A Nanopublication Framework for Biological Networks using Cytoscape.js

We leverage semantic technologies and Cytoscape.js to create a provenance-aware, probabilistic analysis platform for systems biology and evaluate its usefulness in discovering links between drugs and diseases. 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 and display it using Cytoscape.js. 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 postive control, topiramate, allows us to independently reconstruct a positive control of epilepsy and migraine, and potential 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.