Ontology searching and browsing at the Rat Genome Database

• Published in: Database : the journal of biological databases and curation Vol. 2012; p. bas016
• Main Authors: Laulederkind, Stanley J F, Tutaj, Marek, Shimoyama, Mary, Hayman, G Thomas, Lowry, Timothy F, Nigam, Rajni, Petri, Victoria, Smith, Jennifer R, Wang, Shur-Jen, de Pons, Jeff, Dwinell, Melinda R, Jacob, Howard J
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 20-03-2012
• Subjects: Animals; Database Management Systems; Databases, Genetic; Genome; Genomes; Genomics; Humans; Mice; Molecular Sequence Annotation; Ontology; Original; Quantitative Trait Loci; Rats - genetics; User-Computer Interface
• ISSN: 1758-0463; 1758-0463
• DOI: 10.1093/database/bas016

The Rat Genome Database (RGD) is the premier repository of rat genomic and genetic data and currently houses over 40 000 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.