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BMC Bioinformatics. 2007 May 22;8:168.

BioPP: a tool for web-publication of biological networks.

Author information

  • 1Center for Translational Systems Biology and Department of Neurology, Mount Sinai School of Medicine, New York, NY 10029, USA. ganesh.viswanathan@mssm.edu <ganesh.viswanathan@mssm.edu>

Abstract

BACKGROUND:

Cellular processes depend on the function of intracellular molecular networks. The curation of the literature relevant to specific biological pathways is important for many theoretical and experimental research teams and communities. No current tool supports web publication or hosting of user-developed large scale annotated pathway diagrams. Sharing via web publication is needed to allow real-time access to the current literature pathway knowledge-base, both privately within a research team or publicly among the outside research community. Web publication also facilitates team and/or community input into the curation process while allowing centralized control of the curation and validation process. We have developed new tool to address these needs. Biological Pathway Publisher (BioPP) is a software suite for converting CellDesigner Systems Biology Markup Language (CD-SBML) formatted pathways into a web viewable format. The BioPP suite is available for private use and for depositing knowledge-bases into a newly created public repository.

RESULTS:

BioPP suite is a web-based application that allows pathway knowledge-bases stored in CD-SBML to be web published with an easily navigated user interface. The BioPP suite consists of four interrelated elements: a pathway publisher, an upload web-interface, a pathway repository for user-deposited knowledge-bases and a pathway navigator. Users have the option to convert their CD-SBML files to HTML for restricted use or to allow their knowledge-base to be web-accessible to the scientific community. All entities in all knowledge-bases in the repository are linked to public database entries as well as to a newly created public wiki which provides a discussion forum.

CONCLUSION:

BioPP tools and the public repository facilitate sharing of pathway knowledge-bases and interactive curation for research teams and scientific communities. BioPP suite is accessible at http://tsb.mssm.edu/pathwayPublisher/broadcast/

PMID:
17519033
[PubMed - indexed for MEDLINE]
PMCID:
PMC1885811
Free PMC Article

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