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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 15:55:27 PDT 2004


Mike,

There are three dates associated with the file:

1.  (16946 terms as of February 16, 2004), next to a download link 
2. The date in the file header, 
date: 03:06:2004 17:17
3. The date in the ftp listing, 
06/03/2004 10:10AM      5,391,811 gene_ontology.obo

How am I as a user supposed to know which date applies? If as you and
Jane said the file is being regenerated every 24 hours or so, has it not 
changed
since March 6? Oh, I see: one is European style and the other is US, they are
both June 3! 

In any case the initial observation was from several months ago and may have
been addressed with the new update policy. I agree that (1) being out of date
is not a big deal.

Cheers, -Stan



cherry at genome.stanford.edu writes:
Stan,

Yeap, I don't really see a problem with what you mention.  The web page 
says how many terms where present on Feb 16th, that is true.  The file 
tells you the current state as of the minute you retrieve it, thats 
true too.

Is the issue the fact that someone updated the HTML page for the old 
format files and did not update the OBO file totals?

Molecular Function text file (7358 terms as of June 1, 2004)
Biological Process text file (8779 terms as of June 1, 2004)
Cellular Component text file (1414 terms as of June 1, 2004)

Thats just a minor oversight by whoever was editing the HTML.  The 
total for the OBO file on June 1, 2004 was 17,553 with 884 of those 
being obsolete.

-Mike


On Jun 3, 2004, at 1:24 PM, SLetovsky at aol.com wrote:

> 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
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