Researchers and data scientists from dozens of universities, hospitals, and other institutions across the United States have created an online portal that offers free, open access to one of the most comprehensive atlases of the cells, tissues and organ systems of healthy human bodies. Described in Nature Communications, the federally funded portal is designed to help both human researchers and artificial intelligence efforts understand health and disease.
The portal serves as the online home for data from the Human BioMolecular Atlas Program (HuBMAP). This eight-year effort involved more than 600 consortium members at over 60 institutions. According to the researchers, the atlas draws on more than 9,000 datasets from over 500 healthy donors across dozens of organs and tissues, a combination of scope and scale that no other single resource currently offers.
Web-based tools in the HuBMAP Data Portal let researchers worldwide quickly analyze visual, spatial, and biomolecular data from the collection. Users can browse data by organ system, search for gene expression patterns and molecular signatures across tissues, and explore single-cell data across diverse cell populations.
“The HuBMAP program has generated an enormously rich resource for deepening our understanding of human health and disease,” said senior author Nils Gehlenborg from the Blavatnik Institute at Harvard Medical School. “The portal gives users access to the data and also provides tools they can use to explore and analyze the complex relationships between the trillions of cells that make up each healthy human body in a way that’s never been possible before,” he added.
HuBMAP adds to a growing set of biomedical atlases that capture the cellular and biochemical status of people with various diseases. The researchers said a healthy comparison is needed to build a complete picture of human health and disease. “To understand disease, you first need to know what healthy looks like,” said first author Morgan Turner.
According to Turner, the portal combines more than 25 types of molecular and imaging data from dozens of healthy organs and tissues. The data follow community-driven FAIR data and metadata standards, so they can be compared across labs, organs and donors. “Those standards are also what power the portal’s visualization and analysis tools and make the data ready for AI,” Turner said.
A key part of the effort was ensuring that HuBMAP samples, captured with a wide range of tools and technologies, could be compared in a scientifically sound way. The portal team worked with other consortium members to create community-driven standards for contributors to follow when sharing data. They then built standardized processing pipelines so that molecular and imaging data from many labs and technologies are processed uniformly and can be compared.
The portal also lets researchers judge whether the atlas holds information relevant to their questions without first downloading the massive datasets or using heavy computing resources. For more advanced work, users can download data directly and use the portal’s openly available metadata and programming interfaces. Protected data, such as sequencing data that could identify donors, require an approval process.
The portal serves as the online home for data from the Human BioMolecular Atlas Program (HuBMAP). This eight-year effort involved more than 600 consortium members at over 60 institutions. According to the researchers, the atlas draws on more than 9,000 datasets from over 500 healthy donors across dozens of organs and tissues, a combination of scope and scale that no other single resource currently offers.
Web-based tools in the HuBMAP Data Portal let researchers worldwide quickly analyze visual, spatial, and biomolecular data from the collection. Users can browse data by organ system, search for gene expression patterns and molecular signatures across tissues, and explore single-cell data across diverse cell populations.
“The HuBMAP program has generated an enormously rich resource for deepening our understanding of human health and disease,” said senior author Nils Gehlenborg from the Blavatnik Institute at Harvard Medical School. “The portal gives users access to the data and also provides tools they can use to explore and analyze the complex relationships between the trillions of cells that make up each healthy human body in a way that’s never been possible before,” he added.
HuBMAP adds to a growing set of biomedical atlases that capture the cellular and biochemical status of people with various diseases. The researchers said a healthy comparison is needed to build a complete picture of human health and disease. “To understand disease, you first need to know what healthy looks like,” said first author Morgan Turner.
According to Turner, the portal combines more than 25 types of molecular and imaging data from dozens of healthy organs and tissues. The data follow community-driven FAIR data and metadata standards, so they can be compared across labs, organs and donors. “Those standards are also what power the portal’s visualization and analysis tools and make the data ready for AI,” Turner said.
A key part of the effort was ensuring that HuBMAP samples, captured with a wide range of tools and technologies, could be compared in a scientifically sound way. The portal team worked with other consortium members to create community-driven standards for contributors to follow when sharing data. They then built standardized processing pipelines so that molecular and imaging data from many labs and technologies are processed uniformly and can be compared.
The portal also lets researchers judge whether the atlas holds information relevant to their questions without first downloading the massive datasets or using heavy computing resources. For more advanced work, users can download data directly and use the portal’s openly available metadata and programming interfaces. Protected data, such as sequencing data that could identify donors, require an approval process.
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