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Saturday, November 17, 2018

New paper: "Explicit interaction information from WikiPathways in RDF facilitates drug discovery in the Open PHACTS Discovery Platform"

Figure from the article showing the interactive
Open PHACTS documentation to access
interactions.
Ryan, PhD candidate in our group, is studying how to represent and use interaction information in pathway databases, and WikiPathways specifically. His paper Explicit interaction information from WikiPathways in RDF facilitates drug discovery in the Open PHACTS Discovery Platform (doi:10.12688/f1000research.13197.2) was recently accepted in F1000Research, which extends on work started by, among others, Andra (see doi:10.1371/journal.pcbi.1004989).

The paper describes the application programming interfaces (API) methods of the Open PHACTS REST API for accessing interaction information, e.g. to learn which genes are upstream of downstream in the pathway. This information can be used in pharmacological research. The paper discussed examples queries and demonstrates how the API methods can be called from HTML+JavaScript and Python.