  The National Institutes of Health's (NIH) Human Biomolecular Atlas Program
(HuBMAP) aims to create a comprehensive high-resolution atlas of all the cells
in the healthy human body. Multiple laboratories across the United States are
collecting tissue specimens from different organs of donors who vary in sex,
age, and body size. Integrating and harmonizing the data derived from these
samples and 'mapping' them into a common three-dimensional (3D) space is a
major challenge. The key to making this possible is a 'Common Coordinate
Framework' (CCF), which provides a semantically annotated, 3D reference system
for the entire body. The CCF enables contributors to HuBMAP to 'register'
specimens and datasets within a common spatial reference system, and it
supports a standardized way to query and 'explore' data in a spatially and
semantically explicit manner. [...] This paper describes the construction and
usage 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 about
the specimen and donor (the 'who'); (2) a CCF Semantic Ontology, which
describes 'what' part of the body a sample came from and details anatomical
structures, cell types, and biomarkers (ASCT+B); and (3) a CCF Spatial
Ontology, which indicates 'where' a tissue sample is located in a 3D coordinate
system. An initial version of all three CCF ontologies has been implemented for
the first HuBMAP Portal release. It was successfully used by Tissue Mapping
Centers to semantically annotate and spatially register 48 kidney and spleen
tissue blocks. The blocks can be queried and explored in their clinical,
semantic, and spatial context via the CCF user interface in the HuBMAP Portal.
