Section 8 - Creating an Upload Directory

This section describes the basic steps needed to create an upload directory to submit metadata and data uploads to the HIVE (HuBMAP) or CODCC (SenNet). NOTE: The steps required for this differ for Clinical versus non-Clinical assays. Prerequisite: The submission directory has been successfully validated locally.

  1. Getting started
    • HuBMAP members:
      • On the HuBMAP ingest portal
      • Register a single donor, sample, dataset, or publication or bulk register samples or data.
    • SenNet members:
  2. From the Navigation bar:
    • HuBMAP members select REGISTER NEW > BULK > Data
    • SenNet members select: Create an Entity > Data
    • This action initiates the data upload process.
  3. Complete the required fields - Select a title that both you and the HIVE or CODCC can use to recognize the data upload.
  4. Click "Create" - This creates a Globus folder where you upload your dataset files.
  5. Setting up an upload directory - Upload directories have several required components. At minimum, three parts are necessary:
    • An assay metadata file ending in "metadata.tsv" that has been validated using the HuBMAP Metadata Spreadsheet Validator. A list of supported assays can be found here.
    • A contributors metadata file ending with a title of "contributors.tsv" that has been validated using the HuBMAP Metadata Spreadsheet Validator. The contributors metadata template can be found here.
    • Data files required by the assay's directory schema. A list of supported assays can be found here. Each dataset should have a corresponding subdirectory containing all the files in the directory schema. Each row of the metadata file should reference one of these subdirectories via the data_path field.
  6. Need to add or modify files? - Follow the highlighted Globus link.
    • Save: To make changes to the Title or Description fields use the Save button.
    • Submit: Click Submit once all data has been uploaded to Globus.
    • Contact the HuBMAP Helpdesk if further processing by the HIVE is needed.
    • Contact the SenNet Helpdesk if further processing by the CODCC is needed.

This section is for Clinical Assays only:

  1. Email the HuBMAP Helpdesk OR SenNet Helpdesk when ready to upload.
    • Be sure to use an institutional email address (e.g. name@institution.edu).
    • The Help desk relays this request for space on the protected endpoint to the Pitt team.
    • The Pitt team provides the assay team with the protected data endpoint.
  2. Upload your data as compressed / zipped folders, using Globus.

IMPORTANT: This location is distinct from where NON-Clinical HIVE or CODCC data is uploaded.