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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
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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. |
Annotating your data involves the following actions, to be completed in order:
1. Log in to Synapse
2. Ensure your data is properly uploaded
If you haven’t done so already, follow the instructions at How to Upload Data.
3. Navigate to the NF Data Curator app
In order to access the app, you must be logged into Synapse. If you are not already logged into Synapse when you land on this page, you will be prompted to do so. Click the Synapse link provided on the page to log in to Synapse, and then refresh the app page—you should now be able to access it.
4. Find the data you want to annotate
Once in the app, follow the prompts to select the project, folder, and the type of assay you are annotating.
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. Generate metadata template
Click Get Metadata Template, followed by Click to generate google sheets template, 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.
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
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For this step, you may need to reference our full metadata dictionary, including definitions, is available in our Schema spreadsheet. |
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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
If no terms fit, please type in a term that you feel best fits your file
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)
Continue filling in the columns until all required (green columns) and all relevant optional columns (yellow columns) are filled in
7. Submit your manifest
Coming off of step 6, this next step will depend on whether your manifest required custom terms or not.
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