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the true root of GO

Midori Harris midori at ebi.ac.uk
Wed Mar 9 08:47:36 PST 2005


Hello,

These changes are a consequence of the switch to the OBO file format, in
which the former root node GO:0003673 Gene_Ontology is now obsolete,
because it did not represent an actual biological concept.

Some software -- including AmiGO -- relies on there being a root node, so
the developers have created an artificial node in the MySQL database
called "all" that is the root of all possible concepts.

Regards,
Midori

============================
Midori A. Harris, Ph.D.
GO Editor
EMBL - EBI
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD UK

Tel: +44 (0) 1223 494667
Fax: +44 (0) 1223 494468
Email: midori at ebi.ac.uk

On Tue, 1 Mar 2005 Arne.Muller at sanofi-aventis.com wrote:

> Dear All,
> 
> I'm not cutting edge with the recent GO developments, so I may have
> missed some important discussion - please forgive me ...  The
> "historial" root of GO was always "gene_ontology" (GO:0003673) which is
> now an obsolete term (since when?). What was the reason to change the
> dummy root of the DAG from 'gene_ontology' to 'all'?
> 
> Is this an indication for a trend to incoorperate other independent
> branches and different kinds of classifications/namespaces (in addition
> to MF, BC and CC) into GO, and to striclty provide these branches in
> separate files rather than one file with an artifical dummy root?
> 
> 	kind regards,
> 
> 	Arne
> 
> --
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--
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