1)What is GPML ?

A GPML file is a XML file format file. It stands for GenMAPP Pathway Mark-up Language. The root element of the file is always the tag. It has three types of elements, namely:
1. Graphical elements: Shape, Label
2. Elements with a biological elements: DataNode
3. Elements that can connect to elements: Lines

GPML file showing the data nodes

GPML file showing the solid lines to connect elements

GPML file showing the broken/dashed lines to connect elements

What is Javascript viewer in PATHVISIO++?
The main objective was to have a Google maps-type interface for biological pathways. Pathvisio++ provides an interactive web interface to visualize the GPML files and for added functionality. The viewer is provide at a minimum ability to pan, zoom and link out functionality for the diagrams.Users can also get additional information concerning pathways in Javascript viewer. The viewer is provide at a minimum ability to pan, zoom and link out functionality for the diagrams.Users can also get additional information concerning pathways and their elements from information within GPML files. To enable this, the pathway must be first split up into several fragments and it is called as HTML maps which disintegrates the image into several fragments.On clicking the gene of our interest, there will be a simple pop up that will show all the details regarding the gene. In the first module, information like gene type, organism, locat ion, primary source and a general summary about the gene is displayed

Sample Image of Javascript viewer

What is Ontologies for Pathways?
Organizing and categorizing pathways is important to help finding relevant knowledge for a given topic. It can also help to identify related pathways or duplicate information that can be merged. Especially on a Wikipathways, where users are free to create context-specific pathways (e.g. focused at a single tissue, cell-line or experiment); it is important to provide information about this context. Several biological ontologies exist that define a vocabulary of biological context that can be used for pathways. The data and annotated information about all the genes present in the pathway and is stored in a tabular format representing the gene information. This includes information like gene type, organism name, primary source and gene location. This helps in visualizing all the genes information at a single click instead of browsing separately for each individual gene