19 research outputs found

    The future of regulatory toxicity assessment: Adverse Outcome Pathways

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    This poster was presented at byteMAL (Bioinformatics for Young inTernational researchers Expo: Maastricht-Aachen-Liège) 2017, in Maastricht on 23rd of June, 2017

    Identification and development of adverse outcome pathways

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    <div>The vision of EU-ToxRisk is to allow the paradigm shift of toxicity assessment, from in vivo testing towards reliable, animal-free hazard and risk assessment of chemicals. EUToxRisk developed various case studies on five main topics of toxicity: liver, lung, kidney, neuronal system and developmental and reproductive toxicity. The purpose of these case studies is to provide a proof of concept for the use of AOPs by integrating new developments in in vitro and in silico methods to describe the key biological events described in the AOPs. This poster displays the initial efforts towards fully developed AOPs.</div

    Visualizing Linked Open Data

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    <p>A query language called SPARQL has been developed to extract knowledge from Linked Data. Composing a SPARQL query is still mainly for the technical savvy. To expose the potential of Linked Data to other less-technical domains, novel visualization techniques are essential.</p> <p>We introduce “Linked Data” and why and how from a biological perspective it can be visualized graphically and also integrated in different biological software platforms. We present three visualization platforms. These are Pathvisio Loom and Cytoscape Semscape.</p> <p>Cytoscape is a commonly used Open Source platform for analysing and visualizing complex networks, an extensive set of plugins is available. In the last Google Summer of Code 2012, a plugin called Semscape was developed to explore SPARQL endpoints. It allows viewing of linked data as cytoscape network. A second use case is to extract the underlying schema of a given endpoint can be extracted and then represented as a cytoscape network. For overlapping data sources the overlap, which allow the linking, can also be represented.</p> <p>PathVisio is an extensive pathway editor and pathway analysis tool. As an analysis tool it allows the projection of experimental data on pathways. We have developed a plug-in called PathVisio Loom, which provides a framework for knowledge aggregation through menu guided additions. It allows the integration of biological knowledge available in the different formats (including Linked Data). Starting from a single pathway object, the curator is given a set of gene products or metabolites that relate to that pathway object and the relations themselves. This information can be imported as semantic triples or for instance as nanopublications resulting from textmining.</p> <p>Although SPARQL queries are still essential to querying link data, these visualization plugins make exploring linked data in a more intuitive environment.</p

    Identifier interoperability with the BridgeDb framework

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    Poster presented at the BioSB 2018 and ELIXIR All Hands 2018 meetings

    Wikidata and Scholia as a hub linking chemical knowledge

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    Poster presented at the 11th International Conference on Chemical Structures, May 27-31 2018, Noordwijkerhout, The Netherlands

    Poster: Visualizing metabolomics data in directed biological networks

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    <p>We developed a new solution to visualize the biological pathways involved in sparse metabolomics data. Using knowledge from two pathway resources and ontology-based approaches, we can show the directed networks between active metabolites from metabolomics data. The data from both resources is made interoperable by collapsing metabolites in the pathways into single nodes in the biological networks using ontological approaches. This explicit ontological linking allows for precise biological interpretation of the paths. By using Neo4j and Cytoscape, we ensure the computational calculation environment for larger networks as well as advanced visualization functionality to investigate the identified subnetworks. The generic nature of this approach opens up the option to combine with other omics data sources, such as proteomics and transcriptomics.</p

    Curation, Visualization and Analysis of Biological Pathways

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    <p>Pathway diagrams are found everywhere: in textbooks, in review articles, on posters and on whiteboards. Their utility to biologists as conceptual models is obvious. They have also become immensely useful for computational analysis and interpretationof large-scale experimental data when properly modeled. We will highlight the latest developments and newest features of WikiPathways (www.wikipathways.org), a community curated pathway database that enables researchers to capture rich, intuitive models of pathways. WikiPathways and the associated tools PathVisio and pathvisio.js are developed as open source projects with a lot of community engagement.</p> <p>The new interactive JavaScript-based pathway viewer, pathvisio.js (https://github.com/wikipathways/pathvisiojs/), is integrated in the WikiPathways website and enables users to zoom in and click on pathway elements to show linkouts to other databases. In the future pathvisio.js will replace the Java applet editor and introduce a quick and simple way to curate and edit pathways.</p> <p>The standalone pathway editor and analysis and visualization tool, PathVisio (www.pathvisio.org), was refactored with the goal to achieve a better, modular system that can be easily extended with plugins. Plugins are accessible through the new plugin repository and can be installed through the plugin manager from within the application. This is an important aspect of usability that will allow users to build an application with all the necessary modules relevant for their work. The WikiPathways plugin of PathVisio allows searching and browsing WikiPathways from within PathVisio. Furthermore users can upload new pathways or update existing pathways.</p

    Sample WikiPathways Page

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    <p>Each pathway has a dedicated page for viewing and editing content. The pathway diagram is edited with an embedded applet version of PathVisio (inset). The Description and Bibliography sections can be edited in-page as well through applets that facilitate entry. Additional information about the pathway components and version history continue on the page (not shown).</p
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