(In Progress) How to annotate your data

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, and assess whether the data is the type of data that they are looking for. Annotation is not a replacement for sharing experimental methods via a publication method section, in your Synapse project, or via a protocol repository like http://protocols.io.

To annotate your data, first:

1. If you are not yet logged in: log in to Synapse.org.

2. If you have not yet uploaded your data that you would like to annotate:

   1. Navigate to your Synapse Project that was assigned to you at the time of project on-boarding.

   2. Within the “Raw Data” or “Data” folder, create a new folder to house your current data upload.

   3. Upload the data to this folder.

3. Navigate to the NF Data Curator app.

4. Follow the prompts to select the project, folder that you'd like to annotate and the type of assay you are annotating. (Note: If the app is idle for too long, it will disconnect to reduce the load on the server. Simply refresh the page to restart the app).

5. Click "Get Metadata Template" -> "Click to generate google sheets template" to generate a template for your new data, and wait for the app to provide a google sheet link. This may take a few moments, particularly if you have many files or lots of existing annotations on your files.

   1. Note: you may download the manifest as an excel file (File → Download → Microsoft Excel), but we have not extensively tested functionality in Excel. If you encounter any issues filling in the manifest in Excel, please contact us at nf-osi@sagebionetworks.org.

6. Fill in the manifest.

   1. For each column, hover over the column title to get a better idea of what type of information is needed in each column. For example, you can hover over the “individualID” column header to see the definition: “A unique identifier (non-PII) that represents the individual from which the data came. This could be a patient or animal ID.”

   2. Use the dropdown selector for each cell to pick a value. For example, if you are annotating a western blot image, under assay, you’d select “westernBlot”.

   3. If no terms fit, please type in a term that you feel best fits your file.

   4. Our full dictionary, including definitions, is available in our Schema spreadsheet.

   5. For columns without a dropdown, we do not have controlled vocabulary (these are generally project-specific IDs, such as an anonymous patient ID (called `individualID`).

   6. Continue filling in the columns until all required (green columns) and relevant optional columns are filled in.

7. Submit your manifest.

   1. If your manifest did not require any custom terms (as described in step 6c), then you can submit using the NF Data Curator app “Submit and Validate Metadata” tab.

      1. Download the completed manifest as a csv file from Google Sheets (or, if using Excel, save as csv).

      2. Upload the csv into the data curator app, following the on-screen instructions to validate your manifest. Follow the on-screen instructions if validation errors are present.

      3. Once your manifest passes validation, click “Submit to Synapse” to annotate your files. Congratulations, you’re done annotating!

   2. If your manifest did require custom terms (as described in step 6c), please email the completed google sheet or excel file to nf-osi@sagebionetworks.org so that we can add your new terms to our dictionary. We’ll then work with you to get the annotations applied to your data.