Session 3: Open PHACTS

Open PHACTS: Solutions and the Foundation
OpenTox Euro 2014 speaker: Egon L. Willighagen

Egon L. Willighagen


Dept. Bioinformatics - BiGCaT, NUTRIM, Maastricht University


Egon L. Willighagen, Open PHACTS Consortium

Tue, 23. Sep. 2014


1. Williams, A.J.; Harland, L.; Groth, P.; Pettifer, S.; Chichester, C.; Willighagen, E.L.; Evelo, C.T.; Blomberg, N.; Ecker, G.; Goble, C.; Mons, B. Open PHACTS: semantic interoperability for drug discovery. Drug Discovery Today. 2012, 17, 1188-1198.
2. Gray, A.J.G.; Groth, P.; Loizou, A.; Askjaer, S.; Brenninkmeijer, C.; Burger, K.; Chichester, C.; Evelo, C.T.; Goble, C.; Harland, L.; Pettifer, S.; Thompson, M.; Waagmeester, A.; Williams, A.J. Applying Linked Data Approaches to Pharmacology: Architectural Decisions and Implementation. Semantic Web Journal. 2014, 5(20), 101-113.
3. Azzaoui, K.; Jacoby, E.; Senger, S.; Cuadrado Rodríguez, E.; Loza, M.; Zdrazil, B.; Pinto, M.; Williams, A.J.; De la Torre, V.; Mestres, J.; Pastor, M.; Taboureau, O.; Rarey, M.; Chichester, C.; Pettifer, S.; Blomberg, N.; Harland, L.; Williams-Jones, B.; Ecker, G.K. Scientific competency questions as the basis for semantically enriched open pharmacological space development. Drug Discovery Today, 2013. 18(17-18), 843-852.

Egon Willighagen (orcid:0000-0001-7542-0286) is assistant professor at the Department of Bioinformatics - BiGCaT at Maastricht University.

He applies cheminformatics and chemometrics to biological problems, and works on the EU FP7 projects Open PHACTS and eNanoMapper in the area of drug discovery and nanotoxicology.

He contributed to many Open Science projects, including Jmol, the Chemistry Development Kit, Bioclipse, WikiPathways, and BridgeDb. His blog can be found at and his publication are found on his homepage at

Open PHACTS is a five year project of the Innovative Medicines Initiative (IMI), ending in February 2016. It aims to reduce the barriers to drug discovery in industry, academia and for small businesses(1). The Open PHACTS consortium is building a freely available platform, integrating data from a variety of information resources, and providing tools and services to query these integrated data to support life sciences research(2).

Currently, pharmaceutical companies expend significant and often duplicated efforts aligning and integrating internal information with public data sources. This process is difficult and inefficient and the vast majority of data sources cannot easily interoperate, often requiring additional steps to map identifiers or manually curate and correct the content. Open PHACTS is creating a precompetitive infrastructure to make these data integration approaches available both to industry and to academia and smaller companies, who have historically not had access to large-scale integrated data resources.

Here we give an overview of the resulting Open PHACTS Discovery Platform, the semantic web solutions used in this, and describe the integration of the data into dedicated and generic data analysis tools. The platform consists of components that communicate with each other using open standards and cover the full data lifecycle, from data loading to data sharing. Solutions underlying the platform include those for data provenance, data normalization, data standardization, and data access. In particular, we have developed minimal reporting standards for provenance, technologies to express the level of equivalence of entities from different databases, a database identifier mapping infrastructure based on semantic web technologies, unit and end point normalization, as well as chemical structure normalization. For this we use open ontologies (BioAssay Ontology, QUDT, CHEMINF, etc), standards (RDF, SPARQL, REST, etc), and proposed solutions as outlined in published specifications.

On top of these approaches, user oriented solutions have been developed based on a number of research questions selected by the pharmaceutical industry(3). Example questions include: “Give me all oxidoreductase inhibitors active <100 nm in human and mouse” and “Compounds that agonize targets in pathway X assayed in only functional assays with a potency <1 μm”. The OPS platform provides a uniform route by which these questions can be addressed, exposed to the user by a novel pharmaceutical web service platform, called the Linked Data API (LDA).

As well as provided an API and web-portal to access integrated data, the Open PHACTS platform also supports an ecosystem of third-party applications addressing specialised needs such as polypharmacology, hit-selection, target validation and knowledge discovery. Additionally, more generic integrations have been developed too, like client libraries to the LDA in various programming languages, such as JavaScript, Scala, and Java, resulting in integration in generic data analysis platforms like PipeLine Pilot, KNIME, R, and Bioclipse.

Finally, results will be presented based on the sustainability track of the platform, indicating the future of Open PHACTS beyond the initial project. This future is partly covered by an Open PHACTS Foundation which will ensure maintenance and continued development.