A range of databases exist which manage information relating to Brassica genetics, genomics and related activities. There remains achallenge to extend the scope of nomenclature standards, management of 'registries' of widely used resources and information, and development of tools for integrating and navigating between disparate datasets.
Genome browsers and associated sites
- Annotated reference genomes
Brassica Genome Gateway
- Brassica Information Portal at TGAC, UK: a web repository for population and trait scoring information related to the Brassica breeding community. It provides information about quantitative trait loci and links curated Brassica phenotype experimental data with genotype information stored in external data sources. Advanced data submission capabilities and APIs enable users to store and publish their own study results.
- Brassibase: a developing online-accessible knowledge and database system of cross-referenced information and resources on Brassicaceae (Cruciferae) taxonomy, systematics and evolution, including chromosome numbers, traits and characters, germplasm resources, and accurate enumeration of all species, genera and tribes.
Links to external databases
- BRAD - Brassica Database Searchable B. rapa Chiifu-401 genome (from IVF-CAAS)
- Ensembl Plants - Brassica. rapa at EBI
- COGE: Comparative Genomics resource
- BrGDB - Brassica rapa Genome DB (part of PlantGDB)
- GnpIS: Genetic & Genomic Information System (URGI)
- IMSORB genetic marker and QTL database
- NASC Arabidopsis Ensembl with Brassica tracks
- UK BBSRC Physical Mapping DB
- TransPLANT: trans-National Infrastructure for Plant Genomic Science (EU-FP7)
BrassicaDBBrassicaDB was funded until 2003 by BBSRC under the UK-CropNet programme. It aimed to curate a comprehensive set of sequence accessions, bibliography, and a range of genetic maps, markers etc. In addition, this database is currently the original source of information for the 'BBSRC set' of Brassica SSR markers. Martin Trick at JIC ensures that the database is still automatically refreshed with newly deposited Brassica sequences every night and is occasionally rebuilt from scratch. There is also a useful Brassica BLAST server associated with this database.
CropStoreDBCropStoreDB is a relational database that provides a framework for standardised curation and management of data relating to crop genetics. We have adopted Brassica as an exemplar use-base. The CropStore data curation pipeline and database system is being used to collate reference information for the MBGP data repository, including interfaces developed direct through this website, and available using the links below:
InterStoreDBis a suite of closely linked web-based tools, including CropStoreDB designed to assist researchers in navigating from phenotype to genotype. The initial implementation for InterStoreDB is for Brassica.
- InterStoreDB :: Interfaces (this site in process of being moved (2015)
Ensembl (Arabidopsis)The Ensembl genome browser implementation at NASC (AtEnsembl ) provides access to definitive annotation of the Arabidopsis genome (TAIR7), with additional tracks that indicate alignment of homologous Brassica sequences, such s ESTs, BACs etc.
Physical mapsSeveral projects have generated fingerprint and hybridisation data relating to long cloned sequences of Brassica, mostly in BAC libraries. Databases that manage these data include:
- Brassica IGF project (UK) fingerprint and hybridisation of B. rapa and B. oleracea libraries
- Korean Sequencing project B. rapa BAC fingerprinting database