%0 Journal Article
%T GOLink: Finding Cooccurring Terms across Gene Ontology Namespaces
%A Richard W. Francis
%J International Journal of Genomics
%D 2013
%I Hindawi Publishing Corporation
%R 10.1155/2013/594528
%X The Gene Ontology (GO) provides a resource for consistent annotation of genes and gene products that is extensively used by numerous large public repositories. The GO is constructed of three subontologies describing the cellular component of action, molecular function, and overall biological process of a gene or gene product. Querying across the subontologies is problematic and no standard method exists to, for example, find all molecular functions occurring in a particular cellular component. GOLink addresses this problem by finding terms from all subontologies cooccurring with a term of interest in annotation across the entire GO database. Genes annotated with this term are exported and their GO annotation is assigned to three separate GOLink terms lists based on specific criteria. The software was used to predict the most likely Biological Process for a group of genes using just their Molecular Function terms giving sensitivity, specificity, and accuracy between 80 and 90% across all the terms lists. GOLink is made freely available for noncommercial use and can be downloaded from the project website. 1. Introduction With the number of sequenced genomes at various stages of completion being in the tens of thousands [1] and the number of genomic features (genes, RNAs, etc.) identified across these genomes in the millions, the need for accurate and consistent genomic annotation is paramount. The Gene Ontology (GO) [2] was created in 1998 by researchers at FlyBase, The Saccharomyces Genome Database (SGD), and The Mouse Genome Database as a collaborative effort to address the need for consistent descriptions of gene products across different databases. This group has since grown to include 26 consortium members and associates [3] and the GO is a key member of the Open Biological and Biomedical Ontologies (OBO) community [4]. In this context, an ontology can be defined as the specifications of a relational vocabulary [5]. Ontologies provide a controlled vocabulary for representing and communicating knowledge about a topic and a set of relationships that hold among the terms of the vocabulary. The topic for the GO is genes and gene products such as transcripts, proteins, or RNAs that are described in three related subontologies (also called namespaces), Biological Process, the broad biological system in which a gene product is involved; Molecular Function, the specific role a gene product has or potentially has within a Biological Process; and Cellular Component, the location in a cell where the gene product performs its Molecular Function. Each ontology is
%U http://www.hindawi.com/journals/ijg/2013/594528/