Automated Case Definition
Craig Cunningham
OntoReason LLC
Vocabulary Services
Division of Informatics Shared Services
National Center for Public Health Informatics
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Agenda
• Background
• Informatics Foundation
• Case Identification for Reporting
• Case Definition
• Model for Automated Reasoning
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Background
Project Objective: to prove the foundation technologies, public health
knowledge bases, and public health ontology in this proof of concept
capability.
Technical Foundation
• Automated Reasoners for case identification and case classification
• Based upon CSTE Position Statements
• Support to a variety public health mission requirements.
• Including surveillance report content validation, BioSense message classification,
and individual program alerting functions such as drug resistant TB.
• Standard public health informatics model
• Providing standardized domain knowledge representation
• Need for machine processable case reporting and case status classification
definitions
• Reasoning model for automated reasoning
Goal: To demonstrate possible implementation strategies, the presentation will
cover how this technology could be implemented, maintained, and can be
tailored to a variety of programs, target deployment environments, and
maintenance schemes.
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Informatics Foundation
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Public Health Reference Model
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Case Identification for Reporting
•
VI. Criteria for Reporting
•
A. Narrative description of criteria to be used by humans to determine whether a case should
be reported to public health authorities:
• Report any illness to public health authorities that meets any of the following
criteria:
• 1. A person with illness of acute onset AND any of the epidemiologic linkages
listed in table 2.
• 2. A person for whom a diagnostic test specific for anthrax has been ordered (see
table 2).
• 3. A person whose death certificate lists anthrax as a cause of death or a significant
condition contributing to death. [Should this also be listed in table 2?]
•
•
•
•
Other recommended surveillance procedures
ｷ
All cases of anthrax should be reported.
ｷ
Reporting should be on-going and routine.
ｷ
Reporting should be immediate.
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Case Definition
•
VII. Case Definition
•
A. Narrative description of criteria to determine whether a case should be classified as confirmed,
probable (presumptive), or suspected (possible) is provided in table 3:
•
Table 3. Case definition of anthrax (revised 9/96)
•
Clinical description
•
An illness with acute onset characterized by several distinct clinical forms, including the
following:
• Cutaneous: a skin lesion evolving during a period of 2-6 days from a papule,
through a vesicular stage, to a depressed black eschar
• Inhalation: a brief prodrome resembling a viral respiratory illness, followed by
development of hypoxia and dyspnea, with radiographic evidence of mediastinal
widening
• Intestinal: severe abdominal distress followed by fever and signs of septicemia
• Oropharyngeal: mucosal lesion in the oral cavity or oropharynx, cervical
adenopathy and edema, and fever
•
Laboratory criteria for diagnosis
• Isolation of Bacillus anthracis from a clinical specimen, or
• Anthrax electrophoretic immunotransblot (EITB) reaction to the protective antigen
and/or lethal factor bands in one or more serum samples obtained after onset of
symptoms, or
• Demonstration of B. anthracis in a clinical specimen by immunofluorescence
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Table 2 Definitions
(Anthrax Example)
S = This criterion alone is sufficient to report or confirm a case
N = This criterion in conjunction with all other “N” and any “O” criteria in the
same column is required to report or confirm a case. A number following an “N”
indicates that this criterion is only required for a specific clinical presentation
(see below)
O = At least one of these “O” criteria in each category (e.g., clinical presentation
and laboratory findings)—in conjunction with all other “N” criteria in the same
column—is required to report or confirm a case. A number following an “O”
indicates that t
1 = Cutaneous anthrax
2 = Inhalation anthrax
3 = Intestinal anthrax
4 = Oropharyngeal anthrax
* A requisition for any of the “S” or “N” laboratory tests is sufficient to meet the
reporting criteria
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Table 2 Case Classification
Criterion
Reporting
C
N
N
P
S
Cl i ni ca l Presenta ti on
illness with acute onset
skin lesion evolving during a period of 2-6 days from a papule, through a
vesicular stage, to a painless depressed black eschar
brief prodrome resembling a viral respiratory illness
N1
hypoxia
N2
dyspnea
N2
radiographic evidence of mediastinal widening
N2
fever (any)
N2
N3,N4
severe abdominal distress
N3
signs of septicemia
N3
mucosal lesion in the oral cavity
O4
mucosal lesion in the oropharynx
O4
cervical adenopathy
N4
cervical edema
N4
Laboratory findings
[Note that these f indings are not consistent w ith approved tests
or the algorithm f or laboratory diagnosis of anthrax on the CDC BT Website
(http://w w w .bt.cdc.gov/agent/anthrax.]
isolation of Bacillus anthracis from a clinical specimen
S*
O
anthrax electrophoretic immunotransblot (eitb) reaction to the protective
antigen and/or lethal factor bands in one or more serum samples
obtained after onset of symptoms
demonstration of B. anthracis in a clinical specimen by
immunofluorescence
Epidemiological linkages
S*
O
S*
O
exposure to the same environment or objects as persons who have
laboratory-confirmed anthrax
consumption of the same food as persons who have laboratoryconfirmed anthrax
O
O
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Table 3 Informatics Definition
Clinical Findings
Clinical Presentation
Criterion
severe abdominal distress
Text Basis for Coding
AHIC Code
Code System
Name
severe abdominal pain
Code System OID
[21522001|abdominal pain{246112005|severity= SNOMED CT
24484000|severe}]
cervical edema
edema of the neck
[267038008|edema{363698007|finding
SNOMED CT
site=302550007|neck}]
radiographic evidence of mediastinal
radiographic evidence of
[363646005|mediastinal
SNOMED CT
w idening
mediastinal w idening
w idening{418775008|finding
method=302550007|radiographic procedure of
illness w ith acute onset
illness w ith acute onset
[39104002|illness{263502005|clinical
SNOMED CT
course=373933003|acute onset}]
skin lesion evolving during a period of 2-6 painless depressed black eschar [409590008|skin eschar{(116676008|Associated SNOMED CT
days from a papule, through a vesicular
morphology=5960008|Depressed
stage, to a painless depressed black
structure)(103366001|w ith
eschar
color=371252007|black color)(246253006|type of
sensation=255350008|painless)}]
brief prodrome resembling a viral
brief prodrome
[83931009|prodrome{263502005|clinical
SNOMED CT
respiratory illness
course=359535008|brief}
mucosal lesion in the oral cavity
mucosal ulcer in the oral cavity [95356008|mucosal ulcer{363698007|finding
SNOMED CT
site=181220002|oral cavity}]
mucosal lesion in the oropharynx
mucosal ulcer in the oropharynx [95356008|mucosal ulcer{363698007|finding
SNOMED CT
site=31389004|oropharynx}]
signs of septicemia
septicemia
105592009 SNOMED CT
2.16.840.1.113883.6.96
dyspnea
dyspnea
267036007 SNOMED CT
2.16.840.1.113883.6.96
cervical adenopathy
cervical adenopathy
3502005 SNOMED CT
2.16.840.1.113883.6.96
fever (any)
fever
386661006 SNOMED CT
2.16.840.1.113883.6.96
hypoxia
hypoxia
389086002 SNOMED CT
2.16.840.1.113883.6.96
2.16.840.1.113883.6.96
2.16.840.1.113883.6.96
2.16.840.1.113883.6.96
2.16.840.1.113883.6.96
2.16.840.1.113883.6.96
2.16.840.1.113883.6.96
2.16.840.1.113883.6.96
2.16.840.1.113883.6.96
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Table 3 Lab Informatics
LabObservations
Criterion
Text Basis for Coding
AHIC Test Code
Test Code
System Name
Text Basis for
Result Code
AHIC Result
Code
Result Code
System Name
Anthrax electrophoretic immunotransblot (eitb) reaction to the protective antigen B anthracis spore Ag XXX IF
and/or lethal factor bands in one or more serum samples obtained after onset of
symptoms
Demonstration
of B. anthracis in a clinical specimen by immunofluorescence
B anthracis spore Ag XXX IF
44270-7
LOINC
Detected
260373001 SNOMED CT
44270-7
LOINC
Detected
260373001 SNOMED CT
Demonstration of B. anthracis in a clinical specimen by immunofluorescence
B anthracis capsule Ag XXX IF
51976-9
LOINC
Detected
260373001 SNOMED CT
Demonstration of B. anthracis in a clinical specimen by immunofluorescence
B anthracis cell w all Ag XXX IF
44269-9
LOINC
Detected
260373001 SNOMED CT
Demonstration of B. anthracis in a clinical specimen by immunofluorescence
B anthracis Ag Islt Ql IF
33697-4
LOINC
Ordinal value
Demonstration of B. anthracis in a clinical specimen by immunofluorescence
B anthracis Ag XXX Ql IF
22867-6
LOINC
Ordinal value
Demonstration of B. anthracis in a clinical specimen by immunofluorescence
B anthracis Ag Tiss Ql IF
22866-8
LOINC
Ordinal value
Demonstration of B. anthracis in a clinical specimen by immunofluorescence
B anthracis Ab XXX IF-aCnc
11468-6
LOINC
Quantative value
Isolation of Bacillus anthracis from a clinical specimen
B anthracis Islt Ql Phage Lys
33698-2
LOINC
Positive
10828004 SNOMED CT
Isolation of Bacillus anthracis from a clinical specimen
B anthracis XXX Ql Cult
11469-4
LOINC
Isolated
46651001 SNOMED CT
Isolation of Bacillus anthracis from a clinical specimen
Bacteria Shlw Wnd Aerobe Cult 17915-0
LOINC
Bacillus anthracis
21927003 SNOMED CT
Isolation of Bacillus anthracis from a clinical specimen
Bacteria Spt Aerobe Cult
622-1
LOINC
Bacillus anthracis
21927003 SNOMED CT
Isolation of Bacillus anthracis from a clinical specimen
Bacteria Bld Aerobe Cult
17928-3
LOINC
Bacillus anthracis
21927003 SNOMED CT
Isolation of Bacillus anthracis from a clinical specimen
Bacteria XXX Anaerobe+Aerobe 21020-3
Cult
LOINC
Bacillus anthracis
21927003 SNOMED CT
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Model for Automated Reasoning
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Case Definition - Match
Two vocabulary/NND ontology
driven application components
are represented in this
diagram. The presentation
profile data entry with fully
constrained value sets driven
dynamically by the NND
services and the Condition
Reasoner which applies
vocabulary and domain
knowledge to analyze the
presentation profile.
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Case Definition Business Rules
(defrule Case_Definitios_Rule_Condition_I
(EvidenceClassification *CollectFindings*)
(MSG-Observation (obsId ?obsId) (msgId ?msgId) (patientId ?pId) …
(codedValue $?cfObsSet) (obsType ClinicalFinding)
(obsQuality ?obsQuality)… )
(MSG-Observation (obsId ?obsId) (msgId ?msgId) (patientId ?pId) …
(codedValue $?labObsSet) (obsType LabFinding)
(obsQuality ?obsQuality)… )
(PHKB-ClinicalFinding (conditionCode ?condCode)
(codedValue $?cfObsSet) (endType ?endType) … )
(PHKB-LabFinding (conditionCode ?condCode)
(codedValue $?labObsSet) (endType ?endType) … )
(PHKB-Condition (conditionCode ?condCode) …
)
=>
(assert (Endorsement (msgId ?msgId) (endType ?endType)
(Condition ?condCode) (CaseDefinitionStatus *Confirmed*)…
)
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QUESTIONS
Craig Cunningham
OntoReason LLC
(801) 260-1502
[email protected]
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