SorghumBase: a knowledgebase for sorghum genomics, phenomics, and stakeholder engagement

Authors:
Publisher website
Google Scholar
Abstract
Centralizing valuable community data and resources into a user-friendly interface and accessible repository has become essential for agricultural science; embracing Findable Accessible, Interoperable, and Reusable (FAIR) principles is now standard for effective databases. SorghumBase (https://www.sorghumbase.org) is a knowledgebase designed for the sorghum research community. The SorghumBase team curates genomic, transcriptomic, variation, and phenotypic information and aggregates community events, providing rich visualizations and bulk data access. The modular framework of the database is built with open-access software to yield a robust, modifiable, and sustainable data infrastructure. Release 9 of SorghumBase includes: (i) 88 sorghum reference genomes and an updated pan-gene index, (ii) over 100 million variants have been mapped onto the 2 genomes, BTx623 and Tx2783, (iii) assignment of 41 million Reference Cluster SNP identifiers (rsIDs) from BTx623 across the pan-genome, (iv) updated gene search homology, gene expression, and germplasm visualizations and features, (v) added and standardized 234 phenotypic data from 40 community-generated GWAS studies and 148 traits from the Sorghum QTL Atlas (Oz Sorghum), (vi) improved news, funding, and a research content management system for community access and interaction, (vii) outreach materials including training documents and videos, and (viii) community engagement initiatives through training and working groups. SorghumBase serves as a hub for sorghum data and stakeholder engagement while promoting community standards to drive research and multi-omics breeding approaches.
Funding Information
  • U.S. Department of Agriculture (USDA-ARS 8062-21000-051-000D)
  • National Institutes of Health (S10OD028632-01)
  • SCINet project
  • Nemzeti Agrárkutatási és Innovációs Központ (0201-88888-003-000D)
  • Nemzeti Agrárkutatási és Innovációs Központ (0201-88888-002-000D)
  • Salk Institute for Biological Studies
  • Ted Audacious
  • Bezos Earth Fund
  • Advanced Research Projects Agency - Energy
  • U.S. Department of Energy (DE-AR0000594)
  • Bill and Melinda Gates Foundation (OPP1129063)
  • Government Finance Officers Association of the United States and Canada
  • Natural Sciences and Engineering Research Council of Canada
  • Sorghum eFP Browser

This publication has 44 references indexed in Scilit: