Constrained Predictors

How to use the PhenotypeLibrary R package

Here we provide a set of phenotypes that can be used as predictors in prediction models or best practice research.

These phenotypes can be extracted from the PhenotypeLibrary R package. To install the R package run:

remotes::install_github('ohdsi/PhenotypeLibrary')
## Using github PAT from envvar GITHUB_PAT
## Downloading GitHub repo ohdsi/PhenotypeLibrary@HEAD
## cpp11    (NA -> 0.4.7) [CRAN]
## progress (NA -> 1.2.2) [CRAN]
## Installing 2 packages: cpp11, progress
## Installing packages into '/tmp/Rtmp8Zsvqh/temp_libpath27c23f56e899'
## (as 'lib' is unspecified)
## ── R CMD build ─────────────────────────────────────────────────────────────────
## * checking for file ‘/tmp/RtmpgYti1q/remotes31906de79754/OHDSI-PhenotypeLibrary-ebf9e8c/DESCRIPTION’ ... OK
## * preparing ‘PhenotypeLibrary’:
## * checking DESCRIPTION meta-information ... OK
## * checking for LF line-endings in source and make files and shell scripts
## * checking for empty or unneeded directories
## * building ‘PhenotypeLibrary_3.31.0.tar.gz’
## Installing package into '/tmp/Rtmp8Zsvqh/temp_libpath27c23f56e899'
## (as 'lib' is unspecified)

To extract the cohort definition for Alcoholism with an id of 1165, just run:

PhenotypeLibrary::getPlCohortDefinitionSet(1165)
## # A tibble: 1 × 4
##   cohortId cohortName json                                                 sql  
##      <dbl> <chr>      <chr>                                                <chr>
## 1     1165 Alcoholism "{\n\t\"cdmVersionRange\" : \">=5.0.0\",\n\t\"Prima… "CRE…

in general you can extract all the cohorts by running:

phenotypeDefinitions <- PhenotypeLibrary::getPlCohortDefinitionSet(1152:1215)

The full set of predictor phenotypes

Phenotype Name Disorder classification OHDSI Phenotype library ID
Alcoholism Behavioral 1165
Smoking Behavioral 1166
Anemia Blood 1188
Osteoarthritis Bone 1184
Osteoporosis Bone 1185
Cancer Cancer 1215
Atrial fibrillation Cardiovascular 1160
Congestive heart failure Cardiovascular 1154
Coronary artery disease Cardiovascular 1162
Heart valve disorder Cardiovascular 1172
Hyperlipidemia Cardiovascular 1170
Hypertension Cardiovascular 1198
Angina Cardiovascular 1159
Skin Ulcer Debility 1168
Diabetes type 1 Endocrine 1193
Diabetes type 2 Endocrine 1194
Hypothyroidism Endocrine 1171
Obesity Endocrine 1179
Gastroesophageal reflux disease (GERD) GI 1178
Gastrointestinal (GI) bleed GI 1197
Inflammatory bowel disorder (IBD) GI/Rheumatology 1180
Hormonal contraceptives Gynecologic 1190
Antibiotics Aminoglycosides Infection 1201
Antibiotics Carbapenems Infection 1202
Antibiotics Cephalosporins Infection 1203
Antibiotics Fluoroquinolones Infection 1204
Antibiotics Glycopeptides and lipoglycopeptides Infection 1205
Antibiotics Macrolides Infection 1206
Antibiotics Monobactams Infection 1207
Antibiotics Oxazolidinones Infection 1208
Antibiotics Penicillins Infection 1209
Antibiotics Polypeptides Infection 1210
Antibiotics Rifamycins Infection 1211
Antibiotics Sulfonamides Infection 1212
Antibiotics Streptogramins Infection 1213
Antibiotics Tetracyclines Infection 1214
Pneumonia Infection/Respiratory 1199
Sepsis Infection 1176
Urinary tract infection (UTI) Infection 1186
Hepatitis Liver 1169
Anxiety Mood 1189
Depression (MDD) Mood 1161
Psychotic disorder Mood 1175
Antiepileptics (pain) Neurology/Pain 1183
Seizure Neurology 1153
Hemorrhagic stroke Neurology/Vascular 1156
Non-hemorrhagic stroke Neurology/Vascular 1155
Acetaminophen prescription Pain/Infection 1187
Low back pain Pain 1173
Neuropathy Pain/Neurology 1174
Opioids Pain 1182
Acute kidney injury Kidney 1163
Chronic kidney disease Kidney 1191
Asthma Respiratory 1164
Chronic obstructive pulmonary disorder (COPD) Respiratory 1192
Dyspnea Respiratory 1195
Respiratory failure Respiratory 1177
Sleep apnea Respiratory 1167
Rheumatoid arthritis Rheumatology 1200
Steroids Rheumatology/Pain/Pulmonary 1181
Peripheral vascular disease Vascular 1157
Aspirin Vascular 1158
Deep vein thrombosis (DVT) Vascular 1152
Edema Vascular 1196
Inpatient visit NA NA