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


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The Human Disease Ontology (DO), organized as a directed acyclic graph, represents a knowledge base of inherited, environmental, infectious diseases ( DO's textual definition model incorporates a semi-structured format describing the disease etiology built to capture the complex nature of human disease etiology within a is_a hierarchy. DO includes disease concepts for cancer, metabolic disease, infectious disease, mental disorders, genetic disease and syndromes. DO contains disease definitions, external references to resources including ICD, NCI-metathesaurus, SNOMED, MeSH and OMIM and extended relationships that conform to OBO guidelines. DO provides a central ‘switchboard’ for connecting resources, datasets, and computational tools that include disease terms or relationships.

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  • 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
  • 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
  • human disease – classified by disease etiology 8,000 + diseases
  • DO provides a unifying disease terminology DO: a tool for semantic querying and data retrieval
  • 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
  • Human Disease Ontology Project presented at ISB's Biocurator meeting April 2014

    1. 1. Lynn M. Schriml University of Maryland, School of Medicine Institute for Genome Sciences The Disease Ontology: an evolving tool for Disease Curation and Annotation Warren A. Kibbe NU Clinical and Translational Sciences Institute (NUCATS), Northwestern University
    2. 2. disequilibrium and disharmony = disease Hippocrates - the humoral theory for human physiology
    3. 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. 4. 10,000 monogenic human disease 3,076,748 3,043,175 6,800 rare diseases Sequenced Genomes & Metagenomes
    5. 5. Challenge: curation of disease related data among biomedical databases
    6. 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
    7. 7.
    8. 8. DO v3: reorganization by UMLS disease concepts mappings to SNOMED CT and ICD-9 DO 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. 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. 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. 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. 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
    13. 13.
    14. 14. View PubMed annotated records
    15. 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. 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. 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.
    16. 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. 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. • Download DO: