Ontology Support for Influenza and Surveillance

324 views

Published on

This is a presentation about the construction of the influenza ontology to support Influenza research and surveillance as part of the Genomics for Bio-forensics MITRE sponsored research.

Published in: Technology
0 Comments
0 Likes
Statistics
Notes
  • Be the first to comment

  • Be the first to like this

No Downloads
Views
Total views
324
On SlideShare
0
From Embeds
0
Number of Embeds
2
Actions
Shares
0
Downloads
4
Comments
0
Likes
0
Embeds 0
No embeds

No notes for slide

Ontology Support for Influenza and Surveillance

  1. 1. © 2006 The MITRE Corporation. All rights reserved Ontology Support for Influenza Research and Surveillance Joanne Luciano, PhD, Lynette Hirschman, PhD, Marc Colosimo, PhD Approved for Public Release; Distribution Unlimited. 28 April 2008 Case Number 08-0738
  2. 2. © 2008 The MITRE Corporation. All rights reserved Approved for Public Release; Distribution Unlimited. 28 April 2008 Case Number 08-0738 2 Case Study 1: Indonesia ■  Possible Human to Human transmission of H5N1 (May 2006) ■  Samples were collected and epidemiological data obtained –  Know who got sick and their relationship to each other –  Know when they got sick and if they died –  Have some public sequence data from that time ■  It is not known if these sample are from these people! Public Sequence Data 30 Aug 2006 A/Indonesia/CDC595/2006 (2006-05-09) A/Indonesia/CDC594/2006 (2006-05-10) …. A/Indonesia/CDC625L/2006 (2006-05-22) A/Indonesia/CDC644/2006 (2006-05-30) WHO Nature Same person ? GenBank isolation_source="gender:M; age:32; Lung Aspirate" Metadata 23 May 2006 Metadata 12 Jul 2006 Butler “Family tragedy spotlights flu mutations “ Nature 442, 114 - 115 (12 Jul 2006) News
  3. 3. © 2008 The MITRE Corporation. All rights reserved Approved for Public Release; Distribution Unlimited. 28 April 2008 Case Number 08-0738 3 Case Study 2: UK ■  Outbreak of H5N1 in the UK at a turkey farm Feb 1, 2007 ■  What is the source of the outbreak? –  Contact with infected wild birds? ■  But turkeys were in an enclosed “biosecure” unit ■  No H5N1 detected in the region in the 2 previous months –  Govt. veterinarian suggested turkey meat from Hungary might be source of infection ■  Turkey farm is adjacent to a poultry packing plant that had processed poultry products from Hungary ■  Hungary had reported an H5N1 outbreak 2 weeks earlier ■  Sequence data showed that strain infecting the turkeys was 99.96% identical to strain that had infected Hungarian birds ■  Conclusion: Infected Hungarian poultry was source of H5N1 infection –  Open question (relevant to food defense): how did H5N1 spread from processing plant to live turkeys?
  4. 4. © 2008 The MITRE Corporation. All rights reserved Approved for Public Release; Distribution Unlimited. 28 April 2008 Case Number 08-0738 4 Research Agenda ■ Reference Database (Sequences & Metadata) –  What metadata to collect? –  Where to find data and how to connect different sources (bridging the gap)?
  5. 5. © 2008 The MITRE Corporation. All rights reserved Approved for Public Release; Distribution Unlimited. 28 April 2008 Case Number 08-0738 5 Genomic Sequence Data Systems Biology Demographic data Clinical data Research Question: Bridging the Gap - Connecting Genomics and Epidemiology Geospatial data Temporal data Pathogenicity Host Epidemiology: Occurrence of Disease in Host Genomics: Genes of Pathogen Influenza Ontology
  6. 6. © 2008 The MITRE Corporation. All rights reserved Approved for Public Release; Distribution Unlimited. 28 April 2008 Case Number 08-0738 6 ■ Identify the right collaborators ■ Collect metadata terms ■ Identify resources for that include these terms ■ Regularize metadata –  Generate a controlled vocabulary (terms) ■ Validate subset with BioHealthBase CEIRS data ■ Iterate, review with community, publish ■ Integrate Influenza ontology into workflow Influenza Ontology: Development
  7. 7. © 2008 The MITRE Corporation. All rights reserved Approved for Public Release; Distribution Unlimited. 28 April 2008 Case Number 08-0738 7 Influenza Ontology First Draft: Community ■  BioHealthBase: NIAID Influenza Database Point of Contact for –  Centers of Excellence for Influenza Research and Surveillance (CEIRS) ■  Research: Emory, Mt Sinai, St. Jude, Univ. of Rochester ■  Surveillance: St. Jude, UCLA, Univ. of Minnesota –  Los Alamos National Laboratory (LANL) ■  Gemina: Category A-C Pathogen Database Point of contact for –  Children’s Hospital Boston –  Johns Hopkins University ■  MITRE Collaboration with BioHealthBase and Gemina
  8. 8. © 2008 The MITRE Corporation. All rights reserved Approved for Public Release; Distribution Unlimited. 28 April 2008 Case Number 08-0738 8 Influenza Ontology First Draft: Identify metadata 200 controlled vocabulary terms covering several fields
  9. 9. © 2008 The MITRE Corporation. All rights reserved Approved for Public Release; Distribution Unlimited. 28 April 2008 Case Number 08-0738 9 Reuse of existing ontologies & metadata standards OBI – Ontology of Biomedical Investigations EnvO – Environmental Ontology (habitat of pathogen) GAZ – Gazeteer (geographic locations) FMA – Foundational Model of Anatomy DC – Dublin Core (publication metadata) PATO – Phenotype SO – Sequence Ontology (sequence features) Cell – Cell Ontology (types of cells) DO – Disease Ontology IDO – Infectious Disease Ontology Influenza Ontology First Draft: Metadata resources
  10. 10. © 2008 The MITRE Corporation. All rights reserved Approved for Public Release; Distribution Unlimited. 28 April 2008 Case Number 08-0738 10 Influenza Ontology First Draft Excel Spreadsheet Initial steps: • Collect metadata terms • Map and align terms • Group related information • Identify and define relationships • Identify external ontologies Formalize OBO-Edit: Ontology Editing Tool Formalize: • Normalize terms into a CV • Issue unique identifiers • Instantiate class hierarchy • Define properties and values • Link to external ontology terms Status: We have just started the formalization step.
  11. 11. © 2008 The MITRE Corporation. All rights reserved Approved for Public Release; Distribution Unlimited. 28 April 2008 Case Number 08-0738 11 Future Work Ontology development ■ Complete formalization process ■ Validate subset with data from BioHealthBase – Circulate for review and comments ■ Use ontology to annotate influenza data
  12. 12. © 2008 The MITRE Corporation. All rights reserved Approved for Public Release; Distribution Unlimited. 28 April 2008 Case Number 08-0738 12 Team ■  BioHealthBase (UT Southwestern Medical Center) –  Burke Squires –  Richard Scheuermann ■  Institute of Genome Sciences/Gemina (U. Maryland Baltimore) –  Lynn Schriml ■  MITRE –  Joanne Luciano –  Lynette Hirschman –  Marc Colosimo

×