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Lynn M. Schriml
University of Maryland, School of Medicine
Institute for Genome Sciences
lschriml@som.umaryland.edu
The Disease Ontology: an evolving tool for Disease
Curation and Annotation
Warren A. Kibbe
NU 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
Sequenced
Genomes & 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 Foundry
2006
Cell Line Ontology
Susan Tweedie, Nick Brown
Epilepsy Syndromes
Johanna Albers, Ingo
Helbig
IEDB: Disease Finder
2014
2013 PubChemDO Community Development
OMIM
PRO
Reactome
Building DO
The Disease Ontology provides a
unifying structure to map
human disease knowledge
between datasets
patient records
genome sequencing
microbiome samples
drug targets
expression studies
model organism disease models
human genes
KEGG pathways
37, 988 xref mappings
IDs Mapped to DOIDs
ICD9-CM 3,588 3,029
EFO 145
KEGG 42
MeSH 3,305 3,149
NCI Thesaurus 5,307 4,881
OMIM 1,693 1,184
SNOMED_CT 14,227 5,124
UMLS 7,767 7,767
8,720 terms
Subsets:
Tick-borne infectious disease
Gram-negative bacterial infectious disease
Zoonotic infectious disease
Sexually transmitted infectious disease
Gram-positive infectious disease
Term definitions: 29 %
Cross link disease terminologies
and 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
HPO
Human 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 genes
using nearly 100 distinct disease ontology terms based on phenotypes described in
around 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 Diseases
Cardiovascular Diseases
Sleep disorders
Diseases of the Inner Ear
Cancer
Syndromes
pulmonary hypertension
DO to OMIM mappings
DO to SNOMED mappings
sequence variants and genetic disorders
Multiple Sclerosis disease subtypes
DO-EFO mappings
DO-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

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Human Disease Ontology Project presented at ISB's Biocurator meeting April 2014

  • 1. Lynn M. Schriml University of Maryland, School of Medicine Institute for Genome Sciences lschriml@som.umaryland.edu The Disease Ontology: an evolving tool for Disease Curation and Annotation Warren A. Kibbe NU Clinical and Translational Sciences Institute (NUCATS), Northwestern University
  • 2. http://www.hormones.gr/17/article/article.html disequilibrium and disharmony = disease Hippocrates - the humoral theory for human physiology
  • 3. Human Genome Project FISH 2001 Model Organisms Microbial Genomics – Tree of Life 1995 – first bacteria sequenced H. influenzae Metagenome Sequencing Human Microbiome Genomes
  • 4. 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 Sequenced Genomes & Metagenomes
  • 5. Challenge: curation of disease related data among biomedical databases
  • 6. 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
  • 8. 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 Foundry 2006 Cell Line Ontology Susan Tweedie, Nick Brown Epilepsy Syndromes Johanna Albers, Ingo Helbig IEDB: Disease Finder 2014 2013 PubChemDO Community Development OMIM PRO Reactome Building DO
  • 9. The Disease Ontology provides a unifying structure to map human disease knowledge between datasets patient records genome sequencing microbiome samples drug targets expression studies model organism disease models human genes KEGG pathways
  • 10. 37, 988 xref mappings IDs Mapped to DOIDs ICD9-CM 3,588 3,029 EFO 145 KEGG 42 MeSH 3,305 3,149 NCI Thesaurus 5,307 4,881 OMIM 1,693 1,184 SNOMED_CT 14,227 5,124 UMLS 7,767 7,767 8,720 terms Subsets: Tick-borne infectious disease Gram-negative bacterial infectious disease Zoonotic infectious disease Sexually transmitted infectious disease Gram-positive infectious disease Term definitions: 29 % Cross link disease terminologies and concepts
  • 11. 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
  • 12. HPO Human 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
  • 15. Community Relationships and Collaborative Development FlyBase disease model annotation disease annotations to over 1000 different alleles from around 500 different genes using nearly 100 distinct disease ontology terms based on phenotypes described in around 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
  • 16. Ongoing Collaborative Development of Diseases Terms Mental Health Diseases Cardiovascular Diseases Sleep disorders Diseases of the Inner Ear Cancer Syndromes pulmonary hypertension DO to OMIM mappings DO to SNOMED mappings sequence variants and genetic disorders Multiple Sclerosis disease subtypes DO-EFO mappings DO-GWAS catalog disease mappings
  • 17. • 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

Editor's Notes

  1. Genome perspective: genome of organism, diversity of organisms, organisms connected to human healthSelect representative samples, organismsWho and What to Sequence ? what to study, how to sample and analyze the specimen, and the sample descriptive data how the analysis of the microbiome will be impacted if the sample recovery is biased
  2. NIF: Neuroscience Information NetworkNugene: collects and stores genetic (DNA) samples along with EHRs. DO data contributors: [additional] Saul Lozano (Dengue),IDO: Influenza Ontology,Richard Scheuermann: Viral BRC,Gemina: Lynn Schriml
  3. human disease – classified by disease etiology 8,000 + diseases
  4. DO provides a unifying disease terminology DO: a tool for semantic querying and data retrieval
  5. WormBase: Ranjana Kishore @ CaltechPubChem: Evan Bolton & Gang Fu @ NCBIGeneWiki: Andrew Su and Ben Good @ ScrippsNeuroDevNet: Elodie Portales-CasamarEMBL-EBI, EFO/ArrayExpress: Helen Parkinson & James MaloneFlyBase: Susan TweediePomBase: Antonia LockGeorge Washington University, Hive: Raja MazumderPrinceton University: Lewis-Sigler Institute for Integrative Genomics, GO Tools:MichaelLivstoneSifem, Inner ear disease: Marrgie JonesOMIM: Francois Schiettecatte, Joanna Amberger : OMIM APIReactome: BijayJassalCognitive Atlas Project: Russell Poldrack, Univ Texas