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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 , In Publications, With No Comments

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 , In Publications, With No Comments

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 , In Presentations, By ,,,, , With No Comments

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

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

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

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

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

Presentation: Open PHACTS – experience of sustainability

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 , In Presentations, By ,,, , With No Comments

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

Presentation: Implementing chemistry platform for Open PHACTS: Lessons learned

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 , In Presentations, By ,,, , With No Comments

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

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

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

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

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

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?

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

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

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

SWAT4LS International Conference 2015, Cambridge, UK View poster

Poster: Semantic-Web Access to Patent Annotations

SWAT4LS International Conference 2015, Cambridge, UK View poster

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

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

Presentation: Finding novel associations across domains using linked data

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

Presentation: RDFization of DisGeNET

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 , In Presentations, By ,,,,,, , With No Comments

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

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

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

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

Publication: WikiPathways: capturing the full diversity of pathway knowledge

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

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 , In Presentations, By ,, , With No Comments

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

Presentation: ChEMBL resources and KNIME

On October 5, 2015, Posted by , In Presentations, By ,,,, , With No Comments

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