From listmasteranimalgenome.org Fri Jan 3 18:05:48 2020
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 (#1, 2020)
Date: Fri, 03 Jan 2020 18:05:48 -0600
What's new on the NAGRP animal genome web site (#1, 2020)
o Animal QTLdb and CorrDB updates -- Announcing a joint release of the
QTLdb (Release 40) and CorrDB (Release 8):
QTLdb (Dec 29, 2019): A sum of 4,250 new QTL/associations have been curated
into the database. (New additions less obsolete/retracted ones: Catfish: 0;
Cattle: 3,216; Chicken: 478; Horse: 153; Pig: 305; Sheep: 98; Rainbow
trout: 0.) In addition, there are 331 new association data that have been
placed on-hold as they were entered with custom SNP IDs that needs to be
translated to official dbSNP IDs for correct mapping). The current total
number of QTL/associations in the database: 178,491 [break down by species:
Cattle: 130,407; Chicken: 11,818; Horse: 2,413; Pig: 30,170; Sheep: 3,099;
Rainbow trout: 584].
CorrDB (Dec 29, 2019): A sum of 589 new correlations [break down by species:
Pig: 513 (9 new traits); Cattle: 76 (0 new traits)] and a sum of 181 new
heritability data [break down by species: Pig: 68 (0 new traits); Cattle:
104 (9 new traits); Chicken: 9 (5 new traits)] have been curated into the
CorrDB. The current total number of correlations in the database: 18,638
[break down by species: Cattle: 10,076; Chicken: 1,221; Horse: 209; Pig:
5,982; Sheep: 1,150], and heritability data: 3,264 [break down by species:
Cattle: 1,404; Chicken: 272; Horse: 118; Pig: 1,378; Sheep: 92], curated
from 344 publications.
(1) A new version of the QTL/association enrichment analysis tool is
available in the Animal QTLdb (listed under "Search and Analysis" tools).
This version of the tool allows users to select traits and chromosomal
regions of interest to analyze QTL/association representations in the
selected region versus that of the whole genome.
(2) The DOI (Digital Object Identifier) data in the Animal QTLdb has been
made visible on the abstract view and data summary view pages. Users can
follow the DOI link to the full text of a publication when available.
(3) The first phase of curator/editor tools renovation has been undertaken
to accommodate data model and database structural changes due to the
incorporation of eQTL data into the database.
(4) Improvement of Animal CorrDB user interfaces is underway to improve
user access to data. The latest outcome is a new front page for data access
by species. More updates will follow.
(5) Other ongoing improvements of curator tools for both QTLdb and CorrDB.
o Ontology developments
Four (4) data updates were made to the Vertebrate Trait (VT) ontology
(the latest version is 9.5).
o Data repository:
We have ceased to support hosting supplementary data for publications as
a result of a gradual scale-down of the service over a period of 10 months.
Once we finish the ongoing updates of journals information needed for some
late datasets, we will transfer them to the Open Science Framework (OFS,
https://osf.io/). We will continue hosting the current data and initiate
visit redirects after the future transfer.
In the meantime, we encourage users to directly use the OFS.
A new web site has been set up for the upcoming Visions III conference to be
held May 19-20, 2020 at Iowa State University in Ames, Iowa: "Star Gazing
into the Galaxy of Animal Genetics and Genomics". The conference aims to
explore and discuss the challenges and opportunities that the future provides
in animal genetics and genomics.
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