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

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.

AAgAtlas: Human AutoAntigen Db DoCM: Db of Curated Mutations MNDR
ABCkb DOSE: DO Semant & Enrich analysis MOPED
ADEPTUS DOSim MosaicBase
AllEnricher DrugCentral MouseMine
AllerGAtlas DrugNet mTCTScan
Alliance of Genome Resources ECGene: Endometr Cancer Gene Db My Corporis Fabrica Embryo
Arena-Idb EDK: Editome Dis Knowledgebase NCATS Inxight Drugs
Argo Egas NCBO Ontology Recommender
ASDmiR emiRIT: extract miRNA Info from Text ncRNAVar
ATD: Autophagy To Disease EMMA NETME
AuDis ENCODE: Encyc of DNA Elements NutriChem
AutismKB eRAM OCDB: OCD Database
BEAVR EXTRACT OnASSIs
Bio-SimLex FAIRsharing OncoKB
Bio-SimVerb FANTOM OncoMX
Bio2RDF FARNA OncoPDSS
BioASQ FibroAtlas OneStopRNAseq
BioCreative V FlyBase OnTheFly2.0
BioDataome Gemma OntoCAT
BioGrid GEN: Gene Expression Nebulas OntoGene
Biomodels GenCoNet Ontology Extension
BioMuta GeneCards OVA: Ontology Variant Analysis Tool
BioPortal GeneWeaver Pancreatlas
BioWES GeneWiki+ 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 Pharos
CancerMIRNome GWASdb Phen2Gene
cBioportal GXD: Mouse Gene Expression Db PhenCards
CEDAR OnDemand HDncRNA: Heart Disease ncRNA Db Phenolyzer
ChemDIS HERB: Traditional Chinese Med Db Phenomebrowser
ChemDIS-Mixture HFIP: Heart Failure Integr Platform PhenoMiner
ChIPseeker HGPEC Phevor2
Circ2Disease HITSZ_CDR PK-DB: Pharmacokinetics Database
CircR2Cancer HMDC: Human-Mouse: Dis Connect PlasmiR
CIViC HMDD: Human MicroRNA Dis Db PLSDB: plasmid database
CIViCMine hu.MAP: Hum Protein Complex Map POEAS
ClinGen HumanMetagenomeDB Populous
clusterProfiler iCTNet2: integr Complex Traits Netw PORI
COEXPEDIA IEDB: Immune Epitope Database PSINDB: Postsynaptic Interaction Db
COGR: Canadian Open Genet Repo ImmPort pyMeSHSim
comoRbidity IMP: Integrative Multi-species Predict QueryOR
CoNVaQ IMPPAT Quest Diagnostics
COSMONET Integrated Interactions Database R-loopBase
CryptoGene DB InterMine RareDis
CSgator: Compound Set Navigator iProX Reactome
CSGene: Cell Senescence Gene Db IRIDA: Integr Rapid Infect Dis Anal REGene
CTD: Comparative Toxicogenomic Db Isabl Platform ResMarkerDB
CTD2: Cancer Target Discov & Dev IsoDA: Isoform-Dis Assoc predict RGD: Rat Genome Database
CTR-DB iTextMine ROBOT
DAISY: Data Information System JAX Clinical Knowledgebase sem1R
DanioNet JAX Synteny Browser SGD: Saccharomyces Genome Db
Darling Kids Brain Health Network signatureSearch
dbEMT KOBAS SurvExpress
dbGaP Lantern SurvMicro
DcGO LeukmiR Target Central Resource Database
dcGOR LINCS TargetMine
DeCoaD Literome TissueNexus
DeepciRGO LiverAtlas TOXPILOT
DeepGO LiverWiki TRRUST
DEEPScreen Lnc2Meth TSGene
DES-Mutation LncRNADisease UFO
DES-ROD: RNA Oxid & Dis LORD UniCarbKB
DES-Tcell Lynx VectorBase
DEXTER MalaCards VICC
DGA: Disease and Gene Annotations MEDIC VIPR: Virus Pathogen Resource
dictyBase MEDICASCY Viruses.STRING
DincRNA MeFSAT Wikidata
DISEASES MendelVar Wikipathways
DisGeNET MER: Minimal Entity Recognizer WormBase
DISNET MetaSRA Xenbase
DISNOR MetSigDis: Metab Signat of Dis Db XGR: eXploring Genomic Relations
DisSetSim miRTex ZFIN
DisSim MloDisDB

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 eGARD MicroPIE
brainMI EPOM: Epigenome overlap measure Oncodomains
BRWLDA GeneSurrounder ORPheUS
CEDAR IDDAP PreOptique
Cognitive DDx Assistant in Rare Dis InfAcrOnt PRISM
DDA: Disease-Disease Assoc scoring IntNetLncSim RGCNCDA
DLMPM M2PP VRNetzer
Drug-Combo-Generator MEDSHARE
Last updated: May 2022
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