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Output formats

PID data can be output in three graphic formats (SVG, JPG, Silverlight) and two text formats (PID XML, BioPAX). The graphic output is generated by the freely available GraphViz program.

For an explanation of the information displayed in the graphic network maps, see Network maps. All search results are set to display JPG format as a default.

JPG (Joint Photographic Experts Group)

All common web browsers are able to display JPG graphics, but these graphics are less easy to resize and pan on screen than SVG or Silverlight graphics. The elements of the JPG graphics generated by PID (biomolecules, interactions, and so on) are interactive, and clicking on them will open information windows. Click on the molecule list and references tabs to obtain a complete list of molecules and references used in a network map.

SVG (Scalable Vector Graphics)

A free Adobe plug-in is available for older browsers and for browsers that do not have a full implementation of SVG features. Please note that viewing PID SVG graphics requires that the SVG MIME type be set to: image/svg-xml.

Installing SVG Viewer on a Windows platform

For Internet Explorer 5.0 or higher and Netscape Communication 4.x:

For Firefox:

Installing SVG Viewer on a Mac OS X platform:

Netscape on Mac is SVG enabled and does not require that a plug-in be downloaded.


Installing Silverlight on a Windows platform

For Internet Explorer:

For Firefox:

If you have had a previous version of Silverlight installed, or are using Mozilla Firefox, you will need to restart your browser.

PID XML (Extensible Markup Language)

XML is a flexible text format with increasing use in data exchange across different systems. PID XML is both human- and machine-readable, and allows a platform- independent means of exchanging PID data. For further details refer to the PID XML Document Type Definition (DTD) file.


Biological Pathways Data Exchange is a data exchange format for pathway information that has been created by a collaborative effort between a number of groups. PID data can be output in BioPAX Level 2 format to enable it to be added to other pathway databases.

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