PhenoMiner: quantitative phenotype curation at the rat genome database

Database (Oxford). 2013 Apr 19;2013:bat015. doi: 10.1093/database/bat015. Print 2013.

Abstract

The Rat Genome Database (RGD) is the premier repository of rat genomic and genetic data and currently houses >40 000 rat gene records as well as human and mouse orthologs, >2000 rat and 1900 human quantitative trait loci (QTLs) records and >2900 rat strain records. Biological information curated for these data objects includes disease associations, phenotypes, pathways, molecular functions, biological processes and cellular components. Recently, a project was initiated at RGD to incorporate quantitative phenotype data for rat strains, in addition to the currently existing qualitative phenotype data for rat strains, QTLs and genes. A specialized curation tool was designed to generate manual annotations with up to six different ontologies/vocabularies used simultaneously to describe a single experimental value from the literature. Concurrently, three of those ontologies needed extensive addition of new terms to move the curation forward. The curation interface development, as well as ontology development, was an ongoing process during the early stages of the PhenoMiner curation project. Database URL: http://rgd.mcw.edu.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Animals
  • Data Mining / methods*
  • Databases, Genetic*
  • Genome / genetics*
  • Humans
  • Mice
  • Molecular Sequence Annotation
  • Phenotype
  • Rats
  • Software*
  • Workflow