From word models to executable models of signaling networks using automated assembly.

ABSTRACT: Word models (natural language descriptions of molecular mechanisms) are a common currency in spoken and written communication in biomedicine but are of limited use in predicting the behavior of complex biological networks. We present an approach to building computational models directly from natural language using automated assembly. Molecular mechanisms described in simple English are read by natural language processing algorithms, converted into an intermediate representation, and assembled into executable or network models. We have implemented this approach in the Integrated Network and Dynamical Reasoning Assembler (INDRA), which draws on existing natural language processing systems as well as pathway information in Pathway Commons and other online resources. We demonstrate the use of

SUBMITTER: Gyori BM 

PROVIDER: S-EPMC5731347 | biostudies-literature | 2017 Nov

REPOSITORIES: biostudies-literature