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From: "Hu, Zhiliang [AN S]" <zhuiastate.edu>
CC: "Hu, Zhiliang [AN S]" <zhuiastate.edu>
Subject: Re: Limited representation of OMIA causative mutations for cattle in SNP databases
Thread-Topic: 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 21:32:08 -0600
I completely agree with Carrie that journal requirements for data
deposition into a well maintained public database as a pre-request
is an essential first step to not only make the data available to
public, but also for the databases to populate and re-synthesize
the data to make them more useful under a federated database concept.
In this case, it+IBk-s between the OMIA and the dbSNP. Many people,
including the authors of that Korean paper commented by Frank, may
not fully realize what it takes to get information across databases.
For example, in the case for Animal QTLdb, it was a long way to convince
the journal editors for them to believe such requirement will benefit
the whole community in terms of data reuse, meta analysis, structured
analysis, networked analysis, etc. Thanks to the editors of the Animal
Genetics and Journal of Animal Science for their understandings and
visions, we are fortunate to have their endorsement requiring QTL/
association data deposition as their publication pre-requests. Thanks
the team at Iowa State Uinversity led by Jim Reecy, Max Rothschild,
Susan Lamont and Christuggle to have successfully pursued this. We need
to convince more journals to do the same.
Go one step further, suppose you have the data volunteered into a
database by each publication -- are these information get automatically
integrated? One perception often is, for example, when you have a
phenotype located to a genome map (being it cyto OR linkage OR physical),
and you get a bunch of SNPs in the same genome, and one could
subsequently imagine that, through some cyber magics you could
automatically have a list of SNPs mapped to the phenotype. That would
be ideal world if you are lucky. When this does not automatically
happen, whom to ask for? Where to go for an answer? There is an easily
negligible aspect in database development -- data curation. Data curation
takes time, needs man-power, and most importantly, requires someone with
qualified knowledge and skills to comprehend, locate, match, merge, and
synthesize information from different sources. In addition, this job can
be tedious, time consuming, and challenging in terms of coping with
emerging sciences/technologies. We need to convince the funding agencies
for these professional man power to be invested for the post-publication
data curation, along with tool builders to efficiently and effectively
facilitate this process. Frank has been doing an exceptional outstanding
works in OMIA development and data curations. We need more people to
follow, and to support him.
Thirdly, only by effective data integration and exchange between
specialized databases, can information become more useful, and knowledge
extend beyond the horizon. Again the example can be between OMIA and dbSNP
(more such examples exist, such as between OMIA and Uberon, QTLdb, NCBI
Gene DB, dbVAR, ... to link information in a number of different dimensions.
This message has been too long, I will stop here.
The Korea paper on the coming issue of Animal Genetics comes at a good
timing, although it could be better geared towards a more practical
approach to solve their problem.
Zhiliang
-----Original Message-----
.From: Carrie Finno +ADw-cjfinno+AEA-gmail.com>>
.Date: Tue, Jan 31, 2017 at 03:15 PM
.To: OMIA-Supporters +ADw-omia-support+AEA-animalgenome.org>>
.Subject: Re: Limited representation of OMIA causative mutations for cattle in SNP
databases
Resent-From: +ADw-omia-support+AEA-animalgenome.org>>
Resent-Date: Tue, Jan 31, 2017 at 03:15 PM
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 +ACo-require+ACo- 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
----------------------------------+AD0APQA9AD0APQA9AD0------------------------------------
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+IBk-s email:
>> I spotted this note last week, and wrote immediately to its senior authors
>> (who have been cc+IBk-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+ACE-
>> Zhiliang and Jim Reecy (who are also cc+IBk-d in this message) have very
>> generously led two grant proposals to the USDA for funding OMIA
>> enhancements+ADs- 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+IBk-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+IBk-s more to be said, but I+IBk-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+ACE-
>> Regards
>> Frank
>>
>> .From: Hubbard, Suzanne +AFs-mailto:Suzanne.Hubbard+AEA-ARS.USDA.GOV+AF0-
>> .Sent: Saturday, January 28, 2017 1:04 AM
>> .Subject: Excerpt from: Animal Genetics Content Alert (New Articles)
>>
>> Animal Genetics
>> +AKk- Stichting International Foundation for Animal Genetics
>>
>> Early View http://onlinelibrary.wiley.com/...111/(ISSN)
>> 1365-2052/earlyview?campaign+AD0-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+AD0-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+AD0-wolearlyview
>> Aditi Sharma, Yongmin Cho, Bong-Hwan Choi, Han-Ha Chai, Jong-Eun Park and
>> Dajeong Lim
>> Version of Record online: 24 JAN 2017 +AHw- DOI: 10.1111/age.12534
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