Model organism database

Model organism databases (MODs) are biological databases, or knowledgebases, dedicated to the provision of in-depth biological data for intensively studied model organisms. MODs allow researchers to easily find background information on large sets of genes, plan experiments efficiently, combine their data with existing knowledge, and construct novel hypotheses. They allow users to analyse results and interpret datasets, and the data they generate are increasingly used to describe less well studied species. Where possible, MODs share common approaches to collect and represent biological information. For example, all MODs use the Gene Ontology (GO) to describe functions, processes and cellular locations of specific gene products. Projects also exist to enable software sharing for curation, visualization and querying between different MODs. Organismal diversity and varying user requirements however mean that MODs are often required to customize capture, display, and provision of data.

Types of data and services

Model organism databases generate, source and collate species-specific information integratively by combining expert knowledge with literature curation and bioinformatics.

Services provided to biological research communities include:

• Genome sequence annotations
  • Location of genes and regulatory regions in the genome
• Functional curation of gene products
  • Discern functions fulfilled by the gene product by looking at a variety of data including Gene Ontology (GO) annotations, phenotypes, gene expression, pathway information
• Protein/RNA sequence annotations
• Anatomical information
• Stock centres
• Orthology

List of model organism databases