Open PHACTS Foundation

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Poster: DisGeNET RDF: A gene-disease association Linked Open Data resource

On December 12, 2013, Posted by , In Posters, By ,,,,,,,, , With Comments Off on Poster: DisGeNET RDF: A gene-disease association Linked Open Data resource

International SWAT4LS Workshop, Semantic web applications and tools for life sciences, Edinburgh, Scotland View poster

Presentation: Computing Identity Co-reference Across Drug Discovery Datasets

On December 12, 2013, Posted by , In Presentations, By ,,,, , With Comments Off on Presentation: Computing Identity Co-reference Across Drug Discovery Datasets

International SWAT4LS Workshop 2013, Edinburgh, Scotland Alasdair Gray (Heriot-Watt University) View presentation

New source of open chemistry patent data available

On December 11, 2013, Posted by , In News, By ,,,,,, , With Comments Off on New source of open chemistry patent data available

A major new source of open patent chemistry is now available, thanks to the collaboration between Digital Science and the EBI ChEMBL group. We are discussing how this data might be integrated with Open PHACTS and look forward to developing use cases in 2014.

Students build novel apps with Open PHACTS API

On December 11, 2013, Posted by , In News, By ,,,,,, , With Comments Off on Students build novel apps with Open PHACTS API

Undergraduate students from Maastricht University in the Netherlands took part in a Programming in the Life Sciences course. The students created novel applications in six days to consume data via the Open PHACTS API.

Publication: Computing Identity Co-Reference Across Drug Discovery Datasets

On December 10, 2013, Posted by , In Publications, By ,,,,,,,, , With Comments Off on Publication: Computing Identity Co-Reference Across Drug Discovery Datasets

This paper presents the rules used within the Open PHACTS (http://www.openphacts.org) Identity Management Service to compute co-reference chains across multiple datasets. The web of (linked) data has encouraged a proliferation of identifiers for the concepts captured in datasets; with each dataset using their own identifier. A key data integration challenge…

Publication: Nanopublications for exposing experimental data in the life-sciences: a Huntingtion’s Disease case study

On December 10, 2013, Posted by , In Publications, By ,,,,,,,,, , With Comments Off on Publication: Nanopublications for exposing experimental data in the life-sciences: a Huntingtion’s Disease case study

Data from high throughput experiments often produce far more results than can ever appear in the main text or tables of a single research article. In these cases, the majority of new associations is often archived either as supplemental information in an arbitrary format or in publisher-independent databases that can…

Publication: Open PHACTS Explorer: Bringing the web to the semantic web

On December 10, 2013, Posted by , In Publications, By ,,,,,,,,, , With Comments Off on Publication: Open PHACTS Explorer: Bringing the web to the semantic web

The Open PHACTS Explorer is a web application that supports drug discovery via the Open PHACTS API without requiring knowledge of SPARQL or the RDF data being searched. It provides a UI layer on top of the Open PHACTS linked data cache and also provides a javascript library to facilitate…

Over 8 million Open PHACTS API hits

On December 9, 2013, Posted by , In News, By ,, , With Comments Off on Over 8 million Open PHACTS API hits

Since its launch in January 2013 the Open PHACTS API has received over 8 million hits, and over 260 people have registered for it! If you haven’t already, sign up for your free API key now!

Conference: Manchester Informatics Big Data Community Launch

On December 9, 2013, Posted by , In Conferences, By ,,,,, , With Comments Off on Conference: Manchester Informatics Big Data Community Launch

Manchester Informatics Big Data Community Launch, Manchester, UK Carole Goble (University of Manchester) presented Open PHACTS

Presentation: Experimental data guided docking allows to elucidate the molecular basis of drug-transporter interaction

On December 5, 2013, Posted by , In Presentations, By ,,, , With Comments Off on Presentation: Experimental data guided docking allows to elucidate the molecular basis of drug-transporter interaction

Pharma IndoChina VIII, Ho Chi Minh City, Vietnam Gerhard Ecker (University of Vienna) View presentation

Conference: Pharma IndoChina VIII

On December 5, 2013, Posted by , In Conferences, By ,,, , With Comments Off on Conference: Pharma IndoChina VIII

Pharma IndoChina VIII, Ho Chi Minh City, Vietnam Gerhard Ecker (University of Vienna) gave a presentation: Experimental data guided docking allows to elucidate the molecular basis of drug-transporter interaction 

Open PHACTS welcomes e-Therapeutics as an Associated Partner

On December 3, 2013, Posted by , In News, By ,, , With Comments Off on Open PHACTS welcomes e-Therapeutics as an Associated Partner

Open PHACTS extends a warm welcome to our new Associated Partner e-Therapeutics. A full list of Associated Partners can be found here. Find out more about how you can get involved with Open PHACTS!

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 , In Publications, By ,,,,,,,,,,,,,,,, , With Comments Off on 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…

Conference: Autumn School of Chemoinformatics

On November 28, 2013, Posted by , In Conferences, By ,,,,, , With Comments Off on Conference: Autumn School of Chemoinformatics

Autumn School of Chemoinformatics, Nara, Japan Marcus Gastreich (BioSolveIT GmbH) presented ChemBioNavigator

Presentation: WikiPathways: how open source code and open data can make omics technology more useful

On November 26, 2013, Posted by , In Presentations, By ,,, , With Comments Off on Presentation: WikiPathways: how open source code and open data can make omics technology more useful

Life Science Technology Event 2013, Leiden, Netherlands Chris Evelo (Maastricht University) View presentation

Conference: Life Science Technology Event

On November 26, 2013, Posted by , In Conferences, By ,,,, , With Comments Off on Conference: Life Science Technology Event

Life Science Technology Event 2013, Leiden, the Netherlands Chris Evelo (Maastricht University) gave a presentation: WikiPathways: how open source code and open data can make omics technology more useful

Publication: Pav ontology: provenance, authoring and versioning

On November 22, 2013, Posted by , In Publications, By ,,,,,, , With Comments Off on Publication: Pav ontology: provenance, authoring and versioning

We present the Provenance, Authoring and Versioning ontology (PAV): a lightweight ontology for capturing “just enough” descriptions essential for tracking the provenance, authoring and versioning of web resources. We argue that such descriptions are essential for digital scientific content. PAV distinguishes between contributors, authors and curators of content and creators…

Presentation: The biggest problem of science: Ambiguity

On November 22, 2013, Posted by , In Presentations, By ,,, , With Comments Off on Presentation: The biggest problem of science: Ambiguity

HandsOn: Biobanks 2013, The Hague, Netherlands Jan Velterop (AQnowledge) View presentation

Conference: HandsOn: Biobanks 2013

On November 21, 2013, Posted by , In Conferences, By ,,, , With Comments Off on Conference: HandsOn: Biobanks 2013

HandsOn: Biobanks 2013, The Hague, the Netherlands Jan Velterop (AQnowledge) gave a presentation: The biggest problem of science: Ambiguity

Conference: EMBL-EBI Industry Programme Workshop

On November 21, 2013, Posted by , In Conferences, By ,,,, , With Comments Off on Conference: EMBL-EBI Industry Programme Workshop

EMBL-EBI Industry Programme Workshop: Computational Tools for Chemical Biology, Phenotypic Screening and Target De-convolution, Cambridgeshire, UK Bryn Williams-Jones (Connected Discovery) represented Open PHACTS

Target Dossier released

On November 20, 2013, Posted by , In News, By ,, , With Comments Off on Target Dossier released

It is our pleasure to announce the official release of Target Dossier, one of the Example Applications developed within the Open PHACTS project. The Target Dossier uses the Open PHACTS Discovery Platform to answer questions of tissue expression profiles, druggability, pathways and physiological mechanisms. Drug targets can be selected and further investigated….

Publication: Generic Information Can Retrieve Known Biological Associations: Implications for Biomedical Knowledge Discovery

On November 19, 2013, Posted by , In Publications, By ,,,,, , With Comments Off on Publication: Generic Information Can Retrieve Known Biological Associations: Implications for Biomedical Knowledge Discovery

Weighted semantic networks built from text-mined literature can be used to retrieve known protein-protein or gene-disease associations, and have been shown to anticipate associations years before they are explicitly stated in the literature. Our text-mining system recognizes over 640,000 biomedical concepts: some are specific (i.e., names of genes or proteins)…

Project Meeting: Workshop

On November 15, 2013, Posted by , In Project Meetings, By , , With Comments Off on Project Meeting: Workshop

Testing alpha API calls (Beerse, Belgium)

Presentation: Open PHACTS Discovery Platform – Integrating pharmacological and physicochemical data

On November 15, 2013, Posted by , In Presentations, By ,,,, , With Comments Off on Presentation: Open PHACTS Discovery Platform – Integrating pharmacological and physicochemical data

Biochemical Society Workshop: Tools and Strategies to Find Chemical Probes for Your Protein, London, UK Jack Gibb (Royal Society of Chemistry) View presentation

Conference: Biochemical Society Workshop

On November 15, 2013, Posted by , In Conferences, By ,,,, , With Comments Off on Conference: Biochemical Society Workshop

Biochemical Society Workshop: Tools and Strategies to Find Chemical Probes for Your Protein, London, UK Jack Gibb (Royal Society of Chemistry) gave a presentation: Open PHACTS Discovery Platform – Integrating pharmacological and physicochemical data

Over 80% of Open PHACTS publications are open access

On November 12, 2013, Posted by , In News, By , , With Comments Off on Over 80% of Open PHACTS publications are open access

Over 80% of the publications from the Open PHACTS project are open access, available for anyone to read. A full list of our open access publications to date is below. 2013 On the formulation of performant SPARQL queries Scientific competency questions as the basis for semantically enriched open pharmacological space development…

Poster: Accessing Open PHACTS: Interactive exploration of compounds and targets from the semantic web

On November 12, 2013, Posted by , In Posters, By ,,,,,,,, , With Comments Off on Poster: Accessing Open PHACTS: Interactive exploration of compounds and targets from the semantic web

9th German Conference on Chemoinformatics, Fulda, Germany Katrin Stierand (University of Hamburg) View poster

Conference: 9th German Conference on Chemoinformatics

On November 12, 2013, Posted by , In Conferences, By ,,, , With Comments Off on Conference: 9th German Conference on Chemoinformatics

9th German Conference on Chemoinformatics, Fulda, Germany Katrin Stierand (University of Hamburg) presented a poster: Accessing Open PHACTS: Interactive exploration of compounds and targets from the semantic web

Over 3.5 million Open PHACTS API hits since launch

On November 6, 2013, Posted by , In News, By ,, , With Comments Off on Over 3.5 million Open PHACTS API hits since launch

The Open PHACTS API has received over 3.5 million hits since its launch in January 2013.

Open PHACTS Foundation is part of proposal for IMI 9th Call

On November 5, 2013, Posted by , In News, By , , With Comments Off on Open PHACTS Foundation is part of proposal for IMI 9th Call

The recently established Open PHACTS Foundation is part of a proposal for IMI’s 9th Call: WEBAE – Leveraging Emerging Technology for Pharmacovigilance.