HuBMAP Documentation

Developers

Developers may need access to these tools for specific development work:

AWS: Create a Helpdesk ticket to request access to HuBMAP AWS.
Data Authentication: See a diagram of data flow through the HuBMAP authentication process.
DockerHub: HuBMAP uses DockerHub to share containers.
- Create a Helpdesk ticket to request access to the HuBMAP organization on DockerHub.
- You can also contribute new containers to the HuBMAP DockerHub.
GitHub HuBMAP workspace: HuBMAP’s GitHub workspace includes repos for tools related to the Consortium’s work.
Globus Folders: You might need access to HuBMAP data in Globus folders. Globus also provides access to the HuBMAP ingest portal.
- Your Globus identity must be associated with an institution in the dropdown list on this Globus page.
- You cannot use a gmail or an ORCID Globus identity for HuBMAP. NIH eRA Commons accounts are also no longer acceptable.
- Learn how to get Globus access.
HIVE Infrastructure account: Use this application form to request an account. Tips for using the HIVE infrastructure.
- Once approved, you will be contacted via email with account information and login instructions.
Protocols.io: HuBMAP requires that all protocols be publicly available through the HuBMAP Method Development Community.
- You must be a member of this workspace to publish protocols there. Join the HuBMAP Community on protocols.io.

These HuBMAP APIs are not intended for use by external developers or other external users.

Ingest API: Supports writing data and metadata to HuBMAP, used by both TMCs and the HIVE. Links to the SmartAPI site where this API is registered as well as documentation for the API.
UUID API: Supports donor and tissue sample registration, data submission, and collection of provenance information via the Ingest UI. Links to GitHub documentation for this API.
Ontology (UBKG) API: Accesses an instance of a [neo4j] Unified Biomedical Knowledge Graph (UBKG).
- This UBKG links infomation from a variety of biomedical vocabulary systems.
- The HuBMAP UBKG instance includes HuBMAP’s application ontology that represents the HuBMAP operational model.
- Links to the SmartAPI site where this API is registered as well as documentation for the API.

Data Submission Guide: Documents the key steps for TMCs, Assay teams, and others who upload data to the HuBMAP.
Metadata/data schemas: HuBMAP metadata documentation and submission specifications.
- See the HuBMAP Data Upload Guidelines for the latest assay metadata options and specifications.
Metadata Spreadsheet Validator: Use this tool to validate your metadata spreadsheet (template).
- Help documentation for the Metadata Spreadsheet Validator.
HuBMAP Microscope Metadata and Links: View a list of Microscope Metadata, collected to date, and download JSON files for specific instruments.

HuBMAP Member Portal: Find information about how to navigate the consortium, including the calendar, member directory, etc.
Governance: The HuBMAP Steering Committee and Working Groups.
HuBMAP Consortium Google Drive: A shared resource.
- Document Management Guide: For the HuBMAP Consortium Google Drive.
HuBMAP Calendar: A web calendar that combines all shared, internal Consortium events.
- Using Google Groups with Google Calendar
SOPs
other Resources