The Open PHACTS project ( http://www.openphacts.org/) has built a platform for drug discovery that integrates data over diverse sets of public chemistry and biological data. It currently connects linked open data from 12 different data sources, including chemical compounds, protein targets, biological pathways and tissues, and diseases. The diversity and size and of the Open PHACTS data are growing rapidly, and it contains currently more than 3 billion triples. The Open PHACTS project is a unique collaboration between European academic groups, small businesses and large pharmaceutical companies, partially funded by the EU. The driver for the project is to enable scientists to easily access and process data from multiple sources to solve real-world drug discovery problems that were very difficult to solve before. These drug discovery problems formed the basis for selecting what public data sources were integrated in the Open PHACTS project. Anyone can freely access the Open PHACTS data through a well documented API, and numerous workflows to answer specific biomedical questions have been developed and published using the KNIME and Pipeline Pilot pipelining tools. In addition, several custom applications have been built using the API. Open PHACTS has shown that Linked Open Data in the form of RDF triples can be used effectively by the scientific community, and allows queries that were previously very difficult or impossible to run. Future directions include the integration of additional public data sources, integration of internal company data with Open PHACTS data, and the continued development of workflows for scientific questions that can only be answered using linked data.
This work was done as a part of MSc thesis research.
Example of a semantic mind map which can be quickly generated by browsing and selecting linked data.