Using reasoning to guide annotation with gene ontology terms in GOAT

ABSTRACT

High-quality annotation of biological data is central to bioinformatics. Annotation using terms from ontologies provides reliable computational access to data. The Gene Ontology (GO), a structured controlled vocabulary of nearly 17,000 terms, is becoming the de facto standard for describing the functionality of gene products. Many prominent biomedical databases use GO as a source of terms for functional annotation of their gene-product entries to promote consistent querying and interoperability. However, current annotation editors do not constrain the choice of GO terms users may enter for a given gene product, potentially resulting in an inconsistent or even nonsensical description. Furthermore, the process of annotation is largely an unguided one in which the user must wade through large GO subtrees in search of terms. Relying upon a reasoner loaded with a DAML+OIL version of GO and an instance store of mined GO-term-to-GO-term associations, GOAT aims to aid the user in the annotation of gene products with GO terms by displaying those field values that are most likely to be appropriate based on previously entered terms. This can result in a reduction in biologically inconsistent combinations of GO terms and a less tedious annotation process on the part of the user.

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