[Gmod-help] genotype and SNPs

[GMOD Help Desk]

Josef,

I have not dealt with this particular situation before.  I will answer
your questions as best as I can.   I am also sending your question to
the GMOD Schema list, as someone on that list may have dealt with this
before.

A posting from Chris Mungall in 2004 addresses some of your SNP questions:

http://sourceforge.net/mailarchive/message.php?msg_id=Pine.LNX.4.33.0403291606310.21937-100000%40heartbroken.lbl.gov

The relevant paragraph is

  we have two choices; either we create a fake
  feature representing all the chromosome features in the individual; or,
  preferably, we create a chromosome feature for the individual. Most of the
  fields of this feature will be null.

What is not clear to me is how to associate the featureloc records
with both the SNP feature record and the individual's chromosome
feature record.

Does anyone out there have any suggestions or experience with this situation?

Regards,

Dave C.

On Nov 14, 2007 2:46 PM, Josef Jurek <jurek at cs.uchicago.edu> wrote:
>
> Hello Dr. Clements;
>
> Our lab has genotype information,
> (SNPs, microsatelites) for thousands of subjects
> and I am presently trying to figure out how
> we can load this information into the Chado schema.
>
>
>   First, from the available documentation I see how SNP
>   names are put in rows in the table "feature" and that
>   alternate nucleotides are stored in the table "featureloc"
>   and linked to rows in "feature".
>
>
>   Now, in what table do we put rows for our subjects
>   (the people)?  Would this be in the table "genotype"?
>
>
>   And then, if "genotype" is the correct table for
>   our subjects, then how are these subjects linked
>   to a particular nucleotides in "featureloc" for
>   each SNP?
>
>
> I have a ER diagram of the relevant parts
> of the schema here, it that is of help:
> http://jurek.uchicago.edu/gmod
>
> Thank you for your help; Josef
>
>
> Josef Jurek
> Department of Human Genetics
> The University of Chicago
> jurek at cs.uchicago.edu
> 773 834 1304
>
>