PhenotypeLibrary 3.17.1
Minor changes. Remove dependencies from suggests. Fix hyperlinks in vignettes.
PhenotypeLibrary 3.18.0
This release is a clean up of files and cohorts before adding cohorts from HowOften. getPhenotypeLog() now gives additional information about a cohort. These are programmatically derived from Circe model compatible cohort json.
censorWindowStartDate censorWindowEndDate collapseSettingsType
collapseEraPad exitStrategy exitDateOffSetField exitDateOffSet
numberOfInclusionRules qualifyingLimitType primaryCriteriaLimit
numberOfCohortEntryEvents numberOfDomainsInEntryEvents
domainsInEntryEvents continousObservationWindowPrior
continousObservationWindowPost numberOfConceptSets
demographicCriteria demographicCriteriaAge demographicCriteriaGender
useOfObservationPeriodInclusionRule restrictedByVisit
domainConditionOccurrence domainMeasurement domainObservation
domainVisitOccurrence domainDeath domainDrugExposure
criteriaAgePrimaryCriteria domainDeviceExposure
domainProcedureOccurrence criteriaAgeInclusionRules
criteriaGenderPrimaryCriteria criteriaGenderInclusionRules
Accepted Cohorts: No cohorts were accepted in this release.
New Cohorts: No new cohorts were added in this release.
PhenotypeLibrary 3.19.0
This release includes the bulk of the cohorts submitted to the OHDSI PhenotypeLibrary in the month of September 2023, as part of the push for HowOften.
Accepted Cohorts: No cohorts were accepted in this release.
New Cohorts: 252 were added.
311: [P] Parasomnia
742: [P] Parasomnia or Sleep dysfunction with arousal disturbance
743: [P] Diabetic ketoacidosis IP-ER (SNOMED concept)
744: [P] Pulmonary Hypertension
745: [P] Inflammatory Bowel Disease
746: [P] Chronic Thromboembolic Pulmonary Hypertension
747: [P] Pulmonary Arterial Hypertension
748: [P] Psoriatic arthritis
749: [P] Plaque Psoriasis
750: [P] Pulmonary hypertension associated with left heart disease (WHO Group 2)
751: [P] Pulmonary hypertension associated with lung diseases and or hypoxia (WHO Group 3)
752: [P] Firearm Accidents (FA)
753: [P] Motor Vehicle Accidents (MVA)
754: [P] Down Syndrome
755: [P] Non-infectious uveitis and iridocyclitis
756: [P] Cystic Fibrosis
757: [P] Concomitant TNF - alpha Inhibitors and IL23 Inhibitors - GE 30D overlap
759: [P] Concomitant TNF - alpha Inhibitors and IL12_23 Inhibitors - GE 30D overlap
760: [P] Concomitant IL 23 Inhibitors and IL12_23 Inhibitors - GE 30D overlap
761: [P] Pulmonary arterial hypertension with Prior Left Heart or Vice Versa
762: [P] Endothelin receptor antagonists
763: [P] Phosphodiesterase 5 inhibitors and guanylate cyclase stimulators
764: [P] Prostacyclin analogues and prostacyclin receptor agonists
765: [P] Earliest event of Left Heart Failure
766: [P] Earliest event of Right Heart Failure
767: [P] Earliest event of Sarcoidosis
768: [P] Earliest event of Sickle Cell Anemia
769: [P] Scleroderma, first occurrence
770: [P] Essential Hypertension, first occurrence
771: [P] Pulmonary Hypertension (Group 2 Left heart disease, encompassing)
772: [P] Pulmonary Hypertension (Group 3 Chronic lung disease, encompassing)
773: [P] Congenital Heart Disease
774: [P] Portal Hypertension, first occurrence
775: [P] First Inflammatory Bowel Disease
776: [P] Antisynthetase syndrome
777: [P] Mixed connective tissue disease
778: [P] Undifferentiated connective tissue disease
779: [P] Overlap syndrome
780: [P] Raynaud?s disease or Raynaud's phenomenon
781: [P] Antiphospholipid syndrome
782: [P] CTEPH Prevalent (with Echo or RHC) with 2nd dx code 31-365 days after first dx
783: [P] Pulmonary endarterectomy
784: [P] Balloon Pulmonary Angioplasty
785: [P] Skin Burns
786: [P] Non-small cell lung cancer (NSCLC)
787: [P] Lung cancer
788: [P] Breast cancer
789: [P] Glioblastoma multiforme (GBM)
790: [P] Colorectal Cancer
791: [P] Multiple Myeloma
792: [P] Metastatic Hormone-Sensitive Prostate Cancer Synchronous
793: [P] Metastatic Hormone-Sensitive Prostate Cancer Metachronus
794: COPY OF [P][R] Bleeding
795: [P] Antineoplastic drugs against colorectal cancer
796: [P] Potential curative surgery for colorectal cancer
797: [P] Radiotherapy against colorectal cancer
798: [P] Primary adenocarcinoma of the colon or rectum
802: [P] Acute Respiratory Failure 2
803: [P] Fascial dehiscence and evisceration
804: [P] Anastomotic leak or dehiscence
805: [P] Intestinal obstruction (broad)
806: [P] Intraabdominal abscess
807: [P] Perioperative aspiration
808: [P] Postoperative hemorrhage
809: [P] Surgical wound infection (narrow)
810: [P] Distant metastasis following colorectal cancer (wide)
811: [P] Local recurrence after colorectal cancer
812: [P] Primary adenocarcinoma of the colon or rectum, MSI-H or dMMR, no surgery or oncological treatment
813: [P] Primary adenocarcinoma of the colon or rectum treated with potentially curative surgery
814: [P] Primary adenocarcinoma of the colon or rectum, no curative intended surgery and oncological treatment
817: [P] Primary adenocarcinoma of the colon or rectum, no curative intended surgery and oncological treatment2
818: [P] Primary adenocarcinoma of the colon or rectum, MSI-L, MSI-indeterminate, MSS or pMMR
819: [P] Primary adenocarcinoma of the colon or rectum, MSI-L, MSI-indeterminate, MSS or pMMR, treated with curative intended surgery
820: [P] Primary adenocarcinoma of the colon or rectum, MSI-L, MSI-indeterminate, MSS or pMMR, oncological treatment, no curative surgery
821: [P] Primary adenocarcinoma of the colon or rectum, MSI-L, MSI-indeterminate, MSS or pMMR, no surgery or oncological treatment
822: [P] Primary adenocarcinoma of colon or rectum, MSI-H or dMMR, surgical treatment
823: [P] Primary adenocarcinoma of colon or rectum, MSI-H or dMMR, oncological treatment no surgery
824: [P] Primary adenocarcinoma of colon or rectum, MSI-H or dMMR
825: [P] Primary adenocarcinoma of colon
826: [P] Primary adenocarcinoma of colon, no surgery or oncological treatment
827: [P] Primary adenocarcinoma of colon surgical treatment
828: [P] Primary adenocarcinoma of colon oncological treatment, no surgery
829: [P] Primary adenocarcinoma of colon, MSI-L, MSI-indeterminate, MSS or pMMR
830: [P] Primary adenocarcinoma of colon, MSI-L, MSI-indeterminate, MSS or pMMR, surgically treated
831: [P] Primary adenocarcinoma of colon MSI-L, MSI-indeterminate, MSS or pMMR, oncological treatment, no surgery
832: [P] Primary adenocarcinoma of colon MSI-L, MSI-indeterminate, MSS or pMMR, no surgery or oncological treatment
833: [P] Primary adenocarcinoma of colon MSI-H or dMMR
834: [P] Primary adenocarcinoma of colon MSI-H or dMMR, surgical treatment
835: [P] Primary adenocarcinoma of colon MSI-H or dMMR, oncological treatment, no surgery
836: [P] Primary adenocarcinoma of colon MSI-H or dMMR, no surgery or oncological treatment
837: [P] Primary adenocarcinoma of rectum
838: [P] Primary adenocarcinoma of rectum MSI-H or dMMR
839: [P] Primary adenocarcinoma of rectum, MSI-H or dMMR, no surgery or oncological treatment
840: [P] Primary adenocarcinoma of rectum MSI-H or dMMR, oncological treatment, no surgery
841: [P] Primary adenocarcinoma of rectum, MSI-H or dMMR, surgical treatment
842: [P] Primary adenocarcinoma of rectum, MSI-L, MSI-indeterminate, MSS or pMMR
843: [P] Primary adenocarcinoma of rectum MSI-L, MSI-indeterminate, MSS or pMMR, oncological treatment, no surgery
844: [P] Primary adenocarcinoma of rectum MSI-L, MSI-indeterminate, MSS or pMMR, no surgery and no oncological treatment
845: [P] Primary adenocarcinoma of rectum MSI-L, MSI-indeterminate, MSS or pMMR, treated with potentially curative surgery
846: [P] Primary adenocarcinoma of rectum oncological treatment, no surgery
847: [P] Primary adenocarcinoma of rectum surgical treatment
848: [P] Primary adenocarcinoma of rectum, no surgery or oncological treatment
850: [P] Intestinal obstruction (broad 2)
851: [P] Intraabdominal obstruction (broad)
852: [P] Surgical wound infection (broad)
854: [P] Distant metastasis following colorectal cancer (medium)
855: [P] Distant metastasis following colorectal cancer (narrow)
856: [P] Earliest event of Migraine, including history of migraine
857: [P] Earliest event of Migraine
858: [P] Earliest event of Rheumatoid Arthritis
859: [P] Earliest event of Crohns disease
860: [P] Earliest event of Ulcerative colitis
861: [P] Earliest event of Urinary tract infections (UTI)
862: [P] Earliest event of Alzheimer's disease derived from Imfeld, 2
863: [P] Cognitive impairment, incident
864: [P] Earliest event of Dementia
865: [P] Non-Emergent Major Non Cardiac Surgery
866: [P] AAA repair
867: [P] Lower Extremity Bypass
868: [P] Carotid Endarterectomy
869: [P] Lung Resection
870: [P] Esophagectomy
871: [P] Pancreatectomy
872: [P] Colectomy
873: [P] Cystectomy
874: [P] Nephrectomy
875: [P] Coronary Artery Bypass Graft Surgery
876: [P] Aortic or Mitral Valve Repair or Replacement
877: [P] Non-Emergent MNCS (age 18 or greater), post op Afib (parox)
878: [P] Non-Emergent MNCS (age 18 or greater), post op Afib (any)
879: Cxxx Endometriosis indexed on procedure with two or more diagnosis among females 15 to 49
881: [P] Acute myocardial infarction
882: [P] Decreased libido
884: [P] Diarrhea2
888: [P] Gastrointestinal bleeding
889: [P] Hyponatremia
890: [P] Hypotension
891: [P] Nausea
892: [P] Stroke
893: [P] Vertigo
894: [P] Abdominal pain
895: [P] Abnormal weight gain
896: [P] Abnormal weight loss
898: [P] Acute renal failure
899: [P] All-cause mortality
900: [P] Anaphylactoid reaction
901: [P] Anemia
907: [P] All-cause mortality2
910: [P] Anaphylactoid reaction2
913: [P] Anemia2
916: [P] Angioedema2
917: [P] Anxiety
918: [P] Bradycardia
919: [P] Cardiac arrhythmia
920: [P] Cardiovascular disease
921: [P] Cardiovascular-related mortality
922: [P] Chest pain or angina
923: [P] Kidney disease
924: [P] Coronary heart disease
925: [P] Cough
927: [P] Dementia2
928: [P] Depression2
929: [P] Edema2
930: [P] End stage renal disease2
931: [P] Fall2
932: [P] Gout2
933: [P] Headache2
934: [P] Heart failure2
935: [P] Hemorrhagic stroke2
936: [P] Hepatic failure2
937: [P] Hospitalization with heart failure2
938: [P] Hospitalization with heart failure
939: [P] Hospitalization with preinfarction syndrome
940: [P] Hyperkalemia
941: [P] Hypokalemia
942: [P] Hypomagnesemia
943: [P] Impotence
944: [P] Ischemic stroke
945: [P] Malignant neoplasm
946: [P] Measured renal dysfunction
947: [P] Neutropenia or agranulocytosis
948: [P] Rash
950: [P] Rhabdomyolysis2
953: [P] Sudden cardiac death
954: [P] Syncope
955: [P] Thrombocytopenia
956: [P] Transient ischemic attack
957: [P] Type 2 diabetes mellitus
958: [P] Syncope3
959: [P] Thrombocytopenia3
960: [P] Transient ischemic attack3
961: [P] Type 2 diabetes mellitus3
963: [P] Vomiting
964: [P] Chronic kidney disease
965: [P] 3-point MACE
967: [P] 4-point MACE
969: [P] Acute myocardial infarction2
970: [P] 4-point MACE2
975: [P] Acute renal failure2
976: [P] Glycemic control2
979: [P] Hospitalization with heart failure3
980: [P] Revascularization
982: [P] Stroke2
983: [P] Sudden cardiac death2
984: [P] Abnormal weight gain2
985: [P] Abnormal weight loss2
986: [P] Acute pancreatitis2
988: [P] All-cause mortality3
989: [P] Bladder cancer3
990: [P] Bone fracture3
991: [P] Breast cancer3
992: [P] Diabetic ketoacidosis3
993: [P] Diarrhea3
994: [P] Genitourinary infection3
995: [P] Hyperkalemia3
996: [P] Hypoglycemia3
997: [P] Hypotension3
998: [P] Joint pain3
999: [P] Lower extremity amputation3
1000: [P] Nausea3
1001: [P] Peripheral edema3
1002: [P] Photosensitivity3
1003: [P] Renal cancer3
1004: [P] Thyroid tumor3
1005: [P] Venous thromboembolism3
1006: [P] Vomiting3
1007: [P] Earliest event of Epilepsy
1009: [P] Earliest event of Treatment resistant depression (TRD)
1010: [P] Earliest event of Chronic Graft Versus Host Disease (GVHD)
1011: [P] Earliest event of Marginal zone lymphoma
1012: [P] Earliest event of Waldenstrom macroglobulinemia
1013: [P] Earliest event of Ankylosing Spondylitis
1015: [P] Earliest event of Pulmonary arterial hypertension (PAH)2
1016: [P] Earliest event of Polyarticular juvenile idiopathic arthritis (JIA)
1017: [P] Earliest event of Neonatal Thrombocytopenia (NT), less than 1 year old
1018: [P] Earliest event of Warm Autoimmune Hemolytic Anemia (wAIHA), occurring on or after October 2020
1019: [P] All events of Hemolytic Disease Fetus and Newborn (HDFN), RhD type, with a pregnancy episode
1020: [P] Earliest event of Major depressive disorder, with NO occurrence of certain psychiatric disorder
1021: [P] Earliest event of Myasthenia Gravis, inpatient, 2nd diagnosis or treatment, age gte 18
1022: [P] Earliest event of Depressive and Sleep Disorder
1023: [P] Earliest Event of Depressive Disorder with Suicidal Ideation or Attempt Prevalent
1024: [P] Earliest Event of Depressive Disorder with Anhedonia
1025: [P] First event of Attention-deficit hyperactivity (ADHD) disorder or procedure
1026: [P] Earliest Event of Multiple Sclerosis
1027: [P] Earliest event of Chronic Leukocytic Leukemia
1028: [P] Earliest event of Urothelial carcinoma
1029: [P] Earliest event of Mantle Cell Lymphoma
1030: [P] Earliest event of Prostate cancer, among adult males
1031: [P] Earliest event of Coronary artery disease (CAD)
1032: [P] Earliest event of Type 2 Diabetes Mellitus (DM), with no type 1 or secondary DM
1033: [P] Earliest event of Human Immunodeficiency Virus I (HIV), with treatment, lab or 2nd diagnosis
1034: [P] All events of Respiratory syncytial virus infection, with 30 days washout
PhenotypeLibrary 3.20.0
Accepted Cohorts: No cohorts were accepted in this release.
New Cohorts: 37 were added.
1035: [P] New users of Thiazide diuretics
1036: [P] New users of Beta blockers
1037: [P] New users of SGLT2 inhibitor
1038: [P] New users of GLP-1 receptor antagonists
1039: [P] New users of DPP-4 inhibitors
1040: [P] New users of Tumor Necrosis Factor alpha (TNFa) inhibitors
1041: [P] New users of JAK inhibitors
1042: [P] New users of IL-23 inhibitors
1043: [P] New users of Fluoroquinolone systemic
1044: [P] New users of Cephalosporin systemetic
1045: [P] New users of Trimethoprim systemetic
1046: [P] New users of Thiazide diuretics nested in essential hypertension
1047: [P] New users of dihydropyridine calcium channel blockers nested in essential hypertension
1048: [P] New users of dihydropyridine calcium channel blockers
1049: [P] New users of Beta blockers nested in essential hypertension
1050: [P] New users of Beta blockers nested in Left Heart Failure
1051: [P] New users of SGLT2 inhibitor nested in Left Heart Failure
1052: [P] New users of Beta blockers nested in Acute Myocardial Infarction
1053: [P] New users of GLP-1 receptor antagonists nested in Type 2 diabetes mellitus
1054: [P] New users of SGLT2 inhibitor nested in Type 2 diabetes mellitus
1055: [P] New users of DPP-4 inhibitors nested in Type 2 diabetes mellitus
1056: [P] New users of GLP-1 receptor antagonists nested in obesity
1057: [P] New users of IL-23 inhibitors nested in Plaque psoriasis
1058: [P] New users of Tumor Necrosis Factor alpha (TNFa) inhibitors nested in Plaque psoriasis
1059: [P] New users of Tumor Necrosis Factor alpha (TNFa) inhibitors nested in Psoriatic Arthritis
1060: [P] New users of Fluoroquinolone systemic nested in Urinary Tract Infection
1061: [P] New users of Cephalosporin systemetic nested in Urinary Tract Infection
1062: [P] New users of Trimethoprim systemetic nested in Urinary Tract Infection
1063: [P] New users of Fluoroquinolone systemic nested in Acute Typical Pneumonia
1064: [P] New users of Cephalosporin systemetic nested in Acute Typical Pneumonia
1065: [P] New users of Trimethoprim systemetic nested in Acute Typical Pneumonia
1066: [P] New users of Tumor Necrosis Factor alpha (TNFa) inhibitors nested in Rheumatoid arthritis
1067: [P] New users of JAK inhibitors nested in Ulcerative colitis
1068: [P] New users of Tumor Necrosis Factor alpha (TNFa) inhibitors nested in Ulcerative colitis
1069: [P] New users of Tumor Necrosis Factor alpha (TNFa) inhibitors nested in Crohns disease
1070: [P] New users of JAK inhibitors nested in Rheumatoid arthritis
1071: [P] persons at risk at start of year 2012-2022 with 365d prior observation
PhenotypeLibrary 3.21.0
Accepted Cohorts: No cohorts were accepted in this release.
New Cohorts: 20 were added.
1072: [P] CMV Anterior Uveitis
1073: [P] Serious Infection, opportunistic infections and other infections of interest event
1074: [P] Serious Infection
1075: [P] FDA AESI Narcolepsy
1076: [P] FDA AESI Anaphylaxis
1077: [P] FDA AESI Anaphylaxis v2
1078: [P] FDA AESI Bells Palsy
1079: [P] FDA AESI Encephalomyelitis
1080: [P] FDA AESI Guillain Barre Syndrome
1081: [P] FDA AESI Acute Myocardial Infarction
1082: [P] FDA AESI Myocarditis Pericarditis
1083: [P] FDA AESI Immune Thrombocytopenia (ITP)
1084: [P] FDA AESI Disseminated Intravascular Coagulation
1085: [P] FDA AESI Appendicitis
1086: [P] FDA AESI Transverse Myelitis
1087: [P] FDA AESI Hemorrhagic Stroke
1088: [P] FDA AESI Deep Vein Thrombosis (DVT)
1089: [P] FDA AESI Non-hemorrhagic Stroke
1090: [P] FDA AESI Pulmonary Embolism
1091: [P] FDA AESI Thrombosis with Thrombocytopenia (TWT)
PhenotypeLibrary 3.22.0
Accepted Cohorts: No cohorts were accepted in this release.
New Cohorts: No new cohorts were added in this release.
Deleted Cohorts: duplicates. Added in error. Deleted 879, 907, 910, 916, 958, 959, 960, 961
Added new function getPlConceptDefinitionSet() . This new function exposes the concept sets from all circe compatible cohort definitions that are in the library.
Additional computer generated metadata added to cohort definition log
PhenotypeLibrary 3.22.1
- getPhenotypeLog() now returns the original user submitted cohort name, instead of the name forced by atlas-phenotype.
- This is in line with the original requirement. It allows for long names, names with special characters.
- Deprecated listPhenotypes(). This was an older function that did the same as getPhenotypeLog() but returned only two fields.
- Added requirement on R (4.10) because tidyverse seems to cause problems with older versions of R.
PhenotypeLibrary 3.23.0
Accepted Cohorts: No cohorts were accepted in this release.
New Cohorts: No new cohorts were added in this release.
Deleted: 995, 988, 985, 984, 983, 975, 970, 969, 937, 899. Duplicate cohorts from LEGEND Diabetes Import.
Some fixes to issues with meta data for Cohorts
PhenotypeLibrary 3.24.0
Accepted Cohorts: No cohorts were accepted in this release.
New Cohorts: 14 were added.
1093: [P] Abdominal Aoritc Aneurysm repair - post op new Afib (any)
1094: [P] Lower Extremity Bypass - post op new Afib (any)
1095: [P] Carotid Endarterectomy - post op new Afib (any)
1096: [P] Lung Resection - post op new Afib (any)
1097: [P] Esophagectomy - post op new Afib (any)
1098: [P] Pancreatectomy - post op new Afib (any)
1099: [P] Colectomy - post op new Afib (any)
1100: [P] Cystectomy - post op new Afib (any)
1101: [P] Nephrectomy - post op new Afib (any)
1102: [P] Coronary Artery Bypass Graft Surgery - post op new Afib (any)
1103: [P] Aortic or Mitral Valve Repair or Replacement - post op new Afib (any)
1104: [P] RBC Transfusion (adult relevant, no auto 1yr clean window)
1105: [P] Clostridium difficile - first episode
1106: [P] Non-Emergent Major Non Cardiac Surgery no prior Opioid
Thank you for your contributions to the OHDSI Phenotype Library. Over the past month, we’ve added about 300 new cohort definitions to the library. A huge shoutout to all the contributors for making this possible. Special thanks to @agolozar , @Evan_Minty , @Azza_Shoaibi , @Patrick_Ryan , @awrosen , @Jill_Hardin , @jswerdel , and @edward_lee for your contributions.
These contributions span across various OHDSI Workgroups, including but not limited to Oncology, Eye, and Perioperative workgroups. As a part of the HowOften study push, we’ve also added cohort definitions from pivotal OHDSI Studies, notably the Legend Hypertension and Diabetes studies.
For a comprehensive review of all contributed cohorts, please visit here. You can download the entire list for your perusal. If you wish to search by contributor names, simply use the ‘contributors’ field. The ‘cohortId’ corresponds to the unique ID of each cohort in the library. Additionally, the cohort JSON files are accessible here.
You can access the library directly via the Github links provided above. Alternatively, the library is also available as an installable R package. For details on how to utilize the library in a study, please refer to the documentation available here.
The library’s mission is to enable the community to produce high-quality reliable evidence. Please note that the library will temporarily cease accepting cohort definition contributions till the end of October 2023. We will resume acceptance in November 2023.
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