From zhuiastate.edu Wed Apr 24 10:06:20 2013
From: "Hu, Zhiliang [AN S]" <zhuiastate.edu>
Postmaster: submission approved
To: Multiple Recipients of <angenmapanimalgenome.org>
Subject: What's new on the NAGRP animal genome web site (#2, 2013)
Date: Wed, 24 Apr 2013 10:06:20 -0500
What's new on the NAGRP animal genome web site (#2, 2013)
o Announcing Release 20 of the Animal QTLdb. There has been an increase
of 1,314 newly curated QTL/SNP association data with this release (87
pig, 786 cattle, 366 chicken, 36 sheep, and 39 rainbow trout data). The
current total number of QTL/SNP association data in the database is
20,090 [Breakdown by species: Cattle: 7,091; Chicken: 3,808; Pig: 8,402;
Sheep: 789; Rainbow trout: 127]. Thanks to Cari Park of Iowa State
University, as well as Yniv Palti and Sixin Liu from USDA National Center
for Cool and Cold Water Aquaculture for their data curation efforts.
The reaching of 20,000 QTL/SNP association data point is a remarkable
landmark over the history of QTLdb development. Note that it took the
first 6 years to reach 10,000 data points, and the last 3 and 1/2 years to
reach the second 10,000 data points (see the release history for details:
http://www.animalgenome.org/QTLdb/release). A big thanks goes to Cari Park among
The new release also included several improvements on the QTLdb tools:
(1) A number of bug fixes, e.g., where QTL map views could not be
properly displayed under unusual circumstances when a default chromosome
length ratio was not met.
(2) Several options were added to curator tools: Allowed manual search
and import of PubMed references for semi-automated data curation; Added
data review functions with improved data flow for QTL/SNP association data
administration; Added reference-based data summary; Improved data route;
(3) New member to Animal QTLdb data alliances: Data Citation Index (DCI)
on the Web of Knowledge platform from Thomson Reuters. DCI provides a
single point of access to quality research data from repositories across
disciplines around the world.
(4) After welcoming two newly registered curators since the last QTLdb
release, we now have 47 curators on board. As always, we encourage all
interested persons to register for a curator account, and registered
curators to actively use your account to enter new data, whether it is
your data or someone else's data in public domain - as long as you
confirm it's not already in the database.
Please be aware that *biocurator* is a new science professional career.
Valuable experiences you gain from QTLdb data curation, new insight to
help improve the curation tools, may be publishable. There are a number of
scientific conferences and journals where such progress may be reported.
o New pig RH data is available to improve QTL/SNP association information
transfer from the linkage map to the new genome build. Thanks to Bertrand
Servin and coauthors of their BMC Genomics paper (2012, 13:585) "High-
resolution autosomal radiation hybrid maps of the pig genome and their
contribution to the genome sequence assembly" who provided 14,907 RH
markers to serve as new candidate anchors between pig linkage and genome
maps. Work is still in progress to properly utilize the new RH markers
for QTL data transfer to pig genome build 10.2.
o A new "Mail Digest" function on AnGenMap is available for those who do not
wish to receive instant email posts from the listserv. Users now have
the options to receive a weekly mail summary, or receive posts directly.
A new FAQ item has been added to explain how to use it:
o Updates on the NAGRP file-share platform:
(1) Improvement was made to better streamline processes after the data
uploads. Added utility includes sequence file uploads for requesting
(2) New data added to the NAGRP Community Data Repository for sharing:
- Catfish RNA-Seq assembly from John Liu's group from Auburn University;
- Updated chicken 60K SNP mapping data from Hans Cheng of ARS, USDA.
o A new GBrowse instance is set up to display the mapping of predicted
CDS/mRNA on 1670+ oyster scaffolds from a large genome sequencing project
(Zhang, G; Fang, X; et al.: Genomic data from the Pacific oyster -
Crassostrea gigas, GigaScience, http://gigadb.org/pacific_oyster).
Thanks to Steven Roberts of University of Washington for his efforts
facilitating the information flow.
o A new web site is set up as a central location for NRSP-8 community
documents, reports, and outreach information. Thanks to the NIFA NAGRP
Director Lakshmi Matukumalli, and Eric Young of North Carolina State
University, for facilitating the process and providing the needed
o New listserv mailing lists for community activities:
(1) An "OMIA Support Group" listserv mailing list and web site was set up
for 70+ interested subscribers to engage in discussions and information
sharing. Thanks to Frank Nicholas of University of Sydney for his
enthusiasm and leadership on the efforts.
(2) An "Epigenetics Discussion Group" mailing listserv and web site was
created to bring together 190+ researchers in different fields of
epigenetics to share their knowledge and discuss future directions of this
rising field. Thanks to Hasan Khatib of UW-Madison for his leadership in
the creation of the user group.
(3) The "CRI-MAP Users Group" mailing listserv is upgraded with newly
added posts archive browser and search capability. Thanks to Jill Maddox
from Australia for her continuing contributions to the CRI-MAP improvement
efforts. The "CRI-MAP Users Group" list now has 210+ subscribers.
o Thanks to Paris Veltsos of University of St Andrews for providing a
pre-compiled CRI-MAP copy for Mac OSX platform, downloadable from the
Cri-Map Improvement web site:
o Annual reports, newsletters, and NRSP-8 2014-2018 rewrites are updated
on the Aquaculture, Cattle, Pig, Sheep, and Bioinformatics Coordination
o As part of the web site improvements, several centralized web functions
were implemented to serve dynamic web contents, which resulted in a few
web site re-organizations. Here are a few links you need to update if
they are used as links on your web sites or newsletters:
OLD: http://www.animalgenome.org/share/mtg_aqua.html - Aquaculture
OLD: http://www.animalgenome.org/share/mtg_catt.html - Cattle
OLD: http://www.animalgenome.org/share/mtg_chic.html - Chicken
OLD: http://www.animalgenome.org/share/mtg_hors.html - Horse
OLD: http://www.animalgenome.org/share/mtg_pigs.html - Pigs
OLD: http://www.animalgenome.org/share/mtg_shee.html - Sheep
OLD: http://www.animalgenome.org/share/mtg_bioi.html - Bioinformatics
OLD: http://www.animalgenome.org/share/mtg_nagr.html - All above
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We always appreciate your inputs. Please send us your suggestions or
requests at any time.
Check out the daily "what's new" (http://www.animalgenome.org/news/whatsnew)
items for up-to-date information on this site. Thank you for kindly
reporting broken links or web errors on the AnimalGenome.ORG site.
NAGRP Bioinfo Team