Medical College of Wisconsin
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Ontology searching and browsing at the Rat Genome Database. Database (Oxford) 2012;2012:bas016 PMID: 22434847 PMCID: PMC3308169

Pubmed ID

22434847

Abstract

The Rat Genome Database (RGD) is the premier repository of rat genomic and genetic data and currently houses over 40‚ÄČ000 rat gene records, as well as human and mouse orthologs, 1857 rat and 1912 human quantitative trait loci (QTLs) and 2347 rat strains. Biological information curated for these data objects includes disease associations, phenotypes, pathways, molecular functions, biological processes and cellular components. RGD uses more than a dozen different ontologies to standardize annotation information for genes, QTLs and strains. That means a lot of time can be spent searching and browsing ontologies for the appropriate terms needed both for curating and mining the data. RGD has upgraded its ontology term search to make it more versatile and more robust. A term search result is connected to a term browser so the user can fine-tune the search by viewing parent and children terms. Most publicly available term browsers display a hierarchical organization of terms in an expandable tree format. RGD has replaced its old tree browser format with a 'driller' type of browser that allows quicker drilling up and down through the term branches, which has been confirmed by testing. The RGD ontology report pages have also been upgraded. Expanded functionality allows more choice in how annotations are displayed and what subsets of annotations are displayed. The new ontology search, browser and report features have been designed to enhance both manual data curation and manual data extraction. DATABASE URL: http://rgd.mcw.edu/rgdweb/ontology/search.html.

Author List

Laulederkind SJ, Tutaj M, Shimoyama M, Hayman GT, Lowry TF, Nigam R, Petri V, Smith JR, Wang SJ, de Pons J, Dwinell MR, Jacob HJ

Authors

Melinda R. Dwinell PhD Center Associate Director, Associate Professor in the Physiology department at Medical College of Wisconsin
Mary E. Shimoyama PhD Associate Professor in the Biomedical Engineering department at Medical College of Wisconsin




Scopus

2-s2.0-84862262998   14 Citations

MESH terms used to index this publication - Major topics in bold

Animals
Database Management Systems
Databases, Genetic
Genome
Humans
Mice
Molecular Sequence Annotation
Quantitative Trait Loci
Rats
User-Computer Interface
jenkins-FCD Prod-300 626508253d14e4184314fb9f66322a03a5906796