This repository for supplementary data to publications has been serving the
community since 2007. In early 2019 we decided to move all data to Open
Science Framework (OSF; https://osf.io) for better sustainability, and we have
directed future needs for data host to using OSF. As of April 5, 2022,
all valid data were transferred, and URL forwards were set up to direct
incoming web visits to OSF locations ("animalgenome.org" location was used in
the data publications).
-
Apr 26, 2019:
From listmaster
animalgenome.org Fri Apr 26 16:53:53 2019
From: "Hu, Zhiliang [AN S]" <zhuiastate.edu>
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
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
future.
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.
URL: https://www.animalgenome.org/repository/
-
Aug 29, 2019:
From listmasteranimalgenome.org Tlistmaster Aug 29 14:07:09 2019
From: "Hu, Zhiliang [AN S]" <zhuiastate.edu>
To: Members of AnGenMap <angenmapanimalgenome.org>
Subject: What's new on the NAGRP animal genome web site (#3, 2019)
Date: Thu, 29 Aug 2019 14:07:09 -0500
The NAGRP Data Repository has been scaled down in terms of its acceptance
of certain types of files for deposition. In particular, we have ceased to
accept supplementary data for publications. Users are advised to use Open
Science Framework (OFS, https://osf.io/) instead.
-
Jan 03, 2020:
From listmasteranimalgenome.org Fri Jan 3 18:05:48 2020
From: "Hu, Zhiliang [AN S]" <zhuiastate.edu>
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
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.
-
January 2020 - December 2021:
Data are deposited usually prior to manuscript being accepted for publication.
This usually takes up to 4-6 months or longer.
This period of nearly 2 years of time was to wait and complete data tag
with publication citation information to be attached to the data.
By the end of this period, there remain 49 data files (3.6 GB in total size) on
17 manuscripts were dropped for further actions since there is no indication
that their manuscripts would ever get published.
-
Jan 03, 2022:
From listmasteranimalgenome.org Mon Jan 3 17:29:00 2022
From: "Hu, Zhiliang [AN S]" <zhuiastate.edu>
To: Members of AnGenMap <angenmapanimalgenome.org>
Subject: What's new on the NAGRP animal genome web site (#1, 2022)
Date: Mon, 03 Jan 2022 17:29:00 -0600
We have entered the last phase of the transition from hosting supplementary
data for publications at AnimalGenome.ORG to using the Open Science
Framework (OSF, https://osf.io/) for best use of our resources. We will
start to transfer the current data to OSF in the coming months and forward
the data visits to their new home as long as AnimalGenome.ORG is in service.
In the meantime, we encourage users to directly use the OSF.
URL: https://www.animalgenome.org/repository/pub/
-
Mar 29, 2022:
Started data transfer to Open Science Framework (OSF; https://osf.io) on
March 29, 2022.
-
Mar 30, 2022:
Individual email notifications are sent to each data owner.
Below is a sample.
_______________________________________________________________________
From: bioinfo-team <bioinfo-teamanimalgenome.org>
Reply-To: Zhiliang Hu <zhuiastate.edu>
Date: Wed, Mar 30, 2022 at 03:52 PM
To: Bertolini, Francesca <fbertiastate.edu>
Subject: Transfer of your deposited supplementary data to OSF
Dear Bertolini, Francesca,
We have previously (Apr 26, 2019, Aug 29, 2019, Jan 3, 2020, Jan 3, 2022)
announced plans for transfer of all publication supplementary data hosted by
AnimalGenome.ORG to Open Science Framework (OSF, https://osf.io/).
We have started the transfer.
In the coming days you may expect to receive invitation emails from OSF for
your data deposited at OSF and option for you to set up an OSF account in
order to claim the ownership of your data last updated 133 months ago
on May. 5, 2011:
- https://www.animalgenome.org/repository/pub/ISU2016.0617/
"Genomic investigation of piglet resilie..."
by "Francesca Bertolini, John C. S. H ardin..."
Anim Genet. doi:10.1111/age.12522 ...
Please act accordingly. Thanks for your attention,
NAGRP Bioinfo-team
--
Helpdesk | AnGenMap | Animal QTLdb | CorrDB | Data Repository |
NAGRP Databases and Web Sites | USDA-NIFA-NRSP-8 Bioinformatics
ADDR: https://www.AnimalGenome.ORG/
-
Apr 04, 2022:
Data transfer to Open Science Framework (OSF; https://osf.io) completed.
All valid data (a total of 796 data files, 84.25 GB in size, for 92
manuscripts published in 27 scientific journals) have been transferred
to Open Science Framework (OSF; https://osf.io).
Subsequently the URL forwarding (to OSF) for each of the publications
are set up on this site. These URL forwarding will be kept functioning
as long as the AnimalGenome.org website stays alive.
-
Apr 05, 2022:
Individual email notifications are sent to each data owner.
Below is a sample.
_______________________________________________________________________
From: bioinfo-teamanimalgenome.org
Date: Tue, 05 Apr 2022 19:37:47 -0500
Reply-To: zhuiastate.edu
To: mwalugemiastate.edu
Subject: Transfer of your supplementary data to OSF completed
Dear Muhammed Walugembe,
As planned, we have successfully transferred your supplementary data for
"Detection of selection signatures among..."
by "Muhammed Walugembe, Francesca Bertolini..."
Front Genet. 2018; 9: 737 ...
https://www.animalgenome.org/repository/pub/ISU2018.0416/ )
to Open Science Framework (OSF, https://osf.io/).
You should have received OSF email invitation to claim the ownership of
your data (set up your OSF account if you don't yet have one).
Currently your data is under the name of "Zhiliang HU" representing
AnimalGenome.ORG on the data transfer. Once you have claimed the ownership
of your data, "Zhiliang HU" will withdraw from your data contact list.
This is our LAST email communication on the matter. Please act at your
earliest convenience. Thanks for your attention,
NAGRP Bioinfo-team
--
Helpdesk | AnGenMap | Animal QTLdb | CorrDB | Data Repository |
NAGRP Databases and Web Sites | USDA-NIFA-NRSP-8 Bioinformatics
ADDR: https://www.AnimalGenome.ORG/
-
Apr 28, 2022:
From listmasteranimalgenome.org Tlistmaster Apr 28 11:12:08 2022
From: "Hu, Zhiliang[ANS]" <zhuiastate.edu>
To: Members of AnGenMap <angenmapanimalgenome.org>
Subject: What's new on the NAGRP animal genome web site (#2, 2022)
Date: Thu, 28 Apr 2022 11:12:08 -0500
As of April 5, 2022, all NAGRP Data Repository–hosted supplementary data to
publications (total of 796 data files, 84.25 GB in size, for 92 manuscripts
published in 27 scientific journals) has been transferred to Open Science
Framework (OSF; https://osf.io). Automatic web forwarding links for each of
the publications have been set up. The URL forwarding will stay functioning
as long as the AnimalGenome.org website is live.
We have sent notifications to the data owners to sign up on OSF in order to
take ownership of their data. Currently, the transferred data are owned by
one of our representatives (Zhiliang Hu). As soon as the proper ownership
is established at OSF, we will withdraw from our role.
The entire transition process took about four years to finish. (1) In
Spring 2019, we announced our plan and started to scale down the service;
(2) During 2020 and 2021, we provided a time window to update the journal
information for those papers that were in the process of being accepted for
publication. (3) In early 2022, we completed the data transfer. It is worth
mentioning that by the end of this period, there remained 49 data files
(3.6 GB in total size) on 17 manuscripts that were not transferred, since
there is no indication that these manuscripts will ever get published.
URL: https://www.animalgenome.org/repository/pub/
The above changes were only intended to improve long-term data stability.
The data repository service is still available for short-term data sharing.
URL: https://www.animalgenome.org/repository/
