Linking Life Science Data: Design to Implementation, and Beyond

On February 19, 2016, Posted by , In Community Workshops,Conferences,Project Meetings, By ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, , With Comments Off on Linking Life Science Data: Design to Implementation, and Beyond

Open PHACTS project closing conference (Vienna, Austria)

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Poster: Semantic-Web Access to Patent Annotations

On December 7, 2015, Posted by , In Posters, By ,,,,,,,,,,, , With Comments Off on Poster: Semantic-Web Access to Patent Annotations

SWAT4LS International Conference 2015, Cambridge, UK View poster

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Publication: Scientific Lenses to Support Multiple Views over Linked Chemistry Data

On October 19, 2014, Posted by , In Publications, By ,,,,,,,,,,,,,,,,,,,,,,,,, , With Comments Off on Publication: Scientific Lenses to Support Multiple Views over Linked Chemistry Data

When are two entries about a small molecule in different datasets the same? If they have the same drug name, chemical structure, or some other criteria? The choice depends upon the application to which the data will be put. However, existing Linked Data approaches provide a single global view over…

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6th Open PHACTS Community Workshop

On June 26, 2014, Posted by , In Community Workshops, By ,,,,,,,,,,,,,,,,,,,,,,,,,, , With Comments Off on 6th Open PHACTS Community Workshop

Open PHACTS for Academia: Using the Open PHACTS Discovery Platform in undergraduate and postgraduate teaching (London, UK)

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Conference: Bio-IT World Conference & Expo 2014

On April 29, 2014, Posted by , In Conferences, By ,,, , With Comments Off on Conference: Bio-IT World Conference & Expo 2014

Bio-IT World Conference & Expo 2014, Boston, USA Lee Harland (Connected Discovery) gave a presentation: Open PHACTS: Practical Semantics For Drug Discovery

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Presentation: Open PHACTS: Practical Semantics For Drug Discovery

On April 29, 2014, Posted by , In Presentations, By ,,, , With Comments Off on Presentation: Open PHACTS: Practical Semantics For Drug Discovery

Bio-IT World Conference & Expo 2014, Boston, USA Lee Harland (Connected Discovery) View presentation

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Publication: Applying Linked Data Approaches to Pharmacology: Architectural Decisions and Implementation

On January 21, 2014, Posted by , In News,Publications, By ,,,,,,,,,,,,,, , With Comments Off on Publication: Applying Linked Data Approaches to Pharmacology: Architectural Decisions and Implementation

The discovery of new medicines requires pharmacologists to interact with a number of information sources ranging from tabular data to scientific papers, and other specialized formats. In this application report, we describe a linked data platform for integrating multiple pharmacology datasets that form the basis for several drug discovery applications….

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Publication: Nanopublication Guidelines

On December 15, 2013, Posted by , In Publications, By ,,,,,,,,,,,,,,,,,,,,,,,,, , With Comments Off on Publication: Nanopublication Guidelines

This document describes the structure of nanopublications and offers guidelines in their composition, implementation and use. It was produced by members of the Concept Web Alliance (CWA), an open collaborative community that is actively addressing the challenges associated with the production, management, interoperability and analysis of unprecedented volumes of data….

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Publication: Scientific requirements for the next generation semantic web-based chemogenomics and systems chemical biology molecular information system OPS

On December 3, 2013, Posted by , In Publications, By ,,,,,,,,,,,,,,,, , With Comments Off on Publication: Scientific requirements for the next generation semantic web-based chemogenomics and systems chemical biology molecular information system OPS

This book focuses on applications of compound library design and virtual screening to expand the bioactive chemical space, to target hopping of chemotypes to identify synergies within related drug discovery projects or to repurpose known drugs, to propose mechanism of action of compounds, or to identify off-target effects by cross-reactivity…

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Publication: Incorporating private and commercial data into an open linked data platform for drug discovery

On October 22, 2013, Posted by , In Publications, By ,,,,,,,,,,,,,, , With Comments Off on Publication: Incorporating private and commercial data into an open linked data platform for drug discovery

The Open PHACTS Discovery Platform aims to provide an integrated information space to advance pharmacological research in the area of drug discovery. Effective drug discovery requires comprehensive data coverage, i.e. integrating all available sources of pharmacology data. While many relevant data sources are available on the linked open data cloud,…

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Presentation: Real-World Open PHACTS Use Cases

On September 19, 2013, Posted by , In Presentations, By ,, , With Comments Off on Presentation: Real-World Open PHACTS Use Cases

EBI Industry Workshop: Data integration and its application Lee Harland (Connected Discovery) View presentation

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Conference: EMBL-EBI Industry Programme Workshop

On September 19, 2013, Posted by , In Conferences, By ,,,,, , With Comments Off on Conference: EMBL-EBI Industry Programme Workshop

EMBL-EBI Industry Programme Workshop: Data integration and its application, Cambridgeshire, UK Lee Harland (Connected Discovery) gave a presentation: Real-World Open PHACTS Use Cases

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Publication: Dataset Descriptions for the Open Pharmacological Space

On September 12, 2013, Posted by , In Publications, By ,,,,,,,, , With Comments Off on Publication: Dataset Descriptions for the Open Pharmacological Space

This is a specification for the metadata to described datasets, and the linksets that relate them, to enable their use within the Open PHACTS discovery platform. The specification defines the metadata properties that are expected to describe datasets and linksets; detailing the creation and publication of the dataset. Details of…

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Conference: CICAG: New Developments in Chemical Information

On July 3, 2013, Posted by , In Conferences, By ,,,, , With Comments Off on Conference: CICAG: New Developments in Chemical Information

18th CICAG meeting: New Developments in Chemical Information: ‘Best Practice’, London, UK Lee Harland (Connected Discovery) gave a presentation: Mashing Up Drug Discovery: There’s an API for that

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Presentation: Mashing Up Drug Discovery: There’s an API for that

On July 3, 2013, Posted by , In Presentations, By ,,,,,, , With Comments Off on Presentation: Mashing Up Drug Discovery: There’s an API for that

18th CICAG meeting: New Developments in Chemical Information: ‘Best Practice’, London, UK Lee Harland (Connected Discovery) View presentation

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Publication: Scientific competency questions as the basis for semantically enriched open pharmacological space development

On May 20, 2013, Posted by , In Publications, By ,,,,,,,,,,,,,,,,,,, , With Comments Off on Publication: Scientific competency questions as the basis for semantically enriched open pharmacological space development

Molecular information systems play an important part in modern data-driven drug discovery. They do not only support decision making but also enable new discoveries via association and inference. In this review, we outline the scientific requirements identified by the Innovative Medicines Initiative (IMI) Open PHACTS consortium for the design of…

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Presentation: Practical Semantics In The Pharmaceutical Industry – The Open PHACTS Project

On October 12, 2012, Posted by , In Presentations, By ,,,, , With Comments Off on Presentation: Practical Semantics In The Pharmaceutical Industry – The Open PHACTS Project

EKAW 2012: 18th International Conference on Knowledge Engineering and Knowledge Management, Galway City, Ireland Lee Harland (Connected Discovery) View presentation video Read conference paper

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Conference: EKAW 2012

On October 12, 2012, Posted by , In Conferences, By ,,,, , With Comments Off on Conference: EKAW 2012

EKAW 2012: 18th International Conference on Knowledge Engineering and Knowledge Management, Galway City, Ireland Open PHACTS was a Gold Sponsor of the conference, and Lee Harland (Connected Discovery) gave a presentation: Practical Semantics In The Pharmaceutical Industry – The Open PHACTS Project

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Publication: Open PHACTS: A semantic knowledge infrastructure for public and commercial drug discovery research

On September 25, 2012, Posted by , In Publications, By , , With Comments Off on Publication: Open PHACTS: A semantic knowledge infrastructure for public and commercial drug discovery research

Technology advances in the last decade have led to a “digital revolution” in biomedical research. Much greater volumes of data can be generated in much less time, transforming the way researchers work. Yet, for those seeking to develop new drugs to treat human disease, the task of assembling a coherent…

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Conference: 19th EuroQSAR 2012

On August 30, 2012, Posted by , In Conferences, By ,,,,,,,,,,, , With Comments Off on Conference: 19th EuroQSAR 2012

19th EuroQSAR, Knowledge Enabled Ligand Design, Vienna, Austria Open PHACTS hosted a community workshop: Introducing Open PHACTS Mark Forster gave a presentation: Open Innovation Applied to Agrochemical Discovery Steve Pettifer gave a presentation: Utopia Documents Lee Harland gave a presentation: Open Drug Discovery Intelligence: Open PHACTS and SciBite Niklas Blomberg gave a…

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3rd Open PHACTS Community Workshop

On August 30, 2012, Posted by , In Community Workshops, By ,,,,,,,,,,,,,, , With Comments Off on 3rd Open PHACTS Community Workshop

Introducing Open PHACTS (Vienna, Austria) Co-located with the 19th EuroQSAR conference

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Announcing Open PHACTS Workshop at EuroQSAR 2012

On August 10, 2012, Posted by , In News, By ,,,,,,,,,,,,, , With Comments Off on Announcing Open PHACTS Workshop at EuroQSAR 2012

EuroQSAR 2012 in Vienna Open PHACTS Workshop “Introducing Open PHACTS” Thursday 30 August, 13:30-14:45 Presenters : L. Harland, P. Groth, C. Lemmen, L. Wich, J. Mestres, V. de la Torre This workshop will publicly present the first results of the IMI project Open PHACTS, which is producing an open, integrated…

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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: 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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Gold Sponsor at EKAW 2012

On May 11, 2012, Posted by , In News, By ,,,, , With Comments Off on Gold Sponsor at EKAW 2012

Open PHACTS will act as a Gold Sponsor at EKAW 2012 in Galway City, Ireland from 8–12 October, 2012. The 18th International Conference on Knowledge Engineering and Knowledge Management is concerned with all aspects of eliciting, acquiring, modeling and managing knowledge, and its role in the construction of knowledge-intensive systems and…

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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: 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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