Transcript Workshop on Infectious Disease Ontology

Infectious Disease: A New
Challenge for Biomedical
Informatics
September 21, 2007
Cold Spring Harbor Laboratory
Supported by: The Burroughs
Wellcome Fund
Workshop on Infectious
Disease Ontology
September 19 – 20, 2007
Cold Spring Harbor Laboratory
Supported by the Burroughs Wellcome
Fund
Purpose of Infectious Disease
Ontology (IDO)
• Integration of infectious disease relevant
data and information
– Sequence and protein data for various
pathogens
– Case report data for patients
– Clinical trial data
– Epidemiological Data
• Basic biomedical, clinical care, and public
health data
Scope of IDO
• What content is needed to adequately cover the
infectious domain?
– Host-related terms (e.g. carrier, susceptible)
– Pathogen-related terms (e.g. virulence)
– Terms for the biology of disease pathogenesis (e.g.
evasion of host defense)
– Population-level terms (e.g. epidemic)
• What should be in other ontologies?
– Gene Ontology Biological Process Ontology
– Clinical Trial Ontology
Currently Envisioned Structure of
IDO
• Reference ontology with terms relevant to
any infectious disease
• Built on OBO Foundry principles and
ontologies
• Disease-specific ontologies built as
extensions
Preliminary Development Work
•
•
•
•
Generated term list
Discussed definitions
Developed hierarchy
Asserted part_of relations
Future Work
• Identify missing terms
• Identify terms already in existing ontologies
• Create definitions
• UT Southwestern – pathogen terms
– Richard Scheuerman
• University of Michigan – vaccine terms
– Yongqun He
Test IDO by developing diseasespecific ontologies
• U of Michigan - Brucella (Brucilosis)
– Yongqun He
• IMBB: Vector borne diseases (emphasis on malaria)
– Christos Louis
• Colorado State University: Denque fever
– Saul Lozano-Fuentes
• Duke: Tuberculosis
– Carol Dukes-Hamilton
• Cleveland Clinic – Infective Endocarditis
– Sivaram Arabandi
• MITRE, Mt Sinai – influenza
– Joann Luciano, Stuart Sealfon
Getting Involved
• Wiki
– http://www.bioontology.org/wiki/index.php/
Infectious_Disease_Ontology
• Email list
– [email protected]
– https://lists.duke.edu/sympa/
• Infectious Disease Ontology Consortium