Data Submission Guide

This resource documents the key steps for TMCs, Assay teams, and others who need to upload data to the HuBMAP Data Ingest portal.
Additional information about each each step (or section) of the process and additional resources can be found here:

HuBMAP Data Submission Guide  or  Data Ingest Guidance Slide deck 
Links to additional related portals, sites, and other resources are also provided herein.

Download a "tracker" version of this list: HuBMAP Data Upload Checklist
Use this tool to track your team's progress in the data submission/data ingest process.

  • Use the Table of Contents (below) to jump directly to a section of interest.
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      • Enter a term (or part of one) to search for it within this page.

Table of Contents

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  1. Section 1 - Prerequisites
  2. Section 2 - Registering Donors, Organs, and Samples
  3. Section 3 - Add Metadata for an Organ or Samples
  4. Section 4 - Registering RUI Tissue Block Locations
  5. Section 5 - Preparing a Submissions Directory
  6. Section 6 - Preparing Metadata Files
  7. Section 7 - Local Validation
  8. Section 8 - Creating a Data Upload Directory
  9. Section 9 - Data Upload
  10. Section 10 - Data Processing
  11. Section 11 - Review
  12. Section 12 - dbGaP Submission
Section 1 - Prerequisites

Complete the prerequisites listed below prior to registering donors and samples or uploading any data.
Click the provided links in this section to go to related portals or websites, or to access additional relevant information.

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Section 2 - Registering Donors, Organs, and Samples

NOTE: We strongly recommend that you collect this donor information when you get the organ and sample, well before you begin actual preparations to submit data.

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Section 3 - Add Metadata for an Organ or Samples

Click the provided links in this section to access additional relevant information or resources.

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Section 4 - Registering RUI Tissue Block Locations

When registering an organ (sample) on HuBMAP which is supported in the Human Reference Atlas (HRA), you must register a tissue block for the sample with the HRA using the Registration User Interface (RUI).

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Section 5 - Preparing a Submissions Directory

NOTE: The steps below are shared by both Clinical and non-Clinical assays. Highlighted items apply to Clinical assays only.

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Section 6 - Preparing Metadata Files

Click the provided links in this section to access additional relevant information or resources.

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Section 7 - Local Validation

NOTE: TMCs are required to run the submission validation locally BEFORE uploading to Globus. Clinical assays do not need to complete this step.

IMPORTANT: When a new version of a metadata schema is generated, it will be published on the first day of the next month.

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Section 8 - Creating a Data Upload Directory

Use this directory to submit metadata to the HIVE. 

Prerequisite: The submission directory has been successfully validated locally. Highlighted items apply to Clinical assays only.

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Section 9 - Data Upload

Submitting Donor Data

Prerequisite: Your submission donors and samples have already been registered.

NOTE: Donor privacy is a top priority when HuBMAP receives data from the community.

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See the Globus FAQ regarding Globus Connect and Endpoints, see also HuBMAP's data-related policies, or contact the HuBMAP Helpdesk with any additional questions.

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Section 10 - Data Processing

Data Processing: Ingestion, HIVE Validation, and Processing

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Section 11 - Review

Final Review, Data Approval, and Publication

NOTE: For data processed using a HIVE pipeline, the pipeline must complete without throwing a programmatic error prior to the final data review.

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Section 12 - dbGaP Submission

For assays with sequencing data, submit data to dbGaP after publication.

• This is a joint process completed by each data provider and the HIVE.
• We encourage data providers to create a dbGaP study and notify the HIVE as early as possible.

NOTE: The dbGaP submission process can take up to six months after the publication of sequence data in the HuBMAP Portal.

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