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- Title
Pheno Miner: quantitative phenotype curation at the rat genome database.
- Authors
Laulederkind, Stanley J. F.; Weisong Liu; Smith, Jennifer R.; Hayman, G. Thomas; Shur-Jen Wang; Nigam, Rajni; Petri, Victoria; Lowry, Timothy F.; de Pons, Jeff; Dwinell, Melinda R.; Shimoyama, Mary
- 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.
- Subjects
BIOCHEMISTRY databases; FOREIGN associations, institutions, etc.; ANIMAL genome mapping; GENOTYPE-environment interaction; NECESSITY (Philosophy); LABORATORY rats
- Publication
Database: The Journal of Biological Databases & Curation, 2013, Vol 2013, p1
- ISSN
1758-0463
- Publication type
Article
- DOI
10.1093/database/bat015