Integrating large, disparate biomedical ontologies to boost organ development network connectivity

Abstract

There is a significant opportunity to extend the Gene Ontology's (GO) anatomical development hierarchies for use in various bioinformatics analysis scenarios such as systems biology network analysis, for example. In particular there is very little overlap between the anatomical entities referenced in these hierarchies and the corresponding concepts in the Foundational Model of Anatomy (FMA) ontology, despite the fact that the FMA is quite vast and well organized. Both ontologies can be integrated in such a manner that new, biologically meaningful paths can be revealed for use in analysis. In this paper, we present a method for integrating the GO's anatomical development process hierarchies with anatomical concepts in the FMA that correspond to the organs participating in the development processes. We also provide an evaluation of the impact of this integration on the number of paths from diseases and disease genes to the FMA concepts that participate in the development processes that annotate the genes. The results demonstrate a vast number of such paths and therefore the potential to impact biological network analysis of the molecular mechanisms underlying diseases that are involved in anatomical development. © 2012 Springer-Verlag.