From listmaster animalgenome.org Wed May 6 11:56:03 2026
From: "Hu, Zhiliang [ANS]" <zhuiastate.edu>
To: Members of AnGenMap <angenmapanimalgenome.org>
Subject: What's new on the NAGRP animal genome web site (#2, 2026)
Date: Wed, 06 May 2026 11:56:03 -0500
What's new on the NAGRP animal genome web site (#2, 2026)
o ANNOUNCING THE ANIMAL QTLdb RELEASE 59:
(Apr 20, 2026): A sum of 7,562 new QTL/associations have been curated into
the database. (New additions less obsolete/retracted ones: Cattle: 5,291;
Chicken: 1,137; Goat: 322; Horse: 0; Pig: 173; Sheep: 639; Rainbow trout: 0
-- Net increase: 7,562). To date, the current total number of QTL in the
database: 318,441 [Breakdown by species -- Cattle: 212,372 (on 572 traits);
Chicken: 30,465 (on 244 traits); Goat: 3,115 (on 92 traits); Horse: 2,545
(on 71 traits); Pig: 58,517 (on 410 traits); Sheep: 9,226 (on 191 traits);
Rainbow trout: 2,201 (on 35 traits)] curated from 3,038 publications.
In addition, data updates were made to about 1,097 QTL/associations, 67
base traits, and 39 trait variants, partly as a result of active
developments of trait ontologies (VT, LPT, CMO). Base trait updates by
species -- cattle: 17; chicken: 18; goat: 4; pig: 173; horse: 3; pig: 15;
sheep: 10.
Database development notes:
(1) With ongoing improvements in genome assemblies and SNP mappings, the
relevance of several older genome builds has declined, particularly in
terms of their use for lifting QTL and association data. As a result, four
genome builds — Btau4 (cattle), GG4 (chicken), SS10 (pig), and OAR3 (sheep)
— have been retired from the QTLdb supported genome list.
It is important to note that this change only affects their availability
for QTL/association data liftover and downloads. Curation of data
originally reported using these genome builds will continue, and such data
will be lifted to the default genome in future QTLdb releases.
(2) Webtools improvements were continued and a number of bug fixes were
made since the last release.
URL: https://www.animalgenome.org/QTLdb/
o ANNOUNCING THE ANIMAL CorrDB RELEASE 27:
(Apr 21, 2026): A sum of 1,785 new correlations [Breakdown by species --
Pig: 434; Cattle: 1,065; Chicken: 155; Sheep: 131] and a sum of 277 new
heritability data [Breakdown by species -- Pig: 20; Cattle: 186; Chicken:
38; Sheep: 33] have been curated into the CorrDB.
To date, the total number of correlation data in the database: 50,324
[Breakdown by species -- Cattle: 18,998 (on 393 traits, 601 trait
variants); Chicken: 5,825 (on 121 traits, 336 trait variants); Horse: 230
(on 31 traits, 6 trait variants); Pig: 13,479 (on 244 traits, 366 trait
variants); Sheep: 7,669 (on 148 traits, 529 trait variants); Goat: 4,123
(on 93 traits, 190 trait variants)], and total heritability data: 8,490
[Breakdown by species -- Cattle: 3,359 (on 457 traits, 622 trait variants);
Chicken: 923 (on 178 traits, 301 trait variants); Horse: 145 (on 58 traits,
7 trait variants); Pig: 2,127 (on 287 traits, 420 trait variants); Sheep:
1,397 (on 187 traits, 506 trait variants); Goat: 539 (on 88 traits, 156
trait variants)] curated from 868 publications.
In addition, 48 trait-related data updates were made.
URL: https://www.animalgenome.org/CorrDB/
o ONTOLOGY DEVELOPMENTS
(1) Thirteen (13) Vertebrate Trait (VT) Ontology data releases were made,
including structural changes and data addition/deletion updates. The
current term count is 4,055.
URL: https://www.animalgenome.org/bioinfo/projects/vt/
(2) One (1) Livestock Breed Ontology (LBO) data release was made (current
version has 1,142 terms).
URL: https://www.animalgenome.org/bioinfo/projects/lbo/
(3) One (1) Livestock Product Trait Ontology (LPT) data release was made
(current version has 521 terms).
URL: https://www.animalgenome.org/bioinfo/projects/lpt/
(4) The Clinical Measurement Ontology (CMO) data was updated one time from
BioPortal to the local QTLdb/CorrDB curation environment and for ontology
hierarchy browsers and viewers.
URL: https://www.animalgenome.org/bioinfo/projects/cmo/
(5) The data release pipeline has been improved by inclusion of an obo file
syntax verification procedure to facilitate smooth downstream data processes.
The improved release procedure applies to VT, LPT, and LBO data release
pipelines.
o MISC.
(1) The NRSP8 bulletin board (BBS) has been serving its purpose well. A recent
functional addition is to display NRSP8 members posts pulled from ANGENMAP
listserv by an automated weekly process.
(2) The "upcoming community events" has a new calendar view. This is a work
adapted from the NRSP8/RCN communities' "Event calendars" for activity
planning. As usual, we encourage users to submit new events (link on the
lower part of these pages).
URL: https://www.animalgenome.org/community/meetings/
--
NAGRP Bioinfo Team
bioinfo-teamanimalgenome.org
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This work is supported by the Agriculture and Food Research Initiative
competitive award no. 2024-67016-42311 ANIMAL BREEDING-RCN: FARM ANIMAL
GENOMICS COLLECTIVE from the USDA National Institute of Food and Agriculture
and the multistate project NRSP8: Genomic Capacity: Building Applied Genomic
Capacity for Animal Industries.
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