From listmaster animalgenome.org Mon Jan 6 13:03:34 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 (#1,
2025)
Date: Mon, 06 Jan 2025 13:03:34 -0600
What's new on the NAGRP animal genome web site (#1, 2025)
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** A SPECIAL NOTE ABOUT QTLdb AND CorrDB FUTURE RELEASE:
For the past 20 years, we have been regularly rolling out new releases of
the Animal QTLdb (and Animal CorrDB since 2012) with additions of newly
curated data. As we announce the current release (below), we want you be
aware that WE MAY NOT BE ABLE TO DO FUTURE RELEASES IN THE USUAL INTERVALS
DUE TO DISCONTINUATION OF FUNDING. UNLESS NEW SOURCES OF FUNDING ARE SECURED,
WE WILL HAVE TO DEPOSIT ALL CURRENT DATA SOMEWHERE AND CEASE DATABASE
DEVELOPMENT.
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o Announcing the Animal QTLdb Release 55 and CorrDB Release 23:
(Dec 23, 2024): A sum of 11,506 new QTL/associations have been curated into
the database. (New additions less obsolete/retracted ones: Cattle: 89;
Chicken: 9,842; Goat: 324; Horse: 9; Pig: 927; Sheep: 315; Rainbow trout: 0
-- Net increase: 11,506). To date, the current total number of QTL in the
database: 289,348 [Breakdown by species -- Cattle: 192,336 (on 553 traits);
Chicken: 28,444 (on 245 traits); Goat: 2,469 (on 82 traits); Horse: 2,225
(on 60 traits); Pig: 56,615 (on 403 traits); Sheep: 5,058 (on 170 traits);
Rainbow trout: 2,201 (on 35 traits)].
In addition, 13,830 updates were made to previously curated data in cattle,
chicken, goat, pig, and sheep QTLdb.
On database developments:
(1) Miscellaneous updates to the QTLdb FAQ and website.
(2) Numerous improvements were made to the curator tools.
URL: https://www.animalgenome.org/QTLdb
(Dec 23, 2024): A sum of 4,484 new correlations and 7,121 heritability data
have been curated into the CorrDB [New correlations by species -- Pig: 680;
Cattle: 345; Chicken: 1,165; Sheep: 2,066; Goat: 228] and a sum of 693 new
heritability data [Breakdown by species -- Pig: 114; Cattle: 84; Chicken:
84; Sheep: 461; Goat: 27] have been curated into the CorrDB.
To date, the total number of correlation data in the database: 42,436
[Breakdown by species -- Cattle: 16,032 (on 368 traits, 359 trait
variants); Chicken: 3,771 (on 93 traits, 157 trait variants); Horse: 209
(on 27 traits, 131 trait variants); Pig: 12,871 (on 239 traits, 335 trait
variants); Sheep: 5,570 (on 111 traits, 302 trait variants); Goat: 3,983
(on 90 traits, 176 trait variants)], and total of 7,121 heritability data
[Breakdown by species -- Cattle: 2,873 (on 421 traits, 374 trait variants);
Chicken: 620 (on 155 traits, 143 trait variants); Horse: 131 (on 54 traits,
1 trait variant); Pig: 2,044 (on 279 traits, 378 trait variants); Sheep:
1,016 (on 147 traits, 309 trait variants); Goat: 514 (on 84 traits, 142
trait variants)] curated from 719 publications.
Data updates were made to 1,406 correlations (chicken: 147; goat: 466; pig:
745; sheep:48) and 462 heritability data (cattle: 21; chicken: 16; pig:
412; sheep: 13) curated prior to the last data release.
URL: https://www.animalgenome.org/CorrDB
o Ontology developments
(1) Ten (10) Vertebrate Trait (VT) Ontology data releases were made with
structural changes and data addition/deletion updates. The current term
count is 3,817.
URL: https://www.animalgenome.org/...bioinfo/projects/vt/
(2) Three (3) Livestock Breed Ontology (LBO) data releases were made
(current version has 1,125 terms). In addition, the Livestock Breed
Ontology (LBO) data release has a new version naming format that denotes
the version date in 'yyyy-mm-dd' format. For example, its version 9.8 is
now called "version 2024-11-25".
URL: https://www.animalgenome.org/...ioinfo/projects/lbo/
(3) 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/
All trait ontology development works are associated with QTLdb/CorrDB data
curation and maintenance. This is partly reflected in the QTL/CorrDB
updates described above.
o QTLdb and CorrDB functionality may be coming to an end
The QTLdb and CorrDB are no longer actively funded. This means that in the
near future, these data and associated tools will no longer be actively
updated unless additional funding sources are identified. QTLdb and CorrDB
have been actively funded by grants for more than 20 and 10 years
respectively. We will continue to search for alternative funding sources
and will provide additional updates when these resources move to a static
state.
o New funding sources for the NAGRP animal genome web site
The animalgenome.org website is now funded primarily by a new USDA-NIFA
Research Coordination (RCN) Grant, with additional support from the new
NRSP8 multistate project.
Check out our 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 for any questions or
send feedback to the Helpdesk (https://www.animalgenome.org/helpdesk).
--
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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