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[Go-database] Re: error when loading GO process into GO database

SLetovsky at aol.com SLetovsky at aol.com
Thu Jun 3 13:24:11 PDT 2004


Hi Mike,

 At http://www.geneontology.org/index.shtml#downloads the table says:

"The gene ontologies in OBO flat file format: gene_ontology.obo text file 
(16946 terms as of February 16, 2004)"

The linked file has the header:

format-version: 1.0
date: 03:06:2004 17:17
saved-by: jlomax
auto-generated-by: DAG-Edit 1.417
default-namespace: gene_ontology


Cheers, -Stan





In a message dated 6/3/2004 4:11:01 PM Eastern Daylight Time, 
cherry at genome.stanford.edu writes:
Hi Stan,

Where are you looking?  The FTP site 
(ftp://ftp.geneontology.org/go/ontology/) has:

-rw-r--r--   1 0        1          228413 Jun  2 23:15 
component.ontology
-rw-r--r--   1 0        1         1268160 Jun  2 23:15 function.ontology
-rw-r--r--   1 0        1         5391811 Jun  3 10:10 gene_ontology.obo
-rw-r--r--   1 0        1         7770100 Jun  2 23:15 process.ontology

As Jen said, the *.ontology files are generated and committed to CVS 
once a day at 23:15 from the OBO that exists at that moment.  The 
gene_ontology.obo file is committed as it is changed to the GO CVS.  
The FTP site is updated at twice an hour from the GO CVS.  The 
Anonymous CVS is not used much and is updated only nightly, however I 
think we should make that happen more often.

Its the same data for a while, the difference is just the time of 
update and that is never more than 24 hours apart.  Of course the file 
will be different today than it was yesterday because this is an active 
project.  Monthly archives of the *.ontology and OBO files are 
available from the FTP site at:  
ftp://ftp.geneontology.org/go/ontology-archive/

-Mike


On Jun 3, 2004, at 5:45 AM, SLetovsky at aol.com wrote:

> In a message dated 6/3/2004 8:19:29 AM Eastern Daylight Time, 
> jane at ebi.ac.uk
> writes:
> (the old flat file format is now updated once a day),
>
>>> Jane, how often is the OBO file updated? We noticed a while back
> it seemed much older than the OFF (old flat file :-) file. Also, the 
> database
> files, same question. We didn't realize (and I suspect other folk may 
> not)
> that we get different data depending on which format we download...
>
> Cheers, -Stan
> _______________________________________________
> Go-database mailing list
> Go-database at mail.fruitfly.org
> http://mail.fruitfly.org/mailman/listinfo/go-database


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