Ontology searching and browsing at the Rat Genome Database

Area of Science:

• Genomics
• Bioinformatics
• Data Curation

Background:

• The Rat Genome Database (RGD) is a key resource for rat genomic and genetic data.
• RGD curates extensive biological information, including genes, QTLs, and strains, using standardized ontologies.
• Efficiently searching and browsing these ontologies is crucial for data curation and mining.

Purpose of the Study:

• To enhance the ontology term search and browsing capabilities within the Rat Genome Database (RGD).
• To improve the usability and robustness of RGD's ontology features for researchers.
• To facilitate more efficient manual data curation and extraction from the RGD.

Main Methods:

• Upgraded the ontology term search functionality for increased versatility.
• Implemented a 'driller' type browser to replace the traditional tree format for improved navigation.
• Enhanced RGD ontology report pages with expanded functionality for displaying annotations.

Main Results:

• The new ontology search and browser allow users to more effectively find and navigate terms.
• The 'driller' browser enables quicker traversal of ontology hierarchies.
• Upgraded report pages offer greater flexibility in viewing and subsetting annotation data.

Conclusions:

• The RGD's enhanced ontology features significantly improve the efficiency of data curation and extraction.
• These upgrades support researchers in accessing and utilizing the comprehensive rat genomic and genetic information.
• The improved tools contribute to the RGD's role as a premier repository for rat data.