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ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Plant, Soil and Nutrition Research » Research » Publications at this Location » Publication #402154

Research Project: Mapping Crop Genome Functions for Biology-Enabled Germplasm Improvement

Location: Plant, Soil and Nutrition Research

Title: Towards standards for biocuration and interoperability of genetic variation data

item TELLO-RUIZ, MARCELA - Cold Spring Harbor Laboratory
item ALI, KAZIM - University Of Karachi
item Bassil, Nahla
item BEIER, SEBASTIAN - Forschungszentrum Juelich Gmbh
item BOATWRIGHT, LUCAS - Clemson University
item CEZARD, TIMOTHEE - Embl-Ebi
item CHANG, TAO-HO - National Chicken Council
item DYER, SARAH - Embl-Ebi
item Harrison, Melanie
item Ware, Doreen
item KHANGURA, RAJDEEP - Cold Spring Harbor Laboratory
item KUMAR, VIVEK - Cold Spring Harbor Laboratory
item SALAVATI, MAZDAK - University Of Edinburgh
item WEI, SHARON - Cold Spring Harbor Laboratory

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 1/13/2023
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: The Standards for Genetic Variation Data Working Group of the AgBioData Consortium was established in early 2022 to bring together a community of biocurators, data providers, bioinformaticians and computer scientists. One of the primary tasks for this working group was to support the harmonization and adoption of standards for variation data from the various platforms in the plant and animal kingdoms, and to promote interoperability and access to these datasets. The adoption and dissemination of metadata standards for animal genetic variants is already relatively advanced (thanks to the FAANG project), with an online portal that can manage much of the metadata in the form of rule sets and provide tools for central validation - comparable to a data clearing house with links to public repositories such as ENA and EVA. In the Plant Kingdom, the first guidelines on FAIR handling of data from genetic variants were only published at the beginning of 2022. This involved working directly with the EBI on supporting data submission to BioSamples and EVA, by providing a checklist to classify and validate the data. We have begun to survey the AgBioData community, including species-specific and clade-wide databases, germplasm repositories, as well as data producers, on existing and anticipated genetic variation data sets for agriculturally important species. The working group will present a summary of discussions held to identify challenges and progress made towards achieving the above objectives.