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Publication: Publishing DisGeNET as Nanopublications

On March 25, 2015, Posted by wordpressadmin , In Publications, By christine chichester,nuria queralt-rosinach,ferran sanz,laura furlong,disgenet,Michel Dumontier,Tobias Kuhn,semantic web , With Comments Off

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!

On February 27, 2015, Posted by wordpressadmin , In Posters, By knime,christine chichester,swiss institute of bioinformatics,sib,knime user group meeting,knime user group meeting 8,james lumley,eli lilly , With Comments Off

8th KNIME User Group Meeting and Workshops, Berlin, Germany View poster

Conference: 8th KNIME User Group Meeting and Workshops

On February 27, 2015, Posted by wordpressadmin , In Conferences, By knime,christine chichester,swiss institute of bioinformatics,sib,knime user group meeting,knime user group meeting 8 , With Comments Off

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

On December 18, 2014, Posted by wordpressadmin , In Publications, By ronald siebes,gerhard ecker,chris evelo,christine chichester,daniela digles,andra waagmeester,stefan senger,barbara zdrazil,Edgar Jacoby,Emiliano Cuadrado Rodríguez,plos one,Lars Richter,Joseline Ratnam,Jean-Marc Neefs,Hannah Tipney,Glyn Bradley,Chau Han Chau,Jose Brea,Maria Isabel Loza,plos , With Comments Off

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

On October 19, 2014, Posted by wordpressadmin , In Publications, By alasdair gray,chris evelo,anna gaulton,antony williams,lee harland,christine chichester,iswc,daniela digles,paul groth,colin batchelor,iswc 2014,christian brenninkmeijer,mark davies,ian dunlop,carole goble,karen karapetyan,antonis loizou,john overington,steve pettifer,jon steele,robert stevens,valery tkachenko,andra waagmeester,lecture notes in computer science,Egon Willighagen,the semantic web , With Comments Off

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

On September 30, 2014, Posted by wordpressadmin , In Conferences, By imi,christine chichester,swiss institute of bioinformatics,sib,imi 2 , With Comments Off

IMI 2 Open Info Day, Brussels, Belgium Christine Chichester (Swiss Institute of Bioinformatics) represented Open PHACTS.

6th Open PHACTS Community Workshop

On June 26, 2014, Posted by wordpressadmin , In Community Workshops, By pipeline pilot,maastricht,glaxosmithkline,bryn williams-jones,connected discovery,knime,vienna,lee harland,christine chichester,swiss institute of bioinformatics,sib,daniela digles,katrin stierand,hamburg,ian dunlop,chembionavigator,imim,manchester,pharmatrek,jordi mestres,Egon Willighagen,Lars Richter,community workshop 6,community workshop,robert campbell,moe,molecular operating environment , With Comments Off

Open PHACTS for Academia: Using the Open PHACTS Discovery Platform in undergraduate and postgraduate teaching (London, UK)

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

On June 12, 2014, Posted by wordpressadmin , In Publications, By christine chichester,barend mons,paul groth,antonis loizou,Pascale Gaudet,Oliver Karch,Lydie Lane,Amos Bairoch,web semantics,nextprot , With Comments Off

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

On April 5, 2014, Posted by wordpressadmin , In Publications, By anna gaulton,christine chichester,linda zander-balderud,john overington,ola engkvist,drug discovery today,barbara zdrazil , With Comments Off

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

On January 21, 2014, Posted by wordpressadmin , In News,Publications, By alasdair gray,chris evelo,antony williams,lee harland,christine chichester,paul groth,christian brenninkmeijer,carole goble,antonis loizou,steve pettifer,andra waagmeester,Sune Askjaer,Kees Burger,Mark Thompson,semantic web , With Comments Off

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

On December 15, 2013, Posted by wordpressadmin , In Publications, By alasdair gray,lee harland,christine chichester,paul groth,colin batchelor,antonis loizou,steve pettifer,valery tkachenko,andra waagmeester,erik schultes,Carina Haupt,Sune Askjaer,Kees Burger,Mark Thompson,Zuotian Tatum,documentation,Michel Dumontier,Spyros Kotoulas,Miguel Vazquez,José María Fernández,Jahn Saito,Andrew Gibson,Louis Wich,Tobias Kuhn,Jesse van Dam,concept web alliance , With Comments Off

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

On December 3, 2013, Posted by wordpressadmin , In Publications, By gerhard ecker,antony williams,lee harland,christine chichester,stefan senger,matthias rarey,niklas blomberg,olivier taboureau,barbara zdrazil,jordi mestres,Marta Pinto,Kamal Azzaoui,Edgar Jacoby,Emiliano Cuadrado Rodríguez,Mabel Loza,Victor de la Torre,computational chemogenomics , With Comments Off

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

On October 31, 2013, Posted by wordpressadmin , In Community Workshops, By vienna,imi,christine chichester,swiss institute of bioinformatics,sib,daniela digles,managing knowledge about tissues,etox,community workshop,ddmore , With Comments Off

Managing Knowledge about Tissues (Brussels, Belgium)

Presentation: Open PHACTS: How does it work? How can it work for tissue knowledge management?

On October 30, 2013, Posted by wordpressadmin , In Presentations, By christine chichester,swiss institute of bioinformatics,sib,managing knowledge about tissues , With Comments Off

Managing Knowledge about Tissues, Brussels, Belgium Christine Chichester (Swiss Institute of Bioinformatics) View presentation

Conference: NETTAB 2013

On October 18, 2013, Posted by wordpressadmin , In Conferences, By antony williams,royal society of chemistry,nettab,christine chichester,swiss institute of bioinformatics,sib,nettab 2013 , With Comments Off

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

On October 17, 2013, Posted by wordpressadmin , In Presentations, By nettab,christine chichester,swiss institute of bioinformatics,sib,nettab 2013 , With Comments Off

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

On May 20, 2013, Posted by wordpressadmin , In Publications, By bryn williams-jones,gerhard ecker,antony williams,lee harland,christine chichester,steve pettifer,stefan senger,matthias rarey,manuel pastor,niklas blomberg,olivier taboureau,drug discovery today,barbara zdrazil,jordi mestres,Marta Pinto,Kamal Azzaoui,Edgar Jacoby,Emiliano Cuadrado Rodríguez,Mabel Loza,Victor de la Torre , With Comments Off

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

On August 15, 2012, Posted by wordpressadmin , In Publications, By bryn williams-jones,gerhard ecker,antony williams,christine chichester,linda zander-balderud,katrin stierand,john overington,ola engkvist,tim harder,christian lemmen,matthias rarey,oriol massaguer,niklas blomberg,sean ekins,molecular informatics,barbara zdrazil,maria carracosa,jordi mestres,thomas marek,Matthias Hilbig,Marta Pinto,Michael Trauner,Mats Eriksson,Ingemar Nilsson,Thierry Kogej,Christopher Southan,Martin Johansson,Christian Tyrchan,Sorel Muresan,marcus bjareland,alex clark,Poongavanam Vasanthanathan,Anne Hersey , With Comments Off

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

On July 25, 2012, Posted by wordpressadmin , In Publications, By alasdair gray,chris evelo,antony williams,lee harland,christine chichester,paul groth,christian brenninkmeijer,carole goble,antonis loizou,steve pettifer,andra waagmeester,Sune Askjaer,Kees Burger,James Eales,Rishi Ramgolam,Mark Thompson,icbo,icbo 2012,icbo 3 , With Comments Off

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

On June 6, 2012, Posted by wordpressadmin , In Publications, By gerhard ecker,chris evelo,antony williams,lee harland,christine chichester,barend mons,paul groth,carole goble,niklas blomberg,drug discovery today,Stephen Pettifer,Egon Willighagen , With Comments Off

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

On April 16, 2012, Posted by wordpressadmin , In Community Workshops, By glaxosmithkline,bryn williams-jones,connected discovery,jan velterop,aqnowledge,gerhard ecker,vienna,european bioinformatics institute,ebi,antony williams,royal society of chemistry,christine chichester,swiss institute of bioinformatics,sib,barend mons,lumc,john overington,stefan senger,Richard Kidd,community workshop,community workshop 2,tony harmar,iuphar,iuphar-db,anthony harmar , With Comments Off

Working with Open PHACTS (London, UK)

1st Open PHACTS Community Workshop

On September 19, 2011, Posted by wordpressadmin , In Community Workshops, By jan velterop,aqnowledge,imi,christine chichester,swiss institute of bioinformatics,sib,anthony brookes,efpia,evan bolton,national library of medicine,nlm,pubchem,frank schacherer,biobase,gmbh,ann martin,gen2phen,john wilbanks,science commons,creative commons , With Comments Off

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

On March 29, 2011, Posted by wordpressadmin , In Publications, By jan velterop,christine chichester,barend mons,paul groth,herman van haagen,peter-bram 't hoen,johan den dunnen,gertjan van ommen,erik van mulligen,bharat singh,rob hooft,marco roos,joel hammond,bruce kiesel,belinda giardine,erik schultes,nature genetics , With Comments Off

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…