Synapse.org is the data management software for all data hosted and shared on the NF Data Portal. This means that you will upload data to be stored in Synapse, and it will be automatically ultimately be shared on the NF Data Portal. Think of Synapse as the back-end and the NF Data Portal as the front-end for your data.
You will be uploading data into Synapse using a variety of tools. This article will give you a brief guide to ensure you upload data to the correct place, using the appropriate methods.
At the end of this page, you’ll find a video tutorial that covers the steps involved in uploading data (steps 3-4 below). This is the second in a series of three videos on sharing data. Find the first video, Introduction to Sharing Data (steps 1-2), here.
Uploading data involves the following actions, to be completed in order:
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Log into Synapse.org
Click on your profile picture in the upper right hand corner and click Projects
Click on your project—the project title should match the information you provided the NF-OSI coordinators when you registered your project
3. Create a folder for your data (if not already set up)
In most cases, your dataset-specific folders should already be set up. However, here are the general instructions for your creating data folders:
Once you’re in your project, click on Files, and then click the Data or Raw Data folder.
If the data are associated with a particular project milestone (e.g. 6 months, 12 months, etc), navigate to, or create a folder (Folder Tools → > Create Folder) for that milestone (e.g. “6 month deliverables”).
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To upload using the web UI:
navigate to the folder you want to upload to and click Folder Tools → Upload or Link to a File.
To upload using the Python client:
To upload using the command-line client (requires the Python client):
To upload using the R client:
follow the instructions on our R docs site, or
follow the bulk-upload instructions to upload using a manifest on our Synapse docs site
To upload files that already exist in an S3 bucket or Google Cloud Storage Bucket:
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Once your dataset is uploaded, you must annotate it in order to make it findable and understandable. You can find those instructions at How to Annotate Data.
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Video Tutorial: Uploading Data via the Synapse UI
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Links mentioned throughout the video: