Aggregating the Experimental Diversity of Rodent Studies
A vast range of experimental questions have been tested in rodents to understand mechanisms of human skeletal disease. The abundance of bone phenotyping data being generated combined with the diversity of experimental questions being tested makes for an incredibly rich data source. We have designed our data ingestion process to include wide range of experimental approaches including:
- Genetic Perturbation (global knockout, conditional knockout, disease model)
- Preclinical Therapeutic Testing (small molecules, biologics, probiotics, dietary changes, fecal transplants, stem cell transplantation)
- Procedures that Challenge the Skeleton (gonadectomy, mechanical loading and unloading, exercise).
If our existing form does not work for your experimental approach, please contact us to let us know. The ingestion process is modular and can be expanded to include additional experimental categories.
Skeletal Phenotyping Analyses Currently Being Archived
ROSSA will archive and share data generated by investigators within the bone field including universally adopted well-defined methods and standards to phenotype bone tissue. These methods include:
- Dual X-Ray Absorptiometry
- Microcomputed Tomography
- Bone Histomorphometry
- Mechanical Strength Testing
- Clinical Biochemistry Markers (serum, plasma, and/or urine biomarkers)
To learn about specific measurement parameters being archived in this repository, please see the measurement parameters page.
Data File Formats Used for Data Ingestion
Spreadsheet Data
The data ingestion process is designed to accept your own spreadsheet data files, we only ask for you to upload your spreadsheet data in CSV file format only. For database security purposes, we cannot accept spreadsheet data saved in Excel file formats, so please convert your Excel files to CSV before submission. While the data ingestion process has been designed to directly accept your spreadsheet data files, we alternatively provide spreadsheet template files that can be be used for upload.
Image Data
ROSSA will archive images generated from microcomputed tomography analysis and bone histomorphometry. The uploading of image data will be tied to the data submission form to ensure that that each image is appropriately annotated during the archival process. Users can view image data through through a download mechanism.
How Will Your Data be Stored?
ROSSA will store your data in two ways. First, all of your original data files (spreadsheet and image files) are uploaded into ROSSA and stored as object storage in their original form. This is to ensure authenticity of the original data and provide a crucial reference for reading the data into database tables. Spreadsheet data will also be read into database tables (PostgreSQL database) to enable efficient searching via the datacenter and through API access by those interested.
Beginning the Data Submission Process: What to Expect?
This is a multi-page form that you can save and pick up where you have left off after each page is complete. The form follows a logical progression noted by the navigation bar present at the top of each form page. We ask you to fill out the form in the order provided. However, if you need to change or add information that exists on an earlier page, please do so. To start the submission process you need to have a user account and be logged in. Once you have logged in simply click on the "create study" button to start a study. Once you created a study, a unique "study id" will be generated (ROSSA....). Please use this study id in your publications to refer to the archived data in this repository. If you need to leave the website and continue filling the study out on another day, please use the continue study button that now tracks the status of your study.
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