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Disease Ontology - Institute for Genome Sciences - Use Cases

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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) Gend, Sex & Sex Orien Ont (GSSO) Ont Host-Microbiom Interact (OHMI)
Antibiotic Resistance Ont (ARO) Genomic Epi Ont (GenEpiO) Ont of Drug Adverse Events (ODAE)
Apollo Structured Vocabulary Glycoconjugate Ont (GlycoCoO) Ont of Host Pathogen Inter (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)
Cardiovasc Dis Ontology (CVDO) HHEAR Ontology Ontology for Biomed Investig (OBI)
Cell Culture Ontology (CCONT) Hum Physiol Simul Ont (HuPSON) Ontology for Gen Med Sci (OGMS)
Cell Line Ontology (CLO) Human Phenotype Ontology (HP) 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 Histopath Image Ont (QHIO)
Diabetes Mellit Treat Ont (DMTO) 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) Neural Electro Magnet Ont (NEMO) Translational Med Ontology (TMO)
Experimental Factor Ontology (EFO) NIF Standardized Onts (NIFSTD) Vaccine Informed Cons Ont (VICO)
FoodOn Non-Coding RNA Ontology (NCRO) Vaccine Ontology (VO)
Fuzzy Ont Obesity Cancer (FOORC) Obstet and Neonatal Ont (OntONeo) 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 DrugCentral mirDIP
AAgAtlas: Human AutoAntigen Db DrugNet miRTex
ABCkb e-TSN MloDisDB
ADEPTUS ECGene: Endometr Cancer G Db MOPED
African Human Microbiome Portal EDK: Editome Dis Kb MORPHIN
AllEnricher Egas 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 eRAM Mycobacteriaceae Phenome Atlas
ARAX EXPERT MyDisease.info
Arena-Idb EXTRACT MyGeneset.info
Argo FAIRsharing NAFLDkb
ASDmiR FANTOM NCATS Inxight Drugs
ATD: Autophagy To Disease FARNA NCBO Ontology Recommender
AuDis FHOntology ncRNAVar
AutismKB FibroAtlas NetMe
BALDR Flame NutriChem
BEAVR FlyBase OCDB: OCD Database
Bio-SimLex FooDis: Food-disease mining OMIM
Bio-SimVerb GeMI: Genom Meta Integration OnASSIs
Bio2RDF Gemma OncoKB
BioASQ GEN: Gene Expression Nebulas OncoMX
BioASQ-QA GenCoNet OncoPDSS
BioCreative V GeneCards OneStopRNAseq
BioDataome Genekitr OnTheFly2.0
BioGrid GenePlexus OntoCAT
biomappings GeneWeaver Ontoclick
Biomodels GeneWiki+ OntoGene
BioMuta GenIA Ontology Extension
BIONDA GenomeConnect OpenXGR
BioPortal GlutKNOIS: Gluten Interactions Db OVA: Onto Variant Analysis Tool
BioTAGME Glyconnect Pancreatlas
BioThings API ecosystem GlyCosmos Portal PathoPhenoDB
BioWES Glycowork PATRIC
BioXpress GlyGen pBRIT
BLAT2DOLite Google PDX-MI
BO-LSTM GSC: Genomic Stand Consortium PedAM
BrainBase Guide to PHARMACOLOGY Pedican: Pediatric cancer gene Db
BRD: Biosurveillance Resource Dir GVViZ: Vis Genes with Dis Variants Pharmacorank
Cancer Genome Interpreter GWAS Central PharMeBINet
CancerMIRNome GWASdb Pharos
cBioportal GXD: Mouse Gene Expression Db Phen2Gene
CCAS Harmonizome-ML Appyter PhenCards
CEDAR OnDemand HDncRNA: Heart Dis ncRNA Db Phenolyzer
Cell Taxonomy Heart Failure Integrated Platform Phenomebrowser
ChemDIS HemI: Heatmap Illustrator PhenoMiner
ChemDIS-Mixture HERB: Traditional Chinese Med Db Phevor2
ChIPseeker Hetionet PK-DB: Pharmacokinetics Db
Circ2Disease HGPEC PlasmiR
CircR2Cancer HisgAtlas PLSDB: Plasmid Db
circRNADisease HITSZ_CDR POEAS
CIViC HMDC: Human-Mouse Dis Connect Populous
CIViCMine HMDD: Human MicroRNA Dis Db PORI
ClinGen hu.MAP: Hum Prot Complex Map PosMed: Positional MEDLINE
clusterProfiler HumanMetagenomeDB preon
COEXPEDIA iBKH PSINDB: Postsynaptic Inter Db
COGR: Canadian Open Genet Repo iCTNet2 PUTransGCN
CoMentG IEDB: Immune Epitope Db pyMeSHSim
comoRbidity iLncDA-LTR QueryOR
CoNVaQ ImmPort Quest Diagnostics
COSMONET IMPPAT R-loopBase
COVID-19Base Integrated Interactions Db RareDis
CryptoGene DB Integrative Multispecies Prediction Reactome
CSgator: Compound Set Navigator InterMine REGene
CSGene: Cell Senesc Gene Db iProX ResMarkerDB
CTD2: Cancer Target Discov & Dev IRIDA: Integr Rapid Infect Dis Anal RGD: Rat Genome Db
CTD: Compar Toxicogenomic Db Isabl Platform RIscoper
CTR-DB IsoDA: Isoform-Dis Assoc predict RNA2Immune
D2H2 iTextMine RNADisease
DAISY: Data Information System JAX Clinical Kb ROBOT
DanioNet JAX Synteny Browser scMoresDB
Darling KGETCDA sem1R
dbBact Kb KGEV: KGraph Explor and Visual SGD: Saccharomyces Genome Db
dbEMT Kids Brain Health Network signatureSearch
dbGaP KOBAS SPOKE
DcGO Lantern SugarbindDB
dcGOR Leipzig Health Atlas SurvExpress
DeCoaD LeMeDISCO SurvMicro
DeepciRGO LeukmiR SympGAN
DeepGO LINCS Target Central Resource Db
DEEPScreen Linked Open Data Cloud TargetMine
DES-Amyloidosis List2Net TCIA: The Cancer Imaging Archive
DES-Mutation Literome TCMBank: Trad Chinese Med Bank
DES-ROD: RNA Oxid & Dis LiverAtlas TIN-X
DES-Tcell LiverWiki TissueNexus
DEXTER Lnc2Meth TOXPILOT
DGA: Disease and Gene Annot LncPCD TRRUST
dictyBase LncRNADisease TSGene
DincRNA LncTarD UFO
DISEASES LORD UniCarbKB
Diseasomics knowledge system Lynx VectorBase
DisGeNET MalaCards VICC
DiSignAtlas MEDIC VIPR: Virus Pathogen Resource
DISNET MEDICASCY Viruses.STRING
DISNOR MeFSAT Wikidata
DisPhaseDB MendelVar Wikipathways
DisSetSim MER: Minimal Entity Recognizer WormBase
DisSim MetaSRA Xenbase
DoCM: Db of Curated Mutations MethBank XGR: eXploring Genomic Relations
DODO: Dict of Dis Ontologies MetSigDis: Metab Signat of Dis Db YMLA: Yeast Multiple List Analyzer
DOSE: DO Semant Enrich analysis MGI: Mouse Genome Informatics ZFIN
DOSim miR2Disease

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:

BioNELL EPOM: Epigen Overlap Measure MEDSHARE
BPLLDA GeneSurrounder MicroPIE
brainMI GGCDA MultiDS-MDA
BRWLDA IDDAP Oncodomains
CDA-SKAG iLncDA-RSN ORPheUS
CEDAR InfAcrOnt PreOptique
Cognitive DDx Asst in Rare Dis IntNetLncSim PRISM
CVSARRP iPiDA-GCN RGCNCDA
DDCM: Disease-Drug Corr Method iPiDA-LTR RMDGCN
DHOSGR iPiDA-SWGCN SVM-DO
DLMPM iSG-PDA UPHO: Urban Pop Health Observ
Drug-Combo-Generator M2PP VRNetzer
eGARD MAGCNSE
Last updated: June 2024
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