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Presentation: The Open PHACTS project – Progress and Future Sustainability

On February 28, 2014, Posted by , In Presentations, By ,,, , With No Comments

CSHALS, Conference on Semantics in Healthcare and Life Sciences, Boston, USA Tom Plasterer (AstraZeneca) View presentation

Presentation: Linked Data API (LDA)

On February 6, 2014, Posted by , In Presentations, By ,, , With No Comments

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…

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….

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….

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

Publication: Computing Identity Co-Reference Across Drug Discovery Datasets

This paper presents the rules used within the Open PHACTS ( 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…

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

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…

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

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

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

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)…

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

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

Presentation: Open PHACTS: How does it work? How can it work for tissue knowledge management?

Managing Knowledge about Tissues, Brussels, Belgium Christine Chichester (Swiss Institute of Bioinformatics) View presentation

Presentation: Knowledge management for transmembrane transporters

Managing Knowledge about Tissues, Brussels, Belgium Daniela Digles (University of Vienna) View presentation

Presentation: Incorporating Commercial and Private Data into an Open Linked Data Platform for Drug Discovery

On October 25, 2013, Posted by , In Presentations, By ,,, , With No Comments

ISWC 2013, The 12th International Semantic Web Conference, Sydney, Australia Alasdair Gray (Heriot-Watt University) View presentation

Publication: Incorporating private and commercial data into an open linked data platform for drug discovery

The Open PHACTS Discovery Platform aims to provide an integrated information space to advance pharmacological research in the area of drug discovery. Effective drug discovery requires comprehensive data coverage, i.e. integrating all available sources of pharmacology data. While many relevant data sources are available on the linked open data cloud,…

Publication: Including Co-referent URIs in a SPARQL Query

On October 22, 2013, Posted by , In Publications, With No Comments

Linked data relies on instance level links between potentially differing representations of concepts in multiple datasets. However, in large complex domains, such as pharmacology, the inter-relationship of data instances needs to consider the context (e.g. task, role) of the user and the assumptions they want to apply to the data….

Presentation: Including Co-referent URIs in a SPARQL Query

On October 22, 2013, Posted by , In Presentations, By ,,,, , With No Comments

COLD 2013, Fourth International Workshop on Consuming Linked Data, Sydney, Australia Alasdair Gray (Heriot-Watt University) View presentation See also: Full publication: Including Co-referent URIs in a SPARQL Query

Presentation: Facilitating Scientific Discovery through Crowdsourcing and Distributed Participation

NETTAB 2013, Venice Lido, Italy Antony Williams (Royal Society of Chemistry) View presentation

Presentation: Mobile semantic technologies using Open PHACTS

NETTAB 2013, Venice Lido, Italy Christine Chichester (Swiss Institute of Bioinformatics) View presentation

Publication: Guidelines for exposing data as RDF in Open PHACTS

This is a “how to” guide for exposing your data in RDF in the Open PHACTS system. Carina Haupt, Andra Waagmeester, Marc Zimmerman, Egon Willighagen Full publication: Open PHACTS Working Draft 07 October 2013

Presentation: The Open PHArmacological Concepts Triple Store

OpenTox Euro 2013, Mainz, Germany Egon Willighagen (Maastricht University) View presentation

Presentation: Open PHACTS: A novel platform for integrated data-driven drug discovery

Europin Summer School in Drug Design, Vienna, Austria Gerhard Ecker (University of Vienna) View presentation