Re: [SO-devel] so.definitions v. so.obo

[Karen E. <ei...@fr...>]

Hi Steve,
In the old days there were two files needed for GO, an ontology file 
and a definitions file.
Only those terms with a definition made it to the definitions file.
We used this system for SO initially, but moved to the OBO format as 
soon as it was finalized.

Each entry in an obo file has all the information needed for that term. 
Those terms with definitions have a line beginning with 'def'

Most of the terms in SOFA have a definition, but as yet SO has many 
terms that are undefined.

As you can see the term you mentioned is in the so.obo file but has no 
def line.
[Term]
id: SO:0000492
name: D_gene_recombination_feature
is_a: SO:0000301 ! 
recombination_feature_of_vertebrate_immune_system_gene

It appears in the SO.ontology file,
  @is_a@D_gene_recombination_feature ; SO:0000492

but not in the definitions file as it has not yet got a definition.

This is not a sync problem. The files all have the correct info, its 
just a mix up between the two different methods that were used to 
capture the ontology. As you can see from Scotts response, we still 
need to keep the data in the legacy format as some people are still 
using it.

There is documentation on the gene ontology homepage explaining the 
formats.
OBO-http://www.geneontology.org/GO.format.shtml#oboflat

legacy GO format: http://www.geneontology.org/GO.format.shtml#goflat


--Karen




On Aug 26, 2005, at 8:55 AM, Steve Fischer wrote:

> folks-
>
> in the latest CVS, there are terms in so.obo (eg, SO:0000492) that are 
> not in so.definitions.
>
> why is that?  which is the correct file to use for downloading, and 
> loading into our warehouse?
>
> thanks,
> steve
>
>
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