Section 5 - Submissions Directory Preparation

This section decribes setting up the submissions directory. Most steps in this section are shared by both Clinical and non-Clinical assays, except as noted below.

Prepare a Submissions Directory. Use this directory for submitting datasets to the HIVE (HuBMAP) or CODCC (SenNet).

Set up the directory based on the assay-specific directory schema for each assay in Github: (e.g. CODEX Directory structure).
These requirements are defined via a collaborative process.

Include these items:
- One assay metadata spreadsheet per assay type (e.g. assay_metadata.tsv)
- One contributor’s metadata spreadsheet per dataset (e.g. contributors.tsv)
- One antibody metadata spreadsheet per dataset—if applicable—(e.g. antibodies.tsv)
- One data directory for each dataset

Next steps for non-Clinical (most) assays. This includes ANY assay type except the specific clinical types listed below.

2. **Assay-specific directory schema.** Access via GitHub link (e.g., CODEX example) or HuBMAP metadata specifications in the portal. 3. **Organize the dataset components** (i.e., data and metadata files) in a submission directory according to the required directory structure specified in the GitHub page for the assay (e.g., CODEX directory structure).

Next steps for Clinical assays (ONLY). Clinical assays include the following: Body CT, MRI, MicroCT, OCT, and Ultrasound.

2. **Create a root directory.** Inside this directory place the metadata.tsv and contributors.tsv files. 3. **Create a data subdirectory inside the root directory.** When all the files are ready, compress the root directory using a utility (e.g. tar or .zip) to reduce its file size for submission.

NOTE: Clinical assays may have protected patient information (PPI) embedded in the metadata or images.

PPI must be removed before the metadata or images are made available through HuBMAP.
This process allows us to review and remove the information in a way that is Institutional Review Board (IRB) compliant.

4. **Extras directory** (optional, used by both Clinical and Non-Clinical assays). - Use this optional directory for any other files your team wants to include.

NOTE: The contents of this directory will not be vetted by the HIVE. IMPORTANT: Do NOT include TMC-processed data in the extras directory.