Data sharing and ontology use among agricultural genetics, genomics, and breeding databases and resources of the Agbiodata Consortium.

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 'databases' 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. Database URL  https://www.agbiodata.org/databases.

Global agricultural concept space: lightweight semantics for pragmatic interoperability.

Progress on research and innovation in food technology depends increasingly on the use of structured vocabularies-concept schemes, thesauri, and ontologies-for discovering and re-using a diversity of data sources. Here, we report on GACS Core, a concept scheme in the larger Global Agricultural Concept Space (GACS), which was formed by mapping between the most frequently used concepts of AGROVOC, CAB Thesaurus, and NAL Thesaurus and serves as a target for mapping near-equivalent concepts from other vocabularies. It provides globally unique identifiers, which can be used as keywords in bibliographic databases, tags for web content, for building lightweight facet schemes, and for annotating spreadsheets, databases, and image metadata using synonyms and variant labels in 25 languages. The minimal semantics of GACS allows terms defined with more precision in ontologies, or less precision in controlled vocabularies, to be linked together making it easier to discover and integrate semantically diverse data sources.