Long Term Goals of the Bovine Genome Database Consortium

    1. Develop an informatics resource for cattle that combines sequence, haplotype, quantitative trait and gene expression data with graphical search and viewing interfaces.
    We will use open-source software, including modules of the Generic Model Organism Database (GMOD) project, to create the Bovine Genome Database, an integrated resource that will cater to the needs of the bovine genomics community. Furthermore, we will incorporate all cattle genome data from ENSEMBL, NCBI, UCSC Genome Browser and data sources that are specific to the cattle community. The components to be integrated include:
  • Genome viewer based on GMOD
  • Gene expression database based on the Longhorn Array Database, an open-source implementation of the Stanford Microarray Database.
  • Chromosomal context and gene centric views of gene expression data using the SOURCE database and code, with dynamic links to SOURCE GeneReports for predicted orthologs of bovine genes
  • An existing Bovine QTL Viewer with data curated from cattle literature and chromosomal context views of QTL
  • SNP/Haplotype block database with graphical viewers
  • Gene pages with gene structures, splice variants, translations, homologs and orthologs, functional annotations including Gene Ontology, protein domains, database cross references, links to other MODS, Ensembl, NCBI Entrez Gene, NCBI Homologene, OrthoMCL, UniProt, and internal connections to genomes browsers, gene expression, SNP and phenotype information
    2. Maintain and enhance sequence annotations, with an essential level of community support that exceeds what is possible at BCM-HGSC, NCBI and Ensembl.
  • Maintain a single bovine reference gene set.
  • Host an annotation submission website for bovine researchers.
  • Organize, review, map, and submit annotations to NCBI.
  • Port mapping of feature coordinates to updated bovine genome assemblies.
  • Perform computations to supplement annotations available elsewhere.
  • While we are not the official curators of bovine Gene Ontology, we will cooperate with the Gene Ontology Association at EBI, (GOA; the official source of the Bovine GO annotations file), the Gene Ontology Consortium, and AgBase.