The Neural/Immune Gene Ontology: clipping the Gene Ontology for neurological and immunological systems

Here, we propose a new approach to editing the gene ontology, clipping, which is the editing of GO according to biological relevance. Creation of a GO subset by clipping is achieved by removing terms (from all hierarchal levels) if they are not functionally relevant to a given domain of interest. Terms that are located in levels higher to relevant terms are kept, thus, biologically irrelevant terms are only removed if they are not parental to terms that are relevant.Using this approach, we have created the Neural-Immune Gene Ontology (NIGO) subset of GO directed for neurological and immunological systems. We tested the performance of NIGO in extracting knowledge from microarray experiments by conducting functional analysis and comparing the results to those obtained using the full GO and a generic GO slim. NIGO not only improved the statistical scores given to relevant terms, but was also able to retrieve functionally relevant terms that did not pass statistical cutoffs when using the full GO or the slim subset.Our results validate the pipeline used to generate NIGO, suggesting it is indeed enriched with terms that are specific to the neural/immune domains. The results suggest that NIGO can enhance the analysis of microarray experiments involving neural and/or immune related systems. They also directly demonstrate the potential such a domain-specific GO has in generating meaningful hypotheses.An ontology is a formal way for the representation and sharing of knowledge in a certain domain by describing the concepts (or terms) in that domain and the relationships between them. An ontology formalizes the meaning of concepts, or terms, by a set of assertions and rules that characterize them and connects them to other terms within the ontology [1,2].The Gene Ontology (GO), a widely used bio-ontology, is used to describe genes and gene products from numerous organisms [3,4]. GO is constructed from three separate ontologies which capture the three main biological areas of k