Publication: Publishing DisGeNET as Nanopublications

The increasing and unprecedented publication rate in the biomedical field is a major bottleneck for discovery in Life Sciences. Although the scientific community is limited an inability to manually curate facts from published papers, recent approaches enable the automatic, scalable and reliable extraction of assertions from the scientific literature. While the publication of assertions on Read more about Publication: Publishing DisGeNET as Nanopublications[…]

Publication: The Application of the Open Pharmacological Concepts Triple Store (Open PHACTS) to Support Drug Discovery Research

Integration of open access, curated, high-quality information from multiple disciplines in the Life and Biomedical Sciences provides a holistic understanding of the domain. Additionally, the effective linking of diverse data sources can unearth hidden relationships and guide potential research strategies. However, given the lack of consistency between descriptors and identifiers used in different resources and Read more about Publication: The Application of the Open Pharmacological Concepts Triple Store (Open PHACTS) to Support Drug Discovery Research[…]

Publication: Querying neXtProt nanopublications and their value for insights on sequence variants and tissue expression

Understanding how genetic differences between individuals impact the regulation, expression, and ultimately function of proteins is an important step toward realizing the promise of personal medicine. There are several technical barriers hindering the transition of biological knowledge into the applications relevant to precision medicine. One important challenge for data integration is that new biological sequences Read more about Publication: Querying neXtProt nanopublications and their value for insights on sequence variants and tissue expression[…]

Publication: Transporter assays and assay ontologies: useful tools for drug discovery

Transport proteins represent an eminent class of drug targets and ADMET (absorption, distribution, metabolism, excretion, toxicity) associated genes. There exists a large number of distinct activity assays for transport proteins, depending on not only the measurement needed (e.g. transport activity, strength of ligand–protein interaction), but also due to heterogeneous assay setups used by different research Read more about Publication: Transporter assays and assay ontologies: useful tools for drug discovery[…]

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[…]

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: 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[…]

1st Open PHACTS Community Workshop

 

Solving Bottlenecks in Data Sharing in the Life Sciences (Volendam, the Netherlands)

Co-hosted with GEN2PHEN as a project addressing similar issues around data sharing

[…]

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 metrics for citation of data Read more about Publication: The Value of Data[…]