The "GO annotations of Omor contigs" XML document contains the terms of the
Gene Ontology database (July 4 2007). Each GO term in the database is an
element in the document. The nesting of the elements is representative of the
hierarchy of the terms in the database. The start tag for each element is the
term id with ":" substituted with "_". Each element has two attributes: name
and count. The value of the name attribute is the name of the corresponding GO
term. The value of the count attribute represents the number of contigs that
the GO term annotates. For example, for "<GO_0003774 name="motor activity"  count="16">"
"GO_0003774" is the start tag and represents the GO term GO:0003774 which has
the name "motor activity". A total of 16 contigs can be classified as having
'motor activity'. If a given GO term directly annotates contigs, a list of
contig elements follow the GO term start tag. Each contig element has one
attribute: 'ESTs'. The value of the ESTs attribute is the number of ESTs
comprising the contig.  Within each contig element is a list of one or more
EST elements. The character data for each EST element is a genbank accession
for the EST if availible or an in-house identifier otherwise.
Using "<GO_0003774 name="motor activity"  count="16">"
again, while a total of 16 contigs can be classified as having motor activity,
only 3 contigs are assigned directly to the term GO:0003774, motor activity.
The remaining 13 are assigned to child terms of GO:0003774, motor activity
such as GO:0000146, microfilament motor activity (2 contigs) or GO:0003777,
microtubule motor activity (11 contigs).

To view the document, it must be downloaded and decompressed.

On computers running OS X (macs), it is best to use an XML editor such as oxygen
(http://www.oxygenxml.com/). Once the oxygen XML editor has been installed. it
may be necessary to allocate more memory to Java to allow the document to be
viewed. To do this, right-click on the <oXygen/>  application icon in Finder,
in the pop-up menu select Show Package Contents, then in the Contents
directory edit the file Info.plist: in the key VMOptions, modify the parameter
-Xmx###x (where # is an digit and x is a letter) to a larger value such as '-Xmx600m'.
Save the changes; exit, and restart the program.

On computers running Windows XP, simply opening the document with
internet explorer should be sufficient.

The idea behind using a web browser or XML editor to view the document instead
of simply using a text editor is that when viewed using a web browser or XML
editor, the elements are collapsible.