GDR FAQ

About GDR

  1. What is GDR?
  2. What data and information does GDR contain?
  3. How is GDR supported?
  4. How is GDR structured?
  5. How do I cite GDR?
  6. How can I contact GDR?

Data Curation, Submission and Download

  1. Can I submit my data to GDR?
  2. Can I download data from GDR?
  3. Who should I contact if I think I have found a mistake in the database?
  4. Who contributes data and/or assistance to GDR?
  5. How can I find what’s new in GDR?
  6. How do I know what’s coming next in GDR?

GDR Data

  1. What types of markers does GDR house?
  2. Is there a tutorial or help section on how to find marker information?
  3. Can I view a list of all the maps with detailed information, such as genome, population size, etc?
  4. Is there a tutorial or help section on how to use the comparative map (CMap) viewer?
  5. Is there a tutorial or help section on how to use the Genome Browser (GBrowse) viewer?
  6. What genome data are available in GDR?
  7. Do I need a GDR account to access data?
  8. Where can I get the genomic sequences of all the markers that have been aligned to peach genome?

Apple Genome v1.0 Frequently Asked Questions

About GDR

  • What is GDR?
GDR is a curated and integrated web-based relational database providing centralized access to Rosaceae genomics, genetics and breeding data and analysis tools to facilitate basic, translational and applied Rosaceae research.  It has been built using the open-source Tripal database infrastructure. 
  • What data and information does GDR contain?
The current major data components of GDR are:
  • Genome assemblies of various rosaceae species
  • Reference transcriptomes built from the published RNA-Seq and EST data
  • Unigenes for the Rosaceae family and six genus (Prunus, Malus, Fragaria, Pyrus, Rosa and Rubus)
  • Genetic markers and nucleotide sequences
  • Genes and gene products
  • Genetic maps and QTLs
  • Large scale genotypic and phenotypic data  from molecular diversity studies and breeding projects
  • Rosaceae species and germplasm data
  • Relevant bibliographic citations

For details on the number of data, please visit the Data Overview Page.

  • How is GDR Supported?

The GDR project is funded by a partnership of  USDA, NSF, Industry and US Land Grant Universities

  • How is GDR structured?

GDR uses Tripal, a toolkit for construction of online genomic and genetic databases.  Tripal provides a web-front end for the Generic Database schema Chado which houses biological data. Tripal also integrates with Drupal, a Content Management System (CMS) that enables non-techincal users to provide content, provides user management and other social capabilities, and provides  site developers with an interface that facilitates easier construction of websites.

  • How do I cite GDR?

If you use GDR data or tools in your research, please use the following citation. 

Sook Jung, Stephen Ficklin, Taein Lee, Chun-Huai Cheng, Anna Blenda, Ping Zheng, Jing Yu,  Aureliano Bombarely, Ilhyung Cho, Sushan Ru, Kate Evans, Cameron Peace, Albert G. Abbott, Lukas A. Mueller, Mercy A. Olmstead and Dorrie Main. The Genome Database for Rosaceae (GDR): year 10 update. Nucl. Acids Res. (2014) Jan 1; 42(1):D1237-44

  • How can I contact GDR?

The GDR staff can be reached via the Contact Form.

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Data Curation, Submission and Download

  • Can I submit my data to GDR?

Data submission templates are available for you to upload your gene, map, marker, QTL, genotype/phenotype data and breeding data in the data submission page. List of files for genome assembly data submissions are also available in the data submision page. If you have any questions please feel free to contact us via the contact form and we will work with you to get your data into the template.  If you have other types of data, please contact us about how to submit that data to GDR.  We accept data that is peer reviewed via manuscript submission.

For the data that data from manuscripts accepted for publication in Tree Genetics and Genomes, we recommend authors to contact us before filling in the template so that we can work closely with them to ensure this process is expediated quickly and easily. Please refer to the TGG GDR Data Submission site.
  • Can I download data from GDR?

Yes.  There are different ways to download data from GDR:

  • The Download page will direct you to a page where/how to download for each type of data.
  • Via GDR FTP repository
  • GDR genome data can be downloaded from each genome page, accessible from each species page.
  • GDR gene, sequence, marker, QTL, phgenotypic and genotypic data can be downloaded through various search result sites.
  • GDR CMap data can be downloaded via CMap Map Set Info page.
  • GDR genome alignment data and sequences under specific chromosome and region can be downloaded via GDR GBrowse or GDR JBrowse (refer to GDR Tutorial: GBrowse for details). 
  • Sequences can be downloaded from sequence retrieval tool. For sequences aligned to a whole genome, such as genes, transcripts, and genetic markers, users can include a specified number of upstream and downstream bases in the retrieved sequence.
  • Who should I contact if I think I have found a mistake in the database?

Please contact us via the contact form at the top of each page.

  • Who contributes data to GDR?

GDR data is from many contributors around the world.  Refer to Data Contributor page.

  • How can I find what’s new in GDR?

You can find what has recently been accomplished in the Work Completed page, which can be found under 'General'  in the navigation bar.

  • How do I know what’s coming next in GDR?

You can find work in progress at GDR through the Work in Progress page, which can be found under 'General'  in the navigation bar.

GDR Data

  • What types of markers does GDR house?

Please refer to the GDR marker types page.The majority of marker types are: SNP, SSR, AFLP and RFLP.  View the Data Overview page for more details.

  • Is there a tutorial or help section on how to find marker information?

Yes.  Please view GDR Tutorial: Marker Search.

  • Can I view a list of all the maps with detailed information, such as mapping parents, population type and population size?

To view the Map Data Summaries page, where lists all map sets with details in GDR.

  • Is there a tutorial or help section on how to use the comparative map (CMap) viewer?

Yes. Please see CMap User Tutorial.

  • Is there a tutorial or help section on how to use the Genome Browser (GBrowse) viewer?

Yes. Please see GDR Tutorial: GBrowse.

  • What genome data are available GDR?

Please refer to the 'Genome' data in Data overview page

  • Do I need a GDR account to access data?

No. you do not need a GDR account to view any publicly available data: GDR also houses some private breeding data and the breeders need an account to access their own private data.

  • Where can I get the genomic sequences of all the markers that have been aligned to peach genome?​

You can download fasta file from the 'Markers' sub-page of thePrunus persica Genome v1.0