Webinar: Open source software components for chemistry standardisation

Antony Williams (EPA, previously RSC and ChemSpider) and Valery Tkachenko (RSC, previously ChemSpider) discuss the need for mechanisms for the standardisation and validation of chemical structure data, and the development and implementation of a system of software components to achieve this within the Open PHACTS Discovery Platform. Watch webinar video | View webinar slides

Webinar: Open source software components for chemistry standardisation

Our Science and Open PHACTS webinar series returns on 24 October, following our summer break. This month we will discuss the key chemistry software components and datasets that underpin the Open PHACTS Discovery Platform, which are now available as open source software components. Webinar: Science and Open PHACTS: Open source software components for chemistry standardisation Date: Monday, 24 Read more about Webinar: Open source software components for chemistry standardisation[…]

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 are a myriad of issues Read more about Publication: The Chemical Validation and Standardization Platform (CVSP): large-scale automated validation of chemical structure datasets[…]

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: 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[…]

Conference: NETTAB 2013

NETTAB 2013, Venice Lido, Italy Antony Williams (Royal Society of Chemistry) gave a presentation: Facilitating Scientific Discovery through Crowdsourcing and Distributed Participation Christine Chichester (Swiss Institute of Bioinformatics) gave a presentation: Mobile semantic technologies using Open PHACTS

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: Scientific Lenses over Linked Data: An approach to support task specific views of the data. A vision.

Within complex scientific domains such as pharmacology, operational equivalence between two concepts is often context-, user- and task-specific. Existing Linked Data integration procedures and equivalence services do not take the context and task of the user into account. We present a vision for enabling users to control the notion of operational equivalence by applying scientific lenses Read more about Publication: Scientific Lenses over Linked Data: An approach to support task specific views of the data. A vision.[…]

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 Drug Discovery. Maria C. Carrascosa, Oriol L. Read more about Publication: Molecular Informatics Special Issue: Open Innovation in Drug Discovery[…]

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[…]

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 that the data are high Read more about Publication: Towards a gold standard: regarding quality in public domain chemistry databases and approaches to improving the situation[…]

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 2012, Pages 23–25

2011 Conferences

Open PHACTS had a presence at the following conferences and events in 2011:   12–13 December, 2011 Benelux Bioinformatics Conference 2011, Luxembourg 2 December, 2011 STM Innovations Seminar 2011, London, UK 28 November, 2011 Chemical Information and Computer Applications Group (CICAG) meeting: The Future Information Needs of Pharmaceutical & Medicinal Chemistry, London, UK 7 November, 2011 Royal Read more about 2011 Conferences[…]