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)

Conference: Reproducibility of Data-Oriented Experiments in e-Science

Schloss Dagstuhl Conference on Reproducibility of Data-Oriented Experiments in e-Science, Leibniz, Germany Carole Goble and Stian Soiland-Reyes (University of Manchester) presented their work on the research-object-based data release platform developed for Open PHACTS

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…

Conference: ADDS Data Science Workshop

BD2K ADDS Data Science Workshop, Bethesda, USA Barend Mons (LUMC) and Carole Goble (University of Manchester) represented Open PHACTS

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….

Conference: Jointly designing a data FAIRPORT

Jointly designing a data FAIRPORT, Leiden, the Netherlands Bryn Williams-Jones (Connected Discovery), Barend Mons (LUMC), Carole Goble (University of Manchester) and Jan Velterop (AQnowledge) represented Open PHACTS

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…

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…

Conference: Manchester Informatics Big Data Community Launch

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

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…

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

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

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: Theoretical and technological building blocks for an innovation accelerator

Modern science is a main driver of technological innovation. The efficiency of the scientific system is of key importance to ensure the competitiveness of a nation or region. However, the scientific system that we use today was devised centuries ago and is inadequate for our current ICT-based society: the peer…

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…

Publication: Open PHACTS: Semantic interoperability for drug discovery

Open PHACTS is a public–private partnership between academia, publishers, small and medium sized enterprises and pharmaceutical companies. The goal of the project is to deliver and sustain an ‘open pharmacological space’ using and enhancing state-of-the-art semantic web standards and technologies. It is focused on practical and robust applications to solve…

Publication: Toward interoperable bioscience data

To make full use of research data, the bioscience community needs to adopt technologies and reward mechanisms that support interoperability and promote the growth of an open ‘data commoning’ culture. Here we describe the prerequisites for data commoning and present an established and growing ecosystem of solutions using the shared…