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Announcement: GO-EDITOR and GO Revision 2

Midori Harris midori at genome.Stanford.EDU
Fri Mar 16 10:34:34 PST 2001

Dear GO users,

Important notice of changes to GO.

Until now all changes to the three GO ontology files have been made with
generic editing tools (typically emacs) with, in recent months, some
episodic checking for syntactical errors by scripts.

The Berkeley group, especially John Richter, has been working hard for
some months to build an interactive GO editor, as a java app (GO-EDIT).  
This has now been tested by the curators and is ready for prime time.

See the following url for details of the Editor, which is publicly

There are two consequences of this change, one short term and one long

Short term:
The ordering of nodes in the ontologies will change radically, because
GO-EDIT sorts by an alphabetical algorithm.  This means that the first
instantiation of these files on the GO cvs will generate a massive diff
report.  The relationships between nodes will not, of course, change. The
definitions file (doc/GO.defs) will also be handled by GO-EDIT from now.

Long term:
For the moment the GO-EDIT will write out the flat file files of GO.defs,
molecular_function.ontology, biological_process.ontology and
cellular_component.ontology, which will be committed to the GO cvs site in
the normal way.  However, since these files will now be much more rigorous
with respect to their syntax, regular loading into the XML and mySQL
versions will now occur.  In the longer term users of the GO-EDIT will
write directly back to the database, which will then become the
authorative version of GO.  When that occurs we will notify users.

These changes will have effect from Friday, March 16, 2001, around 10:00
AM PST. To avoid any possible confusion between versions the first version
of each of the three ontologies will be numbered 2.1.

Questions or comments to GO by the usual routes please.

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