The Human Disease Ontology Project develops and maintains the Disease Ontology (DO), an open-access ontology of human diseases, phenotypes, and related terms. The DO provides structured terminology to facilitate biomedical research and clinical care. It is funded by the NIH/NHGRI and maintained by researchers at the University of Maryland School of Medicine. The DO contains over 12,000 disease terms, is integrated with other biomedical ontologies, and sees increasing use by researchers around the world.
Human Disease Ontology Project mechanistic profiles of human disease
1. The Human Disease Ontology Project
mechanistic profiles of human disease
for biomedical and clinical research
Funding: NIH/NHGRI Genomic Resource
U41 HG008735-01A1
https://www.disease-ontology.org
https://github.com/DiseaseOntology/HumanDiseaseOntology
Lynn M. Schriml, Ph.D.
University of Maryland School of Medicine
Institute for Genome Science
2. axis of classification
2003
(ICD, MESH, NCI)
Semantic Relationships, DAG
Persistent Identifiers: DOIDs
DO R01 – DO Classification
Website
OBO Foundry domain
ontology
2008
2017
10,598 disease terms
++ ~ 1000 new terms/yr
Term expansion
Outreach
Genetic Diseases
NHGRI U41
Genomic Resource
CCBY → CC0 open license
2020
DO Website (in 2020)
Users: up 15.8 %, 30,207, 142 countries
DO xRefs
GARD:1921; MESH:3466; OMIM:4649; ICD9CM:2117;
ICD10CM:3520; NCI:4397; Orphanet:1845
12,242 cited definition sources (PubMed IDs, databases)
3. Axioms
Alzheimer’s disease
Parkinson’s Disease
pediatric cancers
acute lymphoblastic leukemia
B-lymphoblastic
leukemia/lymphoma
hypersensitivity diseases
genetic diseases:
polygenic, digenic
physical disorders
Syndromes
asthma
diabetes
Term
mappings
DO
Releas
es
DO Slims
databases
tools
(27) ontologies
DO
reports
Disease
re-
classifications
(QC & MESH, NCI, syndromes, synonyms)
(15) DO slims
DO_cancer_slim
DO_AGR_slim
DO citing papers (699)
Linked data
Imports
OBO Foundry
Ontologies
Community
Automated
DO xref
assessment
Term
requests
(ontology enrichment)
GitHub
4. Axiom
s
• Codify disease to disease relationships
• Statements asserting SubClass
• Views/Mechanisms of Disease
6. Wikidata SPARQL queries
Drug-Drug interactions
Drugs – disease – target gene - GO
Linking biomedical data through disease
Gene
Wikidata semantic network linking genes, drugs and
diseases with nodes and edges populated automatically
by ‘bots’ that integrate data from trusted authorities
such as NCBI’s Entrez Gene, PubChem, and the DO.
DO – NDF-RT – ChEMBL
Pathways: Reactome, Wikipathways
7. Clinical Team
Carol Greene, Cynthia Bearer, Richard Lichenstein, Katherine Bisordi
Medical Student
Nicole Campion (Class of 2020)
Connor Oates (Mount Sinai), David Kurland (NYU
Langone Medical Center)
Sue Bello, Melody Swen
Becky Jackson
Mike Schor Dustin Olley
James Munro
Carrie McCracken, Michelle Giglio
IGS - IFX Team
Editor's Notes
Domain – Vocabs to Semantics – Devise Classifications (update) – Update Model – Automated Releases – New term requests – Community Resource -
DO began – combining clinical vocabularies to create a ‘disease focused ontology’
Rex Chisholm and Warren Kibbe – Northwestern
DAG: Rooted Directed Acyclic Graph
1000 terms added by our curation team each year, ~50% from term requests – track in our GitHub site
Textual definitions - available for 75% of the DO’s 10,598 disease terms.
Each definition is written by a DO curator, following specific definition design principles.
Releases – one to two per month – ROBOT tool (http://robot.obolibrary.org) runs
automatically with each GitHub commit, running a series of consistency and rigor checks – Run through Travis CI. Our build process runs further QC tests and produces a suite of reports for quality control assessment.
Domain – all types of disease: common, Mendelian and complex and rare diseases – which we continue to curate and add to the DO
Schematic of DO’s World
- lets begin at the center, now look to the left, paying attention to inward pointing arrows.
Term Requests – Nicole
Nomenclature
Defining mechanisms
GO Biological Process. - can extract Wikidata data