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. 2010 May 15;26(10):1381-3.
doi: 10.1093/bioinformatics/btq143. Epub 2010 Apr 5.

Payao: a community platform for SBML pathway model curation

Yukiko Matsuoka  1 , Samik Ghosh, Norihiro Kikuchi, Hiroaki Kitano
Affiliations

Payao: a community platform for SBML pathway model curation

Yukiko Matsuoka et al. Bioinformatics. .

Abstract

Summary: Payao is a community-based, collaborative web service platform for gene-regulatory and biochemical pathway model curation. The system combines Web 2.0 technologies and online model visualization functions to enable a collaborative community to annotate and curate biological models. Payao reads the models in Systems Biology Markup Language format, displays them with CellDesigner, a process diagram editor, which complies with the Systems Biology Graphical Notation, and provides an interface for model enrichment (adding tags and comments to the models) for the access-controlled community members.

Availability and implementation: Freely available for model curation service at http://www.payaologue.org. Web site implemented in Seaser Framework 2.0 with S2Flex2, MySQL 5.0 and Tomcat 5.5, with all major browsers supported.

Contact: kitano@sbi.jp

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Figures

Fig. 1.
Fig. 1.
Workflow of community pathway curation.
Fig. 2.
Fig. 2.
Payao Model Browser screen—browse the registered models in the list format (left) and the thumbnails with summary data and statistics (right).
Fig. 3.
Fig. 3.
Payao Model Viewer screenshot—model view panel and tag example. In the left panel, tagsets are listed to identify by specified color. In the right panel, under the tagset, assigned model users can add/edit tags associated with the nodes/reactions. Other users can add comments to the tag for providing further information or raising an issue against the tag contents.
See this image and copyright information in PMC

References

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    1. Funahashi A, et al. CellDesigner 3.5: a versatile modeling tool for biochemical networks. Pro. IEEE. 2008;96:1254–1265.
    1. Hucka M, et al. The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics. 2003;19:524–531. - PubMed
    1. Le Novère N, et al. Minimum information requested in the annotation of biochemical models (MIRIAM) Nat. Biotechnol. 2005;23:1509–1515. - PubMed
    1. Le Novère N, et al. Systems biology graphical notation. Nat. Biotech. 2009;8:735–741. - PubMed

Publication types