Open PHACTS

Voices calling for wider access to, and reuse of, data from health and biomedical research are getting louder. Findability, accessibility, interoperability and reusability (aka FAIR) are crucial to allow analyses to be carried out on large-scale datasets in the drug development process. Recognising this, research gatekeepers, including the EU funding bodies, now mandate high quality data management for all projects.###

OpenPHACTS, an early IMI project, was one of the ‘thought incubators’ cited in the drafting of the original FAIR data manifesto, with its OpenPHACTS Discovery Platform cited as an example of a system in which FAIR principles were already being implemented. The online platform links publicly available drug discovery databases to give researchers a one-stop-shop where they can quickly find the data they needed to test their scientific hypotheses. The platform was very innovative - one interface and data integration to allow for very complex (and time consuming) searches all in one spot.

While the key strength of the platform is to make publicly available datasets available through a single, simple query, the pharmaceutical company partners in the project all had confidential data they wanted to integrate for their own use.  OpenPHACTS therefore built infrastructure to allow for this, while guaranteeing the confidentiality of the company data. This functionality led to the founding of Phenaris, a spin-out company that offers data, models, and decision support in all aspects of in silico toxicology.

Find out more

• Read the full news article
• Visit the Phenaris website
• Visit the OpenPHACTS website

The early drug discovery process requires the assembly, overlay and comparison of data from many sources, as well as the development of common standards and semantics. Until now, these data sources were very fragmented and it took researchers significant amounts of time and money to answer basic research questions. IMI’s Open PHACTS project addressed this gap by creating a platform that connects about a dozen different drug discovery databases, allowing researchers to rapidly find and access relevant data in different domains. ###Thanks to the Open PHACTS Foundation, which was set up during the project, the platform is free, open access and sustainable, and will continue to run beyond the lifetime of the project. In an interview with the IMI Programme Office, academic coordinator Gerhard Ecker of the University of Vienna and EFPIA representative Derek Marren of Eli Lilly, explain how the platform is already saving researchers significant amounts of time and money, thus speeding up the drug discovery process. ‘This is the first evidence of that technological approach to deliver anything of this magnitude,’ said Marren. ‘It wasn’t theoretical, it wasn’t on paper, it was real and usable. This is a significant achievement.’

• Read the full interview

IMI’s Open PHACTS project has proven hugely successful, and has delivered a platform that links up diverse and complementary drug discovery databases, allowing researchers to rapidly find and access relevant data. The IMI project has now finished, but the Open PHACTS Discovery Platform will live on thanks to the Open PHACTS Foundation, which was set up to build on the work begun in the project.### The foundation was set up a couple of years ago, and the formal handover from project to foundation took place at the project’s closing meeting in Vienna in late February. Meanwhile the foundation has already established itself as a leader in linking data, and is a partner in two Horizon 2020 projects.

In an article on the Open PHACTS Foundation website, the partners write: ‘Overall the development of the Open PHACTS Discovery Platform has been a remarkable success, demonstrating just what can be achieved when the private and public sectors work together. Several presenters highlighted one key factor in the project’s success: people. Although Open PHACTS began as somewhat of an “arranged marriage”, over the last five years the project has fostered and supported a community that has become much closer to a real family. We managed to bridge not only the cultural divides among different nationalities, but also the divide between scientists and engineers – which some would argue is much bigger!’

Presentations from the closing event, as well as photos, posters and background information, can be viewed via the event web page.

The Open PHACTS Foundation, the organisation set up to continue the work of the Open PHACTS project, now has its first academic member in the form of the University of Vienna. The University of Vienna is the managing entity of the project, and the team brings to both the project and the Foundation a wealth of expertise and experience in linked pharmacological data.### ‘I am very excited that the University of Vienna has become the first academic member of the Open PHACTs Foundation,’ said the Professor Gerhard Ecker of the University of Vienna. ‘This will allow us to participate in the further development of this unique data integration infrastructure and to become an integral part of its sustainability.’

Open PHACTS has delivered a platform that links up diverse and complementary drug discovery databases, allowing researchers to rapidly find and access relevant data. The Open PHACTS Foundation was set up to maintain and further develop the platform. The other members of the Foundation so far are the pharmaceutical companies GSK, Janssen and Lilly.

IMI knowledge management project Open PHACTS will hold a workshop entitled ‘Linking Life Science Data: Design to Implementation, and Beyond’ in Vienna, Austria, on 18-19 February 2016. The conference will include a variety of expert speakers and open discussions on linking data in the life sciences domain. The agenda includes:###

• an overview of what has been achieved so far in this domain, by the Open PHACTS project and by others;
• demonstrations of what can be done with existing linked data;
• how different sectors are moving towards linking more data;
• what concrete steps can be taken to address the challenges still to be met.

Places are limited – register your interest now.

The conference will also include a poster competition for early career researchers. The deadline for poster submissions is 11 January 2016. All successful applicants will be eligible for up to €400 of travel assistance, and the best poster will receive an award of €300.

The Open PHACTS Foundation is part of a new, €30 million project on animal-free chemical safety testing funded by the EU through Horizon 2020. Dubbed EU-Tox-Risk, the project has set itself the ambition of becoming ‘the flagship in Europe for animal-free chemical safety assessment’. The Open PHACTS Foundation was born out of the IMI project of the same name. ###Open PHACTS has delivered a platform that links up diverse drug discovery databases, allowing researchers to rapidly find and access relevant data. The Open PHACTS Foundation was set up to maintain and further develop the platform. In EU-Tox-Risk, the Open PHACTS Foundation will contribute its expertise with interoperable data.

IMI’s Open PHACTS project has been awarded first prize in the Linked Open Data Award category of the European Linked Data Contest.

The ELDC recognises Europe’s top linked data and semantic web achievements. Prizes are awarded for novel and innovative projects, products and industry implementations involving linked data. ###The ELDC also aims to build a directory of Europe’s top linked data and semantic web projects.

An international jury picked Open PHACTS as the winner, judging that the project excelled in all aspects of the competition’s assessment criteria, which cover innovation, networking, the use of open standards, technological maturity, the potential for use in multiple domains, and the level of comprehensibility for users and the public.

‘It is fantastic to see the successes of the Open PHACTS project recognised by the ELDC in this award,’ said project Managing Entity Gerhard Ecker of the University of Vienna. ’Over the course of this project we have been proud to deliver an unprecedented data integration infrastructure to support drug discovery research, thanks to the unparalleled range of expertise of our consortium members. We look forward to continuing to build on these achievements through the successor organisation to this project, the Open PHACTS Foundation.’

• Read the Open PHACTS press release
• Find out more about the awards 
• Read the Open PHACTS entry to the competition

IMI’s Open PHACTS project has now released the latest version of its application programming interface (API). This marks the completion of a large number of improvements and additions to the Open PHACTS API, such as a filter for search fields linked to tissues and a major update of the identity mapping service to allow a greater diversity of possible URLs for retrieving results.### In addition, improvements to the API’s SPARQL protocols allow more intelligent and precise search results. Important new data has been added in this version using adverse events from the Food and Drugs Agency Adverse Event Reporting System (FAERS) and interacting drugs from DrugBank. Furthermore, the Open PHACTS team has been updating the pharmacological data available with the latest ChEMBL release (ChEMBL 20). Along with some bug fixes and quality and consistency assurance, this makes version 1.5 the most versatile version of the Open PHACTS API since launch.

The IMI Open PHACTS project is organising a workshop for the users of their Open PHACTS Discovery Platform, and especially for the users of their workflow tools ‘Pipeline Pilot’ and ‘KNIME’ tools. The platform provides a convenient API (application programming interface) to query across multiple pharmacology datasets.###

The workshop will take place on 19 and 20 May at the VU University in Amsterdam, The Netherlands. This will be a small, informal workshop to introduce users to how the Open PHACTS API can help answer scientific questions. The workshop will explore how the Open PHACTS Discovery Platform can be used to develop solutions for scientific use cases. The Open PHACTS Pipeline Pilot components and KNIME nodes to access the Open PHACTS API will be demonstrated during the workshop in order to learn how different nodes and components can be linked together. The workshop will also look at how data of interest can be extracted from API results, and used as input for downstream nodes and components to generate meaningful results.

The IMI Open PHACTS project’s online data platform is an online; an open access platform that uses semantic web technology to allow scientists to easily access and process data from multiple sources to rapidly solve real-world drug discovery problems.

The workshop is free of charge. More information about the workshop

The IMI Open PHACTS project’s online data platform can help to speed up drug discovery in many ways, as demonstrated by the diverse examples set out in two recent papers published in PLoS ONE and Drug Discovery Today.### Open PHACTS has created an online, open access platform that uses semantic web technology to allow scientists to easily access and process data from multiple sources to rapidly solve real-world drug discovery problems. In these papers, the project partners explain how the platform can be used to deliver rapid results for a number of case studies based around common challenges in drug development. In all cases, manually checking multiple databases one by one would be very time consuming. ‘We hope to encourage the use of the [Open PHACTS] technology to a wide research audience to increase the productivity of both academic and industrial drug discovery projects,’ the authors write in PLoS ONE. Looking to the future, Open PHACTS is planning on integrating additional data, something that will enhance the types of queries that the platform can handle.

The Open PHACTS Foundation will participate in a new BigDataEurope project under Horizon 2020. The project aims to integrate existing big data infrastructures into an extendible stack of semantically interoperable, large-scale, multi-lingual data assets.###

The Open PHACTS Foundation is a not-for-profit membership organisation that maintains and develops the sustainable, open and interoperable information infrastructure established by IMI’s Open PHACTS project. This includes the Open PHACTS Discovery Platform, which provides users with the ability to query multiple integrated and publicly available data sources, and has seen remarkable growth in usage, surpassing 40 million recorded hits in November 2014.

Part of the Foundation’s role in this new project will involve running pilots on services combining data and functionalities from the Open PHACTS Discovery Platform with other project partners, such as the Food and Agriculture Organization of the United Nations. The Foundation will also act as a contact point with the life science R&D community, including industry members of the Foundation (currently GlaxoSmithKline, Janssen, Lilly and Roche), and organise workshops to identify requirements for data and component interoperability among the Open PHACTS API and Discovery Platform, and BigDataEurope's stack and related extensions and plugins.

The Open PHACTS project has taken further steps along the path to sustainability for its outputs by launching a new version of its drug discovery platform and ensuring the long-term financial and technical viability of the infrastructure.### Open PHACTS has developed a powerful cloud-based data platform that allows scientists to draw on diverse databases to answer all kinds of questions relating to drug development. The new version of the platform provides access to two additional data sets and also provides extra information on compounds. Elsewhere, the Open PHACTS Foundation has ensured the sustainability of the Open PHACTS Discovery Platform by funding secure hosting and organising the ongoing technical development of the infrastructure. Looking to the future, the project is now ready to tackle new scientific challenges and use cases by integrating commercial data sources and proprietary in-house data into its platform, adding more platform functionalities, and enhancing connections with workflow tools and engaging existing and upcoming IMI projects and initiatives.

IMI’s Open PHACTS project has announced the first three members of its successor organisation, the not-for-profit Open PHACTS Foundation.### GlaxoSmithKline, Janssen and Roche were the first members to commit to ensuring the sustainability of infrastructure developed by the Open PHACTS project – a freely-accessible drug discovery platform that integrates publicly-available data for applied life science research.

The Open PHACTS community includes academia, industry, application developers and semantic web experts and has delivered a powerful cloud-based data platform demonstrating the effectiveness of robust data integration in answering real scientific questions. Collaboration within existing and future consortia will engage the scientific community and involve relevant applied life science R&D.

• Read the project’s press release

IMI’s Open PHACTS project will hold its 6th Community Workshop in London on 26 June to introduce members of the academic community to the Open PHACTS Discovery Platform.### The Open PHACTS Discovery Platform is a freely-accessible infrastructure that integrates publicly-available data for applied life science research. The workshop will introduce attendees to the Open PHACTS Application Programming Interface (API) and showcase how it can be used to create new or enhance existing applications. Real life case studies will demonstrate how universities can use the Open PHACTS API and associated tools for teaching and research in drug discovery.

• Download the agenda
• Registration is free. To attend, write to london[AT]openphactsfoundation.org.

Open PHACTS recently launched its Target Dossier application (app) which was developed by project partners, the National Centre for Cancer Research (CNIO) in Spain.### This new app allows researchers the ability to work on a specific question or hypothesis using a single entry point to the Open PHACTS integrated data platform. The main goal for the new app is to provide easy access to integrated drug targets data to identify the most productive points for therapeutic intervention. It relies on the Open PHACTS integrated data platform and APIs [application programming interfaces] developed by the consortium. The app allows researchers to explore the interaction between pharmacological, interactive and pathway data through a simple ‘search and browse’ function. This gives researchers a totally new approach for testing their hypotheses using all three types of data in a combined search.  The answers are shown in dynamic graphs which offer a clear visual representation of the search results. Users can go on to manipulate the data in a virtual ‘playground’ area, meaning new hypotheses can be tested from re-working the search results. 

• Find out more about the app and watch a short video how it works on the Open PHACTS website

Professor Carole Goble of IMI’s Open PHACTS project and the University of Manchester has been named as a Commander of the Most Excellent Order of the British Empire (CBE) for her services to science in the UK’s New Year honours list.###

Professor Goble said she was ‘thrilled and honoured to receive this award as a recognition of e-science, and a recognition of the outstanding work of the team at Manchester carried out with many collaborators.’ 

Carole Goble is a proud co-investigator in IMI’s Open PHACTS project. Open PHACTS is a linked data platform and knowledge base of integrated pharmacological data to facilitate drug discovery. She is a full professor in the School of Computer Science in the University of Manchester, UK. She has an international reputation in the semantic web, e-science and distributed computing and has worked closely with life scientists for many years. Since 2001 she has  directed the myGrid project which has produced, amongst other resources,  the widely-used Taverna workflow management system, the BioCatalogue for Web Services and the SEEK data and model management system for Systems Biology.  She is a co-founder of the UK's Software Sustainability Institute and the deputy director of the UK node of ELIXIR.

In 2008 Carole was awarded the Microsoft Jim Gray e-Science award for outstanding contributions to e-Science.

IMI’s knowledge management project Open PHACTS has established the not-for-profit Open PHACTS Foundation to ensure the sustainability of the project’s work when the IMI funding period comes to an end in August 2014.###
The Open PHACTS Foundation will continue to support and develop the Open PHACTS infrastructure, and will act as a hub for relevant research. The scientific community fostered by the Open PHACTS project will be served by the Open PHACTS Foundation, which acts as a unique meeting place for the life sciences industry, pharmaceutical companies, academia, technology partners and small and medium-sized enterprises (SMEs).
More information on the Open PHACTS Foundation, including details of the benefits of membership and how to get involved, can be found on the Open PHACTS Foundation website.

Experts from across Europe and beyond gathered in London at the end of April for the public release of the Open PHACTS application programming interface (API) during the project’s Community Workshop.### The API allows researchers to access and query the vast amounts of data compiled by the Open PHACTS project, creating their own, customised apps to do so if needed. The workshop featured demonstrations of two apps based on the API. PharmaTrek provides researchers with an intuitive tool to explore the reams of target-protein interaction data that are publicly available. Meanwhile, the ChemBioNavigator app allows users to rapidly and easily compare the physicochemical properties of a molecule set. The API generated high levels of interest, and one attendee even incorporated use of the Open PHACTS API into an existing app during the workshop, proving that it is both easy to access and intuitive to use. The workshop also discussed safeguarding the sustainability of the Open PHACTS platform by setting up the not-for-profit Open PHACTS Foundation.
   •   The API is available online
   •   You will find the presentations and a workshop report here

The Open PHACTS project has developed a prototype of an iPhone app that provides rapid access to information on compounds of interest to drug developers.### A video demonstration of the app on YouTube shows how simply typing the name of a drug into the app delivers information on its chemical structure, function, pharmacology, and latest news relating to it. The app is not yet available as it is still in the early stages of development. Meanwhile, the project team points out that ‘the aim is to show that the next generation of drug discovery APIs [application programming interfaces] make app development so much easier’.

IMI knowledge management project Open PHACTS has produced a brochure setting out its work. The project, which is building a platform to integrate data from diverse sources, is attracting growing numbers of associate partners.### Associate partners receive regular updates on the latest developments from the project and are also able to present ideas and use cases to the Open PHACTS team. The project is also presented in a recent edition of Drug Discovery Today.

Scientists from IMI project Open PHACTS have put together a set of guidelines on nanopublications. ‘A nanopublication is the smallest unit of publishable information:### an assertion about anything that can be uniquely identified and attributed to its author,’ the guide reads. The guidelines set out the elements of a nanopublication and outline the developments since the ‘Anatomy of a Nanopublication’ paper. The guidelines explain the Open PHACTS approach to nanopublication and how this relates to real-world data. This first set of guidelines will guide the next stage of implementation within the Open PHACTS project where nanopublications will be integrated with other forms of data to provide a unique view across pharmacology-related data.

A prototype of a novel data mining tool developed by IMI project Open PHACTS has proven its worth, identifying relevant information in just seconds, while a traditional human search took days. Open PHACTS is using semantic web technology to develop a tool called the Open Pharmacological Space (OPS).### The OPS will allow scientists to analyse diverse databases and texts from both public and private sources in their hunt for new drugs and drug targets. A prototype platform is now ready, and when challenged with a simple query (to find compounds that block a given drug target), it delivered the information in a matter of seconds. In contrast, a traditional search took two scientists three working days each. ‘The OPS system not only correctly identified all compounds, it also found one additional drug, which was later on confirmed in a manual search,’ commented Open PHACTS academic coordinator, Gerhard Ecker of the University of Vienna. The team hopes to have a more advanced version ready for the full consortium to test by March.

Researchers from the Open PHACTS project have published a paper in Nature Genetics that proposes representing data and assertions in the form of nanopublications.### The nanopublication is the smallest unit of publication and is essentially a single assertion and its associated data and material. According to the team, using nanopublications will make it easier to place a value on data, support research by tapping into vast, interoperable reserves of information, and also make it easier for scientists and others to follow up individual assertions or develop hypotheses. Open PHACTS will test the nanopublication concept to create an Open Pharmacological Space (OPS). In the OPS, a layer of data and text extraction methods is placed over existing data of different kinds (e.g. rough data, processed datasets and literature). The methods allow close to real time updates of nanopublications from these databases and make them publicly available via the OPS, but do not interfere with local database management. ‘The Open PHACTS consortium thus creates an extra, computer readable layer that works across previously isolated datasets,’ explains the lead author of the paper, Barend Mons of Leiden University Medical Center and the Netherlands Bioinformatics Centre.