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…
Poster: Drug Discovery FAQ: Open PHACTS API and KNIME have the answers!
8th KNIME User Group Meeting and Workshops, Berlin, Germany View poster
Conference: 8th KNIME User Group Meeting and Workshops
8th KNIME User Group Meeting and Workshops, Berlin, Germany Christine Chichester (Swiss Institute of Bioinformatics) presented a poster: Drug Discovery FAQ: Open PHACTS API and KNIME have the answers!
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…
Publication: Scientific Lenses to Support Multiple Views over Linked Chemistry Data
When are two entries about a small molecule in different datasets the same? If they have the same drug name, chemical structure, or some other criteria? The choice depends upon the application to which the data will be put. However, existing Linked Data approaches provide a single global view over…
Conference: IMI 2 Open Info Day
IMI 2 Open Info Day, Brussels, Belgium Christine Chichester (Swiss Institute of Bioinformatics) represented Open PHACTS.
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…
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…
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….
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….
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…
Managing Knowledge about Tissues IMI Workshop
Managing Knowledge about Tissues (Brussels, Belgium)
Presentation: Open PHACTS: How does it work? How can it work for tissue knowledge management?
Managing Knowledge about Tissues, Brussels, Belgium Christine Chichester (Swiss Institute of Bioinformatics) View presentation
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
Presentation: Mobile semantic technologies using Open PHACTS
NETTAB 2013, Venice Lido, Italy Christine Chichester (Swiss Institute of Bioinformatics) View presentation
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: 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: 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…
2nd Open PHACTS Community Workshop
Working with Open PHACTS (London, UK)
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…