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Advanced Temporal Language Aided
Search for the OHDSI community
Juan M. Banda, Ph.D., Alison Callahan, Ph.D., David Kale,
M.S. Vladimir Polony, M.S. Nigam H. Shah, MBBS, Ph.D.

Phenotyping in OHDSI
• Rule based, expert-consensus definitions
• Exemplified by www.phekb.org
• Implemented by ATLAS www.ohdsi.org/web/atlas/
• Probabilistic phenotyping
• Relatively new
• APHRODITE, ANCHOR learning
• https://github.com/OHDSI/Aphrodite

Rule-based phenotypes: www.PheKB.org
• Created by community consensus
• Shared as inclusion / exclusion rules
• Need to be implemented at each local site and can
become quite complex
• This process is facilitate by OHDSI ATLAS

Introducing Advanced Temporal Language
Aided Search
Instead of drop-down menus, we present a
search interface to write phenotype definitions

Example phenotype:
Type 2 diabetes mellitus
PheKB Vanderbilt definition – cases only
Available: https://phekb.org/phenotype/type-2-diabetes-demonstration-project

1) Select people over 18 years old and under 90
2) Define which diagnosis codes our selection can have
Example phenotype – Step 1

3) Define set of non-insulin medications the patient can have
4) Define set of insulin-related medications the patient can have

5) Define abnormal glucose lab tests
6) Define abnormal A1C lab results

7) Define case 1:
Age over 18 AND a T2DM code AND non-insulin medication

8) Define case 2:
Age over 18 AND T2DM code AND abnormal labs AND no history
of non-insulin and insulin medications

9) Define case 3:
Age over 18 AND abnormal lab values AND non-insulin medications

10) Finally, output the union of all different specified cases

Example phenotype search results:
Type 2 diabetes mellitus

OMOP HOI - Acute Myocardial Infarction definition #4:
Available: http://omop.org/sites/default/files/OMOP%20HOI%20Acute%20Myocardial%20Infarction%204.xlsx
Example phenotype:
Acute Myocardial Infarction
Occurrence of the lab test “blood troponin” LOINC codes 42757-5 or 10839-9, and lab test results
≥ the upper limit of normal in two sequential measurements, or ≥ 2 times the upper limit of
normal in one measurement, and falling in a subsequent measurement. The ULN is defined as the
99th percentile of a non-MI control group, or 0.5 ng/mL if not available
OR
Occurrence of the lab test “creatinine phosphokinase MB isozyme (CK-MB)” LOINC codes 49551-5
or 13969-1, and lab test results ≥ the upper limit of normal in two sequential measurements, or ≥
2 times the upper limit of normal in one measurement, and falling in a subsequent measurement.
The ULN is defined as the 99th percentile of a non-MI control group, or 6 ng/mL if not available
}
AND
Occurrence of an EKG test with the LOINC codes 11524-6, 8601-7, 18843-3, 18844-1, 18810-2,
8625-6 or 8634-8 within 10 days prior or after the lab test result and any of the following readings
{
Any Q wave in leads V1 through V3, Q wave ≥ 5 to 30 ms in leads I, II, aVL, aVF, V4, V5, or V6
OR
ST segment elevation: New or presumed new ST segment elevation at the J point in two or more
contiguous leads with the cut-off points _0.2 mV in leads V1, V2, or V3 and ≥ 0.1mV in other leads
(contiguity in the frontal plane is defined by the lead sequence aVL, I, inverted aVR, II, aVF, III)
OR
ST segment depression
OR
T wave abnormalities

1) Find a sequence of high troponin without a low or normal
finding separating them within one day

2) Find a sequence of high CKBM without a low or normal
finding separating them within one day

3) Make sure we check that both lab measurements have the
same trend

4) Define list of EKG CPT codes

5) Finally, output the patients with an EKG CPT code within 10
days of lab sequence in either direction

Example phenotype search results:
Acute Myocardial Infarction

Built for speed
• We have implemented 55 definitions across
46 phenotypes
• Took us 2 hours, in a group of 15 people to
define 38 of them
• With additional curation, about 53 hours of
work

CDM extensions to support
Advanced Temporal Language Aided Search
• Time in all tables (will be added in next CDM version)
• Clinical notes annotations (will be added in CDM next
version)
• Consistent ICD/CPT mappings to SNOMED

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