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….

Linking Life Science Data: Design to Implementation, and Beyond

Open PHACTS project closing conference (Vienna, Austria)

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

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

Conference: SWAT4LS 2015

SWAT4LS International Conference 2015, Cambridge, UK Anna Gaulton (European Bioinformatics Institute) presented a poster: Semantic-Web Access to Patent Annotations Alasdair Gray (Heriot-Watt University) gave a presentation: Validata: An online tool for testing RDF data conformance Ryan Miller (Maastricht University) presented a poster: Where do you go from here? Semantics of directions in biological pathways…

Presentation: Data Integration in a Big Data Context

Ambient Assisted Living (AAL) Forum 2015, Ghent, Belgium Alasdair Gray (Heriot-Watt University) View presentation

Conference: Ambient Assisted Living Forum

Ambient Assisted Living (AAL) Forum 2015, Ghent, Belgium Alasdair Gray (Heriot-Watt University) gave a keynote prsentation at the “Crusade for Big Data in the AAL Domain” workshop: Data Integration in a Big Data Context

Conference: SICSA DEMOfest 2014

SICSA DEMOfest 2014, Edinburgh, UK Alasdair Gray (Heriot-Watt University) gave a presentation: The Open PHACTS Discovery Platform

Presentation: The Open PHACTS Discovery Platform

SICSA DEMOfest 2014, Edinburgh, UK Alasdair Gray (Heriot-Watt University) View presentation

Presentation: Help me describe my data: A demonstration of the Open PHACTS VoID Editor

On October 20, 2014, Posted by , In Presentations, By ,,, , With No Comments

ISWC 2014, The 13th International Semantic Web Conference, Trentino, Italy Alasdair Gray (Heriot-Watt University) View presentation | Paper

Presentation: Scientific Lenses to Support Multiple Views over Linked Chemistry Data

On October 20, 2014, Posted by , In Presentations, By ,,, , With No Comments

ISWC 2014, The 13th International Semantic Web Conference, Trentino, Italy Alasdair Gray (Heriot-Watt University) View presentation See also: Full publication: Scientific Lenses to Support Multiple Views over Linked Chemistry Data

Publication: Scientific Lenses to Support Multiple Views over Linked Chemistry Data

When are two entries about a small molecule in different datasets the same? If they have the same drug name, chemical structure, or some other criteria? The choice depends upon the application to which the data will be put. However, existing Linked Data approaches provide a single global view over…

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….

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: 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…

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 (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: 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…

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…

Conference: ISWC 2013

ISWC 2013, The 12th International Semantic Web Conference, Sydney, Australia Paul Groth (VU University Amsterdam) and Carole Goble (University of Manchester) submitted a paper: Incorporating private and commercial data into an open linked data platform for drug discovery Alasdair Gray (Heriot-Watt University) gave a presentation for the ISWC 2013 Semantic Web…

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,…

Conference: COLD 2013

COLD 2013, Fourth International Workshop on Consuming Linked Data, Sydney, Australia Alasdair Gray (Heriot-Watt University) gave a presentation: Including Co-referent URIs in a SPARQL Query, and a full paper with the same title was submitted

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

Publication: Dataset Descriptions for the Open Pharmacological Space

This is a specification for the metadata to described datasets, and the linksets that relate them, to enable their use within the Open PHACTS discovery platform. The specification defines the metadata properties that are expected to describe datasets and linksets; detailing the creation and publication of the dataset. Details of…

Poster: Scientific Lenses: An Approach to Dynamically Vary the Relationships between Datasets

2013 ISMB/ECCB Conference, Berlin, Germany View poster

Presentation: Enabling Drug Discovery Applications Through a Linked Data Platform

On February 27, 2013, Posted by , In Presentations, By ,,, , With No Comments

CSHALS, Conference on Semantics in Healthcare and Life Sciences, Boston, USA Alasdair Gray (Heriot-Watt University) Presentation details

Conference: CSHALS 2013

On February 27, 2013, Posted by , In Conferences, By ,,, , With No Comments

CSHALS, Conference on Semantics in Healthcare and Life Sciences, Boston, USA Alasdair Gray (Heriot-Watt University) gave a tech talk: Enabling Drug Discovery Applications Through a Linked Data Platform

Publication: Scientific Lenses over Linked Data: An approach to support task specific views of the data. A vision.

Within complex scientific domains such as pharmacology, operational equivalence between two concepts is often context-, user- and task-specific. Existing Linked Data integration procedures and equivalence services do not take the context and task of the user into account. We present a vision for enabling users to control the notion of operational…

Publication: The Pharmacology Workspace: A Platform for Drug Discovery

We present the Open PHACTS linked data platform that is being developed to address a set of example drug discovery research questions and which supports several drug discovery applications. The platform retrieves data from many complementary, but overlapping, data sources to present an integrated view of the data. The platform…