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Nucleic Acids Res. 2015 Jul 1;43(W1):W552-9. doi: 10.1093/nar/gkv399. Epub 2015 May 1.

Pathways with PathWhiz.

Author information

1
Department of Computing Science, University of Alberta, Edmonton, Alberta, T6G 2E8, Canada.
2
Department of Computing Science, University of Alberta, Edmonton, Alberta, T6G 2E8, Canada Department of Biological Science, University of Alberta, Edmonton, Alberta, T6G 2E8, Canada National Institute for Nanotechnology, 11421 Saskatchewan Drive, Edmonton, Alberta, T6G 2M9, Canada david.wishart@ualberta.ca.

Abstract

PathWhiz (http://smpdb.ca/pathwhiz) is a web server designed to create colourful, visually pleasing and biologically accurate pathway diagrams that are both machine-readable and interactive. As a web server, PathWhiz is accessible from almost any place and compatible with essentially any operating system. It also houses a public library of pathways and pathway components that can be easily viewed and expanded upon by its users. PathWhiz allows users to readily generate biologically complex pathways by using a specially designed drawing palette to quickly render metabolites (including automated structure generation), proteins (including quaternary structures, covalent modifications and cofactors), nucleic acids, membranes, subcellular structures, cells, tissues and organs. Both small-molecule and protein/gene pathways can be constructed by combining multiple pathway processes such as reactions, interactions, binding events and transport activities. PathWhiz's pathway replication and propagation functions allow for existing pathways to be used to create new pathways or for existing pathways to be automatically propagated across species. PathWhiz pathways can be saved in BioPAX, SBGN-ML and SBML data exchange formats, as well as PNG, PWML, HTML image map or SVG images that can be viewed offline or explored using PathWhiz's interactive viewer. PathWhiz has been used to generate over 700 pathway diagrams for a number of popular databases including HMDB, DrugBank and SMPDB.

PMID:
25934797
PMCID:
PMC4489271
DOI:
10.1093/nar/gkv399
[Indexed for MEDLINE]
Free PMC Article

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