Harnessing formal concepts of biological mechanism to analyze human disease.

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TitleHarnessing formal concepts of biological mechanism to analyze human disease.
Publication TypeJournal Article
Year of Publication2018
AuthorsDarden, L, Kundu, K, Pal, LR, Moult, J
JournalPLoS Comput Biol
Volume14
Issue12
Paginatione1006540
Date Published2018 Dec
ISSN1553-7358
Abstract

Mechanism is a widely used concept in biology. In 2017, more than 10% of PubMed abstracts used the term. Therefore, searching for and reasoning about mechanisms is fundamental to much of biomedical research, but until now there has been almost no computational infrastructure for this purpose. Recent work in the philosophy of science has explored the central role that the search for mechanistic accounts of biological phenomena plays in biomedical research, providing a conceptual basis for representing and analyzing biological mechanism. The foundational categories for components of mechanisms-entities and activities-guide the development of general, abstract types of biological mechanism parts. Building on that analysis, we have developed a formal framework for describing and representing biological mechanism, MecCog, and applied it to describing mechanisms underlying human genetic disease. Mechanisms are depicted using a graphical notation. Key features are assignment of mechanism components to stages of biological organization and classes; visual representation of uncertainty, ignorance, and ambiguity; and tight integration with literature sources. The MecCog framework facilitates analysis of many aspects of disease mechanism, including the prioritization of future experiments, probing of gene-drug and gene-environment interactions, identification of possible new drug targets, personalized drug choice, analysis of nonlinear interactions between relevant genetic loci, and classification of diseases based on mechanism.

DOI10.1371/journal.pcbi.1006540
Alternate JournalPLoS Comput. Biol.
PubMed ID30586388