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Creating a Vocabulary from Consensus Syndrome Definitions

Creating a Vocabulary from Consensus Syndrome Definitions. Chapman WW, Dowling JN, Baer A, Buckeridge D, Cochrane D, Elkin P, Espino J, Gunn J, Hales C, Hutwagner L, Keller M, Larson C, Lober B, Noe R, Okhmatovskaia A, Olson K, Paladini M, Scholer M, Sniegoski C, Thompson D. Objective.

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Creating a Vocabulary from Consensus Syndrome Definitions

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  1. Creating a Vocabulary from Consensus Syndrome Definitions Chapman WW, Dowling JN, Baer A, Buckeridge D, Cochrane D, Elkin P, Espino J, Gunn J, Hales C, Hutwagner L, Keller M, Larson C, Lober B, Noe R, Okhmatovskaia A, Olson K, Paladini M, Scholer M, Sniegoski C, Thompson D

  2. Objective Develop an ontology for defining and describing clinical conditions appearing in triage chief complaints • based on current practice • has input from a broad base of developers and users of syndromic surveillance systems • can be easily implemented in an automated surveillance system

  3. Scope of Ontology To assist public health in monitoring, characterizing, detecting, and responding to changes in population health based on patients’ initial clinical presentation of acute outbreaks and exposures

  4. Overview • Initial meeting to form consensus definitions • Subsequent work on refining definitions • Description of ontology

  5. 1. ISDS-funded MeetingDevelop consensus syndrome categories and definitions, using the catalogue of existing definitions as a starting point

  6. Characterize Currently Used Syndromic Definitions 10 syndromic surveillance systems • RODS • BioPortal (Univ of Arizona) • Seattle, King County • Biosense • NCDetect • Aegis (Harvard) • Essence • New York State • Boston Public Health Dept • New York City

  7. David Buckeridge Craig Hales Carol Sniegoski Karen Olson Jeremy Espino Cathy Larson Mikaela Keller Lori Hutwagner David Thompson Dennis Cochrane Marc Paladini Julia Gunn Atar Baer Bill Lober Matt Scholer John Dowling Rebecca Noe Peter Elkin Wendy Chapman Participants

  8. Initial Consensus Syndromes

  9. 48 conditions 26 16 Sensitive Specific Respiratory Syndrome Clinical Condition Sens Spec BREATHING DIFFICULTY 1 1 COUGH 1 1 HEMOPTYSIS 1 1 ASTHMA ATTACK 1 1 CROUP 1 1 PNEUMONIA 1 1 WHEEZING 1 1 RUNNY OR STUFFY NOSE 1 0 PLEURITIC PAIN 1 0 SORE THROAT 1 0 URI 1 0 …

  10. 25 conditions 6 3 Sensitive Specific GI Syndrome Clinical Condition Sens Spec ABDOMINAL PAIN 1 0 DIARRHEA 1 1 VOMITING 1 1 NAUSEA 1 0 GASTROENTERITIS 1 1 DEHYDRATION 1 0

  11. 32 conditions 12 Constitutional Syndrome IRRITABLE BABY FEVER WEAKNESS ANOREXIA VIRAL SYNDROME FAINTNESS MALAISE BODY ACHES GENERAL ILLNESS CHILLS LYMPHADENOPATHY SWEATING

  12. 17 conditions 12 Influenza-like Illness Syndrome COUGH SORE THROAT FEVER WEAKNESS VIRAL SYNDROME BODY ACHES BRONCHIOLITIS PNEUMONIA UPPER RESPIRATORY INFECTION MALAISE CHILLS INFLUENZA

  13. 2. Refining the DefinitionsMonthly phone calls

  14. GI Syndrome ABDOMINAL PAIN DIARRHEA VOMITING NAUSEA GASTROENTERITIS DEHYDRATION

  15. The Example of Vomiting What do we mean when we say vomiting? hematemesis vomiting spitting up puke Bloody vomit wretching n/v/d retching peuk Throwing up Blody vomit bringing up

  16. Our Solution Vomiting Self Synonym Related Concept Vomiting Spitting up Hematemesis Throw up Vomit Vommit n/v/d … bringing up spitting up Hematemesis Coffee ground emesis Throw up blood

  17. The definitions are not meant to be the best definitions Provide a starting point

  18. What do you mean by vomiting? Vomiting Self Synonym Related Concept Vomiting Spitting up Hematemesis Throw up Vomit Vommit n/v/d … bringing up spitting up Hematemesis Coffee ground emesis Throw up blood Explicit representation mapped to vocabularies

  19. What do you mean by GI Syndrome? Specific GI … Vomiting Diarrhea Vomiting Spitting up Hematemesis Diarrhea A starting point for conversation and collaboration

  20. Does a chief complaint of nausea really predict GI syndrome of interest to public health? • North Carolina: 11% PPV • Utah: 4% PPV • New York: 28% PPV A starting point for validation

  21. I don’t want to include nausea in my surveillance definition of GI Specific GI Nausea Vomiting Diarrhea Nausea Spitting up Hematemesis Diarrhea Sick to stomach Nausea n/v Flexible and easy to modify

  22. 3. Creating an OWL OntologyDavid BuckeridgeAnya OkhmatovskaiaMichael ConwayJeremy EspinoNigel Collier

  23. Syndrome Syndrome hasSensitiveDefinition: 1 or more hasSpecificDefinition: 1 or more hasSensitiveDefinition: 1 or more hasSpecificDefinition: 1 or more Clinical Condition Clinical Condition hasExternalCoding: 0 or more hasExternalCoding: 0 or more Coding Coding hasExactConcept: exactly 1 hasRelatedConcepts: 0 or more hasSynonymousConcepts: 0 or more hasExactConcept: exactly 1 hasRelatedConcepts: 0 or more hasSynonymousConcepts: 0 or more mapsToCoding: exactly 1 mapsToCoding: exactly 1 Clinical Concept Clinical Concept hasInclusionKeywords: 1 or more hasExclusionKeywords:0 or more hasInclusionKeywords: 1 or more hasExclusionKeywords:0 or more Regular Expression Regular Expression Keyword Keyword matchesKeywords: 1 or more matchesKeywords: 1 or more OWL ontology See poster Syndrome Syndrome hasSensitiveDefinition: 1 or more hasSpecificDefinition: 1 or more hasSensitiveDefinition: 1 or more hasSpecificDefinition: 1 or more Clinical Condition hasExternalCoding: 0 or more Clinical Condition Coding hasExternalCoding: 0 or more Coding hasExactConcept: exactly 1 hasRelatedConcepts: 0 or more hasSynonymousConcepts: 0 or more hasExactConcept: exactly 1 hasRelatedConcepts: 0 or more hasSynonymousConcepts: 0 or more mapsToCoding: exactly 1 mapsToCoding: exactly 1 Clinical Concept Clinical Concept hasInclusionKeywords: 1 or more hasExclusionKeywords:0 or more hasInclusionKeywords: 1 or more hasExclusionKeywords:0 or more Regular Expression Regular Expression Keyword Keyword matchesKeywords: 1 or more matchesKeywords: 1 or more

  24. Functional Uses of Ontology • Generate a document with description of the syndrome definitions • http://surveillance.mcgill.ca/projects/sso/SyndromeDef.html

  25. Functional Uses of Ontology • Perform chief complaint classification

  26. Limitations • Only addresses concepts that are seen in chief complaints • Not validated in any way

  27. Future Community Directions for Chief Complaint Ontology • Perform validation experiments and modify the ontology • Deploy chief complaint classification quickly and easily • Share data across jurisdictions using explicit definitions • Annotate set of chief complaints for chief complaint classifier comparison • Expand to other syndromes

  28. Future Directions • Expand ontology beyond chief complaints • Chest radiography reports • Emergency department • Develop natural language processing applications that use the ontology • More sensitive and specific case detection What other ideas do you have?

  29. Thank you • Ontology available at • www.dbmi.pitt.edu/blulab/resources/syndrome-definitions.xls • http://bioportal.bioontology.org/ontologies/40646 • Will post pointers on ISDS website

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