Lynn M. Schriml University of Maryland, School of Medicine Institute for Genome Sciences [email protected]The Disease Ontology: an evolving tool for Disease Curation and Annotation Warren A. Kibbe NU Clinical and Translational Sciences Institute (NUCATS), Northwestern University
17
Embed
Human Disease Ontology Project presented at ISB's Biocurator meeting April 2014
The Human Disease Ontology (DO), organized as a directed acyclic graph, represents a knowledge base of inherited, environmental, infectious diseases (http://www.disease-ontology.org). 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.
This document is posted to help you gain knowledge. Please leave a comment to let me know what you think about it! Share it to your friends and learn new things together.
Transcript
Lynn M. SchrimlUniversity of Maryland, School of Medicine
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)
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
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.