Re: [Gusdev-gusdev] Controlled Vocabularies data

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

Steve Fischer wrote:

> arnaud-
>
> i should have been more precise about DoTS::GeneInstanceCategory.  We 
> have one row for it:  "unknown".
>
> In general, it seems that our our CVs are either:
>  - loaded from an external source (by a plugin)
>  - our own invention (manually created).
>
> For the latter case, I agree that CBIL might want to make those 
> available to the GUS project in the form of XML.  If my recollection 
> is correct, PSU has a copy of our GUS data from about a year or so 
> ago.  Is that right?  

We've got XML data files used to populate gusdev CV tables 
(ExternalDatabase, AlgorithmParamKey, AlgorithmParamKeyType, 
RNASequenceType and SequenceType). I don't know if they are the ones 
you're talking about.
We've updated ExternalDatabase XML to be used with GUS3. I don't think 
we need to update the other ones.

AFAIK we don't have Anatomy, DevelopmentStage or Disease but I don't 
think we need them at the moment.

I can see another table, SRes.EnzymeClass that we will want to populate. 
How shall we do it ?

cheers
Arnaud

> The basic question is whether our current GUS XML is powerful enough 
> to express, eg, the anatomy CV.   If so, then we could write it to XML 
> and make it available.
>
> steve
>
> Arnaud Kerhornou wrote:
>
>> 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
>>>>
>>>>