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

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...

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Bibliographic Details
Published in:Bioinformatics 2013-06, Vol.29 (11), p.1465-1466
Main Authors: Fried, Jake Y, van Iersel, Martijn P, Aladjem, Mirit I, Kohn, Kurt W, Luna, Augustin
Format: Article
Language:English
Subjects:
Applications Notes
Compatibility
Filtering
Filtration
Freeware
Genes
Humans
Lymphoma - genetics
Models, Biological
Pathways
Proteins - metabolism
Searching
Software
Source code
Systems Biology - methods
User-Computer Interface
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Description
Summary: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. 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.
ISSN:1367-4803
1367-4811
1460-2059
DOI:10.1093/bioinformatics/btt146