Archived Post

From  Wed Jan 11 13:18:09 2017
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From: "Hu, Zhiliang [AN S]" <>
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To: Multiple Recipients of AnGenMap <>
Subject: What's new on the NAGRP animal genome web site (#1,
Date: Wed, 11 Jan 2017 13:18:09 -0600

What's new on the NAGRP animal genome web site (#1, 2017)

o NRSP-8 Bioinformatic Coordination Activity Updates

  The annual updates from NRSP-8 Bioinformatic Coordinators are available
  online.  It covered related works in and supports to a number of areas
  including ontology development, minimal standards development, expanding
  Animal QTLdb functionality, software development, facilitating research,
  multi-species support, community support, user services and reaching out.


o Animal QTLdb updates:

  Announcing Release 31 of the Animal QTLdb.  A sum of 15,237 new QTL
  have been added to the database. The current total number of QTL in
  the database: 121,265 [Break down: Cattle: 95,332; Catfish: 0; Chicken:
  6,633; Horse: 1,245; Pig: 16,516; Sheep: 1,412; Rainbow trout: 127]
  (New additions less obsolete/retracted ones: Catfish: 0; Cattle: 13,680;
  Chicken: 950; Horse: 48; Pig: 483; Sheep: 76; Rainbow trout: 0 -- Net
  QTL number increase: 15,237).  URL:

  New developments:

  (1) The curation tools have been improved to allow automatic verification
  and streamlined curation of SNP information into the database. The
  improvements involve data quality control processes in which multiple
  genome builds are maintained for cattle, chicken, and sheep.


  (2) Curation protocols have been modified so that preliminary SNPs (with
  'ss' numbers only) are allowed to be entered to anchor QTL/association
  mapping locations.  The QTL/association mapping data represented by the
  'ss' SNPs are not subject to normal data release procedures unless the
  manually entered genome map coordinates are also available. The SNP 'ss'
  numbers will eventually be replaced with the corresponding SNP 'rs'
  numbers once they are assigned by dbSNP.


  (3) The Frequently Asked Questions have also been updated to include a
  couple new small items.


  (4) Five people applied to become new Animal QTLdb curators since the last
  update in August.  Training processes are underway to bring them up to
  speed on data curation protocols.


o Ontology developments:

  Three ontologies have been under active development at Iowa State
  University.  New versions of the ontologies have been released:
  Vertebrate Trait (VT) Ontology, version 6.9; Livestock Product Trait
  (LPT) Ontology, version 1.3; and Livestock Breed Ontology (LBO),
  version 1.7. In addition, the VT has been made available for direct
  download at the Github site.


o NAGRP Data Repository:

  The hosted publication supplementary data has now been merged with the
  NAGRP Shared Data Repository. Its contents can be found by searching the
  data repository.


o JBrowse

  Thanks to Ben Rosen from the USDA/ARS and his colleagues for their efforts
  putting together a new goat genome assembly. The new goat assembly is now
  loaded to JBrowse for map alignment views. Currently available tracks
  include NCBI gene model annotations and Gnomon, the NCBI gene prediction


o Misc.:

  (1) US Pig Genome Coordinator's annual report for 2016 was posted.  The
  2016 NRSP-8 pig genome station reports also start to be online.

  (2) Room sharing bulletin boards for PAG, PAG-Asia, and other meetings
  have been improved by adding several administrator tools and a security
  layer to prevent robot-like hackers.

  (3) The AnGenMap listserv moderator's switchbox has been improved to
  include functions to facilitate the list moderator's reviewing and posting
  tasks.  Improvements include functions/tools to clean mail text mixed with
  quoted-printables, and to decode MIME-coded text.


Check out the daily "what's new" ( 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
( for any routine

NAGRP Bioinfo Team



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