From zhuiastate.edu Mon Jan 4 09:39:33 2016
From: "Hu, Zhiliang [AN S]" <zhuiastate.edu>
Postmaster: submission approved by list moderator
To: Multiple Recipients of AnGenMap <angenmapanimalgenome.org>
Subject: What's new on the NAGRP animal genome web site (#1, 2016)
Date: Mon, 04 Jan 2016 09:39:33 -0600
What's new on the NAGRP animal genome web site (#1, 2016)
o Animal QTLdb updates:
Announcing Release 28 of the Animal QTLdb. A total of 6,622 new QTL/
association data were curated into the database since the last release in
August. This brings the total number of QTL/association in the database
to 64,036 [Break down: Cattle: 42,019; Chicken: 5,196; Horse: 1,125;
Pig: 14,479; Sheep: 1,090; Rainbow trout: 127] (New additions less
obsolete ones: Cattle: 5,326; Chicken: 520; Horse: 1; Pig: 521;
Sheep: 254; Rainbow trout: 0). We thank Mirjam Frischknecht, Lichun He,
and Ewa Sell-Kubiak for curating their data into the database.
Recent developmental updates:
(1) New information pages were set up to describe the steps needed to
upload a large quantity of new QTL/association data. An important part
of this information is a set of guidelines regarding the minimum
Information required for preparation of new QTL/association data. Actual
working examples will be added in the coming months.
(2) A new plot tool for whole-genome view of QTL/association data was
created. This is to overcome the space limitations of the current plot
tool where all chromosomes were arranged in a panel with a fixed dimension
(as such, the current whole genome plot only gave a brief overview of
QTL/associations with a limited number of data allowed by the space).
To use it, start from browing by traits, click on a "link out" icon by
a trait name to go to "Find all QTL for this trait type" will do.
Currently the new plot tool is linked from the current tool as an
alternative. The new tool will be made the default, and more query/plot
options will be implemented in the coming months.
(3) A user input portal is added to the QTL/association view page. The
purpose of this function is for users to add annotations or comments and
report problems. Additional annotation data will aid future meta
analysis; problem reports will help with our data quality control
(4) A new curator tool has been added that makes it possible to review
QTL/association data by traits, and to enter the same comments for
multiple QTL/association data for the same trait. This decreases
laborious repeats and improves data review.
(5) A number of bugs in the curator/editor tools were found and fixed.
This continued effort helps to ensure a streamlined data curation
By the way, a new paper on recent developments in the Animal QTLdb will
be published in the Nucleic Acids Research 2016 Database Issue
("Developmental progress and current status of the Animal QTLdb";
Please check it out for more details.
o New home for OMIA:
Working with Dr. Frank Nicholas and Matthew Hobbs of the University of
Sydney, we are in the process of migrating the Online Mendelian
Inheritance in Animals (OMIA) database from its original University of
Sydney site to Iowa State University. We expect the full migration to
be completed in the coming months.
o Livestock Breed Ontology (LBO):
We have been developing a livestock breed ontology (LBO) which was first
started as a utility for Animal QTLdb. A most recent copy of the LBO has
been deposited in Bioportal.ORG, and also made available through AmiGO
hosted on AnimalGenome.ORG.
o FAANG web site:
We have recently developed a number of web modules to support the
Research activities of the Functional Annotation of Animal Genomes
(FAANG) community in terms of organized working groups and activities,
Grant application oriented collaborations and communications, improved
membership management, etc. The functions/tools can be applied to other
groups if such interest exists.
o The NAGRP Data/Tools Repository updates:
New data were continually added to the NAGRP Host of Supplementary Data
to Publications (from Mohamed Salem of Middle Tennessee State University;
Michelle Mousel of USDA/Washington State University), and to the NAGRP
VCF Data Repository (Julia Metzler/Joern Wrede from Institute of Animal
Breeding and Genetics, Germany; Jessica Petersen/Samantha Brooks of
University of Florida).
Check out the daily "what's new" (http://www.animalgenome.org/news/) items
for more up-to-date information on this site. Thanks in advance for kindly
reporting broken links or web errors on AnimalGenome.ORG.
Your input is always appreciated. Feel free to contact us any time with
your needs, requests, and/or suggestions. You can reach us in multiple
ways: contact Jim Reecy (+1-515-294-9269) for new projects/priorities,
email the team at the email address below, or use our online Helpdesk
(http://www.animalgenome.org:bioinfo/services/helpdesk) for specific
NAGRP Bioinfo Team