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Publication: Open PHACTS computational protocols for in silico target validation of cellular phenotypic screens: knowing the knowns

On November 15, 2016, Posted by wordpressadmin , In Publications, With Comments Off

Phenotypic screening is in a renaissance phase and is expected by many academic and industry leaders to accelerate the discovery of new drugs for new biology. Given that phenotypic screening is per definition target agnostic, the emphasis of in silico and in vitro follow-up work is on the exploration of…

Publications referencing Open PHACTS

On September 22, 2016, Posted by wordpressadmin , In Publications, With Comments Off

Read on for a list of articles that refer to Open PHACTS and our work:

Presentation: Exploring available compound data with the Open PHACTS Discovery Platform and KNIME

On August 21, 2016, Posted by wordpressadmin , In Presentations, By acs,knime,vienna,daniela digles,acs 252 , With Comments Off

252nd ACS National Meeting & Exposition, Philadelphia, USA Daniela Digles (University of Vienna) View presentation

Presentation: Mining compounds, targets and indications from the patent corpus with SureChEMBL and Open PHACTS

On July 4, 2016, Posted by wordpressadmin , In Presentations, By european bioinformatics institute,ebi,surechembl,george papadatos,embl-ebi,sheffield conference on chemoinformatics,Sheffield Conference on Cheminformatics 7,sheffield,sheffield 7,Sheffield Conference on Cheminformatics 2016,sheffield 2016 , With Comments Off

Seventh Joint Sheffield Conference on Cheminformatics, Sheffield, UK George Papadatos (European Bioinformatics Institute) View presentation

Publication: Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources

On June 23, 2016, Posted by wordpressadmin , In Publications, By chris evelo,andra waagmeester,ryan miller,martina kutmon,Egon Willighagen,plos,wikipathways,anders riutta,alexander pico,plos computational biology , With Comments Off

The diversity of online resources storing biological data in different formats provides a challenge for bioinformaticians to integrate and analyse their biological data. The semantic web provides a standard to facilitate knowledge integration using statements built as triples describing a relation between two objects. WikiPathways, an online collaborative pathway resource,…

Presentation: Chemical databases – challenges and solutions

On June 14, 2016, Posted by wordpressadmin , In Presentations, By acs,royal society of chemistry,valery tkachenko,green chemistry and engineering,GC&E,gc&e 20,green chemistry and engineering 20 , With Comments Off

20th Annual Green Chemistry & Engineering Conference, Portland, USA Valery Tkachenko (Royal Society of Chemistry) View presentation

Presentation: Adaptive Linked Data-driven Web Components: Building Flexible and Reusable Semantic Web Interfaces

On May 29, 2016, Posted by wordpressadmin , In Presentations, By vu amsterdam,eswc,ali khalili,vu,eswc 2016,eswc 13 , With Comments Off

13th ESWC 2016, Crete, Greece Ali Khalili (VU University Amsterdam) View presentation

Presentation: Open PHACTS – experience of sustainability

On May 18, 2016, Posted by wordpressadmin , In Presentations, By european bioinformatics institute,ebi,nick lynch,embl-ebi,embl-ebi industry programme,mioss,mioss 2016 , With Comments Off

EMBL-EBI Industry Programme Workshop: Molecular Informatics Open Source Software (MIOSS) workshop, Cambridgeshire, UK Nick Lynch (Open PHACTS Foundation) View presentation

Presentation: Open PHACTS: Semantic interoperability for drug discovery

On March 17, 2016, Posted by wordpressadmin , In Presentations, By acs,herman van vlijmen,janssen,acs 251 , With Comments Off

251st ACS National Meeting & Exposition, San Diego, USA Herman van Vlijmen (Janssen) View presentation

Presentation: Implementing chemistry platform for Open PHACTS: Lessons learned

On March 17, 2016, Posted by wordpressadmin , In Presentations, By acs,royal society of chemistry,valery tkachenko,acs 251 , With Comments Off

251st ACS National Meeting & Exposition, San Diego, USA Valery Tkachenko (Royal Society of Chemistry) View presentation

Presentation: Representation of drug discovery knowledge in the ChEMBL and SureChEMBL databases

On March 17, 2016, Posted by anika , In Presentations, By acs,anna gaulton,embl-ebi,acs 251 , With Comments Off

251st ACS National Meeting & Exposition, San Diego, USA Anna Gaulton (EMBL-EBI) View presentation

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….

Presentation: Leveraging Open Chemogenomics Data and Tools with KNIME

On February 25, 2016, Posted by wordpressadmin , In Presentations, By knime,european bioinformatics institute,ebi,george papadatos,embl-ebi,knime spring summit,knime summit,knime spring summit 2016,knime summit 2016 , With Comments Off

KNIME Spring Summit 2016, Berlin, Germany George Papadatos (EMBL-EBI) View presentation

Presentation: Creating workflows for drug-discovery with Open PHACTS and KNIME

On February 25, 2016, Posted by wordpressadmin , In Presentations, By knime,vienna,daniela digles,knime spring summit,knime summit,knime spring summit 2016,knime summit 2016 , With Comments Off

KNIME Spring Summit 2016, Berlin, Germany Daniela Digles (University of Vienna) View presentation

Presentation: The power of open data – Linking transporter interaction profiles to in vivo toxicity

On February 24, 2016, Posted by wordpressadmin , In Presentations, By gerhard ecker,vienna,freie universitat berlin , With Comments Off

Freie Universität Berlin Pharmaceutical Research Colloquium, Winter Semester 2015/2016, Berlin, Germany Gerhard Ecker (University of Vienna) View presentation

Presentation: Linked open data in drug discovery: Where are we?

On February 16, 2016, Posted by wordpressadmin , In Presentations, By herman van vlijmen,janssen,advances and progress in drug design , With Comments Off

Advances and Progress in Drug Design, London, UK Herman van Vlijmen (Janssen) View presentation

Publication: Selectivity profiling of BCRP versus P-gp inhibition: from automated collection of polypharmacology data to multi-label learning

On February 4, 2016, Posted by wordpressadmin , In Publications, By gerhard ecker,daniela digles,barbara zdrazil,Floriane Montanari,journal of cheminformatics , With Comments Off

The human ATP binding cassette transporters Breast Cancer Resistance Protein (BCRP) and Multidrug Resistance Protein 1 (P-gp) are co-expressed in many tissues and barriers, especially at the blood–brain barrier and at the hepatocyte canalicular membrane. Understanding their interplay in affecting the pharmacokinetics of drugs is of prime interest. In silico…

Presentation: Validata: An online tool for testing RDF data conformance

On December 7, 2015, Posted by wordpressadmin , In Presentations, By alasdair gray,heriot-watt,swat4ls,swat4ls 2015 , With Comments Off

SWAT4LS International Conference 2015, Cambridge, UK Alasdair Gray (Heriot-Watt University) View presentation

Poster: Where do you go from here? Semantics of directions in biological pathways

On December 7, 2015, Posted by wordpressadmin , In Posters, By maastricht,chris evelo,swat4ls,andra waagmeester,ryan miller,martina kutmon,anwesha bohler,Egon Willighagen,swat4ls 2015,jonathan melius,nuno nunes,peter woollard , With Comments Off

SWAT4LS International Conference 2015, Cambridge, UK View poster

Poster: Semantic-Web Access to Patent Annotations

On December 7, 2015, Posted by wordpressadmin , In Posters, By anna gaulton,lee harland,daniela digles,mark davies,antonis loizou,john overington,valery tkachenko,stefan senger,nick lynch,Stian Soiland-Reyes,george papadatos,nathan dedman , With Comments Off

SWAT4LS International Conference 2015, Cambridge, UK View poster

Presentation: DisGeNET: A discovery platform for translational research: Usage Tutorial

On December 7, 2015, Posted by wordpressadmin , In Presentations, By swat4ls,nuria queralt-rosinach,disgenet,imim,nuria queralt,swat4ls 2015 , With Comments Off

SWAT4LS International Conference 2015, Cambridge, UK Núria Queralt Rosinach (IMIM) View presentation

Presentation: Finding novel associations across domains using linked data

On December 7, 2015, Posted by anika , In Presentations, By swat4ls,lumc,marco roos,Leiden University Medical Centre , With Comments Off

SWAT4LS International Conference 2015, Cambridge, UK Marco Roos (Leiden University Medical Centre) View presentation

Presentation: RDFization of DisGeNET

On December 4, 2015, Posted by anika , In Presentations, By nuria queralt-rosinach,disgenet,pompeu fabra,nuria queralt,universitat pompeu fabra,BioSB , With Comments Off

BioSB Research School: Managing and Integrating Life Science Information (4th edition): Approaches using Linked Data and Semantics, Utrecht, Netherlands Núria Queralt (Universitat Pompeu Fabra) View presentation

Presentation: DisGeNET – A discovery platform for translational Research – RDF & SPARQL – Usage and Modeling Challenges

On December 3, 2015, Posted by anika , In Presentations, By sib,disgenet,imim,rdf,sparql,semantic web,nuria queralt , With Comments Off

SIB Training Course: Using the Semantic Web for faster (Bio-)Research, Geneva, 30 November – 3 December 2015 Núria Queralt (IMIM) View presentation

Poster: DisGeNET: Applying Semantic Web and Network Analysis Approaches for the Integration and Analysis of Gene-Disease Associationsfor Translational Research and Drug Discovery

On November 17, 2015, Posted by wordpressadmin , In Posters, By nuria queralt-rosinach,disgenet,pompeu fabra,biomedbridges,nuria queralt,universitat pompeu fabra , With Comments Off

BioMedBridges Symposium: Open Bridges for Life Science Data, Hinxton, UK View poster

Poster: Combining various open data sources for P-gp/BCRP selectivity profiling

On November 8, 2015, Posted by wordpressadmin , In Posters, By barbara zdrazil,german conference on chemoinformatics,german conference on chemoinformatics 11 , With Comments Off

11th German Conference on Chemoinformatics, Fulda, Germany View poster

Publication: WikiPathways: capturing the full diversity of pathway knowledge

On October 19, 2015, Posted by wordpressadmin , In Publications, By chris evelo,andra waagmeester,ryan miller,anwesha bohler,Egon Willighagen,wikipathways,jonathan melius,nuno nunes,nucleic acids research,nartina kutmon,anders riutta,kristina hanspers,sravanthi sinha,susan coort,elisa cirillo,bart smeets,alexander pico , With Comments Off

WikiPathways (http://www.wikipathways.org) is an open, collaborative platform for capturing and disseminating models of biological pathways for data visualization and analysis. Since our last NAR update, 4 years ago, WikiPathways has experienced massive growth in content, which continues to be contributed by hundreds of individuals each year. New aspects of the…

Publication: Managing expectations: assessment of chemistry databases generated by automated extraction of chemical structures from patents

On October 6, 2015, Posted by wordpressadmin , In Publications, By anna gaulton,stefan senger,chembl,surechembl,george papadatos,luca bartek,journal of cheminformatics , With Comments Off

First public disclosure of new chemical entities often takes place in patents, which makes them an important source of information. However, with an ever increasing number of patent applications, manual processing and curation on such a large scale becomes even more challenging. An alternative approach better suited for this large…

Presentation: Drug discovery FAQs: Workflows for answering multidomain drug discovery questions

On October 5, 2015, Posted by wordpressadmin , In Presentations, By knime,vienna,daniela digles , With Comments Off

4th KNIME Cheminformatics Workshop, Cambridgeshire, UK Daniela Digles (University of Vienna) View presentation

Presentation: ChEMBL resources and KNIME

On October 5, 2015, Posted by anika , In Presentations, By knime,ebi,chembl,george papadatos,embl-ebi , With Comments Off

4th KNIME Cheminformatics Workshop, Cambridgeshire, UK George Papadatos (EMBL-EBI) View presentation