From listmaster animalgenome.org Fri Jul 14 08:39:00 2017
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From: Frank Nicholas <frank.nicholassydney.edu.au>
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To: OMIA-Supporters <omia-supportanimalgenome.org>
Subject: An OMIA update
Date: Fri, 14 Jul 2017 08:39:00 -0500
Dear OMIA supporters,
A brief report on recent developments, especially to provide background for discussion for
those going to ISAG (which unfortunately I cannot make).
1. A table of OMIA likely causal variants:
We now have a draft table (https://www.animalgenome.org/...db/23.xlsx) that will be mounted on the OMIA web
site in the next few weeks. The table has many omissions and errors but it is a step forward. It includes (in blue) some (but not yet all) of the bovine information provided by Matt and
Jennifer McClure - many thanks, Matt and Jennifer. The uncoloured variant information has been gleaned manually from papers, which means that the more ancient the initial variant report, the
less likely is the information to be correct for the current genome assemblies.
When the table is mounted on the website, I also hope it will be possible to sort it by
any column, and, of course, to download it. I also hope to have by then a strategy for
enabling anyone to help plug the many omissions and correct the many errors.
2. Submitting variants to EVA:
We now have a very fruitful collaboration with Gary Saunders and Cristina Yenyxe Gonzalez
at EBI, creating a system for submitting single variants to EVA. Last night I submitted my
first two variants! I will continue to beaver away on the backlog, contacting the original
researchers wherever possible. When I feel confident with the system, I will contact a few
of you to give it a beta test.
Importantly, all variants in EVA will automatically be mapped to new genome assemblies as
they become available.
For every variant in EVA (including those previously entered through dbSNP), the plan is
to replace the static variant information in the current variant table with information
gathered from EVA, using API to access relevant variants via the variant ID. The ultimate
aim (a long way off!) is to have all OMIA likely causal variants in EVA, and for OMIA to
populate its own tables and the downloadable variant table completely from EVA.
3. Text mining:
>From next week until the end of the year, the University of Sydney is providing me with the services of a bioinformatician for two days per week! We will start with a text-mining project
in collaboration with Zhiyong Lu from PubMed at NCBI and Juan Miguel Cejuela from Munich (https://www.rostlab.org/). The main aim is to use new
text-mining algorithms to locate refs with likely causal variants, and to automate the curation process as far as possible. We will also be looking at ways to automate the conversion of
non-standard descriptions of variants into standard notation.
That's enough for now.
For those of you attending ISAG, I hope the meeting is a great success.
Regards
Frank
For an up-to-date list of animal traits/disorders characterised at the DNA level,
visit Online Mendelian Inheritance in Animals (OMIA): http://omia.angis.org.au
To join the OMIA Support Group, register at http://www.animalgenome.org/...a-support/
OMIA celebrated its 20th birthday on 26 May 2015!
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