The ChEMBL-og

The Open PHACTS Discovery Platform is a freely accessible infrastructure that semantically integrates publicly available data for applied life science R&D. The Platform provides a powerful Application Programming Interface (API) which allows application builders and researchers to query the integrated data using existing applications, to build new applications and to access the API using workflows tools (e.g. KNIME and Pipeline Pilot). Examples of such applications, which illustrate what can be achieved, include the Open PHACTS Explorer, ChemBioNavigator, and PharmaTrek. The Open PHACTS Community Workshop in London on Thursday 26th June aims to introduce members of the academic community to the Open PHACTS Discovery Platform. The workshop will be of interest to: ·         Researchers who would benefit from directly querying the Open PHACTS API using scripting languages or by developing applications to consume the data. ·...

Open PHACTS has released a collection of Pipeline Pilot and KNIME workflow components which integrate with the Open PHACTS API. Integration with these well-established graphical workflow tools allows the pharmacological and physicochemical data within the Open PHACTS Discovery Platform to be easily accessed and consumed. Open PHACTS ( O pen PHA rmacological C oncepts T riple S tore) is a project of the Innovative Medicines Initiative ( IMI ) and has seen SMEs, academia and the pharmaceutical industry work together to create a freely-available online platform to multiple, integrated sources of publicly available pharmacological data. The project ends in 2014 and the project’s not-for-profit successor organisation, the Open PHACTS Foundation, will continue to support and develop the infrastructure created. The Open PHACTS Discovery Platform has been designed to answer various critical pharmacology questions, many of which can be addressed using the newly released Pipeline Pi...

We would like to draw attention to readers of The ChEMBL-og to an excellent new paper in the Journal of Cheminformatics , describing the work of Egon Willighagen and co-authors in building the first published, publicly available version of ChEMBL data in RDF form (ChEMBL RDF). The paper also provides details on a number of linked data based applications built on top of an RDF data model, demonstrating the benefits of the data transformation. More details about the paper are provided here and the link to the paper is here . %T The ChEMBL database as linked open data %A E.L. Willighagen %A A. Waagmeester %A O. Spjuth %A P. Ansell %A A.J. Williams %A V. Tkachenko %A J. Hastings %A B. Chen %A D. J Wild %J J. Cheminf. %D 2013 %V 5 %O doi:10.1186/1758-2946-5-23 The ChEMBL group have been funded by the IMI  OpenPhacts project to build and deploy an RDF version of ChEMBL (which we are currently calling ChEMBL ChEMBL RDF, sorry for the confusion!). With changes in content and cura...

Don’t we just love the fact that these days so much bioactivity data is freely available at no cost (to the end user)? I  think we do. The more, the better. So, what would your answer be if someone asked you if you consider it to be a good idea if they would deposit some of their unpublished bioactivity data in ChEMBL? My guess is that you would be all in favour of this idea. 'Go for it', you might even say. On the other hand, if the same person would ask you what you think of the idea to deposit some of ‘your bioactivity data’ in ChEMBL the situation might be completely different.   First and foremost you might respond that there is no such bioactivity data that you could share. Well let’s see about that later. What other barriers are there? If we cut to the chase then there is one consideration that (at least in my experience) comes up regularly and this is the question:  'What’s in it for me?' Did you ask yourself the same question? If you di...

Open PHACTS is a 3-year EU-funded ( IMI ) project, targeted to enhance and accelerate data intensive drug research for academic and industry partners. It comprises the development of an innovative open source, open standard and open access platform (application), the Open Pharmacological Space (OPS). The project is driven by the Open PHACTS consortium, composed of 14 European core academic and SME partners in close cooperation with 8 major industry partners from pharmacological areas. The realization of the OPS platform and its placement in the targeted pharmaceutical area significantly depends on a proper strategic licensing plan considering all licensing and IP issues of the incorporated sources (data, software components). Main purpose and primary role of required consultancy: The primary role of the consultant is to contribute in depth knowledge with respect to licensing models and IP rights to the Open PHACTS project. Thus, consultancy services are targeted to ensure co...

Just a quick note to say that we have joined the Open PHACTS Project, and as our local contribution (there are multiple strands to the EBI's involvement) we will be enhancing rdf/SPARQL access to ChEMBL, and also developing some improved semantic indexing of some of the assays and targets. Details of the project itself are on the Open PHACTS website  http://www.openphacts.org/ .