PaVESy: Pathway Visualization and Editing System.
A data managing system for editing and visualization of biological pathways is presented. The main component of PaVESy (Pathway Visualization and Editing System) is a relational SQL database system. The database design allows storage of biological objects, such as metabolites, proteins, genes and respective relations, which are required to assemble metabolic and regulatory biological interactions. The database model accommodates highly flexible annotation of biological objects by user-defined attributes. In addition, specific roles of objects are derived from these attributes in the context of user-defined interactions, e.g. in the course of pathway generation or during editing of the database content. Furthermore, the user may organize and arrange the database content within a folder structure and is free to group and annotate database objects of interest within customizable subsets. Thus, we allow an individualized view on the database content and facilitate user customization. A JAVA-based class library was developed, which serves as the database programming interface to PaVESy. This API provides classes, which implement the concepts of object persistence in SQL databases, such as entries, interactions, annotations, folders and subsets. We created editing and visualization tools for navigation in and visualization of the database content. User approved pathway assemblies are stored and may be retrieved for continued modification, annotation and export. Data export is interfaced with a range of network visualization programs, such as Pajek or other software allowing import of SBML or GML data format.


BACKGROUND
http://pavsey.mpimp-golm.mpg.de
Lüdemann
Alexander
A
Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Golm, Germany. luedemann@mpimp-golm.mpg.de
Weicht
Daniel
D
Selbig
Joachim
J
Kopka
Joachim
J
D003628:Database Management Systems; D016208:Databases, Factual; D004282:Documentation / Q000379:methods*; D005786:Gene Expression Regulation / Q000502:physiology*; D016247:Information Storage and Retrieval / Q000379:methods; D008954:Models, Biological; D015398:Signal Transduction / Q000502:physiology*; D014584:User-Computer Interface