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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.

Ontologies

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. http://purl.obolibrary.org/obo/DOID_4) 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) Fuzzy Ont Obesity Cancer (FOORC) Obstet and Neonatal Ont (OntONeo)
Antibiotic Resistance Ont (ARO) Gend, Sex & Sex Orien Ont (GSSO) Ont Host-Microbiom Interact (OHMI)
Apollo Structured Vocabulary Genomic Epi Ont (GenEpiO) Ont of Drug Adverse Events (ODAE)
BioAssay Ontology (BAO) Glycoconjugate Ont (GlycoCoO) Ont of Host Pathogen Inter (OHPI)
Breast Cancer Fuzzy Ont (BCFO) Guideline Provenance Ont (G-Prov) Ont of Precis Med & Investig (OPMI)
Cardiovasc Dis Ontology (CVDO) Hearing Impairment Ontology (HIO) Ontology for Biobanking (OBIB)
Cell Culture Ontology (CCONT) HHEAR Ontology Ontology for Biomed Investig (OBI)
Cell Line Ontology (CLO) Hum Physiol Simul Ont (HuPSON) Ontology for Gen Med Sci (OGMS)
CHEAR Ontology Human Phenotype Ontology (HP) Ontology for MIRNA Target (OMIT)
ChemFOnt Hypertension Ontology (HTN) Ontology of Adverse Events (OAE)
Coronavirus Infect Dis Ont (CIDO) Infectious Disease Ontology (IDO) Pre-Eclampsia Ontology (PE-O)
Data Use Ontology (DUO) Influenza Ontology (FLU) Protein Ontology (PRO)
Dermatological Dis Ont (DermO) Informed Consent Ontology (ICO) Public Health Doc Ont (OntoPH)
Diabetes Mellit Treat Ont (DMTO) Mental Disease Ontology (MFOMD) Quant Histopath Image Ont (QHIO)
Dog Disease Trait Ont (DDTO) Metabolomics Stand Init Ont (MSIO) Quant Imag Biomarker Ont (QIBO)
Drug Interact & Evid Ont (DIDEO) MicrO Radiology Gamuts Ontology (RGO)
Drug Target Ontology (DTO) Mondo Disease Ontology (MONDO) Sickle Cell Disease Ont (SCDO)
eagle-i resource ontology (ERO) Mouse Pathology Ont (MPATH) TOXic Process Ontology (TXPO)
eNanoMapper Ontology (ENM) Myocardial Infarction Ont (MIO) Translational Med Ontology (TMO)
Exercise Med Ontology (EXMO) Neural Electro Magnet Ont (NEMO) Vaccine Informed Cons Ont (VICO)
Experimental Factor Ontology (EFO) NIF Standardized Onts (NIFSTD) Vaccine Ontology (VO)
FoodOn Non-Coding RNA Ontology (NCRO) VEuPathDB Ontology (eupath)

Resources

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 G Db MloDisDB
ADEPTUS EDK: Editome Dis Kb MOPED
African Human Microbiome Portal Egas MORPHIN
AllEnricher EHD dataset MosaicBase
AllerGAtlas emiRIT: extract miRNA Info Text MouseMine
Alliance of Genome Resources EMMA mTCTScan
AlzKB: Alzheimer’s KB ENCODE: Encyc of DNA Elements My Corporis Fabrica Embryo
Annot EnrichDO Mycobacteriaceae Phenome Atlas
ARAX eRAM MyDisease.info
Arena-Idb EXPERT MyGeneset.info
Argo EXTRACT NAFLDkb
ASDmiR FAIRsharing NCATS Inxight Drugs
ATD: Autophagy To Disease FANTOM NCBO Ontology Recommender
AuDis FARNA ncRNAVar
AutismKB FHOntology NetMe
BALDR FibroAtlas NutriChem
BEAVR Flame OCDB: OCD Database
Bio-SimLex FlyBase OMIM
Bio-SimVerb FooDis: Food-disease mining OnASSIs
Bio2RDF GeMI: Genom Meta Integration OncoKB
BioASQ Gemma OncoMX
BioASQ-QA GEN: Gene Expression Nebulas OncoPDSS
BioCreative V GenCoNet OneStopRNAseq
BioDataome GeneCards OnTheFly2.0
BioGrid Genekitr OntoCAT
biomappings GenePlexus Ontoclick
BiomarkerKB GeneWeaver OntoGene
Biomodels GeneWiki+ Ontology Extension
BioMuta GenIA OpenXGR
BIONDA GenomeConnect OVA: Onto Variant Analysis Tool
BioPortal GlutKNOIS: Gluten Interactions Db Pancreatlas
BioTAGME Glyconnect PathoPhenoDB
BioThings API ecosystem GlyCosmos Portal PATRIC
BioWES Glycowork pBRIT
BioXpress GlyGen PDX-MI
BLAT2DOLite Google PedAM
BO-LSTM GSC: Genomic Stand Consortium Pedican: Pediatric cancer gene Db
BrainBase GTO: Gene Therapy Omnibus Petagraph
BRD: Biosurveillance Resource Dir Guide to PHARMACOLOGY Pharmacorank
Cancer Genome Interpreter GVViZ: Vis Genes with Dis Variants PharMeBINet
CancerMIRNome GWAS Central Pharos
CBGDA GWASdb Phen2Gene
cBioportal GXD: Mouse Gene Expression Db PhenCards
CCAS Harmonizome-ML Appyter Phenolyzer
CEDAR HDncRNA: Heart Dis ncRNA Db Phenomebrowser
CEDAR OnDemand Heart Failure Integrated Platform PhenoMiner
Cell Taxonomy HemI: Heatmap Illustrator Phevor2
CFDE: Common Fund Data Ecosystem HERB: Traditional Chinese Med Db PK-DB: Pharmacokinetics Db
ChemDIS Hetionet PlasmiR
ChIPseeker HGPEC PLSDB: Plasmid Db
Circ2Disease HisgAtlas POEAS
CircR2Cancer HITSZ_CDR Populous
circRNADisease HMDC: Human-Mouse Dis Connect PORI
CIViC HMDD: Human MicroRNA Dis Db PosMed: Positional MEDLINE
CIViCMine hu.MAP: Hum Prot Complex Map preon
ClinGen HumanMetagenomeDB PSINDB: Postsynaptic Inter Db
clusterProfiler iBKH PUTransGCN
COEXPEDIA iCTNet2 pyMeSHSim
COGR: Canadian Open Genet Repo IEDB: Immune Epitope Db QueryOR
CoMentG iLncDA-LTR Quest Diagnostics
comoRbidity ImmPort R-loopBase
CoNVaQ IMPPAT RareDis
COSMONET Integrated Interactions Db Reactome
COVID-19Base Integrative Multispecies Prediction REGene
CryptoGene DB InterMine ResMarkerDB
CSgator: Compound Set Navigator iProX RGD: Rat Genome Db
CSGene: Cell Senesc Gene Db IRIDA: Integr Rapid Infect Dis Anal RIscoper
CTD2: Cancer Target Discov & Dev Isabl Platform RNA2Immune
CTD: Compar Toxicogenomic Db IsoDA: Isoform-Dis Assoc predict RNADisease
CTR-DB iTextMine ROBOT
D2H2 JAX Clinical Kb scMoresDB
DAISY: Data Information System JAX Synteny Browser sem1R
DanioNet KGETCDA SGD: Saccharomyces Genome Db
Darling KGEV: KGraph Explor and Visual signatureSearch
dbBact Kb Kids Brain Health Network simona
dbEMT KOBAS SPOKE
dbGaP Lantern SugarbindDB
DcGO Leipzig Health Atlas SurvExpress
dcGOR LeMeDISCO SurvMicro
DDKG: Data Distillery KG LeukmiR SympGAN
DeCoaD LINCS tagger (tagcorpus)
DeepciRGO Linked Open Data Cloud Target Central Resource Db
DeepGO List2Net TargetMine
DEEPScreen Literome TarKG
DES-Amyloidosis LiverAtlas TCIA: The Cancer Imaging Archive
DES-Mutation LiverWiki TCMBank: Trad Chinese Med Bank
DES-ROD: RNA Oxid & Dis Lnc2Meth TIN-X
DES-Tcell LncPCD TissueNexus
DEXTER LncRNADisease ToxDAR
DGA: Disease and Gene Annot LncTarD TOXPILOT
dictyBase LORD TRRUST
Digital Phenotype Explorer LSD600 TSGene
DincRNA Lynx UBKG
Disease Maps MalaCards UFO
DISEASES MarkerDB UniCarbKB
Diseasomics knowledge system MEDIC VarGuideAtlas
DisGeNET MEDICASCY VectorBase
DiSignAtlas MedKG VICC
DISNET MeFSAT VIPR: Virus Pathogen Resource
DISNOR MendelVar Viruses.STRING
DisPhaseDB MER: Minimal Entity Recognizer Wikidata
DisSetSim MetaSRA Wikipathways
DisSim MethBank WormBase
DoCM: Db of Curated Mutations MetSigDis: Metab Signat of Dis Db Xenbase
DODO: Dict of Dis Ontologies MFF-nDA XGR: eXploring Genomic Relations
DOSE: DO Semant Enrich analysis MGI: Mouse Genome Informatics YMLA: Yeast Multiple List Analyzer
DOSim miR2Disease ZFIN
DrugCentral

Methodologies

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:

Alzheimer Gene Assoc Classifier GeneSurrounder MEDSHARE
ANDES GGCDA metaCDA
BioNELL GSWHomoNet MicroPIE
BPLLDA HIT MSMCDA
brainMI IDDAP MultiDS-MDA
BRWLDA iLncDA-RSN OM-GGAT
CDA-SKAG InfAcrOnt Oncodomains
Cognitive DDx Asst in Rare Dis IntNetLncSim ORPheUS
CVSARRP iPiDA-GCN PPDAMEGCN
DDCM: Disease-Drug Corr Method iPiDA-LTR PreOptique
DHOSGR iPiDA-SWGCN PRISM
DLMPM iSG-PDA RGCNCDA
Drug-Combo-Generator LDAGM RMDGCN
eGARD LEDAP SVMDO
EHDChat M2PP UPHO: Urban Pop Health Observ
EPOM: Epigen Overlap Measure MAGCNSE VRNetzer
GCDSAEMDA MedGraphNet
Last updated: June 2025
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