BioPP: a tool for web-publication of biological networks

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/

Figure 1

Schematic illustrating the process of interative manual curation of a biological pathway. Pathway curators initially mine information sources and assemble a pathway draft. Web publication of the resulting annotated pathway can facilitate user access to the information. In addition, web publication facilitates community and domain expert feedback leading to correction, refinement and improvement of the pathway knowledgebase content and user access to the current release.

Figure 2

The upload interface of the BioPP Suite.

Figure 3

The web-accessible pathway repository.

Figure 4

The web-accessible pathway navigator. A sample pathway is shown that represents part of the viral activated signaling pathways in human dendritic immune cells. The entities and links shown in the pathway are clickable to display the corresponding annotations. The content of the individual frames, which are indicated by roman numerals, are as follows: I – Help link. II – brief author provided description of the pathway and contact information for suggesting pathway revisions. III – link for the pathway legend (from CellDesigner), and links for collated lists of the annotations for interactions, protein, genes, and RNAs in the network. IV.1 navigating zoom rectangle. Dragging the zoom rectangle or clicking inside the index window (IV.2) displays the appropriate section of the pathway in IV.3. The arrow in IV.1 is a toggle button to hide/unhide the index window. The zoom facilitates navigating, particularly when the network map is large and fine-grain. V, VII, VIII, IX – sorted, hyperlinked lists of all the interactions, proteins, genes and RNAs, respectively. Clicking on a hyperlink displays the annotations in the annotation frame (VI). Links to the Entrez gene pages and the appropriate page of a public wiki-based discussion forum also launch new windows. VI – annotation frame which displays selected annotations. Clicking an interaction displays the annotations. Clicking a PMID opens a separate PubMed window for that citation.