From listmasteranimalgenome.org Tue Jan 31 21:58:58 2017
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From: Marina Fortes <m.fortesuq.edu.au>
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 21:58:58 -0600
Journals to consider targeting...
Journal of Animal Science and Animal Genetics (already doing it?...)
Livestock Genomics - Frontiers
Animal Production Science
Genetics Selection Evolution
Another thing to think about is more ways to show the value and need of
database curators, so that more of us can justify allocating time to this
Dr Marina Fortes
Lecturer in Genetics
School of Chemistry and Molecular Biosciences – SCMB, room 454 bld 76
Faculty of Sciences | The University of Queensland | Brisbane Queensland 4072 | Australia
telephone +61 7 336 54258 | email m.fortesuq.edu.au |
.From: Fiona McCarthy [mailto:fionamccemail.arizona.edu]
.Sent: Wednesday, 1 February 2017 1:37 PM
.Subject: Re: Limited representation of OMIA causative mutations for cattle in SNP
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.
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
> 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.
> Carrie Finno, DVM, PhD
> Diplomate, ACVIM
> Assistant Professor, Veterinary Genetics University of
> 280 Vet Med II
> One Shields Ave
> Davis, CA 95616
> 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.
>> .From: Frank Nicholas
>> .Sent: Saturday, January 28, 2017 12:10 PM
>> .Subject: RE: Excerpt from: Animal Genetics Content Alert (New
>> 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.
>> 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!
>> .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
>> Brief Notes
>> Limited representation of OMIA causative mutations for cattle in SNP
>> databases http://onlinelibrary.wiley.com/...i/10.1111/age.12534/
>> Aditi Sharma, Yongmin Cho, Bong-Hwan Choi, Han-Ha Chai, Jong-Eun Park
>> and Dajeong Lim Version of Record online: 24 JAN 2017 | DOI:
The AgBase Databases
School of Animal and Comparative Biomedical Sciences & BIO5 University of Arizona