Common evidence network: An integrated approach to investigating gene relationships

A common evidence network is a data structure that integrates evidence for relationships between genes from disparate data sources and across data types. It is an undirected weighted graph where nodes represent genes and edge weights are quantitative measures of confidence in the evidence linking two genes. We describe methods for producing edge weights for two evidence types: literature co-citation and similarity of Gene Ontology annotations. A tool was developed for identifying genes across multiple databases and consolidating selected annotations. Using gene synonym lists obtained from this tool, we extracted co-citations of genes from annotated biomedical abstracts as evidence. We developed a novel approach to interpreting the similarity of Gene Ontology terms annotated to genes. The method produces a score that quantitatively describes the similarity of Gene Ontology term annotations between two genes. We tested both methods on a set of genes sharing a common sequence feature.