# GO Tutorial: Build Your Own Ontology I

### Installing DAG-Edit

First, go to SourceForge and download the installer for DAG-Edit, the ontology editing tool used by the GO consortium. Further down the page you will find the DAG-Edit plugins which you should also download.

Run the DAG-Edit installer file and then install the plugins by dragging them into the DAG-Edit "extensions" folder. Start up the application.

You should see a screen that looks something like this:

#

## Exercise I

### Definitions for biological concepts

Add terms under <new ontology> to create a mini-ontology of biological concepts. To create a new term, click on a parent term (in this case, use <new ontology> as the parent; we will cover relationships in the next exercise), choose "Add term" from the Edit menu and enter a term name into the appropriate box. To create a definition for the term, type some text into the appropriate box and click "Edit" to add a dbxref for the definition. Click "Commit" to add the term to the ontology. Note that you can add a term without definition but that you cannot add a definition without specifying a dbxref.

If you are having problems using DAG-Edit, there is a user guide under the Help menu.

Create new terms with the following strings and try to come up with definitions for them. Don't worry about relationships between terms at the moment.

- cell
- gene
- glycine cleavage system
- lipid binding
- glucose transporter
- retinol isomerase
- glucose catabolism
- signal transduction

In addition to text books and your own knowledge, there are various web resources you can use to find definitions:

- online dictionaries (a collection of these are available at http://www.onelook.com/)
- Enzyme Commission enzyme nomenclature
- MetaCyc
- Transport Classification database
- PubMed literature and book search
- MeSH medical vocabulary

Try to make your answers as non-species-specific as possible. Using definitions from GO is cheating, though!

Looking at the terms you've just defined, how would you split them into cellular components, molecular functions and biological processes? Would a different definition affect how you categorized these terms?

Next exercise