From listmaster animalgenome.org Tlistmaster Aug 29 12:27:41 2024
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From: "Hu, Zhiliang [ANS]" <zhuiastate.edu>
Postmaster: submission approved by list moderator
To: Members of AnGenMap <angenmapanimalgenome.org>
Subject: What's new on the NAGRP animal genome web site (#3,
2024)
Date: Thu, 29 Aug 2024 12:27:41 -0500
What's new on the NAGRP animal genome web site (#3, 2024)
o Celebrating 20 Years of Animal QTLdb
This year marks 20 years since the first public release of the Animal
QTLdb. The database was developed to facilitate G2P research in the
livestock genomics research community. Over the years, this online
database has been run continually by the developers/maintainers at Iowa
State University. We are developing a web page dedicated to highlight
the major progress we have made. We welcome inputs in terms of its past
success and future prospectives.
URL: https://www.animalgenome.org/QTLdb
o Animal QTLdb and CorrDB updates -- Announcing a joint release of the QTLdb
(Release 54) and CorrDB (Release 22):
(Aug 25, 2024): A sum of 11,682 new QTL/associations have been curated
into the database. (New additions less obsolete/retracted ones: Cattle:
1,066; Chicken: 3,021; Goat: 644; Horse: 0; Pig: 6,813; Sheep: 138;
Rainbow trout: 0 -- Net increase: 11,682). To date, the current total
number of QTL in the database: 277,842 [Breakdown by species -- Cattle:
192,247 (on 552 traits); Chicken: 18,602 (on 244 traits); Goat: 2,145 (on
81 traits); Horse: 2,216 (on 60 traits); Pig: 55,688 (on 407 traits);
Sheep: 4,743 (on 167 traits); Rainbow trout: 2,201 (on 35 traits)].
(This is a joint release with the 22nd CorrDB release.)
In addition, as part of our data quality assurance efforts, updates were
performed on 2,020 SNP associations and 115 base trait data.
URL: https://www.animalgenome.org/QTLdb
(Aug 26, 2024): A sum of 935 new correlations [Breakdown by species --
Pig: 44; Cattle: 488; Chicken: 235; Sheep: 104; Goat: 64] and a sum of 164
new heritability data [Breakdown by species -- Pig: 17; Cattle: 68;
Chicken: 40; Sheep: 18; Goat: 21] have been curated into the CorrDB. To
date, the total number of correlation data in the database: 37,952
[Breakdown by species -- Cattle: 15,687 (on 360 traits, 328 trait
variants); Chicken: 2,606 (on 89 traits, 110 trait variants); Horse: 209
(on 27 traits, 0 trait variants); Pig: 12,191 (on 237 traits, 291 trait
variants); Sheep: 3,504 (on 78 traits, 198 trait variants); Goat: 3,755
(on 86 traits, 154 trait variants)], and total heritability data: 6,428
[Breakdown by species -- Cattle: 2,789 (on 414 traits, 340 trait
variants); Chicken: 536 (on 148 traits, 100 trait variants); Horse: 131
(on 54 traits, 1 trait variant); Pig: 1,930 (on 285 traits, 308 trait
variants); Sheep: 555 (on 121 traits, 203 trait variants); Goat: 487 (on
79 traits, 124 trait variants)] curated from 645 publications.
In addition, related updates were made on 12,166 correlations and 825
heritability data as part of our data quality assurance efforts.
URL: https://www.animalgenome.org/CorrDB
Database development notes:
(1) Multiple Genome Support: Local SNP maps have been updated with new EVA
dbSNP release 6 data (https://ftp.ebi.ac.uk/..._releases/;
2024-07-08) for 19 genome assemblies. In addition, SNPs have been lifted
to 3 more genome builds, cattle (ARS_UCD2), pig (MARC1), and sheep
(Rambo1), using our in-house tool. This facilitated QTL/association data
support for 22 genome assemblies in 7 animal species. We will consider
making this in-house tool available for free download if there is
community demand. (2) Towards data curation automations: Thanks to
collaborative work with Yuepei Li and Kang Zhou from Qi Li's group in
computer science at Iowa State University, an AI-powered literature
classification tool has been implemented in the QTLdb data curation
pipeline, which has greatly accelerated literature data processing. (3)
FAQ: the "Frequently asked questions" list has been updated with a few
newly added items. The most recent one is on the "QTL sizes" in downloaded
data. Please check it out for more details. (4) Odd event flag: Warning
flags have been implemented for the rare event when reported heritability
data is outside of the conventional 0-1 range (NOTE these are not data
curation errors!).
o The new websites for NRSP8 and RCN projects
The main pages at AnimalGenome.ORG have been revamped to serve the
purposes of the new NRSP8 (National Research Support Program 8) and RCN
(Research Collaboration Network), both supported by the USDA/NIFA. Here
are some highlights:
- Dynamically displayed banners on top of the entry page to provide lead
information on the main themes of the site. These are the major frontiers
of the new NRSP8 and RCN projects.
URL: https://www.animalgenome.org
- Content TAB featured web pages to serve information for both NRSP8 and
RCN projects (click page-top logos of any page to access). Each site has
the aims, structures, and organizational information at your fingertips.
URL: https://www.animalgenome.org/...e.org/RCN/
- A BBS (Bulletin Board System) to streamline information delivery and
sharing for the community. The use of the BBS is privileged for NRSP8
members only. Check it out to find out how to join NRSP8 and how to use
this system.
URL: https://www.animalgenome.org/community/bbs/
- A community calendar for either or both NRSP8/RCN members to share their
schedules and for the general public to share open events. NRSP8/RCN
schedule entry is available to members only.
URL: https://www.animalgenome.org/RCN/?tab=cal
- Join NRSP8: There are multiple links throughout the site leading to a
new "Join NRSP8" page. All who are interested may take a look at what it
is and how to join.
URL: https://www.animalgenome.org/NRSP8/join
- A road map (or guide) for the site can be found in the upper-right
corner of any page – click on the “list icon” for a pull-down menu to
find your points of interest.
o Active ontology development occurred in the summer of 2024.
(1) Nine Vertebrate Trait (VT) Ontology data releases were made with
structural changes and data addition/deletion updates. The current term
count is 3,796.
URL: https://www.animalgenome.org/...bioinfo/projects/vt/
(2) One Livestock Breed Ontology (LBO) data release was made (current
version has 1,124 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
curation and maintenance. This is partly reflected in the QTL/CorrDB
updates described above.
o Feedback:
Please feel free to contact the new 2024-2027 NRSP8 and RCN project leaders
with your suggestions, inputs, or inquiries, with regard to the web
development at this site or beyond.
** NRSP8 Project:
- Annette McCoy (University of Illinois; mccoyaillinois.edu)
- Molly McCue (University of Minnesota; mccu0173umn.edu)
- Darren Hagen (Oklahoma State University; darren.hagenokstate.edu)
- Ted Kalbfleisch (University of Kentucky; ted.kalbfleischuky.edu)
- James Koltes (Iowa State University; jekoltesiastate.edu)
- Cedric Gondro (Michigan State University; gondrocemsu.edu)
- Rebecca Cockrum (Virginia Tech; rcockrumvt.edu)
- Yanghua He (University of Hawaii; yanghua.hehawaii.edu)
** RCN Project:
- Noelle Cockett (Utah State University; noelle.cockettusu.edu)
- Darren E. Hagen (Oklahoma State University; darren.hagenokstate.edu)
- Andrew S. Hess (University of Nevada–Reno; ahessunr.edu)
- Theodore S. Kalbfleisch (University of Kentucky; ted.kalbfleischuky.edu)
- James E. Koltes (Iowa State University; jekoltesiastate.edu)
- Christian Maltecca (North Carolina State University; cmaltecncsu.edu)
- Fiona M. McCarthy (University of Arizona; fionamccarizona.edu)
- Stephanie D. McKay (University of Missouri; mckaysdmissouri.edu)
- Brenda M. Murdoch (University of Idaho; bmurdochuidaho.edu)
- Timothy P.L. Smith (USDA USMARC, tim.smith2usda.gov)
- Juan P. Steibel (Iowa State University; jsteibeliastate.edu)
- Huaijun Zhou (University of California–Davis; hzhouucdavis.edu)
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.
--
NAGRP Bioinfo Team
bioinfo-teamanimalgenome.org
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