From listmaster animalgenome.org Tue Apr 29 17:37:39 2025
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From: "Hu, Zhiliang [ANS]" <zhuiastate.edu>
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To: Members of AnGenMap <angenmapanimalgenome.org>
Subject: What's new on the NAGRP animal genome web site (#2, 2025)
Date: Tue, 29 Apr 2025 17:37:40 -0500
What's new on the NAGRP animal genome web site (#2, 2025)
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A SPECIAL NOTE:
The Animal QTLdb/CorrDB have been supported by funds from USDA for the past
21 and 13 years respectively. Current lack of funds for the QTLdb/CorrDB
has a direct impect on our efforts to keep it updated. Chances are that we
may have to deposit the current data and discontinue the development work at
some point if the lacking of funding continues.
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o Announcing the Animal QTLdb Release 56 and CorrDB Release 24:
(Apr 24, 2025): A sum of 3,390 new QTL/associations have been curated into
the database. (New additions less obsolete/retracted ones: Cattle: 1,117;
Chicken: 672; Goat: 244; Horse: 257; Pig: 426; Sheep: 674; Rainbow trout: 0
-- Net increase: 3,390). To date, the current total number of QTL in the
database: 292,423 [Breakdown by species -- Cattle: 193,453 (on 558 traits);
Chicken: 29,116 (on 246 traits); Goat: 2,713 (on 90 traits); Horse: 2,482
(on 71 traits); Pig: 57,041 (on 406 traits); Sheep: 5,417 (on 178 traits);
Rainbow trout: 2,201 (on 35 traits)] curated from 2,964 publications.
In addition, updates have been made to 853 QTL/associations, 82 base traits
and 3,771 trait variants on data curated prior to Release 55 (December
2024). (This is a joint release with the 24th CorrDB release.)
Database development notes:
(1) Multiple Genome Support: All currently released data in all 7 species
are lifted to 22 genome assemblies aided by SNP mappings from new (April 2,
2025) dbSNP Release 7 data (direct dbSNP mapping data for 19 genomes, and
our in-house procedures extended the mappings for an additoinal 3 genomes).
(2) "JBrowse2" was introduced a year ago (April 2024; QTLdb Release 53) and
now has been made the default QTL/association map viewer on the "default
genomes" (one per species is supported). The older JBrowse (version 1) is
completely retired from this site as of this release. Links to using
JBrowse2 for QTL/associations are listed on each QTLdb species homepage.
URL: https://www.animalgenome.org/QTLdb/
o Announcing the Animal CorrDB Release 24:
(Apr 25, 2025): A sum of 1,559 new correlations [Breakdown by species --
Pig: 159; Cattle: 1,032; Chicken: 25; Horse: 15; Sheep: 320; Goat: 8] and a
sum of 218 new heritability data [Breakdown by species -- Pig: 37; Cattle:
125; Chicken: 8; Horse: 11; Sheep: 32; Goat: 5] have been curated into the
CorrDB. To date, the total number of correlation data in the database:
43,995 [Breakdown by species -- Cattle: 17,064 (on 370 traits, 457 trait
variants); Chicken: 3,796 (on 93 traits, 169 trait variants); Horse: 224
(on 30 traits, 6 trait variants); Pig: 13,030 (on 240 traits, 354 trait
variants); Sheep: 5,890 (on 116 traits, 341 trait variants); Goat: 3,991
(on 90 traits, 179 trait variants)], and total heritability data: 7,416
[Breakdown by species -- Cattle: 2,998 (on 424 traits, 475 trait
variants); Chicken: 628 (on 155 traits, 151 trait variants); Horse: 142 (on
57 traits, 7 trait variants); Pig: 2,081 (on 285 traits, 413 trait
variants); Sheep: 1,048 (on 152 traits, 326 trait variants); Goat: 519 (on
85 traits, 145 trait variants)] curated from 751 publications.
In addition, data updates have been made to 1,794 correlation data (on 7
base traits and 212 trait variants) and 221 heritability data (on 8 base
traits and 208 trait variants) curated prior to Release 23 (December 2024).
URL: https://www.animalgenome.org/CorrDB/
o Ontology developments
(i) Eleven (11) Vertebrate Trait (VT) Ontology data releases were made with
additions of new terms, synonyms, external resource references (xref), or
structural changes and other updates. The current term count is 3,833.
URL: https://www.animalgenome.org/...bioinfo/projects/vt/
(ii) The Clinical Measurement Ontology (CMO) data was updated two times
from Bioportal to the local QTLdb/CorrDB curation environment and for
ontology hierarchy browsers and viewers.
URL: https://www.animalgenome.org/...ioinfo/projects/cmo/
(iii) Three (3) Livestock Breed Ontology (LBO) data releases were made.
The current version contains a total of 1,130 breed terms.
URL: https://www.animalgenome.org/...ioinfo/projects/lbo/
o NRSP8 website updates:
(i) Community bulletin board system (BBS) was developed last year to accept
meetings, workshops, short courses, open positions, and other announcements
posts from NRSP8 members and display items as a web-based bulletin board.
New development has added a channel to pipe NRSP8 member's posts on
AnGenMap listserv into the BBS (previously, in the BBS posting process
there was already an option for a post to concurrently being sent to
AnGenMap). The reciprocal information flow may better facilitate community
communications.
URL: https://www.animalgenome.org/community/bbs/
(ii) A new tab "Updates" was added to the NRSP8 page to keep the community
informed of its activities, with items like annual/work reports, periodic
newsletters, etc.
URL: https://www.animalgenome.org/NRSP8/?tab=upd
(iii) Community calendar: Please be aware that a community calendar has
been in place to allow sharing events, meetings, and activity schedules
among the community members. Please feel free to make use of it by posting
your items.
URL: https://www.animalgenome.org/NRSP8/?tab=cal
o Support the community:
New web works are dedicated to support community activities. The most
recent addition is the posting of materials (slides, video) for 2025 AG2PI
Single Cell Field Days on FAANG BBS.
URL: https://www.faang.org/...s?s=2025_wkshop..txt
--
NAGRP Bioinfo Team
bioinfo-teamanimalgenome.org
+---------------------------------------------------------------------------+
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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