Table 2.

Ontologies used within the alliance of genome resources to annotate function, phenotype, and disease properties associated with genome features, gene products, genetically defined populations, and other biological entities

		Alliance knowledge center
Ontology	Abbreviation	ZFIN	MGD	SGD	WormBase	FlyBase	RGD	Xenbase
Ascomycete phenotype ontology	APO			✓
Biological spatial ontology	BSPO	✓
C. elegans (nematode) life stage	WBls				✓
C. elegans anatomy	WBbt				✓
C. elegans phenotype	WBPhenotype				✓
Cell ontology	CL		✓				✓
Chemical entities of biological interest	ChEBI	✓	✓	✓	✓		✓
Clinical measurement ontology	CMO						✓
Drosophila development	FBdv					✓
Drosophila gross anatomy	FBdt					✓
Drosophila phenotype ontology	DPO					✓
Embrace data and methods	EDAM			✓
Evidence and conclusion ontology	ECO	✓	✓	✓			✓
Experimental condition ontology	XCO						✓
FlyBase controlled vocabulary	FBcv					✓
Gene ontology	GO	✓	✓	✓	✓	✓	✓	✓
Human disease ontology	DOID	✓	✓	✓		✓	✓	✓
Human phenotype ontology	HP		✓				✓
Mammalian phenotype ontology	MP		✓				✓
Measurement method ontology	MMO						✓
Molecular interactions	MI			✓		✓	✓
Mouse adult gross anatomy	MA		✓				✓
Mouse developmental stage ontology	Mmusdv		✓
Mouse gross anatomy and development, timed	EMAPA		✓
Mouse pathology	MPATH	✓	✓
Ontology for biomedical investigations	OBI			✓
Pathway ontology	PW						✓
Phenotype and trait ontology	PATO	✓	✓		✓
Protein modification	MOD			✓
Protein ontology	PRO		✓
Rat Strain ontology	RS						✓
Relations ontology	RO	✓	✓	✓	✓
Sequence types and features	SO	✓	✓	✓		✓	✓
Uberon	Uberon		✓				✓
Vertebrate trait ontology	VT		✓
Xenopus anatomy ontology	XAO							✓
Xenbase experimental data ontology	XBED							✓
Xenopus phenotype ontology	XPO							✓
Xenopus small molecule ontology	XSMO							✓
Zebrafish anatomy	ZFA	✓
Zebrafish developmental stages	ZFS	✓
Zebrafish experimental conditions ontology	ZECO	✓