Re: [Gusdev-gusdev] Re: GUS 3.0 schema changes: ASCII art redux

[Jonathan C. <cra...@pc...>]

Arnaud-

Returning to some slightly older business...

>>
>>                           <DoTS::GenomicSequence>
>>                           ^      ^      ^    ^  ^
>>                           |      |      |    |  |
>>     <DoTS::GeneFeature (RHS)>    |      |    |  |
>>               ^                  |      |    |  |
>>               |                  |      |    |  |
>>    <DoTS::TransposableElement (INGI)>   |    |  |
>>    ^                ^                   |    |  |
>>    |                |                   |    |  |
>>    |           <DoTS::RepeatRegionNAFeature> |  |
>>    |                   ^                     |  |
>>    |                   |                     |  |
>>    |          2 x <DoTS::RepeatFeature (RIME)>  |
>>    |                                            |
>>    |                                            |
>>    ------------------------<DoTS::GeneFeature (pseudo)>
>>
> 
> My proposal is this representation without the repeat region feature. I would
> see the repeat region feature to cluster together a sequence, whatever the
> sequence is (even one base, or more), repeated X times, but not being used in
> this situation.

Meaning that you would only use the repeat region feature when X > 1, right?
I'm suggesting that we combine the two tables, meaning that we would have one
uniform representation for all X.  I suppose that's probably my strongest
argument against the 2-table representation, namely that it seems arbitrary
to say that something is only a "repeat region" when it contains > 1 copy of
a repeat.  Wouldn't such a thing be better described as a tandem repeat?

>>region".  Specifically, can a repeat region contain things that are not
>>repeats,
>  
> Yes ! a gene for example !! A repeat region would be used to cluster tandemly
> repeated genes. But this should be fine as long as a gene feature can be
> attached to a repeat region.

My question wasn't quite correct; I should have asked whether a repeat region
can contain things that are not repeated.  That is, could you use a repeat region
to cluster tandemly repeated genes if those genes were separated by some
additional non-repeating sequences.  It sounds like the answer is probably "yes",
and that your definition of repeat region is simply any region that contains two
or more copies of some type of sequence.  Is this accurate?

> I think we want to represent a transposable element in a given context, ie at a
> given location because this insertion may have consequences, (in)activating a
> gene or shifting the frame of a gene etc.
> 
> A core transposon should be represented as an entity on its own like genes are.

OK, I agree, and I think that fits with the current schema (except that we have
yet to create a table to represent the transposons independent of their location.)

Jonathan

-- 
Jonathan Crabtree
Center for Bioinformatics, University of Pennsylvania
1406 Blockley Hall, 423 Guardian Drive Philadelphia, PA 19104-6021
215-573-3115