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From listmasteranimalgenome.org  Tue Aug 29 11:54:33 2023
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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 (#3,
Date: Tue, 29 Aug 2023 11:54:33 -0500
What's new on the NAGRP animal genome web site (#3, 2023)

o Animal QTLdb and CorrDB updates -- Announcing a joint release of the QTLdb
  (Release 51) and CorrDB (Release 19):

  (Aug 25, 2023): A sum of 12,478 new QTL/associations have been curated
into the database. (New additions less obsolete/retracted ones: Catfish: 0;
Cattle: 1,113; Chicken: 235; Goat: 429; Horse: 0; Pig: 5,972; Sheep: 4,729;
Rainbow trout: 0 -- Net increase: 12,478). To date, the current total number
of QTL in the database: 278,738 [Breakdown by species: Cattle: 195,011 (on
680 traits); Chicken: 18,646 (on 372 traits); Goat: 558 (on 26 traits);
Horse: 2,649 (on 65 traits); Pig: 54,816 (on 673 traits); Sheep: 4,729 (on
272 traits); Rainbow trout: 2,329 (on 47 traits)].

  URL: https://www.animalgenome.org/QTLdb

  (Aug 26, 2023): A sum of 1,977 new correlations [Break down by species --
Pig: 208; Cattle: 771; Chicken: 16; Sheep: 459; Goat: 523] and a sum of 255
new heritability data [Break down by species -- Pig: 66; Cattle: 46;
Chicken: 3; Sheep: 73; Goat: 67] have been curated into the CorrDB. To date,
the total number of correlation data in the database: 29,947 [Breakdown by
species -- Cattle: 14,839 (on 357 traits, 237 trait variants); Chicken:
2,053 (on 81 traits, 71 trait variants); Horse: 209 (on 27 traits, 0 trait
variants); Pig: 9,308 (on 230 traits, 203 trait variants); Sheep: 2,704 (on
76 traits, 141 trait variants); Goat: 834 (on 42 traits, 27 trait variants)],
and total heritability data: 5,404 [Breakdown by species: -- Cattle: 2,578
(on 406 traits, 250 trait variants); Chicken: 400 (on 107 traits, 60 trait
variants); Horse: 131 (on 54 traits, 1 trait variants); Pig: 1,781 (on 279
traits, 224 trait variants); Sheep: 442 (on 112 traits, 136 trait variants);
Goat: 72 (on 22 traits, 27 trait variants)] curated from 549 publications.

  URL: https://www.animalgenome.org/CorrDB

  Database developments notes:

  (1) We continued the transition from using "sibling traits" to "trait
variants" (see our recent publication "A combinatorial approach implementing
new database structures to facilitate practical data curation management of
QTL, association, correlation and heritability data on trait variants"; DOI:
10.1093/database/baad024). Since April 2023, 1,597 new trait variants have
been created on QTLdb, linked to 3,128 previously curated QTL/association
data, and 1,494 new trait variants created on CorrDB, linked to 7,037
previously curated correlation/heritability data.

  (2) Given the fact that the linkage-map–based QTL/association data being
curated into the QTLdb has significantly diminished in the past 6 years (e.g.
2018, 115; 2019, 84; 2021, 2; 2023, 1), and the fact that all current genome
works have already shifted to using sequence maps, we plan to cease the
curation of linkage-map–based QTL/association data in 2023, and place all
previously curated linkage-map–based QTL/association data in separate
downloads/archives by the next database release. Any comments regarding this
move are welcome.

  URL: https://www.animalgenome.org/PGNET/

o Ontology developments:

  The trait ontology works have been very active in the summer of 2023.

  (1) Seven Vertebrate Trait (VT) Ontology data releases were made (versions
13.2 to 13.9 ) with a number of structural changes and updates, and a
current 3,732 term count.

  URL: https://www.animalgenome.org/...bioinfo/projects/vt/

  (2) Four Livestock Breed Ontology (LBO) data releases were made (versions
8.2 to 8.6) with a current 1,122 terms.

  URL: https://www.animalgenome.org/...ioinfo/projects/lbo/

  (3) The Clinical Measurement Ontology (CMO) data was updated five 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
curations and maintenance. This is partly reflected in the QTL/CorrDB updates
described above.

o Misc.:

  The "room-share bulletin board" tool has been upgraded. This tool has
been serving the Plant and Animal Genome (PAG), PAG-Asia, and International
Conference on Animal Genetics (ISAG) and other meetings since 2005.

  URL: https://www.animalgenome.org/community/#service

Check out the 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 at any time with
your needs, requests, and/or suggestions: Jim Reecy (jreecyiastate.edu),
James Koltes (jekoltesiastate.edu), Fiona McCarthy (fionamccarizona.edu).
Or talk to us using our Helpdesk (https://www.animalgenome.org/helpdesk).

NAGRP Bioinfo Team



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