Table 1.

Landscape of phenotype ontologies

Domain	Ontology	# Classes	Used by
Human and biomedical	DO [36]	11 663	DisGeNet [37]
	HPO [38]	15 381	HPO Database [39] and GWAS Central [40]
	International Classification of Disease version 10, Clinical Modification (ICD10CM) [41]	92 168	Various EHR systems
	ICD9CM [42]	22 533	Various EHR systems
	Medical Subject Headings Thesaurus [43]	261 990	Comparative Toxicogenomic Database [44]
	UMLS [43]		SIDER [45] and DisGeNet [37]
	NCI Thesaurus [46]	118 941	NCI, NIH multiple projects
	Ontology of Adverse Events [47]	5514
	Orphanet Rare Disease Ontology [48]	13 105	Orphanet [49]
	Read Codes Clinical Terminology version 3 [50]	140 065	UK General Practice
	SNOMED-CT [51]	324 129	Various EHR systems
Animal model organism	Dictyostelium Phenotype Ontology [52]	1058	DictyBase [52]
	DPO [53]	506	FlyBase [54]
	MPATH [13]	889	PathBase [55], RGD [56] and MGI [14]
	MPO [22]	30 316	MGI [14], RGD [56]
	Worm Phenotype Ontology (WBPhenotype) [57]	2435	WormBase [58]
Plants and fungi	Ascomycete Phenotype Ontology	619	Saccharomyces Genome Database [59]
	Flora Phenotype Ontology [60]	28 430	African Plants Database [61]
	FYPO [29]	9870	PomBase [62]
	TO [63]	1433	iPlant Collaborative Databases [64] and Planteome [65]
	Solanaceae PATO [30, 31]	397	Sol Genomics Network [66]
	Thesaurus Of Plant traits [67]	950	TRY Database [68]
Cell	Cell Microscopical Phenotype Ontology [69]	813	Cellular Phenotype Database [70]
	Ontology for Microbial Phenotypes (OMP) [71]	1120	Microbialphenotypesȯrg [72]