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Home > Community > Use Cases

Use Cases

The Disease Ontology is utilized extensively in biomedical and bioinformatics research, by both scientists conducting primary research and those creating research tools for others. Some of those research tools designed for reuse by the broader scientific community that have used the Disease Ontology are listed here. These have been grouped into three categories: ontologies, resources and methodologies.


The Disease Ontology is utilized to build other biomedical ontologies. These application ontologies either reuse DO's terms and/or IDs (often as PURLs, unique URL based IDs, e.g. or map to DOIDs as ontology cross references (xrefs), synonyms or annotations. To date, the Disease Ontology is being utilized by more than 50 other biomedical ontologies:

Allotrope Foundation Ont (AFO) Gend, Sex, & Sex Orientat Ont (GSSO) Ont Host-Microbiome Interact (OHMI)
Antibiotic Resistance Ont (ARO) Genomic Epidemiology Ont (GenEpiO) Ont of Drug Adverse Events (ODAE)
Apollo Structured Vocabulary Glycoconjugate Ont (GlycoCoO) Ont of Host Pathogen Interact (OHPI)
BioAssay Ontology (BAO) Guideline Provenance Ont (G-Prov) Ont of Precis Med & Investig (OPMI)
Breast Cancer Fuzzy Ont (BCFO) Hearing Impairment Ontology (HIO) Ontology for Biobanking (OBIB)
Cardiovascular Dis Ontology (CVDO) HHEAR Ontology Ontology for Biomed Investig (OBI)
Cell Culture Ontology (CCONT) Human Phenotype Ontology (HP) Ontology for Gen Med Sci (OGMS)
Cell Line Ontology (CLO) Human Physiol Simul Ont (HuPSON) Ontology for MIRNA Target (OMIT)
CHEAR Ontology Hypertension Ontology (HTN) Ontology of Adverse Events (OAE)
ChemFOnt Infectious Disease Ontology (IDO) Pre-Eclampsia Ontology (PE-O)
Coronavirus Infect Dis Ont (CIDO) Influenza Ontology (FLU) Protein Ontology (PRO)
Data Use Ontology (DUO) Informed Consent Ontology (ICO) Public Health Doc Ont (OntoPH)
Dermatological Dis Ont (DermO) Mental Disease Ontology (MFOMD) Quant Histopathol Image Ont (QHIO)
Diabetes Mellit Treat Ont (DMTO) Metabolomics Stand Init Ont (MSIO) Quant Imaging Biomarker Ont (QIBO)
Drug Interact & Evid Ont (DIDEO) MicrO Radiology Gamuts Ontology (RGO)
Drug Target Ontology (DTO) Mondo Disease Ontology (MONDO) Sickle Cell Disease Ontology (SCDO)
eagle-i resource ontology (ERO) Mouse Pathology Ontology (MPATH) TOXic Process Ontology (TXPO)
eNanoMapper Ontology (ENM) Neural Electro Magnetic Ont (NEMO) Translational Med Ontology (TMO)
Experimental Factor Ontology (EFO) NIF Standardized Onts (NIFSTD) Vaccine Informed Consent Ont (VICO)
FoodOn Non-Coding RNA Ontology (NCRO) Vaccine Ontology (VO)
Fuzzy Ont Obesity Cancer (FOORC) Obstet and Neonatal Ont (OntONeo) VEuPathDB Ontology (eupath)


We actively seek collaborations with other data resources and users to improve data integration, share efforts, and make our data maximally useful to biologists and bioinformaticians. Here are a list of databases, software tools and other web resources that: i) support the use of DO data, ii) have integrated or were built using DO data, or iii) provide data linkages to the DO website. If we are missing your database, software tool or web resource, please contact us.

a GO tool DrugNet mirDIP
AAgAtlas: Human AutoAntigen Db e-TSN miRTex
ABCkb ECGene: Endometr Cancer Gene Db MloDisDB
ADEPTUS EDK: Editome Dis Knowledgebase MOPED
AllEnricher Egas MORPHIN
AllerGAtlas emiRIT: extract miRNA Info from Text MosaicBase
Alliance of Genome Resources EMMA MouseMine
Annot ENCODE: Encyc of DNA Elements mTCTScan
ARAX eRAM My Corporis Fabrica Embryo
Arena-Idb EXPERT
ASDmiR FAIRsharing NAFLDkb: NAFLD Knowledge Base
ATD: Autophagy To Disease FANTOM NCATS Inxight Drugs
AuDis FARNA NCBO Ontology Recommender
AutismKB FHOntology ncRNAVar
BEAVR Flame NutriChem
Bio-SimLex FlyBase OCDB: OCD Database
Bio-SimVerb FooDis: Food-disease mining pipeline OMIM
Bio2RDF GeMI: Genomic Metadata Integration OnASSIs
BioASQ Gemma OncoKB
BioASQ-QA GEN: Gene Expression Nebulas OncoMX
BioCreative V GenCoNet OncoPDSS
BioDataome GeneCards OneStopRNAseq
BioGrid Genekitr OnTheFly2.0
biomappings GenePlexus OntoCAT
Biomodels GeneWeaver Ontoclick
BioMuta GeneWiki+ OntoGene
BIONDA GenomeConnect Ontology Extension
BioPortal GlutKNOIS: Gluten Interactions Db OpenXGR
BioTAGME Glyconnect OVA: Ontology Variant Analysis Tool
BioThings API ecosystem GlyCosmos Portal Pancreatlas
BioWES Glycowork PathoPhenoDB
BioXpress GlyGen PATRIC
BLAT2DOLite Google pBRIT
BO-LSTM GSC: Genomic Stand Consortium PDX-MI
BrainBase Guide to PHARMACOLOGY PedAM
BRD: Biosurveillance Resource Dir GVViZ: Vis Genes with Dis Variants Pedican: Pediatric cancer gene Db
Cancer Genome Interpreter GWAS Central Pharmacorank
CancerMIRNome GWASdb PharMeBINet
cBioportal GXD: Mouse Gene Expression Db Pharos
CCAS Harmonizome-ML Appyter Phen2Gene
CEDAR OnDemand HDncRNA: Heart Disease ncRNA Db PhenCards
Cell Taxonomy HemI: Heatmap Illustrator Phenolyzer
ChemDIS HERB: Traditional Chinese Med Db Phenomebrowser
ChemDIS-Mixture Hetionet PhenoMiner
ChIPseeker HFIP: Heart Failure Integr Platform Phevor2
Circ2Disease HGPEC PK-DB: Pharmacokinetics Database
CircR2Cancer HisgAtlas PlasmiR
CIViC HITSZ_CDR PLSDB: plasmid database
CIViCMine HMDC: Human-Mouse: Dis Connect POEAS
ClinGen HMDD: Human MicroRNA Dis Db Populous
clusterProfiler hu.MAP: Hum Protein Complex Map PORI
COEXPEDIA HumanMetagenomeDB PosMed: Positional MEDLINE
COGR: Canadian Open Genet Repo iBKH: integr Biomed Knowledge Hub PSINDB: Postsynaptic Interaction Db
comoRbidity iCTNet2: integr Complex Traits Netw pyMeSHSim
CoNVaQ IEDB: Immune Epitope Database QueryOR
COSMONET iLncDA-LTR Quest Diagnostics
COVID-19Base ImmPort R-loopBase
CryptoGene DB IMP: Integrative Multi-species Predict RareDis
CSgator: Compound Set Navigator IMPPAT Reactome
CSGene: Cell Senescence Gene Db Integrated Interactions Database REGene
CTD2: Cancer Target Discov & Dev InterMine ResMarkerDB
CTD: Comparative Toxicogenomic Db iProX RGD: Rat Genome Database
CTR-DB IRIDA: Integr Rapid Infect Dis Anal RNA2Immune
DAISY: Data Information System Isabl Platform RNADisease
DanioNet IsoDA: Isoform-Dis Assoc predict ROBOT
Darling iTextMine sem1R
dbBact knowledge base JAX Clinical Knowledgebase SGD: Saccharomyces Genome Db
dbEMT JAX Synteny Browser signatureSearch
dbGaP KGEV: KGraph Explor and Visual SPOKE
DcGO Kids Brain Health Network SugarbindDB
dcGOR KOBAS SurvExpress
DeCoaD Lantern SurvMicro
DeepciRGO Leipzig Health Atlas SympGAN
DeepGO LeMeDISCO Target Central Resource Database
DEEPScreen LeukmiR TargetMine
DES-Amyloidosis LINCS TCIA: The cancer imaging archive
DES-Mutation Linked Open Data Cloud TCMBank: Trad Chinese Med Bank
DES-ROD: RNA Oxid & Dis Literome TIN-X
DES-Tcell LiverAtlas TissueNexus
DGA: Disease and Gene Annotations Lnc2Meth TRRUST
dictyBase LncRNADisease TSGene
Diseasomics knowledge system Lynx VectorBase
DisGeNET MalaCards VICC
DISNET MEDIC VIPR: Virus Pathogen Resource
DisPhaseDB MeFSAT Wikidata
DisSetSim MendelVar Wikipathways
DisSim MER: Minimal Entity Recognizer WormBase
DoCM: Db of Curated Mutations MetaSRA Xenbase
DODO: Dict of Disease Ontologies MethBank XGR: eXploring Genomic Relations
DOSE: DO Semant & Enrich analysis MetSigDis: Metab Signat of Dis Db YMLA: Yeast Multiple List Analyzer
DOSim MGI: Mouse Genome Informatics ZFIN
DrugCentral miR2Disease


Many algorithms, frameworks, software tools, workflows and state-of-the art methods designed for (re)use and implementation by the scientific community incorporate the Disease Ontology. These "methodologies", which have not been incorporated into an existing software tool, database, or web resource or are not freely available, include:

BioNELL EPOM: Epigenome overlap measure MAGCNSE
brainMI GGCDA MicroPIE
CDA-SKAG iLncDA-RSN Oncodomains
Cognitive DDx Assistant in Rare Dis IntNetLncSim PreOptique
DLMPM iPiDA-SWGCN UPHO: Urban Pop Health Observ
Drug-Combo-Generator M2PP VRNetzer
Last updated: Nov 2023