Synapse.org is the data management software for all data hosted and shared on the NF Data Portal. Uploading data to Synapse can be completed using a variety of tools. This article will give you a brief guide to ensure you upload data to the correct place for sharing on the NF Data Portal, and will link you to instruction on using the various Synapse clients to complete this process.
Locate your Synapse workspace. If you have registered your project with the NF-OSI coordinators (see Overview: How to Share Data ), you should have been provided a Synapse project to house your data. You can find this project by logging into Synapse.org, clicking on your profile picture in the upper right hand corner, and clicking “Projects,” which will show you all workspace you have access to. The project title should match the information you provided the NF-OSI coordinators when you first joined the initiative.
Ensure your account is “Certified” (see Overview: How to Share Data ). If your account is certified, there will be an icon indicating so on your profile page.
Navigate to the project, click on “Files”, and click on 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”).
Within this folder, create a new folder for the experiment or data type you plan to upload (e.g. “RNA Seq Experiment 1”).
Then, upload your data using the Synapse.org website, or our Python, R, or command-line clients. For small folders/files, the website upload is generally easiest. For larger uploads (large files, or many files), we recommend using the programmatic clients. Want more information on how to format your data? Please see How to Format Your Data .
To upload using the web UI, simply 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, please follow the documentation on the Python doc site, or follow the bulk-upload instructions to upload using a manifest.
To upload using the command-line client (requires the Python client), please follow the command-line client documentation on the Python docs site.
To upload using the R client, please follow the documentation on the R docs site, or follow the bulk-upload instructions to upload using a manifest.
To upload files that already exist in an S3 bucket or Google Cloud Storage Bucket, please follow the Custom Storage Locations documentation.
Pro tip: if your files are already on GEO, SRA, or another platform that doesn’t require a login, you can link directly to the download HTTPS or FTP URL (for example, the links under the “Data Access” tab on this SRA page) by using the “Link to File” prompt under Folder Tools → Upload or Link to a File. Users will still be able to download the file as if it lived on the NF Data Portal/Synapse, but you only need to upload it once! If you have any questions about whether your repository of choice is compatible with this, please reach out to us (nf-osi@sagebionetworks.org). Please note that annotation on Synapse is still required.
6. When your dataset is uploaded, you must then annotate your data to make it findable and understandable (see How to Annotate Data).
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