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Publication: The FAIR Guiding Principles for scientific data management and stewardship

On March 12, 2016, Posted by wordpressadmin , In Publications, By alasdair gray,jan velterop,chris evelo,barend mons,paul groth,carole goble,andra waagmeester,erik van mulligen,rob hooft,marco roos,erik schultes,niklas blomberg,Susanna-Assunta Sansone,Philippe Rocca-Serra,Tim Clark,Scott Edmunds,Katherine Wolstencroft,Mark Thompson,Albert Mons,anthony brookes,Jun Zhao,Michel Dumontier,Tobias Kuhn,IJsbrand Jan Aalbersberg,Gabrielle Appleton,Myles Axton,Arie Baak,Jan-Willem Boiten,Luiz Bonino da Silva Santos,mark wilkinson,philip bourne,jildau bouwman,Merce Crosas,Ingrid Dillo,Olivier Dumon,Richard Finkers,Alejandra Gonzalez-Beltran,Jeffrey Grethe,Jaap Heringa,Peter t Hoen,Ruben Kok,Joost Kok,Scott Lusher,Maryann Martone,Abel Packer,Bengt Persson,Rene van Schaik,Thierry Sengstag,Ted Slater,George Strawn,Morris Swertz,Johan van der Lei,Peter Wittenburg,scientific data , With Comments Off

There is an urgent need to improve the infrastructure supporting the reuse of scholarly data. A diverse set of stakeholders—representing academia, industry, funding agencies, and scholarly publishers—have come together to design and jointly endorse a concise and measureable set of principles that we refer to as the FAIR Data Principles….

Linking Life Science Data: Design to Implementation, and Beyond

On February 19, 2016, Posted by wordpressadmin , In Community Workshops,Conferences,Project Meetings, By alasdair gray,astrazeneca,heriot-watt,maastricht,glaxosmithkline,bryn williams-jones,gerhard ecker,vienna,european bioinformatics institute,ebi,lee harland,imi,daniela digles,barend mons,lumc,paul groth,herman van vlijmen,janssen,openlink,carole goble,stefan senger,nick lynch,ryan miller,eli lilly,lilly,nuria queralt-rosinach,ferran sanz,manchester,barbara zdrazil,Edgar Jacoby,Jean-Marc Neefs,efpia,ann martin,foundation news,scibite,psmar,elsevier,george papadatos,embl-ebi,nuria queralt,luca bartek,derek marren,emily jamieson,tareq malas,lewis mervin,joseph mullen,pierre meulien,innovative medicines initiative,innomeds,theo meert,hugh williams,strathclyde,jana gurinova,glasgow,cambridge,newcastle upon tyne,jeremy yang,indiana,dean allemang,working ontologist , With Comments Off

Open PHACTS project closing conference (Vienna, Austria)

Conference: DTL On Track

On December 1, 2014, Posted by wordpressadmin , In Conferences, By vu amsterdam,paul groth,dtl,dtl on track,elixir,elixir-nl,dutch techcentre for life sciences , With Comments Off

DTL On Track (DTL and ELIXIR-NL kickoff), Amersfoort, the Netherlands Paul Groth (VU University Amsterdam) represented Open PHACTS

Publication: On the formulation of performant SPARQL queries

On November 15, 2014, Posted by wordpressadmin , In Publications, By paul groth,web semantics,Antonis Louizou,Renzo Angles , With Comments Off

The combination of the flexibility of RDF and the expressiveness of SPARQL provides a powerful mechanism to model, integrate and query data. However, these properties also mean that it is nontrivial to write performant SPARQL queries. Indeed, it is quite easy to create queries that tax even the most optimised…

Presentation: The Knowledge-Remixing Bottleneck – Hidden Decisions

On October 19, 2014, Posted by anika , In Presentations, By iswc,paul groth,iswc 2014,vu,university amsterdam , With Comments Off

Workshop on Context, Interpretation and Meaning, held at the International Semantic Web Conference (ISWC) 2014 at Riva del Garda, Trentino, Italy Paul Groth (VU University Amsterdam) View presentation

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: ProvenanceWeek 2014

On June 13, 2014, Posted by wordpressadmin , In Conferences, By vu amsterdam,paul groth,provenanceweek,provenanceweek 2014 , With Comments Off

ProvenanceWeek 2014, Cologne, Germany Paul Groth (VU University Amsterdam) represented Open PHACTS

Presentation: Provenance: An Introduction to PROV

On June 13, 2014, Posted by anika , In Presentations, By paul groth,prov,provenance,ipaw 2014,ipaw,vu,annotation workshop , With Comments Off

5th International Provenance and Annotation Workshop, Cologne, Germany Paul Groth (Vrije Universitat Amsterdam) View presentation

Conference: IPAW 2014 – 5th International Provenance and Annotation Workshop

On June 13, 2014, Posted by anika , In Conferences, By paul groth,prov,provenance,annotation,ipaw 2014,ipaw , With Comments Off

5th International Provenance and Annotation Workshop, Cologne, Germany Paul Groth (Vrije Universitat Amsterdam) gave a presentation: Provenance: An Introduction to PROV

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…

Conference: 11th ESWC 2014

On May 29, 2014, Posted by wordpressadmin , In Conferences, By vu amsterdam,paul groth,eswc,eswc 2014,eswc 11 , With Comments Off

11th ESWC 2014, Crete, Greece Paul Groth (VU University Amsterdam) represented Open PHACTS

Conference: US NSF Data Citation Workshop

On April 18, 2014, Posted by wordpressadmin , In Conferences, By vu amsterdam,paul groth,nsf,data citation workshop,nsf workshop,linked data,linked open data,data citation , With Comments Off

US National Science Foundation Workshop: Computational Challenges in Data Citation, Philadelphia, USA Paul Groth (VU University Amsterdam) gave a presentation: Data Citation and Linked Open Data – From links to citation?

Presentation: Data Citation and Linked Open Data – From links to citation?

On April 18, 2014, Posted by anika , In Presentations, By paul groth,linked data,linked open data,data citation,vu , With Comments Off

US National Science Foundation Workshop: Computational Challenges in Data Citation, Philadelphia, USA Paul Groth (VU University Amsterdam) View presentation

Conference: European Data Forum 2014

On March 20, 2014, Posted by wordpressadmin , In Conferences, By vu amsterdam,paul groth,european data forum,european data forum 2014 , With Comments Off

European Data Forum 2014, Athens, Greece Paul Groth (VU University Amsterdam) gave a presentation: A Platform for Drug Discovery

Presentation: A Data Platform for Drug Discovery

On March 20, 2014, Posted by wordpressadmin , In News,Presentations, By vu amsterdam,paul groth,european data forum,european data forum 2014 , With Comments Off

European Data Forum 2014, Athens, Greece Paul Groth (VU University Amsterdam) View presentation Watch presentation video

Presentation: Linked Data API (LDA)

On February 6, 2014, Posted by wordpressadmin , In Presentations, By vu amsterdam,paul groth,euclid , With Comments Off

EUCLID Project screencast Paul Groth (VU University Amsterdam) Watch presentation video Read presentation notes

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….

Conference: ISWC 2013

On October 25, 2013, Posted by wordpressadmin , In Conferences, By alasdair gray,heriot-watt,vu amsterdam,iswc 2013,iswc,paul groth,carole goble,manchester,iswc semantic web in use track,iswc 12 , With Comments Off

ISWC 2013, The 12th International Semantic Web Conference, Sydney, Australia Paul Groth (VU University Amsterdam) and Carole Goble (University of Manchester) submitted a paper: Incorporating private and commercial data into an open linked data platform for drug discovery Alasdair Gray (Heriot-Watt University) gave a presentation for the ISWC 2013 Semantic Web…

Conference: COLD 2013

On October 22, 2013, Posted by wordpressadmin , In Conferences, By alasdair gray,heriot-watt,cold 2013,cold,paul groth,christian brenninkmeijer,carole goble,antonis loizou,steve pettifer,Stephen Pettifer,cold 4 , With Comments Off

COLD 2013, Fourth International Workshop on Consuming Linked Data, Sydney, Australia Alasdair Gray (Heriot-Watt University) gave a presentation: Including Co-referent URIs in a SPARQL Query, and a full paper with the same title was submitted

Publication: Provenance: An Introduction to PROV

On September 17, 2013, Posted by wordpressadmin , In Publications, By paul groth,luc moreau,synthesis lectures on the semantic web,prov , With Comments Off

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,…

Webinar: Using the Open PHACTS API

On July 31, 2013, Posted by wordpressadmin , In News,Presentations,Webinars, By vu amsterdam,paul groth,api,developer news,researcher news,webinar , With Comments Off

Paul Groth (VU University Amsterdam) presents a webinar explaining how to use the Open PHACTS API: the data, technical setup, and what can be done with it. Watch presentation video | View presentation slides

Poster: Scientific Lenses: An Approach to Dynamically Vary the Relationships between Datasets

On July 21, 2013, Posted by wordpressadmin , In Posters, By alasdair gray,maastricht,vu amsterdam,chris evelo,ismb eccb 2013,ismb eccb,ismb,eccb,antony williams,royal society of chemistry,paul groth,christian brenninkmeijer,carole goble,steve pettifer,robert stevens,manchester,Egon Willighagen , With Comments Off

2013 ISMB/ECCB Conference, Berlin, Germany View poster

Conference: 10th ESWC 2013

On May 27, 2013, Posted by wordpressadmin , In Conferences, By vu amsterdam,paul groth,eswc,eswc 10,eswc 2013 , With Comments Off

10th ESWC 2013, Montpellier, France Paul Groth (VU University Amsterdam) presented Open PHACTS

Project Meeting: EHR4CR

On January 22, 2013, Posted by wordpressadmin , In Project Meetings, By imi,paul groth,ehr4cr , With Comments Off

Semantic Interoperability meeting for the IMI project EHR4CR (Paris, France). Paul Groth presented Open PHACTS at this meeting.

Publication: Scientific Lenses over Linked Data: An approach to support task specific views of the data. A vision.

On November 12, 2012, Posted by wordpressadmin , In Publications, By alasdair gray,chris evelo,antony williams,paul groth,christian brenninkmeijer,carole goble,steve pettifer,robert stevens,Egon Willighagen,lisc 2012,lisc , With Comments Off

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

On October 4, 2012, Posted by wordpressadmin , In Publications, By barend mons,paul groth,carole goble,erik schultes,Frank van Harmelen,George Kampis,Katy Borner,Peter van den Besselaar,Stuart Anderson,Stefan Decker,Conor Hayes,Thierry Buecheler,Dirk Helbing,the european physical journal,the european physical journal special topics , With Comments Off

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…

Conference: Revaluing Science in the Digital Age

On September 4, 2012, Posted by wordpressadmin , In Conferences, By vu amsterdam,paul groth,royal society,revaluing science in the digital age , With Comments Off

Royal Society Workshop: Revaluing Science in the Digital Age, Chicheley Hall, UK Paul Groth (VU University Amsterdam) presented the Open PHACTS project

3rd Open PHACTS Community Workshop

On August 30, 2012, Posted by wordpressadmin , In Community Workshops, By bryn williams-jones,lee harland,paul groth,euroqsar,christian lemmen,chembionavigator,euroqsar 19,pharmatrek,garfield,target dossier,jordi mestres,Victor de la Torre,Louis Wich,community workshop,community workshop 3 , With Comments Off

Introducing Open PHACTS (Vienna, Austria) Co-located with the 19th EuroQSAR conference

Announcing Open PHACTS Workshop at EuroQSAR 2012

On August 10, 2012, Posted by wordpressadmin , In News, By lee harland,paul groth,euroqsar,christian lemmen,euroqsar 19,jordi mestres,Victor de la Torre,Louis Wich,community workshop,community workshop 3,euroqsar 2012,developer news,researcher news,foundation news , With Comments Off

EuroQSAR 2012 in Vienna Open PHACTS Workshop “Introducing Open PHACTS” Thursday 30 August, 13:30-14:45 Presenters : L. Harland, P. Groth, C. Lemmen, L. Wich, J. Mestres, V. de la Torre This workshop will publicly present the first results of the IMI project Open PHACTS, which is producing an open, integrated…