From listmasteranimalgenome.org Fri Aug 26 13:16:24 2022
From: "Hu, Zhiliang [ANS]" <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 (#3, 2022)
Date: Fri, 26 Aug 2022 13:16:24 -0500
What's new on the NAGRP animal genome web site (#3, 2022)
o Animal QTLdb and CorrDB updates -- Announcing a joint release of the
QTLdb (Release 48) and CorrDB (Release 16):
(Aug 24, 2022): New curation updates made to previously released
QTL/association data: 254,573 [Breakdown by species: cattle: 195,041;
chicken: 16,613; goat: 129; horse: 2,699; pig: 34,793; rainbow trout:
1,225; sheep: 4,202]. These changes related to 2,111 previously curated
traits [Breakdown by species: cattle: 683; chicken: 369; horse: 65; pig:
691; sheep: 264; rainbow trout: 39].
In addition, a sum of 981 new QTL/associations have been curated into the
database. (New additions less obsolete/retracted ones: Catfish: 0; Cattle:
291; Chicken: 19; Goat: 0; Horse: 0; Pig: 462; Sheep: 209; Rainbow trout:0)
(Aug 24, 2022): New data updates made to previously curated correlation
data: 4,526 [Breakdown by species: cattle: 1,758; chicken: 898; pig: 1,096;
sheep: 774]. Updates made on trait data related to correlation data: 1,632
[Breakdown by species: cattle: 395; chicken: 35; horse: 5; pig: 908; sheep:
289]. Updates made on trait data related to heritability data: 92.
[Breakdown by species: cattle: 30; chicken: 3; horse: 1; pig: 39; sheep:18]
In addition, a sum of 281 new correlations [Breakdown by species -- Pig:46;
Cattle: 115; Chicken: 120] and a sum of 93 new heritability data [Break
down by species -- Pig: 38; Cattle: 36; Chicken: 6; Sheep: 13] have been
curated into the CorrDB.
Database developments summary:
(1) The data released above with regard to curation updates reflects our
continued efforts toward implementing a new trait variant management system
(reported in our 2022 WCGALP paper, https://tinyurl.com/yv5wmkxw), as our
work this summer has been focused on extensive data curation changes on all
existing data in the QTLdb and CorrDB. The trait curation changes provide
supporting evidence that the new data management structural change
implemented in the spring works as designed (see our database release 47).
A positive effect from the new trait data management in QTLdb/CorrDB is a
significant reduction in the number of traits maintained in the database
(for correlation data, from 902 to 786, -12.9%; for heritability data, from
1,061 to 928, -14.9%; for QTL/association data, from 2,272 to 2,146, -5.9%).
Overall, this is an approximate 10% reduction in total base trait numbers.
(2) Default genomes: Although the Animal QTLdb has been supporting multiple
genome builds per species since 2021, one genome assembly per species is
now selected as default "reference" genome for the QTLdb web tools searching
and online map display. The selection of the default genome is in alignment
with NCBI/Ensembl updates. The supported "default genome" information can
be found on the "Supported Genome Assemblies for Data Alignments" page on
our website (https://www.animalgenome.org/.../doc/genome_versions).
o Ontology developments:
(1) Two updates were made to the Vertebrate Trait (VT) Ontology data
(versions 12.7 and 12.8).
(2) Four updates were made to the Livestock Breed Ontology (LBO, versions
7.10, 7.11, 7.12, and 7.13).
o FAANG website updates:
The FAANG website has recently been reformatted to accommodate the
consortium's new working structure - new task forces (TF) that have
replaced earlier committees/working groups. Web functions to facilitate the
new working structure include TF membership management (self-elected or
admits by organizers), organizers' ability to add new members, systematic
mechanisms to periodically check TF memberships, a new working mailing
listserv, and introductory web content for each TF. The web contents for
the old working groups have been placed in an archive, accessible by
o ANGENMAP Listserv:
The AnGenMap list and 17 other mailing lists hosted at AnimalGenome.org
have been completely transitioned to using user profiles via web tools for
users' management of their list subscription/alternative emails/mail digest
and other list options. AnGenMap operates on the Smartlist listserv, which
was designed to use auto-responsive email service to handle list
subscribe/unsubscribe commands. Replacement of this default design brings
several advantages, including better security control, ease of use, and
better information transparency to users. Note that this change was built
on our previous efforts developing expanded web functions on the community
directory to couple with the listserv as a "helper" since 2007.
o Data repository:
We have begun a process to clean up the NAGRP Data repository that has been
serving the community since 2005. This effort is aimed at eliminating
out-of-date or redundant files, and those that have remained in an
incomplete status, in order to sustain the support to the community beyond
2023. Ultimately, all must-keep files will be transferred to OSF upon
agreements with data owners. If you have data hosted at the NAGRP Data
Repository, please inform us of your long-term intentions for them or make
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/errors, or suggesting corrections on our site.
Your input is always appreciated. Feel free to contact us at any time with
your needs, requests, and/or suggestions: Jim Reecy (jreecyiastate.edu),
James Koltes (jekoltesiastate.edu), Fiona McCarthy (fionamccarizona.edu).
Or talk to us using our Helpdesk (https://www.animalgenome.org/helpdesk).
NAGRP Bioinfo Team