Output formats
PID data can be output in two graphic formats (SVG, GIF) 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 SVG and GIF network maps, see Network maps. All search results are set to display GIF format as a default.
GIF (Graphics Interchange Format)
All common web browsers are able to display GIF graphics, but these graphics are less easy to resize and pan on screen than SVG graphics. The elements of the GIF 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)
We recommend you use this format for viewing networks, because the graphics can be easily zoomed and panned on screen.
Most recent browsers are already SVG enabled. 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:
- Download and install the Adobe plug-in.
- Once downloaded and installed the plug-in should be automatically recognized by Windows Internet Explorer and Netscape.
- If you see a message pane on the browser indicating that image display has been blocked, right click the mouse in the message pane and select 'Allow Blocked Content'.
For Firefox:
- Download and install a beta version of the Adobe plug-in.
Unfortunately, Firefox is not fully compatible with the current version (version 3) of the plug-in. - Using Windows Explorer, browse to the C:\Program Files\Common Files\Adobe folder.
- Here you will find an SVG Viewer folder and inside it a Plugins folder.
- Inside the Plugins folder you will find two files: NPSVG6.dll and NPSVG6.zip.
- Copy both files into your Firefox plugins folder (which is likely to be C:\Program Files\Mozilla Firefox\plugins).
- In the firefox location bar, type: about:config
- Search for: SVG
- Set 'svg.enabled' to 'false' (you can do this by double clicking on the row)
- Close all browser windows and restart Firefox.
Installing SVG Viewer on a Mac OS X platform:
- You will need to possess at least a Mac OS X 10.3.9
- In Mac OS X, the Adobe SVG Viewer 3.0 is only supported in Internet Explorer 5.1.
- Download and install Adobe plug-in.
- Currently, SVG is poorly supported on Mac OS X and browsers may not support zooming and panning.
Netscape on Mac is SVG enabled and does not require that a plug-in be downloaded.
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.
BioPAX
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.
