Step 4: How to Annotate Data
Once data is uploaded to Synapse, you will need to provide certain metadata in order to describe and annotate your data files.
Annotating your data is the process of labeling files so that users can:
get a general understanding of what information is contained in the file
determine what type of experiment was performed
determine what type of biospecimen was used
assess whether the data is the type of data that they are looking for
Annotating your data involves the following actions, to be completed in order:
1. Ensure your data is properly uploaded
If you haven’t done so already, follow the instructions at Step 3: How to Upload Data .
2. Download relevant metadata template(s)
If you already completed your metadata templates in Step 1.4: How to Assemble Metadata, please
Verify that the template version you filled matches the latest version available.
Once verified, skip forward to 6. Submit your template
Note that metadata templates are subject to change over time as our data standards develop. We recommend that you download templates close to the time when you plan to submit them for validation to ensure that you have the latest version available.
Go to the ELITE Portal Metadata Dictionary and click on “template” in the left bar navigation. Select the required template name(s) and click “download” to download the template file.
At minimum, you will need to have:
One Individual template: select either the “individual human template” or “individual non human template” based on the species your data relates to.
One Biospecimen template: select either the “biospecimen human template” or “biospecimen non human template” based on the species your samples are from.
One Assay template per each type of assay: select the “assay ______ template” corresponding to the assay type of your data. If your data includes multiple assays, you will need to download a template for each.
One File annotation template: this template will be provided to you by the EL DMCC, pre-filled with the Filenames for the files you previously uploaded.
Contact the EL DMCC through your service desk ticket if you are unable to find the specific metadata template(s) you need.
3. Fill in the template
For this step, you may need to reference our full metadata dictionary and definitions. You can browse and search the full dictionary here: https://eliteportal.github.io/data-models/
Fill in the templates by selecting the available variables in each cell’s dropdown menu. Continue filling in the columns until all required columns (highlighted in blue) are filled in.
All required columns must contain either a value or a “Unknown, Not collected, Not applicable, Not specified” option. If you do not see a value you need and require a custom term, please contact us and we can add new value(s) to the template.
Columns without a dropdown do not have controlled vocabulary. Please enter your own values.
Delete any blank rows at the bottom of your completed template.
Once you have filled your template with the necessary metadata, save your file as a CSV (comma-separated values).
4. Submit your template(s)
Go to the Synapse project where you uploaded your data. Locate the folder for “completed metadata templates” and upload your CSV files here.
5. Validate your metadata
The EL DMCC data management team will validate the submitted templates and notify you of any needed revisions. Please respond to any requests to update or revise your provided metadata.
Once validation is complete, the EL DMCC data management team will annotate your files with the provided metadata.
6. (Optional) Updating Annotations
If you need to either update or add to your metadata templates you can do so by contacting the EL DMCC for assistance.
7. Release your data
Once annotations are finished, you are now ready to complete the final checks before releasing your data to the public. See Step 5: How to Release Data .