MecCog: A knowledge representation framework for genetic disease mechanism

Kundu, Kunal; Darden, Lindley; Moult, John

Motivation 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 will greatly enhance its utility. Results 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. Availability and Implementation The MecCog framework is freely available at http://www.meccog.org. Contact [e-mail] Supplementary information Supplementary material is available at Bioinformatics online.