Conference: ISMB 2016

On July 12, 2016, Posted by , In Conferences, By ,,,, , With Comments Off on Conference: ISMB 2016

Intelligent Systems for Molecular Biology (ISMB) 2016, Orlando, USA Chris Evelo (Maastricht University) gave a presentation: Open PHACTS now offers patent information and interactions from pathways

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

On June 23, 2016, Posted by , In Publications, By ,,,,,,,,, , With Comments Off on 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,…

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Publication: The FAIR Guiding Principles for scientific data management and stewardship

On March 12, 2016, Posted by , In Publications, By ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, , With Comments Off on 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….

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

On December 7, 2015, Posted by , In Posters, By ,,,,,,,,,,, , With Comments Off on Poster: Where do you go from here? Semantics of directions in biological pathways

SWAT4LS International Conference 2015, Cambridge, UK View poster

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Publication: WikiPathways: capturing the full diversity of pathway knowledge

On October 19, 2015, Posted by , In Publications, By ,,,,,,,,,,,,,,,, , With Comments Off on 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…

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Poster: Biological Interactions Types for WikiPathways

On April 24, 2015, Posted by , In Posters, By ,,,,,,, , With Comments Off on Poster: Biological Interactions Types for WikiPathways

HARMONY 2015, Wittenberg, Germany View poster

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Conference: BioMedBridges Knowledge Exchange Workshop

On February 18, 2015, Posted by , In Conferences, By ,,, , With Comments Off on Conference: BioMedBridges Knowledge Exchange Workshop

BioMedBridges Knowledge Exchange Workshop: Data strategies for research infrastructures, Garching, Germany Chris Evelo (Maastricht University) represented Open PHACTS

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Publication: The Application of the Open Pharmacological Concepts Triple Store (Open PHACTS) to Support Drug Discovery Research

On December 18, 2014, Posted by , In Publications, By ,,,,,,,,,,,,,,,,,,, , With Comments Off on Publication: The Application of the Open Pharmacological Concepts Triple Store (Open PHACTS) to Support Drug Discovery Research

Integration of open access, curated, high-quality information from multiple disciplines in the Life and Biomedical Sciences provides a holistic understanding of the domain. Additionally, the effective linking of diverse data sources can unearth hidden relationships and guide potential research strategies. However, given the lack of consistency between descriptors and identifiers…

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Conference: SB@NL2014 Systems Biology Symposium

On December 15, 2014, Posted by , In Conferences, By ,,, , With Comments Off on Conference: SB@NL2014 Systems Biology Symposium

SB@NL2014 Systems Biology Symposium: Tackling Complexity through Data Integration, Maastricht, the Netherlands Chris Evelo (Maastricht University) represented Open PHACTS

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

On October 19, 2014, Posted by , In Publications, By ,,,,,,,,,,,,,,,,,,,,,,,,, , With Comments Off on 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…

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Publication: Applying Linked Data Approaches to Pharmacology: Architectural Decisions and Implementation

On January 21, 2014, Posted by , In News,Publications, By ,,,,,,,,,,,,,, , With Comments Off on 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….

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Presentation: WikiPathways: how open source code and open data can make omics technology more useful

On November 26, 2013, Posted by , In Presentations, By ,,, , With Comments Off on 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

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Conference: Life Science Technology Event

On November 26, 2013, Posted by , In Conferences, By ,,,, , With Comments Off on Conference: Life Science Technology Event

Life Science Technology Event 2013, Leiden, the Netherlands Chris Evelo (Maastricht University) gave a presentation: WikiPathways: how open source code and open data can make omics technology more useful

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Publication: Dataset Descriptions for the Open Pharmacological Space

On September 12, 2013, Posted by , In Publications, By ,,,,,,,, , With Comments Off on 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…

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Presentation: Opening Up Pharmacological Space: The Open PHACTS API

On July 23, 2013, Posted by , In Presentations, By ,,,,, , With Comments Off on Presentation: Opening Up Pharmacological Space: The Open PHACTS API

2013 ISMB/ECCB Conference, Berlin, Germany Chris Evelo (Maastricht University) View presentation

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Conference: ISMB/ECCB 2013

On July 23, 2013, Posted by , In Conferences, By ,,,,,, , With Comments Off on Conference: ISMB/ECCB 2013

2013 ISMB/ECCB Conference, Berlin, Germany Chris Evelo (Maastricht University) gave a presentation: Opening Up Pharmacological Space: The Open PHACTS API and presented a poster: Scientific Lenses: An Approach to Dynamically Vary the Relationships between Datasets Andra Waagmeester (Maastricht University) presented a poster at the pre-meeting Tutorials: Visualizing Linked Open Data in Biological Pathways and…

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

On July 21, 2013, Posted by , In Posters, By ,,,,,,,,,,,,,,,, , With Comments Off on Poster: Scientific Lenses: An Approach to Dynamically Vary the Relationships between Datasets

2013 ISMB/ECCB Conference, Berlin, Germany View poster

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

On November 12, 2012, Posted by , In Publications, By ,,,,,,,,,, , With Comments Off on 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…

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Publication: The Pharmacology Workspace: A Platform for Drug Discovery

On July 25, 2012, Posted by , In Publications, By ,,,,,,,,,,,,,,,,,, , With Comments Off on 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…

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Publication: Open PHACTS: Semantic interoperability for drug discovery

On June 6, 2012, Posted by , In Publications, By ,,,,,,,,,,, , With Comments Off on 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…

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Publication: Toward interoperable bioscience data

On January 27, 2012, Posted by , In Publications, By ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, , With Comments Off on 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…

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