Gene Curation Software at the Rat Genome Database (RGD)

Abstract

At model organism databases data is curated for numerous biological categories using various ontologies and vocabularies. The Rat Genome Database (RGD) uses four different ontologies to standardize annotation information for genes and their associations with disease, phenotypes, and pathways. For manual gene curation this is all done in a single user interface of a web-based annotation tool developed at RGD. The same interface can be used for the curation of QTLs and strains. The development of the tool has been achieved through a collaboration of curators and software developers. Features have been tailored to the needs of the curators to allow optimum efficiency of the data entry portion of the curation process. Annotations using the Gene Ontology, Mammalian Phenotype Ontology, Pathway Ontology, and Disease Ontology can be done simultaneously in the same user interface. The search function of the tool has multiple options, giving the curators the opportunity to specify the search according to the immediate need. For ontology terms, gene, QTL, and strain objects the tool searches RGD data tables. For references the tool searches both internal and PubMed reference IDs. If an abstract reference is not already found at RGD, the tool automatically downloads the reference and assigns an RGD ID to it. Data objects, ontology terms, and references can be stored in multiples, providing various options for composing annotations. An editing step allows the composed annotation line to be altered before entering it in the database. The tool displays all current annotations for any gene that is selected. A second editing function is available by hyperlink for any pre-existing annotation displayed in the tool. The curation software has more than doubled literature curation production since replacing spreadsheet curation.