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Publication: Generic Information Can Retrieve Known Biological Associations: Implications for Biomedical Knowledge Discovery

Weighted semantic networks built from text-mined literature can be used to retrieve known protein-protein or gene-disease associations, and have been shown to anticipate associations years before they are explicitly stated in the literature. Our text-mining system recognizes over 640,000 biomedical concepts: some are specific (i.e., names of genes or proteins)…

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

On October 22, 2013, Posted by , In Publications, With No Comments

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

On September 13, 2013, Posted by , In Publications, By ,,, , With No Comments

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: Improving data and knowledge management to better integrate health care and research

Once upon a time, several engineers, biologists and clinicians realized that a lot of information in biomedicine was partitioned into ‘silos’ that do not intercommunicate. These silos were a side effect of the existence of different disciplines required to, for example, develop new drugs. The engineers decided to dispose of the…

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…

Publication: Human diseases through the lens of network biology

On December 7, 2012, Posted by , In Publications, By , , With No Comments

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: Theoretical and technological building blocks for an innovation accelerator

Modern science is a main driver of technological innovation. The efficiency of the scientific system is of key importance to ensure the competitiveness of a nation or region. However, the scientific system that we use today was devised centuries ago and is inadequate for our current ICT-based society: the peer…

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

On September 1, 2012, Posted by , In Publications, By ,, , With No Comments

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: 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…

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: 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…

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…

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…

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: 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…

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…

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…

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…