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July data release

Chris Mungall cjm at fruitfly.org
Wed Jul 3 17:36:53 PDT 2002


Amigo is now pointing at the July 2002 GO database release
http://amigo.geneontology.org

The mysql and xml exports are available from the usual place, see
http://www.godatabase.org/dev/database/

If you have AmiGO or the perl API installed locally, you will need the
latest version of the source code due to changes in the GO schema. This
can be obtained via sourceforge (see url above); or you can get a
compressed snapshot of the code distributed with the mysql/xml dumps.

Note - we shifted email servers for go-database recently, some of you may
not be receiving your go-database emails. You may need to resubscribe (you
should get this twice, if you are on both the mail lists on the header).
see http://www.godatabase.org/dev/database/

 * * *

Some changes in the schema and codebase since the last release - this
shouldn't affect you unless you're seriously hacking either:

the schema has been split into interlocking modules - this should make it
easier to integrate the go schema into your own databases, as you can just
leave out the modules you don't require.

relationship types are now treated as terms themselves

the parsing code has been completely overhauled, an event based mechanism
is now used. You can now turn any of the GO file formats (ontology, xrefs,
defs, associations) directly into an xml-type stream, and write your own
handlers; or you can also use the existing handlers, to turn the events
into object graphs or SQL loading statements. We've also added some
experimental handlers that generate DAML+OIL from GO ontology files; the
results seem to work in OilEd (version 3). The script "go2damloil" can be
run on any of the GO or GOBO ontology files.

more documentation on the new parser/handler modules is forthcoming, I
promise...


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