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Community curation on WikiPathways: How we assist knowledge collection

Chris Evelo¹

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1. Department of Bioinformatics - BiGCat, Maastricht University

PPT (13.7 MB) PDF (8 MB)

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Document Type:

Presentation

Date:

Received 21 April 2009 12:26 UTC; Posted 21 April 2009

Subjects:

Genetics & Genomics, Bioinformatics

Tags:

• knowledge integration
• bioinformatics
• wikis
• pathways
• curation
• wikipathways
• gene ontology
• biocuration
• omics
• GO
• KEGG

Abstract:

Biologists typically use knowledge represented as pathways to better understand the results of genomics experiments. Through integration of data from different omics techniques with what we already know, statistical evaluation and subsequent data visualization the results often start to make sense. An important problem is that we often do not have the relevant pathways, or they may be incomplete or not suitable for usage by analytical tools. Wikipathways is meant to be an answer to the problems described above. It uses mediawiki technology and dedicated open source java code to allow biologists to edit pathway content on the web. We assist this process through the development of helpful software like a Diff tool, Go and KEGG converters, portal mechanism, webservice and pathway extension through automated suggestions.

Collection:

3rd International Biocuration Conference

Presented at:

3rd International Biocuration Conference, 16 April 2009

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5 votes

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2 comments

Luca Toldo on 23 April 2009 06:07 UTC

Dear Chris, very well done. How can one convert SBML V2 to GPML ?

Chris Evelo on 24 April 2009 07:48 UTC

Dear Luca,

It is currently not possible to automatically convert SBML V2 to GPML. The only thing planned so far is a short survey to check the feasibility of such a conversion as part of a support project for the Netherlands Center of Systems Biology. If you would like to be involved please let us know.

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Additional information

License:

This document is licensed to the public under the Creative Commons Attribution 3.0 License

How to cite this document:

Evelo, Chris. Community curation on WikiPathways: How we assist knowledge collection. Available from Nature Precedings <http://dx.doi.org/10.1038/npre.2009.3115.1> (2009)

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Other versions of this document in Nature Precedings

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Other versions of this document elsewhere on the web

• http://www.bigcat.unimaas.nl/tracprojects/pathvisio/attachment/wiki/PresentationMaterial/Wikipathways-Biocurator.ppt (Institutional Repository): On the WikiPathways and PathVisio bugtracker and development (trac) wiki.

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