More rat-related grants are good news for all of us so we’re assembling some information and other resources that might be of help as you plan and write your grants. This is certainly a work in progress so please feel free to contact us with more suggestions and requests for ways in which RGD can help you in your grant writing.
Rat Data and Statistics
The RGD Curation team has a great deal of experience finding and compiling rat data and we may be able to help you find information or even create specific datasets for your grant or publication. If you need statistics we encourage you to contact us.
Current Rat data statistics from NCBI
You can search across all NCBI databases using the term “rattus norvegicus” to see the number of rat records in each database and access the corresponding lists of records: [Run this query at NCBI now].
Data Sharing Plan
RGD makes data readily available to users through our website and tools, as well as tool-specific download functions, our Download page and our Rest APIs. We are happy to work with investigators looking for a particular dataset, and groups building data pipelines for their own purposes, to supply customized data sets and to add new data files to our FTP site or new APIs to our list. Contact us for more information or if you need a particular set of data.
RGD is also a founding member of the Alliance of Genome Resources (https://www.alliancegenome.org. We submit data regularly to the Alliance for integration into their database with data from other model organisms such as yeast, zebrafish, worm, fly and mouse. In addition to providing an additional outlet for data sharing, the Alliance facilitates cross-species comparisons that could be of use to researchers looking to present their work in a larger context.
Most NIH grants now require a section covering the Sharing of Research Data (eg. RO1, Section 2.C.) which requires applicants to describe their plans for sharing data that is created as part of the proposed research. RGD is well positioned to act as a suitable venue for project data to be made available to the research community and we encourage researchers to contact us with any questions they may have on how to do this. Strain, QTL, and gene/allele registration can be done through our submission forms.
Direct submission of new large datasets, or additions and revisions to existing data in RGD are welcome. These would include quantitative phenotype data (i.e. measurement values from low-throughput and high-throughput phenotyping projects), strain-specific variant data from whole genome/exome sequencing, and RNA-Seq data. Please contact our data manager Jennifer Smith for these types of data submissions.
If you need a Letter of Support (LOS) for your grant stating that RGD will make your data publicly available, please do not hesitate to contact us to request a LOS.
Software Sharing Plan
Where third party software exists that meets a specific need at RGD, we use that software. Examples of this include our use of JBrowse (https://jbrowse.org/) for our genome browsers, and Cytoscape.js (http://js.cytoscape.org/) for our InterViewer display. Information about these tools and how to obtain source code for them can be found on the respective websites for the software. For information about RGD’s specific implementations of these tools, please contact us.
Where we have been unable to find software that meets a specific need at RGD, we have developed custom software and tools to support our needs and those of our users. RGD source code is hosted at GitHub (https://github.com/rat-genome-database) and can be used, modified, and distributed under the terms of the GNU Public License version 3. (GPL-3.0).
Model Organism Sharing Plan
Most NIH grants now also contain a section covering the Sharing of Research Resources (e.g., RO1, Section 2.D.) which requires applicants to describe their plans for sharing “unique research resources” that are created as part of the proposed research (see NIH Grants Policy Statement for more information). This includes a Model Organism Sharing Plan that should describe how unique animal models created through the funded research will be made available to the community.
While RGD is unable to help directly with the sharing (i.e. maintenance, preservation and/or distribution) of biological resources such as the rats or other model organisms, investigators are encouraged to contact groups such as the Rat Resource and Research Center (RRRC) in Missouri, USA or the National BioResource Project for the Rat (NBRP-Rat) in Kyoto, Japan, for information about their rat strain repository facilities. We do recommend, however, that you do contact us for correct registration and nomenclature of your strain before submission of the rats to either RRRC or NBRP. The use of official nomenclature and unique identifiers for your biological resources are required for following the “FAIR” principles and for helping to make your research reproducible.
