Archived Post

From  Wed Apr 24 10:06:20 2013
From: "Hu, Zhiliang [AN S]" <>
Postmaster: submission approved
To: Multiple Recipients of <>
Subject: What's new on the NAGRP animal genome web site (#2,
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: A big thanks goes to Cari Park among
  other curators!

  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
  batch blasts.

  (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,
  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
  web sites.


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: - Aquaculture

  OLD: - Cattle

  OLD: - Chicken

  OLD: - Horse

  OLD: - Pigs

  OLD: - Sheep

  OLD: - Bioinformatics

  OLD: - 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" (
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



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