NAGRP Community Data Repository
for Livestock Animal Genomics
Data Repository

Frequently Asked Questions

  1. Does NAGRP Data Repository use DOI to refer to a particular data set?
  2. What's the difference between NAGRP Data Repository and the
  3. I have a large data set to send but it takes forever to upload. Is that normal?
  4. How should I cite the data source for data hosted at this site?
  5. Does the NAGRP Data Repository provide unique accessions number or identifier? What is data locator?
  6. Why NAGRP Data Repository is promoting Open Science Framework (OSF)?
  1. Does NAGRP Data Repository use DOI to refer to a particular data set?

  2. No, we have not implemented DOI system for the supplementary materials we host. This is not only for its cost-dependent system (https://www.doi.org/faq.html), but also for the fact that we are not a publishing platform, and our hosted data may subject to change or removal.

    For supplementary data to publications, the data are not deemed as final upon their first setup, and they may go away depending on if a paper may or may not be finally published. Thus it's not worth setting up DOI for them. The Uniform Resource Locators (URL) we provide are stable and serve as a permanent data locator as long as the domain "animalgenome.org" is alive.

     

  3. What's the difference between NAGRP Data Repository and the NAGRP File Sharing Platform?

  4. In brief, the NAGRP Data Repository is an open platform data host, for any data that members of the community wish to share with the community to benefit the entire research community; while the File Sharing Platform is a file transport service for members of the community to send files to a destination at his/her choice, which include but not limited to the Data Repository.

     

  5. I have a large data set to send but it takes forever to upload. Is that normal?

  6. The NAGRP File Sharing Platform is a web HTTP/CGI based tool which has certain limitations in terms of file sizes and timeout thresholds. When needs to transfer large volumn of data, user can request for our ftp services through our helpdesk.

     

  7. How should I cite the data source for data hosted at this site?

  8. Cite the use of data from this site: please see individual "README" to each file for data owner/credit information. When a specific README is not available for a file, refer to "Data sources/credits" section on the same page (usually below the file list) for data owner/ credit information. Suggested reference formats include but not limited to:
    e.g. 1 Data downloaded from AnimalGenome.ORG Data Repository
           (http://www.animalgenome.org/.../pig/Annot.exon.build10.gff.gz)
           Data source: Martien Groenen, Wageningen University,
           Last updated: 2010-09-30.
    
    e.g. 2 Martien Groenen, Wageningen University, data downloaded from the
           AnimalGenome.ORG Data Repository (http://www.animalgenome.org/
           repository/pig/) on 2013-xx-xx.
    
    e.g. 3 Illumina Pig 60k SNPs mapped to pig genome assembly 10.2, by
           Martien Groenen, Wageningen University, data downloaded from the
           AnimalGenome.ORG Data Repository (http://www.animalgenome.org/
           repository/pig/) on 2013-xx-xx.
    

     

  9. Does the NAGRP Data Repository provide unique accessions number or identifier? What is data locator?

  10. We do not provide “identifiers” (or “accessions” as some users wish to put); We provide “data locators”. This is simply because the deposited files are often multiple, and each may have a different data type or file type. The data locator is for all data from one deposit request and can be accessed with an URL pointing directly to the unique data location.

    Upon successful data deposit, we always inform data owners with the URL as unique data location identifier; and send advice along that this URL should be used in the manuscript and communications with the reviewers. If you only put "data are deposited into the AnimalGenome.ORG" without the URL data locator, it may result in further reader queries about the data from time to time, for which you would have to remember the data location for that specific paper in order to reply users.

     

  11. Why NAGRP Data Repository is promoting Open Science Framework (OSF)?

  12. In order to improve the long term sustainability, we are transitioning the data sharing model from hosting data at AnimalGenome.ORG to using better resources publicly available. One of these resources we recommend is the Open Science Framework (OSF) - https://osf.io/. It has more advantages than what we can offer:
    • Free; supported by Center for Open Science (COS).
    • Long term sustainability: OSF is supported through grants from a variety of supporters, with its current revenue more than $7 million.
    • Preservation fund of $250,000 sufficient for 50+ years of hosting read access to the current data in the event that COS had to curtail.
    • Alliances with many university libraries for data sharing and access.
    • Flexible features for users: it supports both private and public workflows. Projects or components of projects can be kept private for collaborators or made public controlled by users.
    • DOIs available for public projects and registrations.
    • Support API tools.
    See OSF FAQ (http://help.osf.io/m/faqs) for more details.

    While we can continue to host new user data as we did in the past, we want users to be aware that NAGRP program will be funded until the year 2023, and funding after 2023 is unknown. In the meantime, we are helping users to move the currently hosted data at AnimalGenome.ORG to OSF.

Web Access Statistics © 2003-2019 NAGRP - Bioinformatics Coordination Program.
Contact: NAGRP Bioinformatics Team
Helpdesk