Information for HuBMAP data providers
Data Submission Guide
Please see the HuBMAP Data Submission Guide for detailed instructions on the process of submitting data to HuBMAP.
Before you submit data
There are several prerequisites to successfully submitting data to HuBMAP.
Consent and Data Use Agreements on record
Your component must have submitted completed Consent and Data Use Agreements to the Consortium.
Data Use Agreement
Access to HuBMAP space in Globus
To register donors or tissues or to upload data, you must have
- a Globus identity associated with your institutional credentials or your NIH eRA Commons id
- write access to the Globus folder for your HuBMAP component (RTI, TMC or TTD)
If you do not have a Globus identity already, you must create one before you can have access to HuBMAP Globus space. Note that your Globus identity must be associated with an institution or with your NIH eRA Commons account. You cannot use other types of Globus identities, like a gmail or an ORCID Globus identity, for HuBMAP.
You can create a Globus identity by logging in to Globus at app.globus.org.
If your home institution is listed in the organization dropdown on app.globus.org, use your institutional credentials to create a Globus identity. If it is not, you can use your NIH eRA Commons id to create a Globus identity.
Write access to your component's folder
You must have access to upload data to the HuBMAP folder associated with your funded component (your DP, RTI, TMC or TTD) in Globus. This is an additional access level than what is granted by requesting Globus access on the member registration form or through your member profile.
- When you ask for Globus access in the registration form, you are granted read access.
- To register donors, organs or tissues, or upload data, you must have write access to your group's folder.
To request write access to your group's folder, have the PI or the PM of your group send email to firstname.lastname@example.org and request that you be given access to register tissues and upload data. You will receive an email invitation to the appropriate Globus group. Once you accept that invitation, you will be able to register donors and tissues and upload data.
Globus access also provides you with access to the HuBMAP ingest portal.
Transferring files using Globus
Your files must be accessible via a Globus endpoint in order to upload them to HuBMAP.
Globus can transfer data from a variety of different sources:
- From your machine - set up a Globus Connect Personal endpoint.
- An existing Globus account is required.
- Instructions for Windows, Mac, and Linux are available on the Globus How Tos
- Use your primary account when creating a Globus Connect Personal endpoint
- Campus or lab server - Globus may already be installed.
- Your own server - install a Globus server endpoint
- Bridges-2 - Use Globus to transfer
- AWS - AWS connector mapping is available.
Membership in the HuBMAP workspace in GitHub
You must be a member of the HuBMAP workspace in GitHub to prepare files for submission.
How to get GitHub access
Membership in the HuBMAP workspace in protocols.io
HuBMAP requires that all protocols be publicly available through the HuBMAP Method Development Community on protocols.io. You must be a member of this workspace to publish your protocols there.
How to become a HuBMAP research group member on protocols.io
Data ingest portal
The data ingest portal is at https://ingest.hubmapconsortium.org.
See the Data Modality summary spreadsheet.
If you have questions at any time, please email email@example.com.