A Nanopublication Framework for Systems Biology and Drug Repurposing

The interaction among proteins, genes, drugs, and other molecular entities is a core component of systems biology. A number of databases have been developed that serve as a patchwork across the landscape of systems biology, each focused on different experimental methods, many species, and a wide diversity of inclusion criteria. Systems biology has been used in the past to generate hypotheses for drug effects, but has become fragmented under the large number of disparate and disconnected databases. In our efforts to create a systematic approach to discovering new uses for existing drugs, we have developed Repurposing Drugs with Semantics (ReDrugS). ReDrugS is a data curation and publication framework that can take data from nearly any database containing biological or chemical entity interactions. ReDrugS is able to infer probability of the assertions based on its provenance using experimental methods and data sources. A semantic web service API is provided that can search, traverse, and provide composite probabilities for the resulting graph of biological entities using the SADI web service framework and Nanopublications. We show how associations between a positive control, topiramate, allows us to independently reconstruct its use in treatment of epilepsy and migraine, and its consequences on bone health. Future work will incorporate additional protein/disease associations, enabling hypothesis generation on indirect drug targets, and leading to testing the resulting hypotheses using high throughput drug screening.
Speaker Bio:
Jim McCusker is a PhD candidate in Computer Science at the Tetherless World Constellation, Rensselaer Polytechnic Institute; and a Data Scientist at 5AM Solutions, Inc., a software and bioinformatics services company serving the world of life science and medicine.
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