News


Webinar: Workflow tools for Life Science Research: Where next?

Our Science and Open PHACTS webinar series returns this coming Monday, 24 April with a session on the future of drug discovery workflow tools.

Webinar: Workflow tools for Life Science Research: Where Next?
Date: Monday, 24 April, 2017
Time: 15:00 BST (16:00 CEST)
Registration: Free – register now online

Workflow tools have become tremendously useful to scientific researchers for accessing, processing and analysing data. They have enabled the creation of rapid and robust workflows that can support a range of data analytics and informatics, and provide access to leading components for further processing.

How will workflows continue to meet the challenge of increasing volumes of data? How can we support interoperability among different workflow components? Join us for expert presentations on Common Workflow Language (CWL), using KNIME and Open PHACTS to support key life science business questions, and a panel discussion with leading pharmaceutical researchers on where workflows should go next.

This webinar is the latest in our series of monthly webinars about Science and Open PHACTS – keep an eye on our news page and Twitter for more. If you’ve missed any of our previous webinars, you can find full recordings on our YouTube channel, and slides on SlideShare.


Open PHACTS and Big Data Europe: Second community workshop

Last week we held the second Big Data Europe community workshop for societal challenge 1 (Health, Demographic Change and Wellbeing) in Brussels, Belgium.

After demonstrating the progress that has been made translating the Open PHACTS Discovery Platform to Big Data Europe’s architecture, we engaged in a lively roundtable discussion about how the Platform might be extended to tackle new challenges in new domains.

You can read more about the workshop outcomes on the Big Data Europe website – and keep an eye out for details of our follow-up Hangout discussion, which will be held in January 2017.

The Open PHACTS Foundation is a funded partner of Big Data Europe, undertaking foundational work for an open European big data platform.


Webinar: Open source software components for chemistry standardisation

Our Science and Open PHACTS webinar series returns on 24 October, following our summer break. This month we will discuss the key chemistry software components and datasets that underpin the Open PHACTS Discovery Platform, which are now available as open source software components.

Webinar: Science and Open PHACTS: Open source software components for chemistry standardisation
Date: Monday, 24 October, 2016
Time: 15:00 BST
Registration: Free – register now online

Join Antony Williams (EPA, previously at RSC and ChemSpider) and Valery Tkachenko (RSC, previously ChemSpider) as they discuss the software components developed for Open PHACTS, including the Chemical Validation and Standardization Platform, and a proof-of-concept implementation of a platform to address structural standardisation issues. We will also review the Open PHACTS software components that have been made available to the wider community, and possible next steps for supporting and developing them further.

This webinar is the latest in our series of monthly webinars about Science and Open PHACTS. If you’ve missed any of our previous webinars, you can find full recordings on our YouTube channel, and slides on SlideShare.


Datathon: Loading data into Open PHACTS

Interested in running an Open PHACTS environment for your own company or institution? Or in improving the linked open data in the Open PHACTS Discovery Platform?

Introducing Open PHACTS Datathons, a new series of free webinars that will cover everything you need to know about updating or adding to the structured data the Open PHACTS Discovery Platform is built on. Sign up for our first Datathon today:

Datathon #1: Loading data into Open PHACTS
Date: 28 July, 2016
Time: 15:00 BST
Registration: Free – register now

This Datathon will focus on updating existing sources in Open PHACTS with no change in source schema, for example ChEMBL and UniProt. We will be sharing the knowledge and experience of Open PHACTS to help you understand how to load data like these into Open PHACTS for a variety of use cases.

By the end of this Datathon you will understand how to load similar data sources into your own Open PHACTS environment, or indeed into the Open PHACTS Discovery Platform itself. We look forward to seeing you there!


Webinar: Maximising impact for pharmaceutical applications

Next up in our Science and Open PHACTS webinar series, David Wild (Data2Discovery) will demonstrate the work Data2Discovery has been doing to maximise the impact of Open PHACTS for pharmaceutical applications, with systems like their application for phenotypic screening analysis, P3. Register your place now:

Webinar: Integrating data with Open PHACTS: Private and Public
Date: Monday, 27 June, 2016
Time: 15:00 BST
Registration: Free – register now online

Open PHACTS provides a powerful resource for the exploration of biomedical data. However, only when this data is combined with companies’ internal data sources can the power of this dataset be fully leveraged. Data2Discovery, Inc. is creating systems that map proprietary and other data sources into semantic linked form that can be combined with Open PHACTS data in a smart data lake. Combining these data sources will allow researchers across pharmaceutical companies to quickly and easily leverage the power of integrated public and proprietary datasets to make new discoveries.

This webinar is the fourth in our series of monthly webinars about Science and Open PHACTS – keep an eye on our news page and Twitter for more. If you’ve missed any of our previous webinars, you can find full recordings on our YouTube channel, and slides on SlideShare.


Webinar: Integrating data with Open PHACTS: Private and Public

Since completion of the Open PHACTS project, we’ve opened up our regular discussions about using Open PHACTS for science to the whole community, with a series of free monthly webinars. Our next webinar will be about how integrating private data and public Wikidata with Open PHACTS opens up new business question opportunities.

Register now for our webinar on integrating data with Open PHACTS

The ability to search securely across combined public and private data is valuable throughout the drug discovery process, especially in target validation lead identification. This month Jean-Marc Neefs (Janssen) and Luca Bartek (University of Strathclyde) will demonstrate how integrating data with the Open PHACTS Discovery Platform helps meet business needs to query combined public and private datasets, as well as supporting further linked data analysis through resources such as Wikidata.

Date: Monday, 23 May, 2016
Time: 15:00 BST
Registration: Free – register now online

This webinar is the third in our series of monthly webinars about Science and Open PHACTS. If you’ve missed any of our previous webinars, you can find full recordings on our YouTube channel, and slides on SlideShare.


Webinar: Target Validation Protocols

Now that the Open PHACTS project is complete, we’re opening our regular discussions about using Open PHACTS for science up to the whole community, with a series of free monthly webinars. Our next webinar will be about how the Open PHACTS Discovery Platform can be used for in silico target validation.

Register now for our Target Validation Protocols webinar

This month Edgar Jacoby, Senior Principal Scientist in Molecular Informatics at Janssen, will be talking about “knowing the knowns” of phenotypic screening. His talk will cover practical ways that the Open PHACTS Discovery Platform can facilitate seamless integration for phenotypic screening data.

Date: Monday, 25 April, 2016
Time: 15:00 BST
Registration: Free – register now online

You can also sign up for our newsletter to make sure you don’t miss future webinars in this series – and if you missed last month’s webinar on programmatic access to SureChEMBL patent data, you can find the slides on Slideshare and watch the full recording on YouTube.


Open PHACTS Pipeline Pilot Component Collection 2.0

BIOVIA have just released the latest Pipeline Pilot component collection for Open PHACTS:

Download Open PHACTS Component Collection 2.0

This collection connects to the latest version of the Open PHACTS API, version 2.0, and enables protocol developers and users to access the Open PHACTS Discovery Platform through easy-to-use Pipeline Pilot components.

These components provide similar functionality to the API itself, allowing you to more easily integrate Open PHACTS queries into your research workflows.

As a reminder, we will soon be decommissioning version 1.4 of the Open PHACTS API. If you would like help implementing API version 2.0 into your research workflows, please let us know.


Webinar: SureChEMBL Patent Annotations

Now that the Open PHACTS project is complete, we’re opening our regular discussions about using Open PHACTS for science up to the whole community, with a series of free monthly webinars. Our first webinar will be about SureChEMBL Patent Annotations, on Monday, 21 March at 15:00 GMT.

Register now for our SureChEMBL Patent Annotations webinar

This month’s focus is on patent annotations from the SureChEMBL database. Much of the knowledge hidden in patents, including compounds, scaffolds, reaction schemes, biological targets, diseases and bioactivities, is never published elsewhere. Programmatic access to this knowledge could be of exceptional value to the drug discovery and broader life science communities.

George Papadatos (EMBL-EBI) will give an overview of the SureChEMBL data integration with the Open PHACTS Discovery Platform, focussing on practical details of use cases and business questions that can be answered with the combination of the Open PHACTS API and workflow tools.

Date: 21 March, 2016
Time: 15:00 GMT
Registration: Free – register now online

Join us to learn more about the latest updates to the Open PHACTS Discovery Platform, and how they can benefit you and your research. You can also sign up for our newsletter to make sure you don’t miss future webinars in this series.


Completion of the Open PHACTS project

On 18–19 February, 2016, we celebrated the successful completion of the Open PHACTS project with a conference on linking life science data in Vienna, Austria.

79 attendees from a broad cross-section of backgrounds gathered to discuss what lessons have been learned from the success of Open PHACTS, and how the Open PHACTS Foundation will take the project’s outcomes forward.

Conference photos © Samuel Erik Colombo | Optical Engineers

Looking back there have certainly been some challenges along the way – there were several interesting anecdotes shared at the closing conference. But 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!

The Open PHACTS Foundation looks forward to continuing to work with the people who made this project such a success, and with new partners who can contribute novel perspectives and ideas on the future of linked data.

Please contact us for more information about how you can get involved with the next phase of Open PHACTS – or head over to our forums to join in discussions with other members of the Open PHACTS community.


New Foundation Member: University of Vienna

A long-time partner of the Open PHACTS project, the University of Vienna has committed to supporting the Open PHACTS Foundation as our first academic member. Professor Gerhard Ecker and his colleagues bring a wealth of expertise and experience in linked pharmacological data to the Foundation, and we are excited about working together to continue building on the achievements of Open PHACTS.

“I am very excited that the University of Vienna has become the first academic member of the Open PHACTS Foundation. 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.”
–– Professor Gerhard Ecker, University of Vienna

We have several membership options available to industry and academia – contact us today to discuss how you can benefit from joining the Open PHACTS Foundation.


Open PHACTS API 2.0 is here

We’re excited to announce the official release of version 2.0 of the Open PHACTS API, along with major updates to the linked data in the Open PHACTS Discovery Platform.

Try out API version 2.0 now

Highlights include:

  • Complete refresh of chemistry data sets, including ChEMBL 20
  • Reload and refresh of Identity Mapping Service and linksets
  • New Virtual Machine version of Open PHACTS (ask us for details!)
  • Updates to facilitate integration with KNIME and Pipeline Pilot
  • New data from Uniprot, WikiPathways, and OPDDR phenotypic data

For full details please take a look at the release notes on our support portal.

Decommissioning API 1.4

If you are still working from API version 1.4, please note that we will be discontinuing support for this version in February 2016. If you’d like help updating to version 2.0, let us know and we’ll be happy to assist.


Linking Life Science Data: Final speakers and agenda

There are just three weeks to go until our conference, Linking Life Science Data: From Design to Implementation, and Beyond. If you haven’t yet registered, attendance is free and there are still places available:

Register now

The conference will include a variety of expert speakers and open discussions on linking data in the life sciences domain. The full agenda is now finalised and we look forward to seeing you there.

We are also pleased to present the submissions for our poster competition, which will be held at the conference on the evening of 18 February. See below for the list of entrants and poster abstracts.

Continue reading


Linking Life Science Data: Preliminary agenda

We are pleased to present the preliminary agenda for our upcoming conference, Linking Life Science Data: Design to Implementation, and Beyond.

View agenda »

Updates will be announced over the coming weeks as the agenda and speakers are finalised; register your interest now to keep up to date with the latest developments.

As a reminder, the conference will also include a poster competition for early-career researchers, with a first prize of €300 and travel costs reimbursed up to €400. Poster submissions will be accepted until 11 January, 2016.


Call for posters from early career researchers in life science

The Open PHACTS Consortium and Open PHACTS Foundation are pleased to announce a poster competition to be held at our upcoming conference on linking life science data, on 18–19 February 2016.

The competition will be open to early career researchers (from Masters students to post-doctoral fellows), with a prize of €300 for the poster best demonstrating the actual or potential benefits to life science research of using the linked data in the Open PHACTS Discovery Platform. Travel costs for those presenting posters will also be reimbursed up to a maximum of €400.

The deadline for abstract submissions is 11 January, 2016. For full details of how to apply, please see this document.


Event Announcement: Linking Life Science Data: Design to Implementation, and Beyond

Open PHACTS will be hosting a two-day conference in Vienna, Austria on the 18–19 February, 2016.

Places are limited – register your interest now

The conference will include a variety of expert speakers and open discussions on linking data in the life sciences domain.

Day 1 (Thursday, 18 February) will focus on what has been achieved so far in this domain, by the Open PHACTS project and by others. Discussions will include an overview of how the domain has evolved, demonstrations of what can be done with existing linked data, and a poster competition where you can show off your own uses of linked life science data.

Day 2 (Friday, 19 February) will focus on the future of linking life science data. Discussions will consider how various sectors of this domain, including large industries, are moving towards linking more data; what challenges still need to be met; and what concrete steps we can take to keep moving forward.

This conference will be free to attend. To register your interest, please use the form below:

Continue reading


BigDataEurope webinar: Health, Demographic Change and Wellbeing

On 25 November, 14:00–15:00 CET, BigDataEurope will host a webinar update on the societal challenge of Health, Demographic Change and Wellbeing.

If you’re interested in learning more about BigDataEurope and its goals, register now for this free webinar.

The webinar will include a brief overview of the project by Open PHACTS Foundation CEO Bryn Williams-Jones, followed by an update on the technical status of the BDE infrastructure, information about the first pilot in this domain, and the evaluation approach for the project.

You can find more information on the BigDataEurope website.


Press Release: Open PHACTS partners in EU-ToxRisk project

EU-ToxRisk: An Integrated European ‘Flagship’ Program Driving Mechanism-based Toxicity Testing and Risk Assessment for the 21st Century

(PDF) In a large (€30 m) H2020-supported collaborative project, academia joins forces with small and medium-sized enterprises (SMEs), large industry, contract research organisations (CROs) and regulatory bodies to achieve a paradigm shift in toxicology towards a more efficient and animal-free chemical safety assessment.

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Coming soon: API 2.0

Our planned maintenance on 16 October is part of our preparation for the release of version 2.0 of the Open PHACTS API later this month. This will be accompanied by a major data refresh, with all-new sources added to Open PHACTS.

We will then be decommissioning version 1.4 of the API by the end of November 2015. If you haven’t yet upgraded to version 1.5 of the API, and have any questions or concerns about doing so, please let us know.

You can also let us know your thoughts about the API in our survey.


Open PHACTS API questionnaire

We’ve put together a short questionnaire for API users. We’d appreciate it if you could take a few minutes of your time to fill it in:

Open PHACTS API Questionnaire

In particular we would very much like to hear your thoughts on using the API, and your ideas about the future. If you have any other questions or comments you can email us any time.


Planned maintenance: Friday 16 October 2015

Open PHACTS service interruptions from 18:00 – 22:00 CEST, Friday, 16 October 2015

We are planning a service break for maintenance to replace failed drives, and drives marked as close to failure margin, and upgrade the disk topology for better fault tolerance. Not all of this can be done while system is online.

The system will be unstable starting around 18:00 Central European Summer Time on Friday, 16 October, and subsequently COMPLETELY UNAVAILABLE for a period we estimate to not exceed 30 minutes some time between 18:00 and 20:00.

Once the systems are back online, the hosted services may be available, but instability is to be expected for some time further.

We expect all Open PHACTS services hosted by us to operate at nominal capacity no later than 22:00 CEST.

Please let us know if you have any questions, or if this service maintenance may affect a demonstration or key work event.


Press Release: Open PHACTS wins Linked Open Data Award in inaugural European Linked Data Contest

(PDF) Vienna, Austria – The Open PHACTS consortium is proud to have been awarded first prize in the Linked Open Data Award category of the European Linked Data Contest (ELDC).

The ELDC has been established to recognise Europe’s crème de la crème of linked data and semantic web achievements. Prizes are awarded to stories, products, projects or persons presenting novel and innovative projects, products and industry implementations involving linked data. The ELDC also aims to build a directory of the best European projects in the domains of linked data and the semantic web.

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DisGeNET v3.0 RDF now available

DisGeNET has just announced their latest RDF release, including:

For more information see the release notes and DisGeNET’s RDF website.

The DisGeNET-RDF distribution for Open PHACTS, with OMIM dataset included, will be available at the end of September.