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
This repo consists of the following parts.
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.
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.
The translated phenotypes are in the phenotypes directory. Each
phenotype consists of a CQL file and a collection of FHIR ValueSet resources.
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.
- Java 11+
- NodeJS 14+
First install the dependencies:
yarn install
Then run the tests:
yarn test
| # | 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 |