From listmaster animalgenome.org Tue Apr 30 09:44:15 2024
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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,
2024)
Date: Tue, 30 Apr 2024 09:44:15 -0500
What's new on the NAGRP animal genome web site (#2, 2024)
o Announcing a joint release of the QTLdb (Release 53) and CorrDB (Release 21):
(Apr 28, 2024): A sum of 2,676 new QTL/associations have been curated into
the database (New additions less obsolete/retracted ones: Catfish: 0;
Cattle: 512; Chicken: 322; Goat: 300; Horse: 1; Pig: 1,193; Sheep: 348).
To date, the current total number of QTL in the database: 266,160 (less all
linkage-map based QTL data that has been archived since the last release).
[Breakdown by species -- Cattle: 191,181 (on 680 traits); Chicken: 15,581
(on 372 traits); Goat: 1,501 (on 26 traits); Horse: 2,216 (on 65 traits);
Pig: 48,875 (on 673 traits); Sheep: 4,605 (on 272 traits); Rainbow trout:
2,201 (on 47 traits)].
In addition, as part of our data quality assurance efforts, updates were
continually made to previously curated data.
URL: https://www.animalgenome.org/QTLdb
(Apr 29, 2024): A sum of 4,104 new correlations [Breakdown by species --
Pig: 2,735; Cattle: 50; Chicken: 318; Sheep: 696; Goat: 305] and a sum of
313 new heritability data [Breakdown by species -- Pig: 114; Cattle: 31;
Chicken: 45; Sheep: 91; Goat: 32] have been curated into the CorrDB. To
date, the total number of correlation data in the database: 37,017
[Breakdown by species -- Cattle: 15,199 (on 354 traits, 286 trait
variants); Chicken: 2,371 (on 85 traits, 100 trait variants); Horse: 209
(on 27 traits, 0 trait variants); Pig: 12,147 (on 237 traits, 260 trait
variants); Sheep: 3,400 (on 77 traits, 194 trait variants); Goat: 3,691 (on
85 traits, 152 trait variants)], and total heritability data: 6,264
[Breakdown by species -- Cattle: 2,721 (on 407 traits, 296 trait variants);
Chicken: 496 (on 141 traits, 90 trait variants); Horse: 131 (on 54 traits,
1 trait variants); Pig: 1,913 (on 290 traits, 270 trait variants); Sheep:
537 (on 119 traits, 195 trait variants); Goat: 466 (on 79 traits, 124 trait
variants)] curated from 628 publications.
In addition, curation updates have been made to 4,551 correlations on 235
traits, and 263 heritability data on 191 traits.
URL: https://www.animalgenome.org/CorrDB
This release also includes the following updates:
(1) All linkage-map based data are now excluded from data downloads since
they have been separated and archived since the last QTLdb release (#52).
As a result, you may expect to see a reduction in total data number in the
current data summaries on the web.
(2) In addition to mapped data deposition for downloads for supported
genome assemblies, we have also included a copy of all curated data
deposition (data reported on various genome assemblies, in .tsv file
format). This data set has either SNP information OR genome locations on a
particular genome which may be lifted to a target genome by users employing
a method of their choice. In this way, we are not holding back any data
just because of the inability to lift *some* data to some assemblies due to
unavailability of mapped SNPs on that build.
(3) In addition to JBrowse built for QTLdb, we are setting up the newer
JBrowse2 as an experimental alternative to display chromosomal mappings for
default reference genomes. In the meantime, we have retired the GBrowse
display from the site (which was used for QTLdb data display since 2009).
Currently, the JBrowse2 setup is in preliminary tests and you may expect to
see improvements in the next few months. Our goal is to gradually phase out
our in-house chromosomal data display tool.
(4) The Frequently Asked Questions list has been updated with some newly
added Q&A, such as "why the data counts on each build within a species are
not the same", etc.
URL: https://www.animalgenome.org/PGNET/
o Ontology developments:
(1) Vertebrate Trait (VT) ontology data release has adopted a new version
naming format denoted with numeric dates ('yyyy-mm-dd'). For example, its
latest release version is 2024-04-23. This quarter, ten (10) VT data
releases have been made. The number of terms in the ontology has increased
to 3,791.
URL: https://www.animalgenome.org/...bioinfo/projects/vt/
(2) Four (4) Livestock Breed Ontology (LBO) data releases were made
(versions 9.1 to 9.4) with a current total of 1,123 terms.
URL: https://www.animalgenome.org/...ioinfo/projects/lbo/
(3) The Clinical Measurement Ontology (CMO) data was updated seven (7)
times from Bioportal to the local QTLdb/CorrDB curation environment and to
ontology hierarchy browsers and viewers for lookups.
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 QTLdb/CorrDB
updates described above.
o New web face for AnimalGenome.ORG website:
New web page layouts are being developed for the AnimalGenome.ORG website.
The new front page is the start of a redesign of the site for better
support of combined NRSP8 activities, better compatibility with mobile
device views, and to facilitate simpler information access to the site. New
changes on sublayers of the site will be quietly rolled out throughout the
summer.
URL: https://www.animalgenome.org/
o Misc.:
The FAANG website has been updated with new information added and changes
made reflecting consortium activities. See the website
(https://www.faang.org/) for details.
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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