Archived Post

From  Tue Jan  2 16:38:18 2024
Return-Path: <>
From: "Hu, Zhiliang [ANS]" <>
Postmaster: submission approved by list moderator
To: Members of AnGenMap <>
Subject: What's new on the NAGRP animal genome web site (#1,
Date: Tue, 02 Jan 2024 16:38:18 -0600

What's new on the NAGRP animal genome web site (#1, 2024)

o Animal QTLdb and CorrDB updates -- Announcing a joint release of the QTLdb
  (Release 52) and CorrDB (Release 20):

  (Dec 27, 2023): A sum of 3,539 new QTL/associations have been curated into
the database. (New additions less obsolete/retracted ones: Catfish: 0;
Cattle: 1,893; Chicken: 237; Goat: 643; Horse: 35; Pig: 350; Sheep: 381;
Rainbow trout: 0 -- Net increase: 3,539). To date, the current total number
of QTL in the database: 282,277 [Breakdown by species -- Cattle: 196,904 (on
680 traits); Chicken: 18,883 (on 372 traits); Goat: 1,201 (on 26 traits);
Horse: 2,684 (on 65 traits); Pig: 55,166 (on 673 traits); Sheep: 5,110 (on
272 traits); Rainbow trout: 2,329 (on 47 traits)].


  (Dec 27, 2023): A sum of 2,966 new correlations [Breakdown by species --
Pig: 104; Cattle: 310; Goat: 2,552] and a sum of 547 new heritability data
[Breakdown by species -- Pig: 18; Cattle: 112; Chicken: 51; Sheep: 4; Goat:
362] have been curated into the CorrDB.  To date, the total number of
correlation data in the database: 32,913 [Breakdown by species -- Cattle:
15,149 (on 354 traits, 263 trait variants); Chicken: 2,053 (on 81 traits, 75
trait variants); Horse: 209 (on 27 traits, 0 trait variants); Pig: 9,412 (on
228 traits, 214 trait variants); Sheep: 2,704 (on 77 traits, 149 trait
variants); Goat: 3,386 (on 85 traits, 121 trait variants)], and total
heritability data: 5,951 [Breakdown by species -- Cattle: 2,690 (on 406
traits, 276 trait variants); Chicken: 451 (on 138 traits, 68 trait variants);
Horse: 131 (on 54 traits, 1 trait variants); Pig: 1,799 (on 279 traits, 232
trait variants); Sheep: 446 (on 113 traits, 141 trait variants); Goat: 434
(on 78 traits, 117 trait variants)] curated from 596 publications.


  Database development notes:

  (1) Multiple Genome Support: A number of updates were made using the new
EVA dbSNP Release 5 data (Sept. 2023) on 19 genome builds in 7 livestock
species. These updates included the addition of two genome builds (goat
CHIR_1.0 and cattle ARS_UCD2.0). Support for goat CHIR_1.0 was made possible
by the new dbSNP release, and the new cattle ARS_UCD2.0 (July 2023 release)
support was made possible by our in-house SNP liftover procedures. Also
included was the retirement of two chicken genome builds (chicken.GRCg7b and

  (2) Legacy Data: As planned (see QTLdb release #51), a total of 13,309
linkage-map–based QTL/association data curated to the Animal QTLdb during
1999 through 2021 have been deposited to Github as of Dec. 17, 2023. This
step represents the separation of the legacy data from the current QTLdb, as
we move forward with the sequence-based genome maps and SNP-based analysis
results. These legacy data were on 6 livestock species: cattle, chicken,
horse, pigs, sheep, and rainbow trout.

  (3) "Ontologizing" Livestock Trait Terms: As part of our efforts to
"ontologize" livestock trait terms during the process of data annotation into
the QTLdb/CorrDB, two additional ontologies have been introduced for ontology
term mappings: Uberon anatomy/tissue ontology, and RGD Disease Ontology. The
outcomes from this work may be visible to the public in the near future.

  (4) Misc. Updates and Bug Fixes: (a) Continued efforts to stay current on
QTLdb link-outs in agreement with usage in public citations for journal
articles. (b) Fixes of missing or incorrect DOI brought in by erroneous
extraction of outdated PubMed XML structure. (c) Debugging of data status
control in the CorrDB curation pipeline.

  (5) Continued "Sibling Traits" to "Trait Variants" Transitions: As a result
of our implementation of experiment-level curation of traits with modifiers
(trait variants), continued reductions in the number of base traits and
increase in trait variants are observed. This continues to have a positive
impact on the QTLdb/CorrDB with regard to future developments.

  (6) New Data Summary Statistics: With the new developments (described
above) and our continued efforts on data curations, several new statistics
have been added to the data summary page for each species. These include
1) Counts of each trait appearance in experiments, 2) Counts of each trait
variant appearance in experiments, and 3) Number of data in the curation


o Ontology developments:

  (1) Five Vertebrate Trait (VT) Ontology data releases were made (versions
13.10 to 13.14) with a number of structural changes and updates, and a
current 3,731 term count.


  (2) Four Livestock Breed Ontology (LBO) data releases were made (versions
8.7 to 8.10) with a current total of 1,121 terms.


  (3) The Clinical Measurement Ontology (CMO) data was updated four times
from Bioportal to the local QTLdb/CorrDB curation environment and for
ontology hierarchy browsers and viewers.


  All trait ontology development works are associated with QTLdb/CorrDB data
curations and maintenance. This is partly reflected in the QTL/CorrDB updates
described above.

o Misc.:

  Some extensive website updates were made at to reflect
the transition of the USDA-supported NRSP8 program into a new phase. This
includes retirements of all websites supporting coordinator programs on
multiple species (pig, cattle, chicken, sheep, and aquaculture).


Check out our daily "what's new" ( 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 with your
feedback or suggestions: Jim Reecy (, James Koltes
(, Fiona McCarthy ( Or write
to our Helpdesk directly (

NAGRP Bioinfo Team



© 2003-2024: USA · USDA · NRPSP8 · Program to Accelerate Animal Genomics Applications. Contact: Bioinformatics Team