> Back to seminars list


Thursday, June 21st, 2018
From 11h30 To 12h30
Centre de Recherche - Paris - Amphithéâtre Hélène Martel-Massignac

WikiPathways: Curation, Visualization and Analysis of Biological Pathways

Martina Kutmon , Kristina Hanspers, Jonathan Mélius, Ryan Miller, Nuno Nunes, Anders Riutta,
Denise Slenter, Egon L. Willighagen, Chris T. Evelo, Alexander R. Pico

WikiPathways ( www.wikipathways.org ) is a community curated pathway databases that enables
researchers to capture rich, intuitive models of pathways. In this talk, I will highlight the latest
developments, newest features and ongoing projects of WikiPathways and the associated tools
pathvisio.js, PathVisio and the WikiPathways app for Cytoscape. The database and the associated
tools are developed as open source projects with a lot of community engagement.
Tools: The interactive JavaScript-based pathway viewer, pathvisio.js, is integrated in the
WikiPathways website and enables users to zoom in and click on pathway elements to show links
to other databases. The standalone pathway editor, analysis and visualization tool, PathVisio
provides easy-to-use drawing and annotation tools to capture identities, relationships, comments
and literature references for each pathway element and interaction. The WikiPathways app for
Cytoscape can be used to import biological pathways in Cytoscape for data visualization and
network analysis.
Data: The WikiPathways database is improved by continuous data curation and updates through
an expanding community: more than 630 individual contributors and more than 2,500 edits on
nearly 900 pathways in 2017. We have now reach a total number of pathways of 2,652 for 27
different species. Recently, we have decided to adopt the Creative Commons CC0 waiver for our
content on WikiPathways. Our data is available for download from our website, through our REST
webservice or in RDF format from our SPARQL endpoint. We are also in the progress of importing
our content into WikiData ( www.wikidata.org ).


Martina KUTMON

Maastricht University

Invited by


Institut Curie