[Gusdev-gusdev] Re: Phenotype tables - Interactions

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

Hi Chris

I didn't include anything about genetic interactions even if in the 
future we will want to store them. I've reviewed the interaction table 
and I've got some thoughts about this table.

Genetic interactions may involve more than one effector/target. If we 
want to make the Interaction table generic, we need to store more than 
one effector and more than one target. I don't have any use cases yet, 
but I can ask around one if needed.
An extra controlled vocabulary is needed. This controlled vocabulary 
will be used to classify the behaviour of the effector for a given 
interaction.
e.g. Allele1 "inhibits" the expression of Allele2.

Regarding physical interactions, there are two cases in which it will be 
useful to annotate them:
    * Transient interactions associated with a function, e.g. a protein 
regulating the transcription will be interacting with DNA.
    * Structural interactions involved in the formation of a complex. In 
that case, we can associate component interactions with the complex they 
are involved in. Some of these interactions are experimentally 
characterized, others are hypothetical.

Currently in GUS, a complex is a set of components. Would it be possible 
to associate a complex with a set of interactions as well ?

The other point I didn't mention in my previous email was the review of 
the phenotype table. Would it be possible to associate phenotypic data 
with GO terms ?

cheers
Arnaud

Chris Stoeckert wrote:

> Hi Arnaud,
> These look fine to me and represent what we've discussed. Thanks for 
> putting this together!
> Cheers,
> Chris
>
> On Monday, November 11, 2002, at 06:53  AM, Arnaud Kerhornou wrote:
>
>>  Hi everyone
>>
>> I've attached SQL statements and doc for draft tables and views for 
>> holding genetic data.
>>
>> You'll find statements for:
>>
>> Allele tables:
>>
>> * Allele table,
>> * AlleleInstance table,
>> * AlleleFeature view,
>>
>> * A Complementation table which stores complementation data. It works 
>> as a reference table to another allele. It can be an internal or an 
>> external reference. There are three types of complementation 
>> references : "complements", "complemented_by", "fails_to_complement".
>>
>> Controlled vocabulary tables:
>> * PhenotypeClass - controlled vocabulary to classify the allele 
>> effects - recessif/dominant - lethal,
>> * Mutagen - controlled vocabulary of chemical products used to 
>> generate mutants,
>>
>> and
>> * AllelePhenotypeClass,
>> * AlleleMutagen,
>> * AllelePhenotype,
>> * AlleleComplementation,
>>
>> * RNAi table to store RNAi constructs data,
>> * RNAiPhenotype table.
>>
>> Please let me know if you have any questions or comments.
>> cheers
>> Arnaud
>> <phenotype.tar.gz>
>
>