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Bioinformatics Advance Access originally published online on July 23, 2009
Bioinformatics 2009 25(21):2860-2862; doi:10.1093/bioinformatics/btp453
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© The Author 2009. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

PathBuilder—open source software for annotating and developing pathway resources

Kumaran Kandasamy 1,2,3, Shivakumar Keerthikumar 1,2, Rajesh Raju 1,2, T. S. Keshava Prasad 1, Y. L. Ramachandra 2, Sujatha Mohan 1,4 and Akhilesh Pandey 3,*

1 Institute of Bioinformatics, International Tech Park, Bangalore 560066, 2 Department of Biotechnology and Bioinformatics, Kuvempu University, Shankarghatta, Karnataka, India, 3 McKusick-Nathans Institute of Genetic Medicine and the Departments of Biological Chemistry, Pathology and Oncology, Johns Hopkins University, Baltimore, Maryland 21205, USA and 4 Research Unit for Immunoinformatics, Research Center for Allergy and Immunology, RIKEN Yokohama Institute, Kanagawa, Japan 230-0045

* To whom correspondence should be addressed.


  Abstract

Summary: We have developed PathBuilder, an open-source web application to annotate biological information pertaining to signaling pathways and to create web-based pathway resources. PathBuilder enables annotation of molecular events including protein–protein interactions, enzyme–substrate relationships and protein translocation events either manually or through automated importing of data from other databases. Salient features of PathBuilder include automatic validation of data formats, built-in modules for visualization of pathways, automated import of data from other pathway resources, export of data in several standard data exchange formats and an application programming interface for retrieving existing pathway datasets.

Availability: PathBuilder is freely available for download at http://pathbuilder.sourceforge.net/ under the terms of GNU lesser general public license (LGPL: http://www.gnu.org/copyleft/lesser.html). The software is platform independent and has been tested on Windows and Linux platforms.

Contact: pandey{at}jhmi.edu

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Alex Bateman

Received on May 11, 2009; revised on July 16, 2009; accepted on July 17, 2009

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