Customize Your Gene Ontology

Jie Bao, baojie@cs.iastate.edu

2005-04-07

Gene Ontology is a very large DAG, and usually only a small part is useful for you.

Use the most updated version of INDUS ontology editor, you can customize a subset of gene ontology and use it in your research.

INDUS is available at http://boole.cs.iastate.edu/indus/Indus-2005-04-07.jar

A simple instruction:

1. Create a new AVH(attribute value hierarchy) type, say, "myGO", with supertype "AVH"

2. type of the tree is ISA (no part-of so far)

3. Choose template 'go'

4. Now the tree is created with a default root 'myGO_AVH'. You can add a subtree of GO into that tree. Right click on any node, choose from the popup menu "add subtree from template". The start node will be the selected node value, or the GO root* if given value is null. You also need to give a cutoff value: only the nodes within given cutoff depth from start node will be added. cutoff -1 means importing the whole sub tree. Don't try it on high level nodes like 0008150, 0000575 unless it is very necessary - it takes long time to import a big subtree.

* Actually GO has no single root node. We added a meta root '0000000' as the root for all of its three hierarchies.

5. Here is the result for start node '0000000' and cutoff 1

6. you can also build the tree with a given set of GO id. choose "Add a id set from template" from the popup menu:

You will be asked for a set of GO id, one id per line

7. those nodes and their ancestors up to the root will be added into the tree

Limitation:

• Actually GO is DAG, not tree. If a node has multiple ancestors, we will only choose the first one.
• No part-of relationship is handled in this version
• We store all user created tree on the server and anybody can view, edit and delete it. That means one user could mess up another user's work. A user-space or local storage will be provided in the next version.

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