Section 6 - Preparing Metadata

This section provides links to access relevant metadata templates, and provides information for assays that include antibodies or assay-specific channel IDs. Click the provided links in this section to access additional relevant information or resources.

Create metadata files. Download and complete the latest version of each required metadata template:

• assay-specific
• contributors
• antibodies (if relevant)

Lists of assay-specific templates are available from the HuBMAP consortium’s Data Upload Guidelines page.

Note: Many HuBMAP metadata schemas are shared by SenNet. The murine source schema is unique to SenNet.

1. Assay-specific templates
   • Clicking on an assay type (on the page linked above) takes you to a page for that type.
   • Select the Excel template on that page.
   • Each page includes field name descriptors, format requirements.
2. Contributors template
   • Lists the names, institutions, and ORCID ID’s of contributors to the dataset.
   • If ALL datasets listed in your assay metadata use the same set of contributors, you may submit just one contributors file.
   • Point to the file in the contributors_path field for the corresponding datasets.
3. Antibodies template
   • Required for all assays that use antibodies.
   • If ALL datasets in your assay metadata use the same set of antibodies, you may submit just one antibodies file.

NOTE: A separate antibody validation report is also required.

If datasets in the submission use Different sets of antibodies — OR — the same set, but different lots…

• Each unique antibody set must be listed in a separate antibody.tsv with a unique name:
  • (e.g., dataset1_antibodies.tsv, dataset2_antibodies.tsv, etc).
  • Different lot numbers for different datasets
• Custom antibodies
  • Indicate the batch date (format: yyyy-mm-dd) in the lot_number field.
• Assay-specific channel_id
  • The channel_id field in the antibodies TSV is populated with assay-specific information in the following formats:
    • CODEX: cycle#_CH# > The cycle/channel information is generated by the Akoya instrument used for CODEX.
    • Cell DIVE: cycle#_CH# > The following 3 assays do not involve cycles:
      • Light sheet: channel_id is the name of the fluorophore tag on the antibody.
      • MIBI: channel_id is the name of the metal tag on the antibody.
      • IMC: channel_id is the name of the metal tag on the antibody.

Check for RRID registration: If an RRID (Research Resource Identifier) has not been assigned for an antibody, register the antibody.