1. Department of Veterans Affairs Veteran Health Administration
Knowledge Based Systems
Informatics Architecture Support Services
Identify Negation for Special Handling
Kirsten Haake, MD
Tim Williams
Veterans Health Administration, Office of Informatics & Analytics and Health Informatics Informatics Architecture Support Services Contract VA C-0039
CLIN Bi Weekly Web Based Workshops
9/5/2017

2. Agenda Discussion Topics Facilitator Slide # Introduction
Project Overview
“Negation” Within the SNOMED CT Concept Model
Kirsten Haake
3 – 4
Keywords Used to Identify Data
Tim Williams 5
Process to Evaluate 6
Heuristics / Rules to Determine Negation
7 – 15
Results
Tim Williams, 16
Modeling Issues
17-19
Next Steps 20
Questions? 21

3. Introduction Project Overview
SNOMEDT CT CONTENT REQUIRING SPECIAL HANDLING
Concepts may require special handling for a number of reasons:
Hierarchies may be incorrect and could affect retrieval
Concepts may require retirement or movement to the “Situation” hierarchy
Use of concepts may have to be limited
The focus for content that requires special handling was defined for three categories:
Concepts including Negation
Concepts including compound observations
Concepts including a Subject of Record Other Than the Patient
Initial task was to evaluate 50,000 concepts from Findings, Procedures, and Body Structure hierarchies
This presentation will describe our strategy for identifying, collecting and evaluating “Negation” concepts

4. “Negation” Within the SNOMED CT Concept Model
Introduction
“Negation” Within the SNOMED CT Concept Model 
“Negation” vs. “Affirmation” are two polar opposite paradigms within the SNOMED CT Concept Model. Where “Affirmation” represents a statement that e.g. a finding or a disorder is present, negation states their absence.
Example:
|Swelling (finding)| vs |Swelling absent (situation)|
“Negation” concepts are generally located in the “situation” with explicit context” hierarchy, where the Context terminological model is consistently applied. However, the logical hierarchy remains “upside-down”.
Concepts including or implying negation, which are located outside this hierarchy pose challenges for the logical semantic hierarchies they reside in.
|No headache (situation)| is a subtype of |No pain (situation)|, but “no headache” does not mean, the patient has no pain.

5. Keywords Used to Identify Data
The following keywords were used to identify potential members of the “Negation” RefSet by query: No
Not
Without
None (or non-xyz)
Only
Unable
Inability
Stated Negation
Unilateral
Other than
Implied Negation

6. Process to Evaluate
Evaluated concepts that were compound observations and where the patient was not the subject of record at the same time
Used keyword searches over all terms to identify concepts
Expanded set of concepts by including descendants (51,093)
Concepts were grouped into assignments based on criteria
Two reviewers independently reviewed each concept

7. Heuristics / Rules to Determine Negation
Besides clearly stated negation in the SNOMED CT (SCT) Fully Specified Names (FSN), implied negation has to be considered in a number of contexts
Symptom not changed (finding) vs. Late syphilis with clinical manifestations other than neurosyphilis (disorder)
Proposed Rules for Inclusion in “Negation” RefSet *:
FSN states, that something about the Subject of Record is “absent”, e.g.
Ankle movement absent in “No ankle movement (finding)”
FSN states, that something about a procedure is “absent” (Assumption: Procedures are documented, when they are carried out on a Subject of Record), e.g.
Use of contrast media absent in “Magnetic resonance imaging without contrast (procedure)”
FSN negates everything “other” than what it describes, e.g.
Perception of anything other than light in “Perceives light only (finding)”
* SCT “Situations with explicit context” hierarchy is deliberately excluded

8. Heuristics / Rules to Determine Negation
The following keywords helped to identify potential members of the “Negation” RefSet during the manual review: No
Not
Without
None (or non-xyz)
Only
Unable
Inability
Stated Negation
Unilateral
Other than
Absence
Decreased
Implied Negation

9. Heuristics / Rules to Determine Negation
Stated Negation
Examples: Keyword “NO”
SCT ID
FSN
INCLUSION
COMMENT
No help available (finding) 
Something about the subject of record is “absent”
No ankle movement (finding)
Electrocardiogram: no heart block (finding)
Adverse incident resulting in no harmful effect (finding)
No beef diet (finding) 
“No beef” is not about the subject of record – it is about the diet.

10. Heuristics / Rules to Determine Negation
Stated Negation
Examples: Keyword “NOT”
SCT ID
FSN
INCLUSION
COMMENT
Does not eat (finding) 
Something about the subject of record is “absent”
Not yet walking (finding)
Not getting enough sleep (disorder)
Reduction of dislocated joint, not prosthetic (procedure)
Something about the procedure is “absent”
Recommendation not to eat (procedure) 
“Not” does not apply to the procedure itself

11. Heuristics / Rules to Determine Negation
Stated Negation
Examples: Keyword “WITHOUT”
SCT ID
FSN
INCLUSION
COMMENT
Akinetic seizure without atonia (finding) 
Something about the subject of record is “absent”
Incontinence without sensory awareness (finding)
Blister without infection (disorder)
Magnetic resonance imaging without contrast (procedure)
Something about the procedure is “absent”

12. Heuristics / Rules to Determine Negation
Stated Negation
Examples: Keyword “NON” or “NON-X”
SCT ID
FSN
INCLUSION
COMMENT
Sensory nerve conduction block - none (finding) 
Something about the subject of record is “absent”
Immature white blood cells - none present (finding)
Nonerosive nonspecific gastritis (disorder)
Nonexcisional debridement of burn (procedure)
Something about the procedure is “absent”
Compression of lymphedema using nonelastic compression device (procedure) 
“Nonelastic” does not apply to the procedure itself

13. Heuristics / Rules to Determine Negation
Stated Negation
Examples: Keyword “ONLY”
SCT ID
FSN
INCLUSION
COMMENT
Perceives light only (finding) 
Everything other than what the FSN states is negated
Diabetic on diet only (finding)
Blind or low vision - one eye only (disorder)
Mediastinoscopy - inspection only (procedure)
Progestogen-only pill failure (finding) 
“Progestogen-only” is about the pill, not the subject of record

14. Heuristics / Rules to Determine Negation
Stated Negation
Examples: Keyword “Unable”
SCT ID
FSN
INCLUSION
COMMENT
Unable to run (finding) 
Something about the subject of record is “absent”
Unable to eat (finding)
Examples: Keyword “Unable”
SCT ID
FSN
INCLUSION
COMMENT
Inability to cope (finding) 
Something about the subject of record is “absent”
Inability to imitate tongue movements (finding)

15. Heuristics / Rules to Determine Negation
Stated Negation
Examples: Keyword “Rejected”
SCT ID
FSN
INCLUSION
COMMENT
Sample rejected (finding) 
Something about the subject of record is “absent”
Assumption: “Sample/Specimen” was taken from the subject of record.
Specimen rejected / not processed (finding)
Excision of rejected transplanted kidney (procedure) 
“rejected” is not about the procedure – it is about the kidney.

16. Results 4,573 concepts identified in keyword search
98% (4,473) were agreed to be negated by reviewers
0.82% (381) of the concepts that were not in the keyword search were agreed to be negated by reviewers
Reviewers agreed 96% (48,993/51,093) on concepts reviewed for negation

17. Modeling Issues
Parent concept is unilateral, but children do not explicitly state unilateral

18. Modeling Issues
Child concepts do not necessarily mean there are no caregivers

19. Modeling Issues

20. Next Steps Reviewing final content for discrepancies
Testing concepts identified for negation to see if children are also negated
Determine whether concepts need to be moved to Situation hierarchy
Testing final heuristics/rules with a sample of concepts (1,273)
Two reviewers agreed on 89%
Reviewing the results to determine needed changes to heuristics/rules.

21. Questions
Not sure if we want to use a bird here, but they did for the HSPC Workshop.