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Infectious Disease: A New Challenge for Biomedical Informatics

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.

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Infectious Disease: A New Challenge for Biomedical Informatics

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  1. Infectious Disease: A New Challenge for Biomedical Informatics September 21, 2007 Cold Spring Harbor Laboratory Supported by: The Burroughs Wellcome Fund

  2. Workshop on Infectious Disease Ontology September 19 – 20, 2007 Cold Spring Harbor Laboratory Supported by the Burroughs Wellcome Fund

  3. 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

  4. 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

  5. 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

  6. Preliminary Development Work • Generated term list • Discussed definitions • Developed hierarchy • Asserted part_of relations

  7. 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

  8. Test IDO by developing disease-specific 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

  9. Getting Involved • Wiki • http://www.bioontology.org/wiki/index.php/Infectious_Disease_Ontology • Email list • ido@duke.edu • https://lists.duke.edu/sympa/ • Infectious Disease Ontology Consortium

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