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,…
Publication: Including Co-referent URIs in a SPARQL Query
Linked data relies on instance level links between potentially differing representations of concepts in multiple datasets. However, in large complex domains, such as pharmacology, the inter-relationship of data instances needs to consider the context (e.g. task, role) of the user and the assumptions they want to apply to the data….
Publication: Guidelines for exposing data as RDF in Open PHACTS
This is a “how to” guide for exposing your data in RDF in the Open PHACTS system. Carina Haupt, Andra Waagmeester, Marc Zimmerman, Egon Willighagen Full publication: Open PHACTS Working Draft 07 October 2013
Publication: Provenance: An Introduction to PROV
The World Wide Web is now deeply intertwined with our lives, and has become a catalyst for a data deluge, making vast amounts of data available online, at a click of a button. With Web 2.0, users are no longer passive consumers, but active publishers and curators of data. Hence,…
Publication: Encoding units and unit types in RDF using QUDT
This guideline describes how units for data are preferably encoded, setting a standard that can then be handled uniformly by data consumers. Egon Willighagen Full publication: Open PHACTS Working Draft 13 September 2013
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…
Publication: Human diseases through the lens of network biology
One of the challenges raised by next generation sequencing (NGS) is the identification of clinically relevant mutations among all the genetic variation found in an individual. Network biology has emerged as an integrative and systems-level approach for the interpretation of genome data in the context of health and disease. Network…
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…
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…
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,…
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…
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…
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…
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…
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…
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…
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…
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…