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GO December data release, sourceforge site

Chris Mungall cjm at fruitfly.bdgp.berkeley.edu
Thu Dec 6 16:32:45 PST 2001


The december2001 GO data release is available. This was created from a
snapshot of the GO repository from 2001-12-01, but was a few days late in
arriving.

This release includes over 10,000 terms and GO associations from a number
of new sources, including human GO annotation from SwissProt. It also
encompasses sequence data.

You can peruse this data in a number of ways

The AmiGO browser
~~~~~~~~~~~~~~~~~~

AmiGO is now pointing at the december data

http://amigo.geneontology.org
or
http://www.godatabase.org

Download the MySQL data dumps
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

To create your own copy of the GO MySQL database. See:

http://www.godatabase.org/dev/database/

You can choose whether to download

* just the terms
* terms plus associations
* the above plus sequence data

RDF XML
~~~~~~~~

You can also get the GO RDF-XML data export from
http://www.godatabase.org/dev/database/

DAG-Edit
~~~~~~~~~

Point DAG-Edit at the files in
ftp://ftp.geneontology.org/go/ontology-archive/

FASTA Format
~~~~~~~~~~~~~

A Fasta file of gene products that have at least one non IEA assignment
and a corresponding SPTR sequence is available here:

ftp://ftp.geneontology.org/go/sequence

You can also use the MySQL database with sequences to build custom FASTA
files, for example a FASTA of all ATP binding proteins. There are scripts
to help you build these files.

Sourceforge Site
================

In other news, the GO software project has moved its cvs repository from
Berkeley to SourceForge. The page is:

http://geneontology.sourceforge.net

We have also given the software/database pages a facelift. The new site is
http://www.godatabase.org/dev

(You can still use the old fruitfly URLs, they will redirect to the above
site)

The new site includes more database documentation and some example SQL
queries of varying complexity.

There have been a few changes to the schema, there will be a seperate
announcement on the go-database list detailing these.

We realise that we could still be providing a lot more introductory
documentation on the database schema, and more up to date schema diagrams.
There are also a few teething problems with the new website and the
sourceforge site. We're working hard to remedy these, so please keep us
informed of any problems.

Cheers,
Chris

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