From listmaster animalgenome.org Fri Aug 29 12:38:54 2025
From: "Hu, Zhiliang [ANS]" <zhuiastate.edu>
To: Members of AnGenMap <angenmapanimalgenome.org>
Subject: What's new on the NAGRP animal genome web site (#3, 2025)
Date: Fri, 29 Aug 2025 12:38:54 -0500
What's new on the NAGRP animal genome web site (#3, 2025)
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A SPECIAL NOTE:
The Animal QTLdb and CorrDB currently do not have stable funding and are
supported on a month by month basis. We wish to acknowledge the current
support from the NRSP8 program and a seed grant from the Translational
artificial intelligence center at Iowa State University.
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o Announcing the Animal QTLdb Release 57:
(Aug 26, 2025): A sum of 4,105 new QTL/associations have been curated into
the database. (New additions less obsolete/retracted ones: Cattle: 642;
Chicken: 212; Goat: 0; Horse: 9; Pig: 371; Sheep: 2,871; Rainbow trout: 0
-- Net increase: 4,105). To date, the current total number of QTL in the
database: 296,528 [Breakdown by species -- Cattle: 194,095 (on 558 traits);
Chicken: 29,328 (on 243 traits); Goat: 2,713 (on 90 traits); Horse: 2,491
(on 71 traits); Pig: 57,412 (on 410 traits); Sheep: 8,288 (on 182 traits);
Rainbow trout: 2,201 (on 35 traits)] curated from 2,991 publications.
In addition, our efforts to improve data quality since the last release
have involved updates to 3,385 QTL, 1,399 base traits, and 3,901 trait
variants.
Database development notes:
(1) A new set of curation tools to tag tissue information has been
developed to allow animal tissues to be identified where applicable, and
unambiguously linkable to related database resources involving expression
studies, functional annotations, etc. This tool set includes an animal
tissue vocabulary collection and maintenance tool (based on UBERON anatomy
ontology and BRENDA tissue ontology, it currently has 1600+ active terms),
a curation portal to allow adding or excluding terms, an automated keyword
tagging pipeline to pre-compute possible tissue tags, and a curator
confirmation and editing interface to finalize the results.
(2) Miscellaneous debugs and web interface adjustments have been performed
to improve data searches. (3) The curation pipeline has been fine-tuned in
terms of data status tracking, monitoring, and reporting on web portals.
For example, a weekly updated number of newly curated (pre-release) data
counts can be seen along with other data summaries ("Data in Curation
Pipeline") for each species, when newly curated data are found in the
curation pipeline.
URL: https://www.animalgenome.org/QTLdb/
o Announcing the Animal CorrDB Release 25:
(Aug 26, 2025): A sum of 2,567 new correlations [Breakdown by species --
Pig: 15; Cattle: 156; Chicken: 1,653; Sheep: 731; Goat: 12] and a sum of
455 new heritability data [Breakdown by species -- Pig: 18; Cattle: 38;
Chicken: 233; Sheep: 162; Goat: 4] have been curated into the CorrDB. To
date, the total number of correlation data in the database: 46,562
[Breakdown by species -- Cattle: 17,220 (on 370 traits, 467 trait
variants); Chicken: 5,449 (on 113 traits, 290 trait variants); Horse: 224
(on 30 traits, 6 trait variants); Pig: 13,045 (on 241 traits, 356 trait
variants); Sheep: 6,621 (on 124 traits, 432 trait variants); Goat: 4,003
(on 90 traits, 179 trait variants)], and total heritability data: 7,871
[Breakdown by species -- Cattle: 3,036 (on 428 traits, 487 trait variants);
Chicken: 861 (on 171 traits, 262 trait variants); Horse: 142 (on 57 traits,
7 trait variants); Pig: 2,099 (on 288 traits, 418 trait variants); Sheep:
1,210 (on 162 traits, 417 trait variants); Goat: 523 (on 85 traits, 145
trait variants)] curated from 800 publications.
Since the last CorrDB data release, our continued efforts to fine tune the
base traits have resulted in updates that affected 646 correlations and 730
heritability data. In addition, data updates relating 18 heritability were
made.
Database development notes:
(1) The curation pipeline has been updated in terms of currently curated
data (pre-release) status tracking and reflection of data in public
portals. For example, a weekly updated number of newly curated data counts
can be seen on the front page.
o Ontology developments
(i) Ten (10) Vertebrate Trait (VT) Ontology data releases were made with
updates on synonyms, external resource references (xref), and/or other
changes along with addition of 63 new terms. The current term count is 3,896.
URL: https://www.animalgenome.org/...bioinfo/projects/vt/
(ii) Two (2) Livestock Breed Ontology (LBO) data releases were made. The
current version contains a total of 1,133 breeds.
URL: https://www.animalgenome.org/...ioinfo/projects/lbo/
(iii) Two (2) Livestock Product Ontology (LPT) data releases were made
since its last update more than two years ago. The current version contains
a total of 500 terms. Now the LPT data versioning has changed to a new
naming convention denoted with dates in 'yyyy-mm-dd' format, replacing the
earlier incremental numbers. For example, its "version 4.4" is now "version
2025-08-13". Version 2025-08-14 of the LPT ontology data with 500 terms is
updated to the public portal.
URL: https://www.animalgenome.org/...ioinfo/projects/lpt/
o NRSP8/RCN website updates:
A new web space is under development for making RCN project information
available. This is aimed at public awareness of our progress and to gather
potential collaboration possibilities.
o NRSP8 server maintenance:
We have recently observed a steady web server workload increase due to an
abnormal steady increase of web hits to our site. For example, over the
last 6 months, web hits to our site has increased more than 60 folds; the
number of unique visiting IP addresses has increased over 100 folds.
Obviously, the majority of these hits increase are not from regular human
activities but web bots (likely for AI training). As a result, our server
got overloaded more often than before. To safeguard the server and to
maintain its normal operations, we have to take measures to block the
aggressive visiting IPs and tune for a better workload balance for normal
web visitors. As a side effect, users may find unable to visit our site due
to excessive activities by some others in your institute, or ISP. While you
may contact us to arrange for better alternatives when justified, we wish
to remind users that the best way to utilize our data resource is by direct
data downloads, not by automated interactive web searches that generate
intensive web hits.
--
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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