title: PathVisio-Faceted Search: an exploration tool for multi-dimensional navigation of large pathways.
abstract: OBJECTIVE
  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.
  
  
  BACKGROUND
  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.
authors.affiliation: Computer Engineering, University of Maryland, College Park, MD 20740, USA. jakeyfried@gmail.com
authors.forename: Jake Y
authors.initials: JY
authors.lastname: Fried
authors.forename: Martijn P
authors.initials: MP
authors.lastname: van Iersel
authors.forename: Mirit I
authors.initials: MI
authors.lastname: Aladjem
authors.forename: Kurt W
authors.initials: KW
authors.lastname: Kohn
authors.forename: Augustin
authors.initials: A
authors.lastname: Luna
mesh_terms: D005796:Genes; D006801:Humans; D008223:Lymphoma / Q000235:genetics; D008954:Models, Biological; D011506:Proteins / Q000378:metabolism; D012984:Software; D049490:Systems Biology / Q000379:methods; D014584:User-Computer Interface
chemical_list: D011506:Proteins
references.citation: Bioinformatics. 2011 Feb 1;27(3):431-2
references.pmid: 21149340
references.citation: Nat Biotechnol. 2010 Sep;28(9):935-42
references.pmid: 20829833
references.citation: PLoS Biol. 2008 Jul 22;6(7):e184
references.pmid: 18651794
references.citation: BMC Bioinformatics. 2008 Sep 25;9:399
references.pmid: 18817533
references.citation: Database (Oxford). 2011 Sep 18;2011:bar041
references.pmid: 21930507
references.citation: BMC Bioinformatics. 2013 Jan 16;14:17
references.pmid: 23324051
references.citation: BMC Bioinformatics. 2011 May 17;12:167
references.pmid: 21586134
references.citation: Nat Genet. 2002 May;31(1):19-20
references.pmid: 11984561
references.citation: Nat Biotechnol. 2009 Aug;27(8):735-41
references.pmid: 19668183
references.citation: BMC Bioinformatics. 2010 Jan 04;11:5
references.pmid: 20047655