Archived Post

From  Tue Aug 29 19:28:18 2017
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From: "Hu, Zhiliang [AN S]" <>
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To: Members of AnGenMap <>
Subject: What's new on the NAGRP animal genome web site (#3,
Date: Tue, 29 Aug 2017 19:28:18 -0500

What's new on the NAGRP animal genome web site (#3, 2017)

o Animal QTLdb updates:

  Announcing Release 33 of the Animal QTLdb.  A sum of 10,384 new QTL
  have been added to the database. The current total number of QTL in the
  database: 136,137 [Breakdown: Cattle: 99,652; Chicken: 7,812; Horse:
  1,278; Pig: 25,610; Sheep: 1,658; Rainbow trout: 127] (New additions
  less obsolete/retracted ones: Catfish: 0; Cattle: 1,562; Chicken: 1,021;
  Horse: 3; Pig: 7,655; Sheep: 143; Rainbow trout: 0 -- Net QTL number
  increase: 10,384).

  Thanks to Chunyan Bai from Jilin University (China) and Codie Durfee
  from Washington State University for adding their pig and sheep QTL/
  association data respectively.

  Database developments:

  (1) A "permanent record locator" has been implemented in the AnimalQTLdb
      to provide unique and stable links to all curated QTL/association
      data for a publication. The new "permanent record locator" is a
      replacement of a "URL Link" function introduced two years ago and
      overcomes some of its shortcomings. It can be used by the authors to
      refer to their published data, to provide proof of evidence of data
      entry at the Animal QTLdb to journal editors/manuscript reviewers,
      and to serve other purposes. All QTLdb curators/editors have access
      to this tool for their curated data.

  (2) The backend database structure and processes to handle curation of
      QTL traits paralleled with VT/LPT/CMO ontology developments have been
      undergoing further improvements in terms of facilitating curation of
      trait terms modified by a diversified list of entities such as time,
      anatomical locations, measurement methods, etc. This is in conjunction
      with Animal Correlation Database (CorrDB) development. Stay tuned for
      further news.

  (3) We have registered 5 users for new curator accounts this year. We
      encourage users to apply for an Animal QTLdb curator account to learn
      how it may help their research, and to possibly be more involved in
      database development. We love to work with you and appreciate your
      useful ideas, suggestions, and/or requests, which all help to make the
      database/tools more useful to the community.

  (4) Periodic data checks on "on-hold", "conditionally released" (such as
      QTL/associations marked with 'ss' SNPs), and "suspended" data have been
      automated. This helps to make sure no sub-optimal data goes unnoticed.


o Data repository:

  The NAGRP Data Repository for publication supplementary data files has
  been actively used, partly due to the requirements by journals for
  depositing supplementary data as online resources. To cope with the
  increasing demands, we have performed the following restructuring of the

  (1) addition of a customized file description area to allow authors to
      better describe what files are hosted (optional; in addition to what
      they can put in their publications). This was made retrospectively
      compatible for 10+ publications having custom file descriptions.

  (2) modification of the web interface for supplementary data uploads for
      better collection of metadata when initiating the data hosting

  (3) addition of a new mechanism to allow only reviewers to access a set
      of deposited data while the data is considered confidential prior to
      publication (e.g., public access to the data is not possible during
      the review period, or until authors request removal of the

  (4) automation of checking with authors for publication status updates.

  (5) The new NCBI pig genome annotation data for the assembly build version
      11.1 has been made available at the NAGRP shared data repository.


o Secured web servers:

  After a five-month testing period during which both HTTP and HTTPS visits
  were served, the web services on https://www.AnimalGenome.ORG are now
  completely switched to Secure Sockets Layer (SSL) protocols for secured
  data transfer to/from the website. Currently all traffic to the
  traditional HTTP protocol (i.e. "http://www.AnimalGenome.ORG") is now
  automatically served by the HTTPS server (so you don't have to worry about
  which protocol your visits are using - it will automatically switch).


  Likewise, the website for the Functional Annotation of ANimal Genomes
  (FAANG) consortium,, is now also operating on an
  SSL-implemented web server; thanks to Barry Horne from Roslin Institute
  for supplying the permits/keys for the domain name.


o Website content updates:

  Continual web content updates have been carried out on a daily basis.
  Check out the daily "what's new" items for more up-to-date information.


o Feedback:

  Thanks in advance for kindly reporting broken links or out-of-date
  information on AnimalGenome.ORG. Feel free to contact us at any time with
  your needs, requests, and/or suggestions. You can reach us in multiple
  ways: Email the team at the address below, or write us with Helpdesk web
  form, or contact Jim Reecy ( for projects/priorities.


NAGRP Bioinfo Team



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