Applying linked data approaches to pharmacology: Architectural decisions and implementation

Abstract

The discovery of new medicines requires pharmacologists to interact with a number of information sources ranging from tabular data to scientific papers, and other specialized formats. In this application report, we describe a linked data platform for integrating multiple pharmacology datasets that form the basis for several drug discovery applications. The functionality offered by the platform has been drawn from a collection of prioritised drug discovery business questions created as part of the Open PHACTS project, a collaboration of research institutions and major pharmaceutical companies. We describe the architecture of the platform focusing on seven design decisions that drove its development with the aim of informing others developing similar software in this or other domains. The utility of the platform is demonstrated by the variety of drug discovery applications being built to access the integrated data. An alpha version of the OPS platform is currently available to the Open PHACTS consortium and a first public release will be made in late 2012, see http://www.openphacts.org/ for details.

A new wave of innovation in Semantic web tools for drug discovery

“…Along similar lines, Open PHACTS (Open Pharmacological Concept Triple Store) [70], was created as part of the Open PHACTS project to answer complex questions in drug discovery [71]. It essentially provides an application layer on top of the Open PHACTS API, such that users can search for drug discovery data without needing to understand the RDF data behind it, or even understand SPARQL [72].…”

DisGeNET-RDF: harnessing the innovative power of the Semantic Web to explore the genetic basis of diseases

“…In recognition of the interest in the RDF representation of DisGeNET, we note that from October 31st, 2014 to October 31st, 2015 the dataset web site had more than 11,000 page views according to Google Analytics report. Remarkably, DisGeNET-RDF is integrated in the Open PHACTS Discovery Platform [7], which is an application for drug discovery based on Semantic Web technology and RDF linked datasets.…”

On the Formulation of Performant SPARQL Queries

“…In order to achieve this goal, the platform must tackle the problem of public domain data integration in the pharmacology space and provide efficient access to the resulting integrated data. The development of the OpenPHACTS platform is driven by a set of concrete research questions presented in [9], and the platform architecture is described in [7].…”