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Bioinformatics. 2013 Jun 1;29(11):1465-6. doi: 10.1093/bioinformatics/btt146. Epub 2013 Apr 1.

PathVisio-Faceted Search: an exploration tool for multi-dimensional navigation of large pathways.

Author information

1
Computer Engineering, University of Maryland, College Park, MD 20740, USA. jakeyfried@gmail.com

Abstract

PURPOSE:

The PathVisio-Faceted Search plugin helps users explore and understand complex pathways by overlaying experimental data and data from webservices, such as Ensembl BioMart, onto diagrams drawn using formalized notations in PathVisio. The plugin then provides a filtering mechanism, known as a faceted search, to find and highlight diagram nodes (e.g. genes and proteins) of interest based on imported data. The tool additionally provides a flexible scripting mechanism to handle complex queries.

AVAILABILITY:

The PathVisio-Faceted Search plugin is compatible with PathVisio 3.0 and above. PathVisio is compatible with Windows, Mac OS X and Linux. The plugin, documentation, example diagrams and Groovy scripts are available at http://PathVisio.org/wiki/PathVisioFacetedSearchHelp. The plugin is free, open-source and licensed by the Apache 2.0 License.

PMID:
23547033
PMCID:
PMC3661049
DOI:
10.1093/bioinformatics/btt146
[Indexed for MEDLINE]
Free PMC Article
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