Lynn M. SchrimlUniversity of Maryland, School of Medicine
Institute for Genome [email protected]
The Disease Ontology: an evolving tool for Disease Curation and Annotation
Warren A. KibbeNU Clinical and Translational Sciences Institute (NUCATS),
Northwestern University
http://www.hormones.gr/17/article/article.html
disequilibrium and disharmony = disease
Hippocrates - the humoral theory for human physiology
Human Genome Project
FISH 2001
Model Organisms
Microbial Genomics – Tree of Life
1995 – first bacteria sequenced H. influenzae
Metagenome Sequencing
Human Microbiome
Genomes
10,000 monogenic human disease
3,076,748
http://www.ncbi.nlm.nih.gov/pubmed/?term=disease
3,043,175
http://www.ncbi.nlm.nih.gov/nuccore/?term=disease
6,800 rare diseases
SequencedGenomes & Metagenomes
Challenge: curation of disease related data among biomedical databases
genetic disease
disease of mental health
disease of infectious agent
disease of cellular proliferation cancer benign neoplasm
disease of anatomical entity
NCI
DSM- IV
[C04] neoplasms
[F03] mental disorders
[C01] bacterial infections and mycoses[C02] virus diseases[C03] parasitic diseases
[C19] endocrine system diseases[C20] immune system diseases
disease of metabolism inherited metabolic disorder
MeSH[C] Diseases OMIM
phenotypes
phenotypes
ICD9
neoplasms
mental disorders
infectious and parasitic
diseases
disease of … system
congenital anomalies
Challenge: Cross-mapping disease concepts,disparate representation of disease across vocabularies
Orphanet: Rare Diseases
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245088/
DO v3: reorganization by UMLS disease concepts mappings to SNOMED CT and ICD-9
DO http://www.disease-ontology.org 2011
2004
Rex Chisholm & Kibbe (Northwestern): founded DO
DO v1: ICD-9 as foundational vocabulary
DO v2: DO reorganized by process, system affected, and cause (genetic disorders, infectious diseases, metabolic disorders) MeSH added
2008
DO R01 (ARRA, NIH/NCRR, R01RR025342) DO Advisory Board (Michael Ashburner, Suzi Lewis, Barry Smith, Alan Ruttenberg, Chris Mungall, Judy Blake, Rex Chisholm)
DO submitted to OBO Foundry2006
Cell Line Ontology
Susan Tweedie, Nick Brown
Epilepsy SyndromesJohanna Albers, Ingo Helbig
IEDB: Disease Finder
2014
2013 PubChemDO Community DevelopmentOMIM
PROReactome
Building DO
The Disease Ontology provides a unifying structure to map human disease knowledge
between datasets
patient recordsgenome sequencing
microbiome samples drug targets
expression studiesmodel organism disease models
human genesKEGG pathways
37, 988 xref mappings IDs
Mapped to DOIDs ICD9-CM 3,588
3,029 EFO 145KEGG 42MeSH 3,305
3,149NCI Thesaurus 5,307
4,881OMIM 1,693
1,184SNOMED_CT 14,227 5,124 UMLS 7,767 7,767
8,720 termsSubsets: Tick-borne infectious diseaseGram-negative bacterial infectious diseaseZoonotic infectious diseaseSexually transmitted infectious diseaseGram-positive infectious disease
Term definitions: 29 %
Cross link disease terminologiesand concepts
Domain Ontology Application Ontologies
IDO: Influenza Ontology
ADO: Alzheimer’s disease ontology
Pathogenic disease ontology version 0.1
ProteomeXchange
Sample annotation:- Cell type. Use the “Cell Type” ontology (CL);- Disease. Use the “Human Disease” ontology (DOID).
Metadata Standard and Data Exchange Specifications to Describe, Model, and Integrate Complex and Diverse High-Throughput Screening Data from the Library of Integrated Network-based Cellular Signatures (LINCS)
GSC MIxS metadata standard: diseases status, for humans the terms should be chosen from DO (Disease Ontology)
- a concept mapping tool- a data annotation tool
HPOHuman Phenotype
Ontology
Gene Wiki
DO Community
Samples, Phenotypes, Ontology Team
Sifem Inner Ear disease
Improving the quality and content of DO
Serving Our Community• Term requests & review• Integrating rare diseases• Coordinating development with clinicians
Providing support for disease curation & annotation
http://testpubchem.ncbi.nlm.nih.gov/classification/#hid=1
View PubMed annotated records
Community Relationships and Collaborative Development
FlyBase disease model annotation disease annotations to over 1000 different alleles from around 500 different genesusing nearly 100 distinct disease ontology terms based on phenotypes described inaround 300 papers. http://flybase.org
WormBase: Human disease model data Curated and orthology-based human disease related data for genes Currently, over 250 genes have been manually curated, for their relevance to human disease and several hundred genes are flagged as potential models, based on orthology to human disease genes.http://www.wormbase.org
OMIM: DOs 947 OMIM xref annotations utilized for OMIM API
Reactome: To identify disease-associated entities and events, a new‘disease’ attribute is added, taking its value terms from a disease ontology.
Protein Ontology (PRO): Disease references are curated DO mappings.http://pir.georgetown.edu/pro/pro.shtml
Ongoing Collaborative Development of Diseases Terms
Mental Health DiseasesCardiovascular DiseasesSleep disordersDiseases of the Inner EarCancerSyndromespulmonary hypertensionDO to OMIM mappingsDO to SNOMED mappingssequence variants and genetic disordersMultiple Sclerosis disease subtypesDO-EFO mappingsDO-GWAS catalog disease mappings
• Follow DO on twitter
• Send us your disease terms DO Term Tracker - Submit new terms, definitions or suggestions for the Disease Ontology to the DO Term Tracker.
http://sourceforge.net/p/diseaseontology/feature-requests/
• Download DO:http://sourceforge.net/p/diseaseontology/code/HEAD/tree/trunk/HumanDO.obo