From listmasteranimalgenome.org Wed Jan 3 15:10:44 2018
From: "Hu, Zhiliang [AN S]" <zhuiastate.edu>
Postmaster: submission approved by list moderator
To: Members of AnGenMap <angenmapanimalgenome.org>
Subject: What's new on the NAGRP animal genome web site (#1, 2018)
Date: Wed, 03 Jan 2018 15:10:44 -0600
What's new on the NAGRP animal genome web site (#1, 2018)
o Animal QTLdb and CorrDB updates:
This is a joint release of the QTLdb (Release 34) and CorrDB (Release 2).
QTLdb: A sum of 9,705 new QTL/associations have been added to the database
(New additions less obsolete/retracted ones: Catfish: 0; Cattle: 8,388;
Chicken: 551; Horse: 26; Pig: 466; Sheep: 274; Rainbow trout: 0 -- Net
increase: 9,705). The current total number of QTL in the database: 145,842
[Breakdown: Cattle: 108,040; Chicken: 8,363; Horse: 1,304; Pig: 26,076;
Sheep: 1,932; Rainbow trout: 127]
CorrDB: A sum of 842 new correlations (Genetic correlations: 521;
Phenotypic correlations: 303; Residual correlations: 18) and 113
heritability data on 64 cattle traits have been added.
(1) Pig genome build version 11.1 is now supported by the QTLdb.
(2) The development of the initial set of curator tools has been completed
for the Animal Trait Correlation Database (CorrDB). With this release,
we open CorrDB curation for free registration for anyone who wishes
to be a curator to enter his/her own or public correlation and
(3) As part of the Animal QTLdb/CorrDB co-development efforts, functions
have been developed to link QTL data with trait correlation data through
common trait terms where such data exist. For example, within the
CorrDB, under the Table View of correlation data, a hyperlinked red
"QTL" label is added when QTL data exist for the trait; likewise,
within the QTLdb on the trait search results, a hyperlinked tag is
added on traits where correlation data are found.
(4) New web portals have been developed for display of "gene-centric view"
and "trait-centric view" of QTL/association data where underlying gene
information is available. This tool helps users to relatively quickly
interrogate and understand genotype-to-phenotype information in a
synopsis. A quick way to use the tool to view information is to try
a search by genes or by traits (e.g., try a species "general search,"
then go to "genes" or "traits"), or go from a "Trait Details" page to
the “Explore Further” link to "List all QTL/association data where a
gene may exist." The returned query results are displayed in one of two
ways ("gene-centric" or "trait-centric" view) at user's choice.
o Data repository:
(1) A process is underway to replace the "aquaculture" data area with
separate aquaculture species data areas. For example, the existing data
have been moved to the respective "catfish" and "rainbow trout" folders
but are still available in the current "aquaculture" location during the
transition period. This process started on September 1, 2017, and is
to be made final on March 1, 2018. The aquaculture genomics community
has been informed of this change.
(2) A new "Frequently Asked Questions" page is being developed to address
the problems/questions most often encountered by users.
(3) In the past year we had an unprecedented number of 22 requests from
authors of journal papers who needed their supplementary data files
hosted at AnimalGenome.ORG. This is a 3-4 fold increase from
- The "AnGenMap Frequently Asked Questions" has been updated to address
several confusing problems mostly seen by new users.
- Pig Genome Update No. 125 is online (Nov. 1, 2017)
- Aquaculture Genomics Newsletter 44 is online (Dec. 22, 2017)
Check out the daily "what's new" (https://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 site to send
any requests (https://www.animalgenome.org/...fo/services/helpdesk).
NAGRP Bioinfo Team