From listmasteranimalgenome.org Wed Apr 28 08:22:16 2021
From: "Hu, Zhiliang [AN S]" <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, 2021)
Date: Wed, 28 Apr 2021 08:22:17 -0500
What's new on the NAGRP animal genome web site (#2, 2021)
o Animal QTLdb and CorrDB updates -- Announcing a joint release of the
QTLdb (Release 44) and CorrDB (Release 12):
QTLdb (Apr 26, 2021): A sum of 3,853 new QTL/associations have been
curated into the database. (New additions less obsolete/retracted ones:
Cattle: 1,116; Chicken: 1,173; Pig: 1,028; Sheep: 25; Rainbow trout: 509
-- Net increase: 3,853). In addition, 453 previously curated data were
updated as part of our data quarantine routine. The current total number
of QTL in the database: 214,876 [Breakdown: Cattle: 161,756; Chicken:
14,049; Horse: 2,470; Pig: 31,825; Sheep: 3,571; Rainbow trout: 1,205]
(Apr 26, 2021): A sum of 1,368 new correlations [Breakdown by species --
Pig: 233 (12 new traits); Cattle: 945 (24 new traits); Chicken: 190 (6
new traits)] and a sum of 313 new heritability data [Breakdown by species
-- Cattle: 177 (32 new traits); Chicken: 24 (3 new traits); Sheep: 8 (0
new traits)] have been curated into the CorrDB. To date, the total
number of correlation data in the database: 22,404 [Breakdown by species
-- Cattle: 12,222; Chicken: 1,437; Horse: 209; Pig: 6,968; Sheep: 1,568],
and total heritability data: 4,079 [Breakdown by species -- Cattle: 2,058;
Chicken: 311; Horse: 118; Pig: 1,396 (after recall of 1,241 heritability
data entered prior to 2012 that did not meet data quality standards);
Sheep: 196], curated from 344 publications.
(1) Links to the Animal QTLdb and CorrDB are published on the Figshare
open access platform through the Iowa State University Library.
Subsequently, each database has a universal Digital Object Identifier
(DOI), and all data are covered by the Creative Commons licenses. As a
result, there can be alternative ways for the users of the QTLdb or
CorrDB to properly cite the use of the database resources and/or tools.
Please check each database website to find more details (click on
respective web page footers for copyright claims and citation details;
the same information is pre-pended to all data download files as well).
(2) Continued improvements are ongoing to facilitate the curation of eQTL
information into the database. For example, cis/trans eQTL information
are curated to the Animal QTLdb and can be seen on QTL details and data
summary (by publication) pages where such data is available.
(3) We have been engaged in continued developmental works to transition
the QTLdb from linkage map–based database infrastructure to be genome map
based, and to accommodate more structural genomics data types.
(4) Progress is being made to improve the CorrDB web interface for better
data summary, query, and data representation reports. The initial visible
change is the new front page with new data summary tables. Further changes
will include sub-page reformats to reflect multiple reports on the same
pairs of traits, and/or correlation types (phenotypic, genetic,
environmental, residual), and reports by species. These improvements are
made possible by the recent addition of a database routine for
post-curation data processing to improve structured data queries. This is
an ongoing process; stay tuned for new updates.
(5) Data curation tools are undergoing continued improvement, including
the addition of data summaries for curators to be better informed when at
certain parts of the curation process, and the creation of direct work
flow links between tools.
o FAANG website updates
The FAANG website is undergoing a revamp to reflect the advancement of
the consortium for the next decade of FAANG research (FAANG to Fork
strategy) to link G2P in diverse populations of animals and apply
innovative new technologies to model G2P at the cell, tissue, and whole
animal levels. More changes will be visible in the coming weeks.
o Ontology developments:
(1) Four updates were made to the Vertebrate Trait (VT) Ontology data
(versions 11.1, 11.2, 11.3, and 11.4).
(2) Two updates were made to the Livestock Breed Ontology (LBO, versions
6.1 & 6.2).
(1) NRSP8 annual reports for 2020 are being made available on the
website as they became available from each species coordinator.
(2) The website has been updated for the upcoming VISIONS III conference:
Star Gazing into the Galaxy of Animal Genetics and Genomics, with new
information on the date change, updated speakers and sponsors.
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