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The National Institutes of Health's (NIH) Human Biomolecular Atlas Program(HuBMAP) aims to create a comprehensive high-resolution atlas of all the cellsin the healthy human body. Multiple laboratories across the United States arecollecting tissue specimens from different organs of donors who vary in sex,age, and body size. Integrating and harmonizing the data derived from thesesamples and 'mapping' them into a common three-dimensional (3D) space is amajor challenge. The key to making this possible is a 'Common CoordinateFramework' (CCF), which provides a semantically annotated, 3D reference systemfor the entire body. The CCF enables contributors to HuBMAP to 'register'specimens and datasets within a common spatial reference system, and itsupports a standardized way to query and 'explore' data in a spatially andsemantically explicit manner. [...] This paper describes the construction andusage of a CCF for the human body and its reference implementation in HuBMAP.The CCF consists of (1) a CCF Clinical Ontology, which provides metadata aboutthe specimen and donor (the 'who'); (2) a CCF Semantic Ontology, whichdescribes 'what' part of the body a sample came from and details anatomicalstructures, cell types, and biomarkers (ASCT+B); and (3) a CCF SpatialOntology, which indicates 'where' a tissue sample is located in a 3D coordinatesystem. An initial version of all three CCF ontologies has been implemented forthe first HuBMAP Portal release. It was successfully used by Tissue MappingCenters to semantically annotate and spatially register 48 kidney and spleentissue blocks. The blocks can be queried and explored in their clinical,semantic, and spatial context via the CCF user interface in the HuBMAP Portal.

Construction and Usage of a Human Body Common Coordinate Framework Comprising Clinical, Semantic, and Spatial Ontologies