Publication: Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources

The diversity of online resources storing biological data in different formats provides a challenge for bioinformaticians to integrate and analyse their biological data. The semantic web provides a standard to facilitate knowledge integration using statements built as triples describing a relation between two objects. WikiPathways, an online collaborative pathway resource,…

Poster: Where do you go from here? Semantics of directions in biological pathways

SWAT4LS International Conference 2015, Cambridge, UK View poster

Publication: WikiPathways: capturing the full diversity of pathway knowledge

WikiPathways (http://www.wikipathways.org) is an open, collaborative platform for capturing and disseminating models of biological pathways for data visualization and analysis. Since our last NAR update, 4 years ago, WikiPathways has experienced massive growth in content, which continues to be contributed by hundreds of individuals each year. New aspects of the…

Poster: Biological Interactions Types for WikiPathways

HARMONY 2015, Wittenberg, Germany View poster

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: OpenTox Euro 2014

OpenTox Euro 2014, Athens, Greece Egon Willighagen (Maastricht University) gave a presentation: The Open PHArmacological Concepts Triple Store: Solutions and the Foundation

Presentation: The Open PHArmacological Concepts Triple Store: Solutions and the Foundation

OpenTox Euro 2014, Athens, Greece Egon Willighagen (Maastricht University) View presentation | Overview

6th Open PHACTS Community Workshop

Open PHACTS for Academia: Using the Open PHACTS Discovery Platform in undergraduate and postgraduate teaching (London, UK)

Poster: Open PHACTS: Solutions and the Foundation

On June 5, 2014, Posted by , In Posters, By ,, , With No Comments

10th ICCS, International Conference on Chemical Structures, Noordwijkerhout, the Netherlands View poster

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: 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

Conference: OpenTox Euro 2013

OpenTox Euro 2013, Mainz, Germany Egon Willighagen (Maastricht University) gave a presentation: The Open PHArmacological Concepts Triple Store

Publication: Encoding units and unit types in RDF using QUDT

On September 13, 2013, Posted by , In Publications, By ,,, , With No Comments

This guideline describes how units for data are preferably encoded, setting a standard that can then be handled uniformly by data consumers. Egon Willighagen Full publication: Open PHACTS Working Draft 13 September 2013

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: Open PHACTS: meaningful linking of preclinical drug discovery knowledge

On April 11, 2013, Posted by , In Presentations, By ,,, , With No Comments

245th ACS National Meeting & Exposition, New Orleans, USA Egon Willighagen (Maastricht University) View presentation

Conference: 245th ACS National Meeting & Exposition

On April 11, 2013, Posted by , In Conferences, By ,,, , With No Comments

245th ACS National Meeting & Exposition, New Orleans, USA Egon Willighagen (Maastricht University) gave a presentation: Open PHACTS: meaningful linking of preclinical drug discovery knowledge

Conference: QualityNano 2013

QualityNano 2013, Prague, Czech Republic Egon Willighagen (Maastricht University) presented a 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: 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…