Open PHACTS Foundation

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Poster: Open PHACTS Use Cases

On September 3, 2012, Posted by , In Posters, By ,,,,,,,,,, , With Comments Off on Poster: Open PHACTS Use Cases

EFMC-ISMC 2012, 22nd International Symposium on Medicinal Chemistry, Berlin, Germany View poster

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Publication: Open data for drug discovery: learning from the biological community

On September 1, 2012, Posted by , In Publications, By ,,, , With Comments Off on Publication: Open data for drug discovery: learning from the biological community

Drug discovery is undergoing a transformational change. Early-stage target identification, lead generation and optimization work is now undertaken in a much more diverse set of organizations, involving biotechnology companies and academia as well as large pharmaceutical companies. Anne Hersey, Stefan Senger, John Overington Full publication: Future Medicinal Chemistry, Volume 4,…

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Publication: Druggable and biopharmable genome annotation pipeline development

On September 1, 2012, Posted by , In Publications, By ,, , With Comments Off on Publication: Druggable and biopharmable genome annotation pipeline development

The identification of proteins which could be potential targets for new pharmaceutical products is invaluable for the continued improvement people’s quality of life and expansion of available treatment options. In order to aid the discovery of new drug targets, predictions of every human gene likely to be exploitable by compounds…

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Poster: Open PHACTS Architecture: Building the extensible platform

On August 30, 2012, Posted by , In Posters, By , , With Comments Off on Poster: Open PHACTS Architecture: Building the extensible platform

19th EuroQSAR, Knowledge Enabled Ligand Design, Vienna, Austria View poster

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Poster: Open PHACTS Scientific Competency Questions: Guiding the technical development

On August 30, 2012, Posted by , In Posters, By , , With Comments Off on Poster: Open PHACTS Scientific Competency Questions: Guiding the technical development

19th EuroQSAR, Knowledge Enabled Ligand Design, Vienna, Austria View poster

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Poster: Open PHACTS Examplars: Using the Open PHACTS Platform API

On August 30, 2012, Posted by , In Posters, By ,,,,, , With Comments Off on Poster: Open PHACTS Examplars: Using the Open PHACTS Platform API

19th EuroQSAR, Knowledge Enabled Ligand Design, Vienna, Austria View poster

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Publication: Molecular Informatics Special Issue: Open Innovation in Drug Discovery

On August 15, 2012, Posted by , In Publications, By ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, , With Comments Off on Publication: Molecular Informatics Special Issue: Open Innovation in Drug Discovery

Several publications about Open PHACTS were included in this Special Issue of Molecular Informatics. Open Innovation in Drug Discovery. Gerhard F. Ecker, Bryn Williams-Jones; Molecular Informatics 31: 519–520 Taking Open Innovation to the Molecular Level – Strengths and Limitations. Barbara Zdrazil, Niklas Blomberg, Gerhard F. Ecker; Molecular Informatics 31: 528–535 PharmaTrek: A Semantic Web Explorer for Open Innovation in Multitarget…

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Publication: The Pharmacology Workspace: A Platform for Drug Discovery

On July 25, 2012, Posted by , In Publications, By ,,,,,,,,,,,,,,,,,, , With Comments Off on Publication: The Pharmacology Workspace: A Platform for Drug Discovery

We present the Open PHACTS linked data platform that is being developed to address a set of example drug discovery research questions and which supports several drug discovery applications. The platform retrieves data from many complementary, but overlapping, data sources to present an integrated view of the data. The platform…

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Publication: Microattribution and nanopublication as means to incentivize the placement of human genome variation data into the public domain

On July 23, 2012, Posted by , In Publications, By ,,,,,,,,,, , With Comments Off on Publication: Microattribution and nanopublication as means to incentivize the placement of human genome variation data into the public domain

The advances in bioinformatics required to annotate human genomic variants and to place them in public data repositories have not kept pace with their discovery. Moreover, a law of diminishing returns has begun to operate both in terms of data publication and submission. Although the continued deposition of such data…

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Publication: Solving Bottlenecks in Data Sharing in the Life Sciences

On June 18, 2012, Posted by , In Publications, By ,,,,,,,,,, , With Comments Off on Publication: Solving Bottlenecks in Data Sharing in the Life Sciences

The joint Open PHACTS/GEN2PHEN workshop on “Solving Bottlenecks in Data Sharing in the Life Sciences” was held in Volendam, the Netherlands, on September 19 and 20, 2011, and was attended by representatives from academia, industry, publishing, and funding agencies. The aim of the workshop was to explore the issues that…

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Publication: Open PHACTS: Semantic interoperability for drug discovery

On June 6, 2012, Posted by , In Publications, By ,,,,,,,,,,, , With Comments Off on Publication: Open PHACTS: Semantic interoperability for drug discovery

Open PHACTS is a public–private partnership between academia, publishers, small and medium sized enterprises and pharmaceutical companies. The goal of the project is to deliver and sustain an ‘open pharmacological space’ using and enhancing state-of-the-art semantic web standards and technologies. It is focused on practical and robust applications to solve…

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Presentation: The Open Pharmacological Concepts Triple Store

On May 30, 2012, Posted by , In Presentations, By ,,,, , With Comments Off on Presentation: The Open Pharmacological Concepts Triple Store

IMI Stakeholder Forum 2012, Brussels, Belgium Bryn Williams-Jones (Connected Discovery), Gerhard Ecker (University of Vienna) View presentation

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Publication: Towards a gold standard: regarding quality in public domain chemistry databases and approaches to improving the situation

On March 8, 2012, Posted by , In Publications, By ,,, , With Comments Off on Publication: Towards a gold standard: regarding quality in public domain chemistry databases and approaches to improving the situation

In recent years there has been a dramatic increase in the number of freely accessible online databases serving the chemistry community. The internet provides chemistry data that can be used for data-mining, for computer models, and integration into systems to aid drug discovery. There is however a responsibility to ensure…

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Presentation: Open PHACTS: an introduction and explanation

On March 1, 2012, Posted by , In Presentations, With Comments Off on Presentation: Open PHACTS: an introduction and explanation

Information on the Open PHACTS Project View presentation

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Publication: The Innovative Medicines Initiative: A European Response to the Innovation Challenge

On February 8, 2012, Posted by , In Publications, By , , With Comments Off on Publication: The Innovative Medicines Initiative: A European Response to the Innovation Challenge

The Innovative Medicines Initiative (IMI) was launched in 2008 as a large-scale public–private partnership between the European Commission and the European Federation of Pharmaceutical Industries and Associations (EFPIA). With a total budget of €2 billion, the IMI aims to boost the development of new medicines across Europe by implementing new…

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Publication: It’s all about the data: an exclusive interview with Dr. Antony J. Williams

On January 30, 2012, Posted by , In Publications, By ,, , With Comments Off on Publication: It’s all about the data: an exclusive interview with Dr. Antony J. Williams

Thousands of professionals in the life sciences and other industries rely on external chemical data in their decision matrices. Just how reliable is publicly available data? Don Alexander of Carlyle & Conlan interviewed Dr. Antony J. Williams for perspective on this issue. Antony J. Williams Full publication: Life Science Trends…

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Publication: Toward interoperable bioscience data

On January 27, 2012, Posted by , In Publications, By ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, , With Comments Off on Publication: Toward interoperable bioscience data

To make full use of research data, the bioscience community needs to adopt technologies and reward mechanisms that support interoperability and promote the growth of an open ‘data commoning’ culture. Here we describe the prerequisites for data commoning and present an established and growing ecosystem of solutions using the shared…

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Publication: Of possible cheminformatics futures

On December 30, 2011, Posted by , In Publications, By ,,, , With Comments Off on Publication: Of possible cheminformatics futures

For over a decade, cheminformatics has contributed to a wide array of scientific tasks from analytical chemistry and biochemistry to pharmacology and drug discovery; and although its contributions to decision making are recognized, the challenge is how it would contribute to faster development of novel, better products. Here we address…

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Publication: Systems chemical biology and the Semantic Web: what they mean for the future of drug discovery research

On December 29, 2011, Posted by , In Publications, By ,,,,,, , With Comments Off on Publication: Systems chemical biology and the Semantic Web: what they mean for the future of drug discovery research

Systems chemical biology, the integration of chemistry, biology and computation to generate understanding about the way small molecules affect biological systems as a whole, as well as related fields such as chemogenomics, are central to emerging new paradigms of drug discovery such as drug repurposing and personalized medicine. Recent Semantic…

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Publication: Representing Text Mining Results for Structured Pharmacological Queries

On October 23, 2011, Posted by , In Publications, By ,,,, , With Comments Off on Publication: Representing Text Mining Results for Structured Pharmacological Queries

Several approaches integrating life science data using Semantic Web technologies have been described in the literature. However, these approaches have largely ignored the vast amount of content only available within the scientific literature. In this article, we present an RDF schema for text mining results that enables queries in SPARQL…

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Presentation: Integrating and curating internet based chemistry resources to serve life scientists

On June 15, 2011, Posted by , In Presentations, By ,,, , With Comments Off on Presentation: Integrating and curating internet based chemistry resources to serve life scientists

PharmSciFair 2011, Prague, Czech Republic Antony Williams (Royal Society of Chemistry) View presentation

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Publication: Knowledge Driven Drug Discovery goes Semantic

On April 18, 2011, Posted by , In Publications, By ,,,,,, , With Comments Off on Publication: Knowledge Driven Drug Discovery goes Semantic

While the availability of freely accessible information sources relevant to medicinal chemistry and drug discovery has grown over the past few years, the knowledge management challenges of this data have also grown enormously: how to get consistent answers, how to manage different interfaces, how to judge data quality, and how…

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Publication: The Value of Data

On March 29, 2011, Posted by , In Publications, By ,,,,,,,,,,,,,,,, , With Comments Off on Publication: The Value of Data

Data citation and the derivation of semantic constructs directly from datasets have now both found their place in scientific communication. The social challenge facing us is to maintain the value of traditional narrative publications and their relationship to the datasets they report upon while at the same time developing appropriate…

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