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Presentation: The DisGeNET Discovery Platform

BioHackathon 2015 Symposium, Nagasaki, Japan Núria Queralt-Rosinach (IMIM) View presentation

DNAdigest interviews Open PHACTS

On August 24, 2015, Posted by , In News, By ,,, , With No Comments

Open PHACTS Foundation CTO Nick Lynch recently spoke to DNAdigest about the benefits that Open PHACTS can offer researchers, as well as about the issues of limited data sharing and ethical data sharing in life sciences. You can read the full interview at DNAdigest’s website.

DisGeNET v3.0 RDF now available

DisGeNET has just announced their latest RDF release, including: More GDAs comprising 17 000 genes and more than 14 000 diseases as linked data in the Semantic Web New disease-phenotype annotation data from the Human Phenotype Ontology New linksets A new full metadata description of the dataset compliant with the…

Presentation: Topliss batchwise scheme reviewed in the era of Open Data

On August 20, 2015, Posted by , In Presentations, By ,,, , With No Comments

250th ACS National Meeting & Exposition, Boston, USA Gerhard Ecker (University of Vienna) View presentation

Presentation: Workflow-based data integration for drug discovery

250th ACS National Meeting & Exposition, Boston, USA Richard Kidd (Royal Society of Chemistry) View presentation

Conference: 250th ACS National Meeting & Exposition

250th ACS National Meeting & Exposition, Boston, USA Richard Kidd (Royal Society of Chemistry) gave a presentation: Workflow-based data integration for drug discovery Gerhard Ecker (University of Vienna) gave a presentation: Topliss batchwise scheme reviewed in the era of Open Data George Papadatos (EMBL-EBI) gave a presentation: SureChEMBL: An open patent chemistry…

Node.js library OPS.js now available

On July 27, 2015, Posted by , In News, By ,, , With No Comments

OPS.js is a JavaScript library you can use to fetch and parse responses from the Open PHACTS API. It is now available via the Node Package Manager which means that anyone using Node-based JavaScript applications can easily include it. It is also available as a single file download for standard…

Biological annotations in SureChEMBL

Biological patent annotations are now displayed on the SureChEMBL interface. In collaboration with Open PHACTS and SciBite, the EBI have implemented a mechanism to allow users to highlight biological entities (such as genes and diseases) within SureChEMBL patent documents. For more information see the SureChEMBL blog. This is a first step towards full integration…

Conference: Gordon Research Conference on Computer Aided Drug Design

Gordon Research Conference on Computer Aided Drug Design, West Dover, USA Barbara Zdrazil (University of Vienna) presented a poster: Assessing multi target SAR by using pharmacological and pathway data from the public domain

ChemBioNavigator Webinar

On July 17, 2015, Posted by , In News, By ,, , With No Comments

ChemBioNavigator is a web application that was specifically designed to visualise the small-molecule and pharmacological data integrated by Open PHACTS. Last week BioSolveIT hosted a webinar showing how ChemBioNavigator can be used to: discover new target-compound interactions identify multi-target as well as target-specific compound sets retrieve small-molecule data from a variety…

Project Meeting: Tech Team

On July 15, 2015, Posted by , In Project Meetings, By , With No Comments

Tech Team Meeting (Amsterdam, the Netherlands)

Publication: Medicinal chemistry in the era of big data

In the era of big data medicinal chemists are exposed to an enormous amount of bioactivity data. Numerous public data sources allow for querying across medium to large data sets mostly compiled from literature. However, the data available are still quite incomplete and of mixed quality. This mini review will…

Conference: Bioinformatics Open Source Conference 2015

On July 11, 2015, Posted by , In Conferences, By , , With No Comments

Bioinformatics Open Source Conference (BOSC) 2015, Dublin, Ireland Ian Dunlop (University of Manchester) gave a lightning presentation: Visualising Open PHACTS linked data with widgets

Presentation: Visualising Open PHACTS linked data with widgets

On July 11, 2015, Posted by , In Presentations, By ,,,, , With No Comments

Bioinformatics Open Source Conference (BOSC) 2015, Dublin, Ireland Ian Dunlop (University of Manchester) Watch presentation video | View presentation slides

Pipeline Pilot Component Collection 1.5 Released

On July 10, 2015, Posted by , In News, By ,, , With No Comments

We are pleased to announce the release of version 1.5 of the Open PHACTS component collection. There are no major changes to the components, but this version is needed to connect to version 1.5 of the Open PHACTS API, which has refreshed data and several other improvements. Version 1.5 of the Open PHACTS…

Open PHACTS API Milestone

On June 26, 2015, Posted by , In News, By ,, , With No Comments

The Open PHACTS Discovery Platform passed an exciting milestone this month of having served over 250,000,000 hits since it passed into production in 2013. Our API is averaging over 25 million hits a month, and is now at version 1.5. If you would like information about moving to API version 1.5, please get…

Publication: The Chemical Validation and Standardization Platform (CVSP): large-scale automated validation of chemical structure datasets

There are presently hundreds of online databases hosting millions of chemical compounds and associated data. As a result of the number of cheminformatics software tools that can be used to produce the data, subtle differences between the various cheminformatics platforms, as well as the naivety of the software users, there…

Open PHACTS now operational

On June 9, 2015, Posted by , In News, By ,, , With No Comments

The Open PHACTS API and other services (Explorer) have been restored early this morning. We have done some testing on this and things seem to be back to normal. Thank you for your patience during the outage. We are carrying out an analysis on the outage and will report back….

Open PHACTS temporarily unavailable

On June 8, 2015, Posted by , In News, By ,, , With No Comments

Update: Service has been restored as of 9 June 2015, with both the API and Explorer back online. Apologies for any inconvenience caused by this downtime. On Sunday 7 June our Open PHACTS & API hosting environment suffered a major hardware fault. As a result the Open PHACTS API and…

Project Meeting: ENSO & Technical Coordination

ENSO & Technical coordination meeting (London, UK)

Open PHACTS Newsletter 7

Contents: Open PHACTS Discovery Platform Updates Open PHACTS Pipeline Pilot Collection 1.4 Open PHACTS Explorer 2.0 View newsletter Sign up for the Open PHACTS Newsletter

First Big Data Europe workshop complete

As a funded partner of the Big Data Europe project, the Open PHACTS Foundation played a key role in the first BDE Community Workshop, which focussed on the health and demographic change societal challenge. A full report will be released soon; in the meantime Bryn Williams-Jones has written a preview of the…

Open PHACTS API version 1.5 is here!

On May 28, 2015, Posted by , In News, By ,,,, , With No Comments

We’ve been working hard to update and improve the Open PHACTS Discovery Platform, and are excited to report that version 1.5 of the Open PHACTS API is now live for public use. Try out the updated API now See the full release notes at our support portal This marks the…

Open PHACTS Drug Discovery Workflow Workshop

Drug Discovery Workflow Workshop: Using Open PHACTS (Amsterdam, the Netherlands)

Big Data Europe Workshop: Big Data in the Health Sector

As a funded partner of the Big Data Europe project, the Open PHACTS Foundation will be helping facilitate a workshop on big data in the health sector this 21 May, 2015. This workshop will provide a key opportunity for stakeholders in the health sector to influence the design of Big…

Open PHACTS – a story through publications

With all that Open PHACTS has achieved in the past few years, it can be hard to keep track of everything! Paul Groth has put together a post summarising the story of Open PHACTS to date, with links to publications demonstrating the various successes of the project: I was proud…

Presentation: The Open PHACTS Discovery Platform – Semantic Data Integration for Life Sciences

Swedish Linked Data Network Meet-up, Gothenburg, Sweden Ola Engkvist (AstraZeneca) Watch presentation video | View presentation slides

Conference: Swedish Linked Data Network Meet-up

Swedish Linked Data Network Meet-up, Gothenburg, Sweden Ola Engkvist (AstraZeneca) gave a presentation: The Open PHACTS Discovery Platform – Semantic Data Integration for Life Sciences

Poster: Biological Interactions Types for WikiPathways

HARMONY 2015, Wittenberg, Germany View poster

Conference: HARMONY 2015

HARMONY 2015, Wittenberg, Germany Ryan Miller (Maastricht University) presented a poster: Biological Interactions Types for WikiPathways