Programmatic Interface to HuBMAP Ontology

Work Group

Project Lead(s)

Project Status


Project Deliverables

Tool for programmatic interaction with HuBMAP ontology


HMS Department

Center for Computational Biomedicine

Project Description

The NIH Human BioMolecular Atlas Program (HuBMAP) is building tables that describe cell types, their characteristic biomarkers, and their relationships to other cell types and anatomical structures in the healthy human body. These so-called “ASCT+B” tables—one per organ—are compiled into the so-called “HuBMAP ontology,” which can be queried via Web APIs that support specific, pre-canned queries. Alternatively, the HuBMAP ontology can be queried directly using the SPARQL query language. 

The main objective of this project is to develop tooling to allow scientists to programmatically interact with the HuBMAP ontology in meaningful ways. This includes first eliciting HuBMAP-related queries of interest, then developing a suite of ontology queries. Finally we will develop a tool to perform queries programmatically or through a command line interface. We particularly aim to facilitate the automatic annotation of cells in single-cell experiment data with cell types described in the HuBMAP ontology based on biomarker expression and anatomical location.


Contact Genoa Polumbo with questions about this project.