Utopia Documents integrates with Discovery Platform
Utopia Documents is a free PDF reader that connects the static content of scientific articles to the dynamic world of online content and allows data to be extracted from figures and tables within the scientific literature. Interesting concepts and words can be further investigated using a variety of tools –…
Open PHACTS Explorer updated
The Open PHACTS Explorer now uses version 1.3 of the Open PHACTS API. This includes an update of the pharmacology data (from ChEMBL 13 to ChEMBL 16). Changes with this update: pChEMBL values (a unification over different activity types) are now available. They can be used to sort and filter…
Presentation: Linked Data API (LDA)
EUCLID Project screencast Paul Groth (VU University Amsterdam) Watch presentation video Read presentation notes
Publication: Toxins in transit
The Pharmacoinformatics Research Group seeks to further understanding of transporter proteins and their interactions with drugs, with a particular focus on multidrug resistance in cancer. The development of the eTOX and Open PHACTS databases should encourage greater integration of pharmacoinformatics datasets so that more efficient in silico models can be…
Open PHACTS API 1.3 released
We are excited to release the Open PHACTS API 1.3. Among the features are: Over 2,900 million triples New compound API calls: drug type (approved, experimental) New pharmacology API calls: pChEMBL, assay type, generic name, literature DOI/PMID, target type and component New target info API calls: ChEMBL URIs, UniProt protein-protein interactions,…
Publication: Applying Linked Data Approaches to Pharmacology: Architectural Decisions and Implementation
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….
The Open PHACTS Foundation joins the project
We are pleased to announce that the Open PHACTS project’s successor organisation, the Open PHACTS Foundation, has joined the project as a partner. The Open PHACTS Foundation aims to ensure the sustainability of the Open PHACTS Discovery Platform infrastructure. Furthermore, it acts as a hub for scientific research and development relevant…
Conference: 5th Annual aDREAM Conference
5th Development of Robust Experimental Assay Methods (aDREAM) Conference, Madison, USA Linda Zander-Balderud (AstraZeneca) gave a presentation: Applying BioAssay Ontology to facilitate HTS analysis
Presentation: Applying BioAssay Ontology to facilitate HTS analysis
5th Development of Robust Experimental Assay Methods (aDREAM) Conference, Madison, USA Linda Zander-Balderud (AstraZeneca) View presentation
Publication: Nanopublication Guidelines
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: ERCIM 2013
ERCIM 2013, London, UK Open PHACTS participated in the 6th International Conference of the ERCIM Working Group on Computational and Methodological Statistics
Conference: SWAT4LS 2013
International SWAT4LS Workshop 2013, Edinburgh, Scotland Núria Queralt (Universitat Pompeu Fabra) presented a poster: DisGeNET RDF: A gene-disease association Linked Open Data resource Alasdair Gray (Heriot-Watt University) gave a presentation: Computing Identity Co-reference Across Drug Discovery Datasets Ian Dunlop (University of Manchester) presented a publication: Open PHACTS Explorer: Bringing the web to the semantic…
Award-winning Open PHACTS publications
Open PHACTS publications won the top two best paper awards at SWAT4LS 2013: Computing Identity Co-Reference Across Drug Discovery Datasets (Christian Y.A. Brenninkmeijer, Ian Dunlop, Carole Goble, Alasdair J.G. Gray, Steve Pettifer and Robert Stevens) Nanopublications for exposing experimental data in the life-sciences: a Huntingtion’s Disease case study (Eleni Mina, Mark…
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
International SWAT4LS Workshop 2013, Edinburgh, Scotland Alasdair Gray (Heriot-Watt University) View presentation
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
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
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
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
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
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
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
Pharma IndoChina VIII, Ho Chi Minh City, Vietnam Gerhard Ecker (University of Vienna) View presentation
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
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!