From listmasteranimalgenome.org Mon Apr 30 13:40:53 2018
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, 2018)
Date: Mon, 30 Apr 2018 13:40:53 -0500
What's new on the NAGRP animal genome web site (#2, 2018)
o Animal QTLdb and CorrDB updates:
This is a joint release of the QTLdb (Release 35) and CorrDB (Release 3).
QTLdb: A sum of 7,308 new QTL/association data were added to the database.
(New additions less obsolete/retracted ones: Catfish: 0; Cattle: 5,216;
Chicken: 615; Horse: 45; Pig: 1,389; Sheep: 43 -- Net increase: 7,308).
The current total number of QTL in the database: 153,150 [Breakdown:
Cattle: 113,256; Chicken: 8,978; Horse: 1,349; Pig: 27,465; Sheep: 1,975;
Rainbow trout: 127]
CorrDB: A sum of 7,541 new correlations [Breakdown by species -- Cattle:
4,823 (on 139 traits); Chicken: 421 (on 42 traits); Pig: 1,217 (on 84
traits); Sheep: 1,080 (on 38 traits)]. A sum of 1,015 heritability data
[Break down by species -- Cattle: 706 (on 188 traits); Chicken: 75 (on 43
traits); Pig: 177 (on 57 traits); Sheep: 57 (on 40 traits).
(1) In order to maintain a high standard for data integrity and quality
control, a total of 3,628 historic correlation data were taken offline
and are currently being re-entered into the database with data integrity
check mechanisms newly built into the CorrDB. Even with this reduction,
the total number of data records still increased by 3,913 from the last
release, representing a 87% net data increase in the database - THANKS to
Cari Park for her vigorous and diligent curation works!
(2) The Animal QTLdb has introduced the use of DOI (Digital Object
Identifiers) on data that have a DOI record. This is to facilitate the
link-out service useful for unification of identified records and database
federation. Where applicable, DOI will become part of the required data for
submission to the Animal QTLdb.
(3) Active curator/editor tool improvements have continued. The most
recent improvements include managing the trait list with modifiers (for
traits that are the "same" by nature but slightly different in terms of
attached information, such as time, location, and other conditions as
"modifiers"), which helps the curators better manage the curation
environment. Another improvement is to wrap the critical database internal
identifiers in the backend process to avoid situations where errors might
(4) We are in the process of upgrading the web interfaces for the CorrDB as
the increase in number of newly curated data adds to the complexity of data
representations and queries. Stay tuned for the coming improvements on the
o Jbrowse data alignments
Thanks to Marcela Maria de Souza, Luciana Correia de Almeida Regitano, et al
from Brazil for providing the data from their recent study "A comprehensive
manually-curated Compendium of Bovine Transcription Factors." A total of
1,645 cattle transcription factors (TFs), including 865 sequence-specific
DNA-binding bovine TFs and 780 putative transcription cofactors (TcFs)
derived from known interactions with the identified TFs, have been added to
NAGRP Jbrowse tracks to align with QTL/association data among other genomic
features on the bovine genome.
o Data repository developments
(1) To solve platform dependency problems, a virtual machine (VM) was set up
to host the Virtual Comparative Map (VCmap) Visualization Tool. Please
update your bookmark or URL link.
OLD URL: https://www.animalgenome.org/VCmap
NEW URL: http://vcmap.animalgenome.org
(2) In response to some community requests, we have created HISAT2 indexes
for the most recent genome builds of cattle, chicken, horse, pigs, and sheep
and made them available through the NAGRP Data Repository (see links below).
The HISAT2 is a fast and sensitive alignment program for mapping next-
generation sequencing reads. Based on the HISAT and Bowtie2 implementations,
HISAT2 aligns reads in SAM format, which can be used by any tool that uses
SAM format, for example, SAMtools, GATK, etc.
o Community information updates:
Thanks to Mohamed Salem who helped make the current NRSP-8 annual reports
from aquaculture, bioinformatics, cattle, horse, poultry, sheep/goat, and
swine coordinators available online. Also now online are a work summary of
NRSP-8 accomplishments during 2013-2018, a proposal for the next 5 years
(2019-2023), and an updated list of current community leaders.
o Data sharing platform:
There has been a significant increase in the use of the NAGRP Data Sharing
Platform since 2017, especially regarding the supplementary data depositions
for publications, which have more than doubled compared to the previous year.
To increase the visibility of the tools (in response to increasing number
of inquiries from users), we have made improvements on the web layouts with
clearer guides for users to access the tools more easily.
More current/on-going updates can be found at the daily "what's new" web page
(https://www.animalgenome.org/news/) on this site. We appreciate your kind
reporting of broken links or web errors on AnimalGenome.ORG.
Your inputs are always appreciated. Feel free to contact us with your needs,
requests, and/or suggestions. You can reach us in multiple ways: contact Jim
Reecy (+1-515-294-1609) for new projects/priorities, email the team at the
email address below, or use our online Helpdesk web site to write to us
NAGRP Bioinfo Team