From listmasteranimalgenome.org Tlistmaster Apr 28 11:12:08 2022
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 (#2, 2022)
Date: Thu, 28 Apr 2022 11:12:08 -0500
What's new on the NAGRP animal genome web site (#2, 2022)
o Animal QTLdb and CorrDB updates -- Announcing a joint release of the
QTLdb (Release 47) and CorrDB (Release 15):
(Apr 25, 2022): A sum of 17,360 new QTL/associations have been curated into
the database. (New additions less obsolete/retracted ones: Catfish: 0;
Cattle: 15,726; Chicken: 366; Goat: 60; Horse: 31; Pig: 1,042; Sheep: 135;
Rainbow trout: 0 -- Net increase: 17,360). To date, the current total
number of QTL in the database: 253,330 [Breakdown: Cattle: 192,925 (on 701
traits); Chicken: 16,637 (on 443 traits); Goat: 128 (on 25 traits); Horse:
2,636 (on 65 traits); Pig: 35,384 (on 716 traits); Sheep: 4,207 (on 281
traits); Rainbow trout: 1,413 (on 41 traits)]
(Apr 26, 2022): A sum of 752 new correlations [Break down by species --
Pig: 156; Cattle: 172; Chicken: 170; Sheep: 254; ] and a sum of 155 new
heritability data [Break down by species -- Pig: 44; Cattle: 47; Chicken:
24; Horse: 1; Sheep: 36; Goat: 3; ] have been curated into the CorrDB.
To date, the total number of correlation data in the database: 24,856
[Breakdown by species -- Cattle: 13,003 (on 393 traits); Chicken: 1,625
(on 90 traits); Horse: 209 (on 27 traits); Pig: 7,737 (on 267 traits);
Sheep: 1,971 (on 93 traits) Goat: 311 (on 32 traits)], and total
heritability data: 4,474 [Breakdown by species -- Cattle: 2,243 (on 426
traits); Chicken: 343 (on 120 traits); Horse: 123 (on 53 traits); Pig:
1,491 (on 306 traits); Sheep: 269 (on 124 traits) Goat: 5 (on 2 traits)],
curated from 441 publications.
(1) The curator tools in both QTLdb and CorrDB have been extensively
re-developed (involving 15 scripts serving 47 curator views/functions)
in order to facilitate curation of "trait variants" (called "sibling
traits" previously). This improvement is intended not only to improve
consistency of livestock trait curation, but also to provide a better data
management structure to facilitate information dissemination and trait
ontology developments. We have submitted a paper for the upcoming WCGALP
to describe the new data structure and tools.
(2) Batch data download from the CorrDB is now possible. A new section has
been added to the CorrDB home page listing livestock animal trait
correlation and heritability data. The data for download will be synced
with the current database release.
o Ontology developments:
(1) Six updates were made to the Vertebrate Trait (VT) Ontology data
(versions 12.1, 12.2, 13.3, 12.4, 12.5, and 12.6).
(2) Nine updates were made to the Livestock Breed Ontology (LBO, versions
7.1, 7.2, 7.3, 7.4, 7.5, 7.6, 7.7, 7.8, and 7.9).
o Data repository:
As of April 5, 2022, all NAGRP Data Repository–hosted supplementary data to
publications (total of 796 data files, 84.25 GB in size, for 92 manuscripts
published in 27 scientific journals) has been transferred to Open Science
Framework (OSF; https://osf.io). Automatic web forwarding links for each of
the publications have been set up. The URL forwarding will stay functioning
as long as the AnimalGenome.org website is live.
We have sent notifications to the data owners to sign up on OSF in order to
take ownership of their data. Currently, the transferred data are owned by
one of our representatives (Zhiliang Hu). As soon as the proper ownership
is established at OSF, we will withdraw from our role.
The entire transition process took about four years to finish. (1) In
Spring 2019, we announced our plan and started to scale down the service;
(2) During 2020 and 2021, we provided a time window to update the journal
information for those papers that were in the process of being accepted for
publication. (3) In early 2022, we completed the data transfer. It is worth
mentioning that by the end of this period, there remained 49 data files
(3.6 GB in total size) on 17 manuscripts that were not transferred, since
there is no indication that these manuscripts will ever get published.
The above changes were only intended to improve long-term data stability.
The data repository service is still available for short-term data sharing.
(1) NRSP8 annual reports for 2020 are being made available on the
website as they became available from each species coordinator.
(2) The website supporting the FAANG 2022 Workshop held in February has
video recordings and slides available online.
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