FAQ Outline
- What is GDR?
- What data and information does GDR contain?
- How is GDR supported?
- How is GDR structured?
- How do I cite GDR?
- How can I contact GDR?
Data Curation, Submission and Download
- Can I submit my data to GDR?
- Can I download data from GDR?
- Who should I contact if I think I have found a mistake in the database?
- Who contributes data and/or assistance to GDR?
- How can I find what’s new in GDR?
- How do I know what’s coming next in GDR?
- Do I need a GDR account to access data?
- What types of markers does GDR house?
- Is there a tutorial or help section on how to find marker information?
- Can I view a list of all the maps with detailed information, such as genome, population size, etc?
- Is there a tutorial or help section on how to use the comparative map (CMap) viewer?
- Is there a tutorial or help section on how to use the Genome Browser (GBrowse) viewer?
- What genome data are available in GDR?
- Where can I get the genomic sequences of all the markers that have been aligned to peach genome?
GDR Breeding Information Management System (BIMS)
Apple Genome v1.0 Frequently Asked Questions
About GDR
GDR is a curated and integrated web-based relational database providing centralized access to Rosaceae genomics, genetics and breeding data and analytic tools to facilitate basic, translational and applied Rosaceae research. It has been built using the open-source Tripal database infrastructure.
The current major data components of GDR are:
- Genome assemblies of various Rosaceae species
- Reference transcriptomes built from published RNA-Seq and EST data
- Unigenes for the Rosaceae family and six genera (Fragaria, Malus, Prunus, Pyrus, Rosa and Rubus)
- Feature sequences (contig, EST, gene, mRNA)
- Genetic markers
- Genetic maps
- Genotypes of SNP and SSR markers
- Phenotypic trait evaluations from molecular diversity studies and breeding projects
- Rosaceae species and germplasm data, including images
- Publications of relevant Rosaceae research
- SNP haplotype data for Prunus avium and cerasus
- Quantitative Trait Loci (QTL) and Mendelian Trait Loci (MTL)
More information on searching these data types can be found in the GDR User Manual: Data Searches. For details on data numbers, please see the Data Overview Page.
The GDR project is funded by a partnership of USDA, NSF, Industry and US Land Grant Universities
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-technical users to provide content, provides user management and social capabilities, and provides site developers with an interface that facilitates easier construction of websites.
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
To cite original data sources, look for the "Publication" link in the left-hand menu of GDR feature pages.
The GDR staff can be reached via this contact form, or by selecting "Contact" under Help in the header menu.
Data Curation, Submission and Download
We accept data that is peer reviewed via manuscript submission. Data submission templates are available for uploading gene, map, marker, QTL, genotype/phenotype and breeding data. A list of the files and information needed for genome assembly data submissions can be found here. If you have any questions please contact us using this contact form and we will work with you to input your data. If you have other types of data, please contact us about how to submit it to GDR.
For manuscripts accepted by Tree Genetics and Genomes, please contact us before filling in the template so we can work with you to expedite the process. Please refer to the TGG GDR Data Submission page for further details.
Yes. There are different ways to download data from GDR:
- The Download Data page provides links and instructions for downloading the major data types available on GDR.
- Via the MainLab FTP repository
- Genome data can be downloaded from species pages by using the "Downloads" or "Genomes" links in the left-hand menus.
- GDR search pages can be used to download gene, sequence, marker, QTL, phenotype and genotype data. After completing a search you have the option to download the matching data (refer to the GDR User Manual: Data Searches for instructions)
- GDR CMap data can be downloaded via the CMap Map Set Info page.
- Genome alignment data and sequences under a specific chromosome and region can be downloaded via GDR JBrowse (refer to this JBrowse video tutorial for instructions).
- Specific sequences can be found by name and downloaded using the GDR sequence retrieval tool. For sequences aligned to a whole genome, such as genes, transcripts, and genetic markers, users can specify the number of upstream and downstream bases to include with the retrieved sequence. For more instructions, see the GDR User Manual: Sequence Retrieval.
Please contact us via this contact form, or by selecting "Contact" under Help in the header menu.
GDR data is from many contributors around the world. A list can be found on the Data Contributors page.
A list of recent accomplishments can be found on the Work Completed page, under 'General' in the navigation bar.
A list of work in progress at GDR can be found on the Work in Progress page, under 'General' in the navigation bar.
GDR Data
No, you do not need a GDR account to view publicly available data. GDR also houses private breeding data for which breeders need an account to access and transfer.
Please refer to the GDR Marker Types page. The majority of markers are SNP, SSR, AFLP or RFLP. Numbers of each marker type in GDR, by genus, can be found on the Data Overview page.
Yes. Please see the GDR User Manual: Search Markers.
- Can I view a list of all the maps with detailed information, such as mapping parents, population type and population size?
A comprehensive list with map details can be found on the Search Maps page. This list can be filtered by species.
Yes. Please see the CMap User Tutorial.
Yes. Please refer to this JBrowse video tutorial for instructions.
Twenty-four genomes across six genera (Fragaria, Malus, Prunus, Pyrus, Rosa and Rubus) are available on GDR JBrowse.
These can be downloaded in fasta format from the Prunus persica Genome v1.0 page, under "Markers" in the left-hand menu.
GDR Breeding Information Management System (BIMS)
GDR BIMS is a Tripal module being developed by Mainlab Bioinformatics which allows users to explore the publically available breeding data in GDR while also providing a data management solution for private breeding programs. It is being continually developed to provide individual breeders with a comprehensive breeding management system that allows storage, management and analysis of their private data as well as secure integration with publicly available resources.
The GDR BIMS User Manual provides instructions for using the various functions provided by BIMS.