From listmaster animalgenome.org Sat Jan 28 10:38:54 2017
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From: Frank Nicholas <frank.nicholassydney.edu.au>
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To: OMIA-Supporters <omia-supportanimalgenome.org>
Subject: Limited representation of OMIA causative mutations for cattle in SNP databases
Date: Sat, 28 Jan 2017 10:38:54 -0600
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/...munity/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/...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/...munity/omia-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/...learlyview
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
|
