# Submitting Assay Data and Metadata

As stated in Data Submission Introduction, data submission involves two key steps:

  1. Uploading assay data files to Synapse; and
  2. Completing and validating metadata using the Data Curator App (DCA).

This page provides details regarding those steps.

HTAN Data Submission Process
HTAN Data Submission Process

# Data Submission Steps

  1. Complete Pre-submission Tasks
  2. Submit Data Files
  3. Submit metadata

Please read the rest of this page for more information about each of these steps.

# Pre-submission Tasks

  • Have at least one user with Certified User status on Synapse.

To upload files to the Synapse Platform, you need to be a Synapse Certified User. You can complete your certification by taking a short certification quiz. Please see the Synapse Certified User Documentation for more information.

  • Contact your Data Liaison

When you are ready to upload data, please contact your data liaison. Please have users obtain certified user status prior to contacting your data liaison.

  • Ensure the dataset conforms to the HTAN Data Model and uses HTAN Identifiers.

The HTAN Data Model is built upon data standards described on the Data Standards page. All HTAN Centers are required to encode their clinical, biospecimen and assay data and metadata using the HTAN Data Model. If you have a new data type which is not currently represented in the HTAN Data Model, please contact your data liaison.

All data should be identified using HTAN identifiers. Please see the Identifiers and Creating HTAN Identifiers sections of this manual for more information regarding HTAN identifiers.

  • Ensure that your data does not contain PHI.

Please review your data to ensure that it does not contain PHI. The HTAN DCC cannot accept data with PHI, including dates less than a year. For example, dates in metadata must be converted to days from an index date and all image files must have PHI removed from file headers.

# Submit Data Files

Organize your data using the flattened data layout described in Synapse's Data Ingress Docs

Data files can be transferred using the Synapse User Interface (Synapse UI) or programmatically.

# Submit Metadata

The DCA contains HTAN-specific manifests (metadata templates) which can be

  1. completed on the app, or
  2. downloaded, completed and uploaded back to the DCA.

Manifests for assay data will be pre-populated with assay file entityIDs once they are associated with a particular Synapse dataset folder.

Once the manifests are completed by your center, they should then be validated and submitted via the DCA. The DCA will perform validation checks for a subset of common errors. If any of these errors are found, you can edit the metadata, revalidate and submit.

Please see Synapse's Data Ingress Docs for more details regarding the web app.

# Useful Links and Guides

# Synapse and the DCA

# Understanding the HTAN Data Model

  • To understand the general structure of the HTAN Data Model and HTAN Identifiers, please see the HTAN Data Model section of this manual.
  • To understand the Data Model Manifests/Metadata Attributes, please see the Data Standards section of the HTAN Portal. There, you can download manifest summaries. These cannot be used for metadata submission, but can help you prepare your metadata.