[Bioc-devel] Request for Comment: SNP Annotation package design

Seth,

It seems like there is more information available than that in your proposed
table structure.  Do you really want to drop those accessory data (like Avg
Het. or from what database the snps are derived)?  If you stuck with the
table structure from UCSC, then on the implementation side of things, one
could envision being able to use RMySQL, RSQLite, or RdbiPgSQL to access the
tables which could be easily obtained from bioc (RSQLite) or via a local
database (which probably several of us already have running).  I don't do
much SNP work, so I shouldn't really be saying much, but disk space is
pretty cheap, so it seems like more might be better (or at least not worse)
here?

Sean

Greetings all,

Some of us have been working on a design for annotation packages for
SNP chips.

We would like to get input from the community at large.  A summary of
our current design notes is available here:

http://wiki.fhcrc.org/bioc/SNP_Annotation_Package_Discussion

You can comment either by replying to this thread or creating an
account on the wiki (see above URL) and adding comments directly to
the page.  Adding to the wiki directly is preferred.

We will let the discussion evolve for 1 week before beginning
implementation work.

Best Wishes,

+ seth

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Hi Sean,

It seems like there is more information available than that in your
proposed table structure.  Do you really want to drop those
accessory data (like Avg Het. or from what database the snps are
derived)?  

That's a good question.  What is in the proposal is the info
specifically requested by Rafael and his collaborators.

If you stuck with the table structure from UCSC, then on
the implementation side of things, one could envision being able to
use RMySQL, RSQLite, or RdbiPgSQL to access the tables which could
be easily obtained from bioc (RSQLite) or via a local database
(which probably several of us already have running).

Interesting.  We are planning to use a database (SQLite) as the
backend for the SNP annotation.  If we are not going to integrate any
information from any other data source, then mirroring the UCSC
structure has a number of advantages.

I don't do much SNP work, so I shouldn't really be saying much, but
disk space is pretty cheap, so it seems like more might be better
(or at least not worse) here?

Yes, disk space is cheap, but network bandwidth is not.  There is some
value in keeping just the annotation data that is needed and having
smaller downloads, etc.

+ seth

Hi,

I'm posting this for Carsten who isn't yet subscribed to bioc-devel.

A couple notes:

1. If you want to post to this list, you need to subscribe.  See:
   http://www.stat.math.ethz.ch/mailman/listinfo/bioc-devel

2. If you want to update the wiki, create an account for yourself by
   going to http://wiki.fhcrc.org/bioc/UserPreferences, filling out
   the form and clicking on 'create profile'.  Then login using your
   new username/password and you should see an edit link on each page.

3. The wiki uses reST markup.  See notes and links on the main page:
   http://wiki.fhcrc.org/bioc/MyStartingPage

   Unfortunately, the markup hints on the edit page are totally
   wrong.  Sorry, working on a fix for that.

Here is Carten's post:

From: <carsten_rosenow at agilent.com>
Subject: FW: [Bioc-devel] Request for Comment: SNP Annotation package design
To: <bioc-devel-bounces at stat.math.ethz.ch>
Cc: <SMurray at illumina.com>, <eric_boyer at agilent.com>
Date: Wed Feb 15 12:22:54 2006 -0800

 
Dear Seth,

It would be great to get involved in this discussion. I had a quick
look at the page and couldn't figure out how to comment in Wiki.

I think it is very important to include flanking sequences. A
certainly longer discussion is the strandedness of the SNPs in
dbSNP. Coming up with a solution would clearly ease the use of the
database.

In addition you might want to check with Illumina on their SNP
annotations.

We are currently working on proposals and will keep you posted. Is
there an Email list I can subscribe to?

 

Thanks

Carsten

CARSTEN ROSENOW, Ph.D.
Product Manager Genotyping and Systems Biology
IBS Informatics
Agilent Technologies 
5301 Stevens Creek Blvd 
Santa Clara, CA 95051