About Human Reference Atlas (HuBMAP)
The NIH HuBMAP atlas of the healthy adult body, built as ASCT+B tables for 30+ organs: anatomical structures (UBERON), the cell types in them (Cell Ontology) and the biomarkers that characterise each cell type, with the supporting papers. Look up a cell type, an organ or tissue, or a marker gene, list the organ tables and 3D reference organs, or query the knowledge graph directly. CC BY 4.0.
Questions you can ask Human Reference Atlas
Type them into Kahubi’s chat once Human Reference Atlas is connected.
“Which cell types are found in the human kidney cortex, and which marker genes identify each one?”
What comes back: Anatomical structures with the cell types located in them (Cell Ontology ids) and their biomarker genes, from the HRA kidney ASCT+B table.
“Which cell types does PODXL mark, and which papers support it?”
What comes back: Each cell type, structure and organ table where PODXL is a marker, then the full marker set and supporting DOIs for the cell type.
Human Reference Atlas MCP tools
The 6 tools the Human Reference Atlas server offers to Kahubi. The assistant picks the right one for each question.
hra_search_termsFind anatomical structures, cell types or biomarkers in the Human Reference Atlas by label substring.
hra_cell_typeWhere a cell type is found and how it is recognised: for each organ ASCT+B table, the anatomical structures it is located in, its biomarker genes/proteins and the DOIs of the su...
hra_anatomical_structureCell types located in an anatomical structure and in all of its parts (e.g.
hra_biomarkerWhich cell types a gene or protein marks, in which anatomical structures and organ tables.
hra_list_datasetsList HRA digital objects, latest version of each: ASCT+B organ tables (asct-b), 3D reference organs (ref-organ), 2D functional tissue unit illustrations (2d-ftu), organ mapping...
hra_sparqlRun a read-only SPARQL SELECT query on the HRA knowledge graph (lod.humanatlas.io).
Using Human Reference Atlas in Kahubi
- Hosted by Kahubi. Kahubi runs this server itself so it stays reliable enough for research use.
- Cited, checkable answers. Results are treated as retrieved material and cited with the source’s own identifiers, so you can open every record the answer relied on.
- Your files stay private. Only the search the assistant writes for your question is sent to Human Reference Atlas.
More life science sources
- TogoMCP (UniProt, ChEMBL, PubChem, PDB, Reactome, NCBI)One service across 30+ life-science databases: proteins, genes, compounds, structures, pathways, variants and MeSH.
- Open Targets PlatformTarget–disease–drug associations with the evidence behind them, from EMBL-EBI.
- Protein structures (PDB, AlphaFold)Search experimental and predicted protein structures, find similar folds, track ligands and fetch annotations.
- NCBI E-utilitiesGene, ClinVar, dbSNP, Taxonomy, Nucleotide, Protein, PMC and other NCBI databases.
- GBIF (biodiversity occurrences)2.5 billion species occurrence records from museums, surveys and citizen science worldwide.
- iNaturalistCitizen-science observations with photos, research-grade identifications and places.