Information for HuBMAP data providers
On this page, you will find information about:
Data submission
- Data submission office hours and how to make an appointment
- Links to detailed guidance on data submission, including the Data Submission Guide and a video recording of the 2023 data submission workshop
- Prerequisites for submitting data
- Assay metadata and directory schemas
- The data ingest portal
- The data ingest board, to track your data submissions
Other
- Comparison table for spatial transcriptomic methods
Questions? Email help@hubmapconsortium.org.
Data submission office hours
By appointment only
12 PM to 2 PM Eastern time, Tuesdays and Thursdays
Data submission office hours are hosted by the HIVE IEC to help with the data submission process. This a great opportunity for data providers to get their data submission questions answered and to enlist troubleshooting help.
Data Submission Guidance
Please see the HuBMAP Data Submission Guide for detailed instructions on the process of submitting data to HuBMAP.
You can also review this video about data submission from our 2023 annual meeting workshop.
Prerequisites for submitting data
There are several prerequisites to successfully submitting data to HuBMAP. You must have:
Consent and Data Use Agreements on record
Your component must have submitted completed Consent and Data Use Agreements to the Consortium.
- See the Data Use Agreement
Write 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 for an institution listed in the organization dropdown at https://app.globus.org. If your institution is not listed there, please contact the helpdesk at help@hubmapconsortium.org. NIH eRA Commons ids are no longer acceptable.
- 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 from the organization dropdown on https://app.globus.org. NIH eRA Commons identities are no longer acceptable. 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, please contact the helpdesk at help@hubmapconsortium.org.
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.
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.
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.
Assay metadata and directory schemas
As metadata and directory schemas can be reviewed and revised at any time, be sure that you are using the most up-to-date schemas for your data uploads.
You can always find the updated schemas at https://software.docs.hubmapconsortium.org/metadata.
Data ingest portal
Data submission is done via the data ingest portal at https://ingest.hubmapconsortium.org.
Note that you must log in to the ingest portal with your HuBMAP credentials.
Data ingest board
You can follow your data through the ingest process on the Data Ingest Board.
You can view both your data uploads and your datasets through this interface.
Questions? Email help@hubmapconsortium.org.