From listmasteranimalgenome.org Fri Apr 26 16:53:53 2019
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, 2019)
Date: Fri, 26 Apr 2019 16:53:53 -0500
What's new on the NAGRP animal genome web site (#2, 2019)
o Animal QTLdb and CorrDB updates -- Announcing a joint release of
the QTLdb (Release 38) and CorrDB (Release 6):
QTLdb (Apr 24, 2019): 3,881 new QTL/associations have been added to the
database. (New additions less obsolete/retracted ones: Cattle: 2,771;
Chicken: 197; Horse: 7; Pig: 325; Sheep: 581; Rainbow trout: 0. This
results in a net increase of 3,881 new data). The current total number
of QTL in the database: 168,143 [Break down: Cattle: 122,893; Chicken:
11,141; Horse: 2,030; Pig: 29,045; Sheep: 2,906; Rainbow trout: 128].
CorrDB (Apr 24, 2019): 3,903 new correlations have been added to the
database. [Break down by species -- Cattle: 1,913 (0 new traits); Horse:
201 (26 new traits); Pig: 1,789 (21 new traits) ], and a sum of 430 new
heritability data [Break down by species -- Cattle: 224 (61 new traits);
Horse: 114 (52 new traits); Pig: 91 (0 new traits); Sheep: 1 (0 new traits)]
have been curated into the CorrDB.
(1) Extensive improvements have been made to the QTLdb curator tools to
streamline workflows and create more intuitive curation environments.
The development efforts focused on reducing the chances for a curator to
manually enter some critical info where automatic information passage can
be implemented. At-the-site user instructions were developed/revised to
offer better helps to curators.
(2) Debugging of curator/editor tools has continued. This effort was aimed
to help improve data debugs (improvement/implementation of some data quality
(3) The CorrDB curator tools have also been improved to refine workflows and
better data handling.
o Data repository:
The NAGRP Data Repository at AnimalGenome.ORG is taking forward-looking
steps to safeguard the hosted data for long-term sustainability. A new
message is posted on the website to encourage users to start using Open
Science Framework (https://osf.io) for their open data host options in the
The Repository has been serving the community for over 10 years. While we
continue to improve our services to meet community needs, new opportunities
and infrastructures have emerged, such as Open Science Framework and Dryad
(https://datadryad.org/pages/faq). Our move is for better use our fund and
leverage existing resources that are available to the community.
In order to improve the long-term sustainability of data availability, we
plan to transit from hosting user data at AnimalGenome.ORG to facilitating
the use of publicly available resources when these services offer better
technical support and increased sustainability.
The Open Science Framework has more advantages than what we can offer
(See http://help.osf.io/m/faqs for more details):
- Free to use.
- Long term sustainability: OSF is supported through grants from a
variety of supporters, with current revenue of more than $7 million.
- A $250,000 preservation fund sufficient for 50+ years of
hosting read access to the current data in the event that the Center for
Open Science has to curtail.
- Alliances with many university libraries for data sharing and access.
- Flexible features for users: supports both private and public
workflows. Projects or components of projects can be kept private
for collaborators or made public and controlled by users.
- DOIs available for public projects and registrations.
- API tools available.
The Dryad data repository:
- Nonprofit organization.
- Collects only a one-time Data Publishing Charge (DPC) of $120 US
(or an annual fee).
- Provides long-term access to data at no access cost for data less
than 20GB (increment charges for every 10GB beyond 20GB).
- Includes clear instructions on how to prepare data, submit data, and
how to write README files, etc. to help users.
(See https://datadryad.org/pages/faq for more details.)
At AnimalGenome.ORG, while we can continue to host new user data as we
have in the past, we want users to be aware of the fact that the NAGRP
program currently has funding until the year 2023. For this reason, we are
helping users to move the currently hosted data at AnimalGenome.ORG to OSF.
With this change, it is a great time to obtain feedback from the community
and other stakeholders on what they need most, and what would be the best
approaches to leverage the current and future support from USDA/NIFA and
elsewhere considering the community as a whole.
o Ontology developments
New data releases were made for Livestock Breed Ontology (LBO)
(three times; the latest version is v.4.3).
URL: https://www.animalgenome.org/...ioinfo/projects/lbo/ (LBO)
o FAANG website:
FAANG past meeting archives are gathered and made available. The plans are
to add future meeting outcomes to the meeting archive resource. A scheme
has been set up so that at the FAANG meetings/events page one can look for
future meetings OR go for past meeting archives.
- Both NAGRP Data Repository FAQ and AnGenMap FAQ were updated to address
new developments on these two sites.
- New information have been posted at
o NRSP8 leadership site (https://www.animalgenome.org/community/NRSP-8/)
o Aquaculture Genomics site (https://www.animalgenome.org/aquaculture/)
- Room sharing bulletin board for PAG-Asia 2019 is open
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 simply use our online Helpdesk to make a request
NAGRP Bioinfo Team