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. The functionality offered by the Read more about Publication: Applying Linked Data Approaches to Pharmacology: Architectural Decisions and Implementation[…]

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. Paul Groth, Erik Schultes, Mark Read more about Publication: Nanopublication Guidelines[…]

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 analysis. Both ligand-based and structure-based Read more about Publication: Scientific requirements for the next generation semantic web-based chemogenomics and systems chemical biology molecular information system OPS[…]

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, their content needs to be Read more about Publication: Incorporating private and commercial data into an open linked data platform for drug discovery[…]

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 deploying dataset descriptions and an Read more about Publication: Dataset Descriptions for the Open Pharmacological Space[…]

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 an open pharmacological space (OPS) Read more about Publication: Scientific competency questions as the basis for semantically enriched open pharmacological space development[…]

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 picture of existing knowledge from Read more about Publication: Open PHACTS: A semantic knowledge infrastructure for public and commercial drug discovery research[…]

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 presentation: Is it just me or Read more about Conference: 19th EuroQSAR 2012[…]

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 and sustainable knowledge resource for Read more about Announcing Open PHACTS Workshop at EuroQSAR 2012[…]

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 exploits two entity resolution services: Read more about Publication: The Pharmacology Workspace: A Platform for Drug Discovery[…]

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 specific questions in drug discovery Read more about Publication: Open PHACTS: Semantic interoperability for drug discovery[…]

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 services for the semantic web, Read more about Gold Sponsor at EKAW 2012[…]

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 Web technologies such as RDF Read more about Publication: Systems chemical biology and the Semantic Web: what they mean for the future of drug discovery research[…]