From listmasteranimalgenome.org Mon Aug 30 22:27:44 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 (#3, 2021)
Date: Mon, 30 Aug 2021 22:27:44 -0500
What's new on the NAGRP animal genome web site (#3, 2021)
o Animal QTLdb and CorrDB updates -- Announcing a joint release of the
QTLdb (Release 45) and CorrDB (Release 13):
This database release is highlighted by two major events: (1) The Goat
QTLdb/CorrDB is live! The first batch of goat QTL/association data has
been curated into the Goat QTLdb and CorrDB, and (2) Progress toward
supporting only genome coordinate-based maps for QTL/association data
reports (more details below), with revised procedures and structures to
support multiple genome assemblies in terms of QTL/association mappings.
(Aug 23, 2021): A sum of 4,166 new QTL/associations have been curated into
the database. (New additions less obsolete/retracted ones: Catfish: 0;
Cattle: 1,944; Chicken: 1,417; Goat: 64; Horse: 1; Pig: 397; Sheep: 180;
Rainbow trout: 163 -- Net increase: 4,166). The current total number of
QTL in the database: 220,401 [Breakdown: Cattle: 163,725; Chicken: 15,475;
Goat: 64; Horse: 2,473; Pig: 33,540; Sheep: 3,752; Rainbow trout: 1,372]
Thanks are due to Dr. Holly Neibergs from Washington State University, and
Gabrielle Becker from University of Idaho for their commitment curating
their data into the QTLdb.
(Aug 23, 2021): A sum of 1,148 new correlations [Breakdown by species --
Pig: 193 (7 new traits); Cattle: 579 (26 new traits); Chicken: 18 (1 new
traits); Sheep: 47 (4 new traits); Goat: 311 (32 new traits)] and a sum of
194 new heritability data [Breakdown by species -- Pig: 48 (6 new traits);
Cattle: 115 (25 new traits); Chicken: 7 (2 new traits); Sheep: 22 (5 new
traits); Goat: 2 (1 new traits)] have been curated into the CorrDB. To
date, the total number of correlation data in the database: 23,552
[Breakdown by species -- Cattle: 12,801; Chicken: 1,455; Goat: 311; Horse:
209; Pig: 7,161; Sheep: 1,615], and total heritability data: 4,273
[Breakdown by species -- Cattle: 2,173; Chicken: 318; Goat: 2; Horse: 118;
Pig: 1,444; Sheep: 218]
(1) Multiple genome support: The current Animal QTLdb currently supports
20 genome builds for 7 species. This is a result of progress in database
restructuring and new data pipeline developments, along with several tools
for data lift-over between assemblies (more below).
(2) We have developed an in-house procedure to map known SNPs to a genome
assembly using flanking sequences, which can be lifted over from older
genome builds. This has greatly accelerated our progress on supporting
multiple/new genomes when they become available without extended waiting
periods for official SNP identifiers ('rs' numbers) to become available,
which presented a bottleneck for timely QTLdb data release. The
procedures developed also can help to match SNPs when 'rs' numbers are
missing from a data set.
(3) As a result of changes made in (2), modifications have been made to
the policy on minimum information required for Animal QTLdb data entry.
The change clarifies the minimum information for SNP-based data reports,
and opens avenues for new types of SNP information, such as those SNPs
without official 'rs' numbers must provide flanking sequences.
(4) A new hierarchy display tool has been developed for the Animal QTLdb
web portal for data access using traits from the Vertebrate Trait (VT)
Ontology, Livestock Product Trait (LPT) Ontology, and Clinical Measurement
Ontology (CMO). The display tool also includes search capability, which
helps users to quickly find relevant terms in large ontologies. The tool
has been implemented on all species QTLdb front pages, as well as on the
VT/LPT/CMO home pages at AnimalGenome.ORG.
(5) As a result of the changes made in (4), the Animal QTLdb web portal
structure has been reorganized to improve data access by requiring fewer
browse/search steps before reaching the level of pages for data.
(6) Animal CorrDB: A Data Summary text table has been added on several
pages to provide extended information on the current data window. A
featured function is a display of median and interquartile ranges of
heritability data when multiple measurement results exist for the same
(7) Animal CorrDB: The web portal on the Animal CorrDB website has been
extensively reformed. A number of new data filters along with search/
browse functions help to provide the scope of data so users have an
idea of what to expect rather than needing to guess what to search for.
Added links and flags on web pages can effectively enable users to
traverse from one data type to another (e.g., from traits to
QTL/association data; from heritability data to correlation data; from a
table view to graphic view). Linking traits to VT/LPT/CMO ontologies
facilitates data links with external databases where such ontologies are
o FAANG website updates
New updates are continually made to the FAANG website to cope with changes
on 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. The FAANG website updates serve an important role to
inform our peers and the public what we do and how we are doing better.
o Tool developments
Thanks to the individuals and groups (see data source acknowledgement on
the web page cited below) who shared their SNP names, custom SNP ID data
from their SNP discovery works that helped us to be able to upgrade the
previous tool for matching SNP names/'ss'/'rs' numbers into a livestock
SNP ID/name match repository with a new collection of over 7.8 million
non-redundant matches between various types of SNP names, identifiers, and
their final dbSNP 'rs' IDs. This dataset and tools are part of the NAGRP
Tool Box and useful for SNP-related data annotations and integrations. We
will continue to seek and accept new data contributions.
o Ontology developments:
(1) Five updates were made to the Vertebrate Trait (VT) Ontology data
(versions 11.6, 11.7, 11.8, 11.9, and 11.10).
(2) Three updates were made to the Livestock Breed Ontology (LBO, versions
6.3, 6.4, and 6.6).
(1) Data repository:
SNP liftover (an in-house procedure, see above) from chicken assembly
Gallus_gallus-5.0) to more recent builds Chicken GRCg7b and GRCg7w are
deposited at the NAGRP data repository as requested by users. More
data deposits can be made upon user requests.
(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