Hi,

You're not looking for a tree viewer, you're looking for a DAG viewer ;-) In your example, if it were a true GO graph, E would, for example, be a child of D and I.

The EBI's QuickGO tools allows you to do what you want.

For example, I selected a few terms that were related to Apoptosis and generated the following ancestor chart for comparison: http://www.ebi.ac.uk/QuickGO/GMultiTerm#a=64%240AaC0E%5Bq0Nkg&tab=chart&c=

Instructions:

1. Go to the QuickGo website home page Near the top of the page, there is a search box with the "QuickGO" logo next to it. There are also the links "Web services", "Dataset" and "Term Basket".
2. Click on Term Basket and it will open a popup.
3. In the textarea, enter the list of GO terms you would like to visualise (new-line delimited works OK) and click on the "add to basket" button - these terms will appear as a list at the top of the popup
4. At the bottom of the popup there are a number of other buttons - "Use terms", "Display terms in ancestor chart", "find annotations", etc. If you click on "Display terms in ancestor chart", it will load a visualisation of how these terms relate to one another. Note that if the terms are from the the 3 different ontologies (MF, BP, CC) they will be displayed in different charts and you may need to scroll to see them all.

Hope this helps!

Sarah

There are cytoscape plugins, one such is ClueGO.

http://supfam.org/dnet/visDAG.html

You may want to check FDA's GOFFA tool.

website: http://www.fda.gov/ScienceResearch/BioinformaticsTools/ucm233315.htm

Paper: http://www.biomedcentral.com/content/pdf/1471-2105-7-S2-S23.pdf

I built a graph viewer for gene ontologies with D3.js and some python scripts, following this blog post. You can do it too.

I also built a graph viewer with the vivagraph javascript library, it is much more efficient (thanks webgl) but less flexible.

I think there is also some GEPHI tools to do that.

If you are really interested, i can give you some advices.

cytoscape