From listmaster animalgenome.org Tue Jan 31 15:15:39 2017
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From: Carrie Finno <cjfinnogmail.com>
Subject: Re: Limited representation of OMIA causative mutations for cattle in SNP databases
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To: OMIA-Supporters <omia-supportanimalgenome.org>
Date: Tue, 31 Jan 2017 15:15:39 -0600
Dear group,
I agree that this is problematic that these variants are not being uploaded
to open-access databases. Unfortunately, I think that this will only solved
once journals *require* the upload prior to publication. This is the way
that next-gen sequence data is getting uploaded to SRA now...you cannot
even submit a paper unless you have already uploaded your data to NCBI
SRA. So, although uploading to SRA is quick a time-consuming task (as is
dbSNP), it will get done in order to submit a manuscript.
So, perhaps we need to rally to encourage journal editors to require any
new putative functional variants are uploaded to dbSNP in the same manner?
I look forward to further discussion.
Best,
Carrie
-------------------------------------------------------------------------------------
Carrie Finno, DVM, PhD
Diplomate, ACVIM
Assistant Professor, Veterinary Genetics
University of California-Davis
280 Vet Med II
One Shields Ave
Davis, CA 95616
(530)-752-2739
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On Sat, Jan 28, 2017 at 8:38 AM, Frank Nicholas wrote:
> Dear OMIA colleagues,
> The following correspondence is self-explanatory.
> I look forward to some fruitful discussion and,
> ultimately, to resolving the problem.
> Regards
> Frank
>
> .From: Frank Nicholas
> .Sent: Saturday, January 28, 2017 12:10 PM
> .Subject: RE: Excerpt from: Animal Genetics Content Alert (New Articles)
>
> Dear Suzanne
> Thank you very much for circulating this just-published
> note in Animal Genetics.
> To everyone included in Suzanne’s email:
> I spotted this note last week, and wrote immediately to its senior authors
> (who have been cc’d in this message). In my message to the authors, I
> thanked them for highlighting a problem that has been occupying my mind for
> several years, namely that many likely causal variants in OMIA are not
> included in dbSNP or any other variant database.
> Because the Korean team has raised such an important
> issue, and because the discussion needs to include a wider group than is
> included in this email list, I suggest that we transfer this discussion to
> the OMIA Support Group discussion list http://www.animalgenome.org/
> community/omia-support/ , kindly set up a few years ago by Zhiliang Hu.
> If you are not on this list and wish to continue with this conversation,
> please join up!
> Zhiliang and Jim Reecy (who are also cc’d in this message) have very
> generously led two grant proposals to the USDA for funding OMIA
> enhancements; both were near-misses. Solving the problem highlighted in the
> Animal Genetics note is one of three projects that comprised the USDA grant
> proposals (the other two being text mining and ontologies).
> For several years I have been compiling manually a table
> of OMIA likely causal variants, aiming to provide for each variant its
> location on the relevant current assembly. For any variant that has been
> entered in dbSNP, this is an easy task. For the many that have not been so
> entered, it can be very time-consuming to dig out the relevant information,
> especially for variants published in the pre-assembly era. Ensembl’s
> Variant Effect Predictor (VEP) http://asia.ensembl.org/info/
> docs/tools/vep/index.html has proved to be very useful, enabling the
> table to be populated with relevant information on-the-fly via REST APIs.
> My plan has been to place an abbreviated form of this table on the OMIA web
> site, highlighting those variants that are not in dbSNP or Ensembl
> Variation, hoping that this will stimulate authors to submit their variant
> to one of the databases.
> Also, in recent times, whenever anyone publishes a new
> likely causal variant, I write to them, asking if they would submit the
> variant to a database, and explaining about the OMIA table. Interestingly,
> I am often told that entering single variants in dbSNP is a very tedious
> business and, consequently, authors are often reluctant to make the
> submission. Having never submitted a variant to any database, I have no
> first-hand experience. But if anyone in this email list has had some
> experience, it would be very helpful to hear from you via the OMIA Support
> Group discussion list. http://www.animalgenome.org/...a-support/
> Another strategy on the OMIA to-do list is to ask journal
> editors to require any likely causal variant to be submitted to a variant
> database prior to publication. Zhiliang and Jim and I have also planned to
> ask editors to require relevant OMIA IDs to be included in any paper
> publishing a likely causal variant.
> There’s more to be said, but I’ll leave further discussion
> to the OMIA Support Group discussion list.
> Suffice to say that I welcome the Korean team highlighting
> this problem, and, with the support of people in this list and of the wider
> OMIA community, I am optimistic that we will be able to work with
> colleagues at NCBI and Ensembl to solve it!
> Regards
> Frank
>
> .From: Hubbard, Suzanne [mailto:Suzanne.HubbardARS.USDA.GOV]
> .Sent: Saturday, January 28, 2017 1:04 AM
> .Subject: Excerpt from: Animal Genetics Content Alert (New Articles)
>
> Animal Genetics
> © Stichting International Foundation for Animal Genetics
>
> Early View http://onlinelibrary.wiley.com/...urnal/10.1111/(ISSN)
> 1365-2052/earlyview?campaign=wolearlyview (Online Version of Record
> published before inclusion in an issue)
>
> These Early View articles are now available on Wiley Online Library
> http://onlinelibrary.wiley.com?campaign=wolearlyview
>
> Brief Notes
>
> Limited representation of OMIA causative mutations for cattle in SNP
> databases http://onlinelibrary.wiley.com/...i/10.1111/age.12534/
> abstract?campaign=wolearlyview
> Aditi Sharma, Yongmin Cho, Bong-Hwan Choi, Han-Ha Chai, Jong-Eun Park and
> Dajeong Lim
> Version of Record online: 24 JAN 2017 | DOI: 10.1111/age.12534
|
