From listmaster animalgenome.org Tue Jan 31 21:36:43 2017
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From: Fiona McCarthy <fionamccemail.arizona.edu>
Subject: Re: Limited representation of OMIA causative mutations for cattle in SNP databases
Postmaster: submission approved by list moderator
To: OMIA-Supporters <omia-supportanimalgenome.org>
Date: Tue, 31 Jan 2017 21:36:43 -0600
I strongly agree that we need to ensure that SNPs are uploaded to dbSNP as
a part of publication and that accessions are reported in the article. In
addition to contacting Journal Editors, we all need to do our part as
reviewers to insist on this.
The argument of not wanting to submit data to a public archive because the
process is tedious also applies to SRA data and yet we all still manage
that process.
Frank - do you have a list of Journals where you most commonly find SNP
data? It may be that a general statement targeting these editors would be a
great starting place. I would be happy to sign a statement like this
showing my support.
Fiona
On Tue, Jan 31, 2017 at 2:15 PM, Carrie Finno <cjfinnogmail.com> wrote:
> 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
> ------------------------------------------------------------
> --------------------------------------------------
>
>
> 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/...111/(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
--
The AgBase Databases
School of Animal and Comparative Biomedical Sciences
& BIO5
University of Arizona
Phone: 520-626-7321
http://www.agbase.msstate.edu/
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