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)

Globus identities

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.

• How to create a Globus identity using eRA Commons credentials

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 help@hubmapconsortium.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.

• How to get Globus access

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
  • Globus Connect Server
• Bridges-2 - Use Globus to transfer
  • Bridges-2 User Guide
• AWS - AWS connector mapping is available. 
  • How to Access Your Files on AWS S3 with Globus.

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.

Data modalities

See the Data Modality summary spreadsheet.

Questions

If you have questions at any time, please email help@hubmapconsortium.org.