MecCog: a knowledge representation framework for genetic disease mechanism.

Abstract

Experimental findings on genetic disease mechanisms are scattered throughout the literature and represented in many ways, including unstructured text, cartoons, pathway diagrams and network graphs. Integration and structuring of such mechanistic information greatly enhances its utility. MecCog is a graphical framework for building integrated representations (mechanism schemas) of mechanisms by which a genetic variant causes a disease phenotype. A MecCog mechanism schema displays the propagation of system perturbations across stages of biological organization, using graphical notations to symbolize perturbed entities and activities, hyperlinked evidence tagging, a mechanism ontology and depiction of knowledge gaps, ambiguities and uncertainties. The web platform enables a user to construct, store, publish, browse, query and comment on schemas. MecCog facilitates the identification of potential biomarkers, therapeutic intervention sites and critical future experiments. The MecCog framework is freely available at http://www.meccog.org. Supplementary data are available at Bioinformatics online.