Re: [Gusdev-gusdev] Controlled Vocabularies data

[Arnaud K. <ax...@sa...>]

Hi Steve

Steve Fischer wrote:

> Arnaud-
>
> first, about DoTS::GeneInstanceCategory.  we don't seem to be using 
> this table.  its empty in our instance. 

We want to generate gene, RNA and protein entries and link them to 
corresponding gene, RNA and protein feature entries. This is done using 
the Gene, RNA and Protein Instance entries.
There is a FK to a GeneInstanceCategory entry in GeneInstance and this 
can not be null. The same for RNAInstance and for ProteinInstance, I'm 
not sure what they are for.

>
>
> second, about the other vocabs.  there is no central resource 
> available. each is dealt with individually.  for example, sres.taxon 
> has a plugin which loads data from ncbi.  sres.anatomy exists uniquely 
> in our db and was created manually.

I'm thinking of CVs such as Taxon with has its own plugin and that the 
data can be retrieve from NCBI.
There are a few ones, GUS specific, that we could share, e.g. 
SRes::OntologyRelationshipType 
<http://www.gusdb.org/cgi-bin/schemaBrowser?db=CBILBLD&table=SRes::OntologyRelationshipType&path=SRes::OntologyRelationshipType> 
(AFAIR two entries "part_of" and "is_a"). They could be stored in XML 
format or as SQL statements. I'm thinking of others CVs, I'll prepare a 
list.

>
> so, to best answer your question we would need to know which CVs you 
> want to populate.
>
> steve
>
> Arnaud Kerhornou wrote:
>
>> Hi
>>
>> We would like to populate some of the GUS Controlled Vocabulary 
>> tables. I'm thinking of DoTS::GeneInstanceCategory, and of a bunch of 
>> SRes tables.
>> Are these resources available in XML format or in SQL statements from 
>> gusdb website or from CVS ?
>>
>> cheers and happy thanksgiving !!
>> Arnaud
>>
>>