Fwd: [GET-Editors] adding dbSNP IDs

[Barbara Ruef]

Accidentally went off the get-editors list, so forwarding the response.


---------- Forwarded message ----------
From: Madeleine Ball <mpball at gmail.com>
Date: Mon, Oct 10, 2011 at 10:58 AM
Subject: Re: [GET-Editors] adding dbSNP IDs
To: Barbara Ruef <bjruef at gmail.com>


So, it looks like the issue here is that the dbSNP ID was added quite
recently to dbSNP (it's not in build 130 or 132, I think the page indicates
it was created in build 134, which is the most recent build). I don't think
the answer is to add by hand.

This is the sort of thing that should be addressed automatically. Ideally,
we should create an automatic addition or update of all amino acid changes
predicted by the latest dbSNP build, something we could run again whenever
new updates come out. Unfortunately, my last experience with dbSNP was that
it was actually hard to find out what the nonreference genotypes are -- the
database is focused on reporting *locations* of polymorphisms but not the
nucleotide variants themselves. This variant was added to GET-Evidence
because it was seen in a PGP genome, but those genomes were build 36 which
means it is forced to use build 130 of dbSNP. Build 37 genomes can use the
latest dbSNP build (now up to 134) -- this sort of thing should hopefully
get addressed automatically as we start receiving and processing build 37
genomes instead of build 36.

I think "without dbSNP entries" was a rough proxy for "probably rare" (if
not in dbSNP yet) when making this report? In this case it looks like this
is the case (.7% allele frequency in the population study that reported the
variant to dbSNP). Presumably there *were* web hits to the variant, and so
there was info to find there -- I'm guessing that's how you ended up there?
Web hits needs updating but it's not trivial; maximizing the dbSNP IDs would
also surely help with search results.

Please go ahead and forward this email to the get-editors if you're okay
with having it go there? I wasn't sure if you intentionally dropped this
conversation off the list. :-)

  -- Madeleine

On Fri, Oct 7, 2011 at 11:34 AM, Barbara Ruef <bjruef at gmail.com> wrote:

> Hi Madeleine,
>
> I think I had gone to the reports page and randomly selected a variant from
> a list that said 'no dbSNP'. This was the one I looked at.
>
> http://evidence.personalgenomes.org:80/ZP1-Val93Ile
>
> I went to dbSNP and found the record and put the ID in the comment field of
> the publication I added. Is this one that should have been loaded? I didn't
> know if there was a way for editors to add external data IDs or links.
>
> Thanks,
> Barbara
>
>
> On Oct 7, 2011, at 6:16, Madeleine Ball <mpball at gmail.com> wrote:
>
> > It depends what you're talking about, you're right that it should be
> > added automatically for any nonsynonymous variants. Can you tell me
> > the particular case here? If it's missing and should've been added,
> > then it's useful to know what needs to get fixed.
> >
> > Thanks!
> > Madeleine
> >
> > On Thu, Oct 6, 2011 at 5:16 PM, Barbara Ruef <bjruef at gmail.com> wrote:
> >> Is there a way to add the SNP IDs if they're not brought in
> automatically?
> >> Or is this something that will be updated in batch in the future?
> >> Thanks,
> >> Barbara
> >> _______________________________________________
> >> GET-Editors mailing list
> >> GET-Editors at lists.freelogy.org
> >> http://lists.freelogy.org/mailman/listinfo/get-editors
> >>
> >>
>
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