You will need to load the latest version of the GO file into OBO-Edit, so choose 'Load Terms' from the 'File' menu. A 'Load Ontology' window will appear; ensure that the data adapter pull-down menu is set to 'OBO Flat File Adapter', and set to 'Basic' by clicking the Basic button at the top of the window. Now enter the URL http://www.geneontology.org/ontology/gene_ontology.obo into the 'load files' box and click 'Okay'; this will upload the GO file directly from the GO website into OBO-Edit. Alternatively, you can browse for a local copy of the GO file. When the 'Load Ontology' window disappears, the file is loaded.
In term editing panel, and you should see listed three nodes: 'Classes', 'Relations' and 'Obsolete'. 'Classes' is the Gene Ontology itself, 'Relations' is a list of ontology relationships and 'Obsolete' is a list of all the terms deleted from GO. Expand the node 'Classes' to display the top three nodes of GO: biological process, cellular component and molecular function. Expand a few nodes to have a look at the terms.
Select the term 'biological process' and click the 'Subsets' tab in the Text Editor. Subsets are explained in more detail in the text editing and An Introduction to OBO Ontologies sections. You'll see a list of GO slims that currently exist in the GO file; notice that biological process is in all of the existing subsets. Terms are removed from a GO slim subset in the same way as from other subsets, by ticking the box next to the subset name and clicking 'Commit'.
To add your own GO slim subset, use the Subset Manager from the Metadata menu. Give your new subset a name (e.g. 'my_own_slim') and description (e.g. 'My Favourite GO Slim'), and save it.
Now select 'biological process' again, and click the 'Subsets' tab. You should now see your GO slim subset listed with the others. If you tick the box next to your subset and press 'Commit', the term 'biological process' will be added to that subset.
The next step is to go through the ontology and add terms to your GO slim. The easiest way to do this is to use a term renderer, so you can keep track of which terms you've added already. For information about how to use renderers, see the Rendering section. For the GO slim example described above, the pull-down menus should be set to, from left to right, [Self] [Subset] [equals], and the text box should contain 'my_own_slim' (without quotes). It would be useful to save your filter at this stage, so that you can reload it when you want to save your file; see the Reusing filters section.
Try adding a new term to your subset; after you press 'Commit', the term name should also become rendered.
You may also want to see just the terms in your GO slim, so to do this you can use a Term Filter, using the same pull-down menu settings as for the renderer. For more information about filters, see the Filtering section.
Note: GO contains part_of, regulates, negatively_regulates, positively_regulates, and is_a relationships. The is_a relationship is built in to OBO-Edit and is included in the exported file automatically, but the others are not, so you will need to add this relationship to your subset manually. To do this, open the 'Relations' node, which is adjacent to the 'Classes' node and appears as blue text. Select 'part of', and add to the subset as you would an ordinary term; repeat for the regulates relationships. For a more detailed discussion of relationships, see the Introduction to OBO Ontologies section.
To save your GO slim in a separate file, select 'Save As' from the 'File' menu. Make sure the data adapter is still set to 'OBO Flat File Adapter'.
Enter or browse for a path to save your file, and click the 'Advanced' button at the top of the box to switch to the advanced save options. Now tick the 'Filter terms' tick box in the middle of the window, and you should see a filtering interface similar to the one you used to apply a filter to your terms. See the end of the section on the OBO Adapter for more information on saving with filters. Set the filters in the same way as above, or reload your saved filter.
Click 'Ok' to save the file.