creating a vocabulary from consensus syndrome definitions chapman ww, dowling jn, baer a, buckeridge...
TRANSCRIPT
![Page 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,](https://reader035.vdocuments.site/reader035/viewer/2022062517/56649f295503460f94c428ab/html5/thumbnails/1.jpg)
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
![Page 2: 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,](https://reader035.vdocuments.site/reader035/viewer/2022062517/56649f295503460f94c428ab/html5/thumbnails/2.jpg)
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
![Page 3: 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,](https://reader035.vdocuments.site/reader035/viewer/2022062517/56649f295503460f94c428ab/html5/thumbnails/3.jpg)
Scope of OntologyTo 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
![Page 4: 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,](https://reader035.vdocuments.site/reader035/viewer/2022062517/56649f295503460f94c428ab/html5/thumbnails/4.jpg)
Overview
1. Initial meeting to form consensus definitions
2. Subsequent work on refining definitions
3. Description of ontology
![Page 5: 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,](https://reader035.vdocuments.site/reader035/viewer/2022062517/56649f295503460f94c428ab/html5/thumbnails/5.jpg)
1. ISDS-funded MeetingDevelop consensus syndrome categories
and definitions, using the catalogue of existing definitions as a starting point
![Page 6: 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,](https://reader035.vdocuments.site/reader035/viewer/2022062517/56649f295503460f94c428ab/html5/thumbnails/6.jpg)
Characterize Currently Used Syndromic Definitions
10 syndromic surveillance systems
1. RODS2. BioPortal (Univ of Arizona)– Seattle, King County– Biosense– NCDetect– Aegis (Harvard)– Essence– New York State– Boston Public Health Dept– New York City
![Page 7: 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,](https://reader035.vdocuments.site/reader035/viewer/2022062517/56649f295503460f94c428ab/html5/thumbnails/7.jpg)
Participants
• 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
![Page 8: 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,](https://reader035.vdocuments.site/reader035/viewer/2022062517/56649f295503460f94c428ab/html5/thumbnails/8.jpg)
Initial Consensus Syndromes
![Page 9: 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,](https://reader035.vdocuments.site/reader035/viewer/2022062517/56649f295503460f94c428ab/html5/thumbnails/9.jpg)
Respiratory Syndrome
48 conditions
2616
Sensitive Specific
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
…
Clinical Condition Sens Spec
![Page 10: 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,](https://reader035.vdocuments.site/reader035/viewer/2022062517/56649f295503460f94c428ab/html5/thumbnails/10.jpg)
25 conditions
6 3
Sensitive Specific
Clinical Condition Sens Spec
ABDOMINAL PAIN 1 0
DIARRHEA 1 1
VOMITING 1 1
NAUSEA 1 0
GASTROENTERITIS 1 1
DEHYDRATION 1 0
GI Syndrome
![Page 11: 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,](https://reader035.vdocuments.site/reader035/viewer/2022062517/56649f295503460f94c428ab/html5/thumbnails/11.jpg)
32 conditions
12
Constitutional Syndrome
IRRITABLE BABY
FEVER
WEAKNESS
ANOREXIA
VIRAL SYNDROME
FAINTNESS
MALAISE
BODY ACHES
GENERAL ILLNESS
CHILLS
LYMPHADENOPATHY
SWEATING
![Page 12: 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,](https://reader035.vdocuments.site/reader035/viewer/2022062517/56649f295503460f94c428ab/html5/thumbnails/12.jpg)
Influenza-like Illness Syndrome
17 conditions
12
COUGH
SORE THROAT
FEVER
WEAKNESS
VIRAL SYNDROME
BODY ACHES
BRONCHIOLITIS
PNEUMONIA
UPPER RESPIRATORY INFECTION
MALAISE
CHILLS
INFLUENZA
![Page 13: 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,](https://reader035.vdocuments.site/reader035/viewer/2022062517/56649f295503460f94c428ab/html5/thumbnails/13.jpg)
2. Refining the Definitions
Monthly phone calls
![Page 14: 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,](https://reader035.vdocuments.site/reader035/viewer/2022062517/56649f295503460f94c428ab/html5/thumbnails/14.jpg)
ABDOMINAL PAIN
DIARRHEA
VOMITING
NAUSEA
GASTROENTERITIS
DEHYDRATION
GI Syndrome
![Page 15: 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,](https://reader035.vdocuments.site/reader035/viewer/2022062517/56649f295503460f94c428ab/html5/thumbnails/15.jpg)
The Example of Vomiting
What do we mean when we say vomiting?
vom
iting
vom
iting
spitting up
spitting uphematemesis
hematemesisw
retc
hing
wre
tchi
ng
n/v/dn/v/dThrowing
up
Throwing up
Bloody vomit
Bloody vomit
pukepuke
retchingretchingBlody vomitBlody vomit
peukpeuk bringing up
bringing up
![Page 16: 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,](https://reader035.vdocuments.site/reader035/viewer/2022062517/56649f295503460f94c428ab/html5/thumbnails/16.jpg)
Our Solution
Vomiting
Vomiting Spitting up Hematemesis
Throw upVomitVommitn/v/d…
bringing upspitting up
HematemesisCoffee ground emesisThrow up blood
Self Synonym Related Concept
![Page 17: 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,](https://reader035.vdocuments.site/reader035/viewer/2022062517/56649f295503460f94c428ab/html5/thumbnails/17.jpg)
The definitions are not meant to be the best definitions
Provide a starting point
![Page 18: 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,](https://reader035.vdocuments.site/reader035/viewer/2022062517/56649f295503460f94c428ab/html5/thumbnails/18.jpg)
What do you mean by vomiting?
Vomiting
Vomiting Spitting up Hematemesis
Throw upVomitVommitn/v/d…
bringing upspitting up
HematemesisCoffee ground emesisThrow up blood
Self Synonym Related Concept
Explicit representation mapped to vocabulariesExplicit representation mapped to vocabularies
![Page 19: 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,](https://reader035.vdocuments.site/reader035/viewer/2022062517/56649f295503460f94c428ab/html5/thumbnails/19.jpg)
What do you mean by GI Syndrome?
Vomiting
Vomiting Spitting up Hematemesis
Specific GI
Diarrhea
Diarrhea
…
A starting point for conversation and collaborationA starting point for conversation and collaboration
![Page 20: 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,](https://reader035.vdocuments.site/reader035/viewer/2022062517/56649f295503460f94c428ab/html5/thumbnails/20.jpg)
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 validationA starting point for validation
![Page 21: 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,](https://reader035.vdocuments.site/reader035/viewer/2022062517/56649f295503460f94c428ab/html5/thumbnails/21.jpg)
I don’t want to include nausea in my surveillance definition of GI
Vomiting
Spitting up Hematemesis
Specific GI
Diarrhea
Diarrhea
Nausea
Nausea
Sick to stomachNausean/v
Flexible and easy to modifyFlexible and easy to modify
![Page 22: 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,](https://reader035.vdocuments.site/reader035/viewer/2022062517/56649f295503460f94c428ab/html5/thumbnails/22.jpg)
3. Creating an OWL Ontology
David BuckeridgeAnya Okhmatovskaia
Michael ConwayJeremy Espino
Nigel Collier
![Page 23: 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,](https://reader035.vdocuments.site/reader035/viewer/2022062517/56649f295503460f94c428ab/html5/thumbnails/23.jpg)
OWL ontology
See posterSee poster
![Page 24: 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,](https://reader035.vdocuments.site/reader035/viewer/2022062517/56649f295503460f94c428ab/html5/thumbnails/24.jpg)
Functional Uses of Ontology
• Generate a document with description of the syndrome definitions
• http://surveillance.mcgill.ca/projects/sso/SyndromeDef.html
![Page 25: 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,](https://reader035.vdocuments.site/reader035/viewer/2022062517/56649f295503460f94c428ab/html5/thumbnails/25.jpg)
![Page 26: 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,](https://reader035.vdocuments.site/reader035/viewer/2022062517/56649f295503460f94c428ab/html5/thumbnails/26.jpg)
Functional Uses of Ontology
• Perform chief complaint classification
![Page 27: 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,](https://reader035.vdocuments.site/reader035/viewer/2022062517/56649f295503460f94c428ab/html5/thumbnails/27.jpg)
![Page 28: 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,](https://reader035.vdocuments.site/reader035/viewer/2022062517/56649f295503460f94c428ab/html5/thumbnails/28.jpg)
![Page 29: 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,](https://reader035.vdocuments.site/reader035/viewer/2022062517/56649f295503460f94c428ab/html5/thumbnails/29.jpg)
Limitations
• Only addresses concepts that are seen in chief complaints
• Not validated in any way
![Page 30: 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,](https://reader035.vdocuments.site/reader035/viewer/2022062517/56649f295503460f94c428ab/html5/thumbnails/30.jpg)
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
![Page 31: 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,](https://reader035.vdocuments.site/reader035/viewer/2022062517/56649f295503460f94c428ab/html5/thumbnails/31.jpg)
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?
![Page 32: 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,](https://reader035.vdocuments.site/reader035/viewer/2022062517/56649f295503460f94c428ab/html5/thumbnails/32.jpg)
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