Prokaryotic GO subset README 
============================

For those users of GO who would rather not view eukaryote-specific terms
(such as mitochondrial and nuclear terms), we now have available as part
of the OBO format ontology file a new category of GO terms: a
prokaryotic subset used to filter out eukaryotic terms.


What is it for? 
=============== 
This category is intended to be used as an annotator aid, and allows an
annotator to browse and choose from a smaller set of terms, although 
obviously no-one is ever restricted to using just these terms.


Is this just a type of GO slim? 
=============================== 
This is not the same as a GO slim, as it does not provide a set of high 
level terms, rather it is a reduced set of terms.


Will this subset be generated as a separate file?
================================================= 
This category of terms will not be generated as a separate file like 
GO slims, but will be part of the gene_ontology.obo file, and can be viewed
using a filter in DAG-Edit (see
http://www.godatabase.org/dev/java/dagedit/docs/index.html
and below for instructions). We also soon hope to provide a filter in 
AmiGO for viewing the prokaryote subset terms.


Will this subset be updated regularly?
====================================== 
The subset will be updated approximately twice yearly, to take in to account
terms that have been added to the ontologies.


How can I view the prokaryotic subset?
====================================== 
Using DAG-Edit version 1.418 or above, load the gene_ontology.obo file. In the
'Find Terms' box, select the following from the pull-down menus:

[Term] has [self] with [category id] that [equals]

and enter the following in the search box:

gosubset_prok

Drag the yellow highlighted writing over the term editing panel on the
left, and choose 'add as filter' for the pop-up menu. You'll now just
see the prokaryote terms. Choose 'add as renderer' if you just want the
prokaryotic terms in a different colour/font. See
http://www.godatabase.org/dev/java/dagedit/docs/index.html for more
information on using DAG-Edit. We also soon hope to provide a filter in
AmiGO for viewing the prokaryote subset terms.


For more infomation about the prokaryotic subset, please contact Jane
Lomax on jane@ebi.ac.uk.