Ontology registry

Which ontology owns which kind of term, what OLS calls it, and a branch root to constrain against. Every ontology id and branch label below was resolved against OLS in July 2026.

Prefix to OLS ontology id

The OLS ontology id is almost always the lowercased CURIE prefix. Note the exceptions.

CURIE prefix	OLS id	Covers
`UBERON`	`uberon`	Anatomy, tissues, organs, body fluids (cross-species)
`CL`	`cl`	Cell types
`CLO`	`clo`	Cell lines
`MONDO`	`mondo`	Diseases (the merged disease ontology; prefer over DOID/NCIT)
`DOID`	`doid`	Human Disease Ontology (largely subsumed by MONDO)
`HP`	`hp`	Human phenotypic abnormalities — id is `hp`, not `hpo`. `HPO` is a Bioregistry synonym; Identifiers.org rejects `HPO:…`
`EFO`	`efo`	Experimental factors, assays, platforms, cell lines
`CHEBI`	`chebi`	Chemical entities, drugs, metabolites
`NCBITaxon`	`ncbitaxon`	Organisms
`GO`	`go`	Biological process, molecular function, cellular component
`OBI`	`obi`	Assays, devices, protocols, study design
`PATO`	`pato`	Qualities — sex, colour, magnitude, `normal`
`SO`	`so`	Sequence features
`HsapDv`	`hsapdv`	Human developmental stages
`MmusDv`	`mmusdv`	Mouse developmental stages
`ENVO`	`envo`	Environmental materials and biomes
`FOODON`	`foodon`	Food
`NCIT`	`ncit`	NCI Thesaurus (clinical/oncology breadth)
`MS`	`ms`	Mass spectrometry instruments and methods
`BAO`	`bao`	BioAssay descriptions
`Orphanet`	`ordo`	Rare diseases — id is `ordo`, prefix in CURIEs is `Orphanet`, and OLS reports `preferredPrefix: ORDO`

Not in OLS at all: Cellosaurus (cell line identity, RRID CVCL_*) — query https://api.cellosaurus.org instead. Vendor and instrument vocabularies generally are not there either.

Branch roots for constraint checks

Pass these to --branch to assert a term is the right kind of thing.

Root	Label	Use for
`UBERON:0001062`	anatomical entity	any anatomy
`UBERON:0000465`	material anatomical entity	tissues and organs
`CL:0000000`	cell	cell types
`MONDO:0700096`	human disease	human disease fields
`HP:0000118`	Phenotypic abnormality	phenotype fields
`CHEBI:24431`	chemical entity	compounds
`NCBITaxon:1`	root	organisms
`OBI:0000070`	assay	assay fields
`PATO:0000001`	quality	qualities including sex
`GO:0008150`	biological_process	GO BP only
`GO:0003674`	molecular_function	GO MF only
`GO:0005575`	cellular_component	GO CC only
`EFO:0000001`	experimental factor	EFO breadth
`SO:0000110`	sequence_feature	sequence features
`HsapDv:0000001`	life cycle	human developmental stage
`MmusDv:0000001`	life cycle	mouse developmental stage
`ENVO:00010483`	environmental material	environmental samples
`CLO:0000031`	cell line	cell lines
`NCIT:C7057`	Disease, Disorder or Finding	NCIT disease subtree
`DOID:4`	disease	DOID subtree

MONDO:0000001 resolves (label disease) but only through the IRI fallback described in ols4-api.md; prefer MONDO:0700096 as a human-disease root.

A branch check does not substitute for a prefix check. CARO places cell under anatomical structure, so cell types pass an anatomy branch test. Constrain both.

Choosing between overlapping ontologies

Disease: MONDO. It is the merge target for DOID, Orphanet, OMIM, and NCIT disease terms, and it carries cross-references back to all of them. Use DOID or NCIT only when a downstream consumer demands that namespace.
Disease vs phenotype. MONDO for the diagnosis (asthma), HP for the observed abnormality (Wheezing). Metadata fields usually want one or the other, not either.
Tissue vs cell type. UBERON for the sample's anatomical origin, CL for what the cells are. liver is UBERON, hepatocyte is CL — even though a search for hepatocyte restricted to uberon will return the CL term as an imported copy.
Assay: EFO first, OBI second. Genomics platforms and library strategies are richer in EFO; OBI is better for general laboratory assay classes.
Chemicals: ChEBI for anything with a structure. Drug products by trade name belong in a drug vocabulary (RxNorm, DrugBank), not ChEBI.
Sex: PATO (PATO:0000384 male, PATO:0000383 female). Not NCIT, not free text.
"Normal" / healthy control: PATO:0000461 (normal) is the conventional filler for a disease field with no disease, and is what several submission schemas require.

Common metadata fields and their expected ontology

Field names differ per archive, but the ontology behind each concept is stable:

Concept	Ontology
tissue / organ / anatomical site	UBERON
cell type	CL
cell line	CLO, or Cellosaurus for identity and contamination status
disease	MONDO (`PATO:0000461` when none)
phenotype	HP
organism	NCBITaxon
assay / platform	EFO
developmental stage	HsapDv, MmusDv
sex	PATO
chemical / treatment compound	ChEBI
environmental material	ENVO

Submission schemas — CELLxGENE, HCA, ENA/BioSamples checklists, ISA-Tab configurations — pin both the field names and the permitted ontologies, and they revise them. Read the schema version the submission targets rather than relying on this table or on memory; the ontology choices above are the stable part, the field names are not.