PheKB Phenotypes

Collection of PheKB phenotypes translated as part of the PhEMA phenotype variability project.

Brandt PS, Pacheco JA, Rasmussen LV. Development of a repository of computable phenotype definitions 
using the clinical quality language. JAMIA Open. 2021 Dec 3;4(4):ooab094. 
doi: 10.1093/jamiaopen/ooab094. PMID: 34926996; PMCID: PMC8672934.

☝️ citation

Overview

This repo consists of the following parts.

CQL to ELM Translator

A compiled version of the cql-to-elm translator is in the tools directory. This is necessary because the testing framework used only works with ELM and not directly with CQL.

Value Set Cache Builder

There is a small script in the scripts directory that creates a cache from ValueSet resources (in phenotype valuesets directories) in the format expected by the testing framework.

PheKB Phenotypes

The translated phenotypes are in the phenotypes directory. Each phenotype consists of a CQL file and a collection of FHIR ValueSet resources.

Test Cases

Inside each phenotype directory there is a test folder, which contains the test configuration (cqlt.yaml) and a set of tests cases (in the cases directory). The test are executed using AHRQ's CQL Testing Framework.

Documentation

• 📝 Contributing
• ❄️ Phenotype Patterns

Running The Tests

Prerequisites

• Java 11+
• NodeJS 14+

First install the dependencies:

yarn install

Then run the tests:

yarn test

Phenotype List

#	id	slug	Translated By	Validated By	Status
1	8	cardiac-conduction-qrs	Pascal	Luke	✅ Done
2	9	cataracts	Luke	Pascal	✅ Done
3	12	high-density-lipoproteins-hdl	Pascal	Luke	✅ Done
4	13	height	Pascal	Luke	✅ Done
5	14	hypothyroidism	Luke	Pascal	✅ Done
6	15	lipids	Luke	Pascal	✅ Done
7	16	peripheral-arterial-disease-2012	Luke	Pascal	✅ Done
8	17	red-blood-cell-indices	Pascal	Luke	✅ Done
9	18	type-2-diabetes-mellitus	Luke	Pascal	✅ Done
10	19	white-blood-cell-indices	Pascal	Luke	✅ Done
11	68	resistant-hypertension	Pascal	Luke	✅ Done
12	73	type-2-diabetes-demonstration-project	Pascal	Luke	✅ Done
13	74	rheumatoid-arthritis-demonstration-project	Pascal	Luke	✅ Done
14	76	multiple-sclerosis-demonstration-project	Pascal	Luke	✅ Done
15	77	crohns-disease-demonstration-project	Pascal	Luke	✅ Done
16	78	atrial-fibrillation-demonstration-project	Pascal	Luke	✅ Done
17	88	clopidogrel-poor-metabolizers	Pascal	Luke	✅ Done
18	112	herpes-zoster	Pascal	Luke	✅ Done
19	115	asthma-response-to-inhaled-steroids	Pascal	Luke	✅ Done
20	135	drug-induced-liver-injury	Luke	Pascal	✅ Done
21	155	steroid-induced-osteonecrosis	Pascal	Luke	✅ Done
22	156	warfarin-doseresponse	Pascal	Luke	✅ Done
23	162	autism	Pascal	Luke	✅ Done
24	170	statins-and-mace	Pascal	Luke	✅ Done
25	602	familial-hypercholesterolemia	Pascal	Luke	✅ Done
26	615	sickle-cell-disease	Pascal	Luke	✅ Done
27	797	developmental-language-disorder	Pascal	Luke	✅ Done
28	1053	multimodal-analgesia	Pascal	Luke	✅ Done
29	1058	systemic-lupus-erythematosus-sle	Pascal	Luke	✅ Done
30	1070	phema-bph-benign-prostatic-hyperplasia-cases	Pascal	Luke	✅ Done
31	1205	digital-rectal-exam	Luke	Pascal	✅ Done
32	1404	urinary-incontinence	Luke	Pascal	✅ Done
33	1197	bone-scan-utilization	Luke	Pascal	✅ Done