integration of datasets which requires data sharing, along with structured vocabularies and\/or ontologies. Two AgBioData working groups, focused on Data Sharing and Ontologies, respectively, conducted a Consortium-wide survey to assess the current status and future needs of the members in those areas. A total of 33 researchers responded to the survey, representing 37 databases. Results suggest that data-sharing practices by AgBioData databases are in a fairly healthy state, but it is not clear whether this is true for all metadata and data types across all databases; and that, ontology use has not substantially changed since a similar survey was conducted in 2017. Based on our evaluation of the survey results, we recommend (i) providing training for database personnel in a specific data-sharing techniques, as well as in ontology use; (ii) further study on what metadata is shared, and how well it is shared among databases; (iii) promoting an understanding of data sharing and ontologies in the stakeholder community; (iv) improving data sharing and ontologies for specific phenotypic data types and formats; and (v) lowering specific barriers to data sharing and ontology use, by identifying sustainability solutions, and the identification, promotion, or development of data standards. Combined, these improvements are likely to help AgBioData databases increase development efforts towards improved ontology use, and data sharing via programmatic means.<\/jats:p><jats:p>Database URL: https:\/\/www.agbiodata.org\/databases<\/jats:p>","DOI":"10.1093\/database\/baad076","type":"journal-article","created":{"date-parts":[[2023,11,16]],"date-time":"2023-11-16T16:34:36Z","timestamp":1700152476000},"source":"Crossref","is-referenced-by-count":7,"title":["Data sharing and\u00a0ontology use among agricultural genetics, genomics, and\u00a0breeding databases and\u00a0resources of\u00a0the Agbiodata Consortium"],"prefix":"10.1093","volume":"2023","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2723-7249","authenticated-orcid":false,"given":"Jennifer L","family":"Clarke","sequence":"first","affiliation":[{"name":"Department of Statistics and Department of Food Science and Technology, University of Nebraska\u2013Lincoln , 340 Hardin Hall North Wing, Lincoln, NE 68583, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6379-8932","authenticated-orcid":false,"given":"Laurel D","family":"Cooper","sequence":"additional","affiliation":[{"name":"Department of Botany and Plant Pathology, Oregon State University , 2503 Cordley Hall, Corvallis, OR 97331, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4584-6056","authenticated-orcid":false,"given":"Monica F","family":"Poelchau","sequence":"additional","affiliation":[{"name":"USDA, Agricultural Research Service, National Agricultural Library , 10301 Baltimore Ave, Beltsville 20705, USA"}]},{"given":"Tanya Z","family":"Berardini","sequence":"additional","affiliation":[{"name":"The Arabidopsis Information Resource and Phoenix Bioinformatic , 39899 Balentine Drive, Suite 200, Newark, CA, USA"}]},{"given":"Justin","family":"Elser","sequence":"additional","affiliation":[{"name":"Department of Botany and Plant Pathology, Oregon State University , 2503 Cordley Hall, Corvallis, OR 97331, USA"}]},{"given":"Andrew D","family":"Farmer","sequence":"additional","affiliation":[{"name":"National Center for Genome Resources , 2935 Rodeo Park Dr. E., Santa Fe, NM 87505, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9138-6292","authenticated-orcid":false,"given":"Stephen","family":"Ficklin","sequence":"additional","affiliation":[{"name":"Department of Horticulture, Washington State University , 249 Clark Hall, PO Box 646414, Pullman, WA 99164, USA"}]},{"given":"Sunita","family":"Kumari","sequence":"additional","affiliation":[{"name":"Cold Spring Harbor Laboratory , One Bungtown Road, Cold Spring Harbor, NY 11724, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8461-9745","authenticated-orcid":false,"given":"Marie-Ang\u00e9lique","family":"Laporte","sequence":"additional","affiliation":[{"name":"Digital Inclusion, Bioversity International , Parc Scientifique Agropolis II, 1990 Bd de la Lironde, Montpellier 34397, France"}]},{"given":"Rex T","family":"Nelson","sequence":"additional","affiliation":[{"name":"USDA, Agricultural Research Service, Corn Insects and Crop Genetics Research Unit , Iowa State University, 716 Farmhouse Lane, Ames, IA 50011, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2861-5288","authenticated-orcid":false,"given":"Rie","family":"Sadohara","sequence":"additional","affiliation":[{"name":"Department of Plant, Soil, and Microbial Sciences, Michigan State University , 1066 Bogue St, East Lansing, MI 48824, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7151-4445","authenticated-orcid":false,"given":"Peter","family":"Selby","sequence":"additional","affiliation":[{"name":"School of Integrative Plant Science, College of Agriculture and Life Sciences, Cornell University , 215 Garden Avenue, Ithaca, NY 14850, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2908-3327","authenticated-orcid":false,"given":"Anne E","family":"Thessen","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics, University of Colorado Anschutz , 1890 N. Revere Court, Mailstop F600, Aurora CO 80045, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0337-8610","authenticated-orcid":false,"given":"Brandon","family":"Whitehead","sequence":"additional","affiliation":[{"name":"Data Science and Informatics, Manaaki Whenua\u2014Landcare Research, Ltd. , Riddet Road, Massey University, Palmerston North 4472, New Zealand"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5553-6190","authenticated-orcid":false,"given":"Taner Z","family":"Sen","sequence":"additional","affiliation":[{"name":"USDA, Agricultural Research Service, Crop Improvement Genetics Research Unit, Western Regional Research Center , 800 Buchanan St, Albany 94710, USA"},{"name":"Department of Bioengineering, University of California , 306 Stanley Hall, Berkeley, CA 94720, USA"}]}],"member":"286","published-online":{"date-parts":[[2023,11,16]]},"reference":[{"key":"2024032916250415700_R1","doi-asserted-by":"crossref","DOI":"10.1038\/sdata.2016.18","article-title":"The FAIR guiding principles for\u00a0scientific data management and\u00a0stewardship","volume":"3","author":"Wilkinson","year":"2016","journal-title":"Sci. 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