Quick question: A total of 6 phenotypes in the OHDSI phenotype library have “Accepted” status right? I’m looking for all accepted phenotypes.
Yes. It’s very low (compared to some 300+ cohort definitions in library that have not been peer reviewed). I think there is 1 more that has been accepted but it’s waiting next release of library.
Note - you may use the 300+ cohort definitions in the library in your project. As described here
you can use > PhenotypeLibrary::listPhenotypes()
to get a log of all available. You can filter definitions based on the many columns in that data frame object.
You can get the full cohort definition set as follows
cohortDefinitionSet ← PhenotypeLibrary::getPlCohortDefinitionSet(cohortIds = c(1, 2, 3))
cohortDefinitionSet
Note: the cohort definitions that have [P] are guaranteed to be consistent within the released version of PhenotypeLibrary R package. So you may use it as part of a renv in a HADES package, as long as you reference the right version number of the R package.
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Gowtham and I have been discussing what a phenotype library dashboard would look like on the community dashboard. We would be very interested in getting other suggestions you would like to see and potentially tracked about the use of phenotypes.
Phase 1:
- add phenotype library to a new section of the community dashboard using github api and current based on cohort.csv content with linking to the cohorts themselves. This will allow easy search and retrieve for users. It will also be a good landing place to identify publications and network studies using those phenotypes.
Phase 2:
- Need standard template way for network studies to identify cohort definitions so we can link from phenotypes to network studies. This is a good metric of validity to see if phenotypes are being used in network studies and publications.
- Work with SOS challenge participants to help them submit their Phenotypes.
- Work with a DOI Agency(identified) to assign DOI’s to each Phenotype. https://www.doi.org/
- publish a paper on how to cite referenceable phenotypes as computable artifacts
Phase 3:
- linking phenotypes identified in publications along with network studies, show on phenotype library
- Build an queryable REST terminology server for phenotypes to be electronically searchable and retrievable via a Rest API. This would be an excellent way of building an extension to Atlas to query and retrieve phenotypes.
– FHIR would be an interesting and possible approach with some modifier extensions Terminology-module - FHIR v5.0.0-cibuild
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PhenotypeLibrary version 3.11.0 has been released. This release has the two additional cohort definitions that were accepted into the library during PhenotypePhebruary 2023.
Accepted Cohorts: 2 were accepted.
234: Appendicitis (1Pe, 180Era)
213: Acquired Neutropenia or unspecified leukopenia (21Pe, 365Era)
New Cohorts: 9 were added.
339: [P] Hypotension (1Pe, 3Era)
340: [P] Hives, Erythema, Eruption, Urticaria (1Pe, 7Era)
341: [P] Loss of mentation including coma, loss of consciousness, altered consciousness (1Pe, 3Era)
342: [P] Urinary Incontinence (1Pe, 3Era)
343: [P] Fecal Incontinence (1Pe, 3Era)
344: [P] Doctors office or clinic visit without other overlapping visits (0Pe, 0Era)
345: [P] Doctors office or clinic visit (0Pe, 0Era)
346: [P] Non urgent outpatient visit without overlapping inpatient or emergency visit (0Pe, 0Era)
347: [P] Ambulance utilization (0Pe, 0Era)
PhenotypeLibrary version 3.13.0 has been released. This release has 5 cohort definitions that were contributed by @MaximMoinat as part of the OHDSI Phenotype Pheburary 2023 here. The cohort definitions were peer reviewed by the OHDSI Phenotype Development and Evaluation workgroup and accepted (Video recording here) . Thank you @MaximMoinat for the contribution to OHDSI.
Previous release - missed announcement
See two additional announcement regarding OHDSI PhenotypeLibrary. Current version is 3.15.0. The versions 3.14.0 and 3.15.0 had additions of several symptom cohorts.
PhenotypeLibrary 3.15.0
Accepted Cohorts: No cohorts were accepted in this release.
New Cohorts: 7 were added.
410: [P] Acute Urinary tract infections UTI (1Pe, 30Era)
411: [P] Sepsis or Septic Shock (1Pe, 7Era)
412: Transverse myelitis indexed on diagnosis (1Ps, 0Era, 365W)
414: [P] Acute Skin Eruption symptoms (1Pe, 7Era)
415: [P] Skin Erythema (1Pe, 7Era)
416: [P] Skin Rash (1Pe, 7Era)
417: [P] Acute gastrointestinal bleeding events (7Pe, 30Era)
PhenotypeLibrary 3.14.0
Accepted Cohorts: No cohorts were accepted in this release.
New Cohorts: 44 were added.
363: [P] Joint Stiffness (3Pe, 7Era)
364: [P] Sleep disorder (3Pe, 7Era)
365: [P] Dysuria (3Pe, 7Era)
366: [P] Streptococcal throat infection (14Pe, 30Era)
367: [P] Allergic Rhinitis (14Pe, 30Era)
368: [P] Sinusitis (7Pe, 30Era)
369: [P] Allergic condition (14Pe, 30Era)
370: [P] Allergic disorder (14Pe, 30Era)
371: [P] Claudication Pain (365Pe, 365Era)
372: [P] Otitis media (3Pe, 30Era)
373: [P] Iron deficiency Anemia (365Pe, 365Era)
374: [P] Drug Dependence Disorder (30Pe, 365Era)
375: [P] Gall stone disorder (30Pe, 365Era)
376: [P] Skin Bleeding (1Pe, 7Era)
377: [P] Skin Petechiae (1Pe, 7Era)
378: [P] Skin Purpura (1Pe, 7Era)
379: [P] Ecchymosis (1Pe, 7Era)
380: [P] Jaundice (1Pe, 7Era)
381: [P] Skin Itching (1Pe, 7Era)
382: [P] Prurititc Rash (1Pe, 7Era)
383: [P] Eczematous Atopic Dermatitis and non hyperkeratotic dermatosis (1Pe, 365Era)
384: [P] Contact Dermatitis (14Pe, 60Era)
385: [P] Intertrigo (14Pe, 60Era)
386: [P] Seborrheic dermatitis (14Pe, 60Era)
387: [P] Photodermatitis (14Pe, 60Era)
388: [P] Peripheral Neuritis (FP)
389: [P] Peripheral Neuropathy or Neuritits (FP)
391: [P] Hearing Loss (30Pe, 365Era)
392: [P] Otalgia or Otitis (3Pe, 30Era)
393: [P] Low Back Pain or Injury (3Pe, 7Era)
394: [P] Gastroesophageal reflux disease (365Pe, 365Era)
395: [P] Dysmenorrhea (90Pe, 365Era)
396: [P] Osteoarthritis (FP)
397: [P] Benign Prostatic Hyperplasia (FP)
398: [P] Bladder Outflow Obstruction (0Pe, 180Era)
399: [P] Kidney Stone (1Pe, 30Era)
400: [P] Prostate Cancer among adult males (FP)
401: [P] Uterine Fibroids (FP)
402: [P] Ventilatory assist for respiratory findings with Acute Respiratory Failure (0Pe, 0Era)
403: [P] Acute Respiratory Failure in inpatient or Emergency room (0Pe, 0Era)
404: [P] Ventricular Tachycardia, in an Inpatient or Emergency room setting (1Pe, 7Era)
405: [P] Atrial Fibrillation or Flutter (1Pe, 365Era)
406: [P] Intellectual Disability (FP)
407: [P] Hemorrhoids (1Pe, 30Era)
In our last meeting (link to recording), at the OHDSI Phenotype Development and Evaluation Workgroup - we discussed a paper we are collaboratively writing about the OHDSI PhenotpyeLibrary. We discussed about the importance of FAIR and democratization of the OHDSI PhenotypeLibrary. The current submission and review process is labor-intensive and is dependent on mostly me - the librarian. Today, in the OHDSI Phenotype Development and Evaluation Workgroup we will discuss the conceptual idea of trying to make this community resource more democratized and self sustaining.
An idea that some of us (@Paul_Nagy , @jpegilbert ) are discussing is to use Zenodo/InvenioRDM as a DOI service provider. We think that this new framework would enable anyone to submit their cohort definitions to the OHDSI PhenotpyeLibrary without need to engage me i.e. they can post their cohort definitions into the OHDSI PhenotypeLibrary Zenodo organization. The posted definitions are immediately available via Zenodo/InvenioRDM and have a DOI. These are thus immediately retrievable. We then add a layer of controlled vocabulary/metadata using a community curation process (e.g. peer review, librarian review etc). The controlled vocabulary would help provide markers of trust. A snapshot of the posted definitions would be periodically converted into a release via OHDSI Github R package for PhenotypeLibrary. This R package will continue to be release version 3 and backward compatible. The R package is designed for use in OHDSI Studies like HowOften (@hripcsa). We think this this will streamline the OHDSI PhenotpyeLibrary and also make sure it both democratic and FAIR compliant. Maybe we can get it ready for OHDSI Symposium 2023.
@Paul_Nagy and I are looking for community volunteers to lead this effort. We are also hoping to get the support of the OHDSI technology advisory committee and/or open source committees to detail the feasibility of this idea, perform a proof of concept and help develop it further.
Hoping to talk about this today at the OHDSI Phenotype Development and Evaluation workgroup meeting
Good day: OHDSI Phenotype Library has now stopped taking any additional community contributions till after OHDSI Global Symposium 2023.
PhenotypeLibrary 3.15.0
Accepted Cohorts: No cohorts were accepted in this release.
New Cohorts: 7 were added.
410: [P] Acute Urinary tract infections UTI (1Pe, 30Era)
411: [P] Sepsis or Septic Shock (1Pe, 7Era)
412: Transverse myelitis indexed on diagnosis (1Ps, 0Era, 365W)
414: [P] Acute Skin Eruption symptoms (1Pe, 7Era)
415: [P] Skin Erythema (1Pe, 7Era)
416: [P] Skin Rash (1Pe, 7Era)
417: [P] Acute gastrointestinal bleeding events (7Pe, 30Era)
PhenotypeLibrary 3.16.1
Updated readme file and CohortDefinitionsubmissionRequirement document Removed some rogue files.
PhenotypeLibrary 3.16.0
Metadata documentation has improved in this release.
Reference Cohorts: 251 cohort definitions called reference cohorts have been added. These came from version 2 of the OHDSI PhenotypeLibrary. Those definitions are simple cohort definitions that have a template of one entry event criteria with conceptId and descendants. These have prefix of [P][R] in their name. There is also an indicator field called isReferenceCohort.
444: [P][R] Neck pain
445: [P][R] Hypoglycemia
446: [P][R] Eosinophilic esophagitis
447: [P][R] Esophagitis
448: [P][R] Dysphagia
449: [P][R] Nausea
450: [P][R] Constipation
451: [P][R] Myasthenia gravis
452: [P][R] Joint pain
453: [P][R] Osteoarthritis
454: [P][R] Dermatomyositis
455: [P][R] Fetal growth restriction
456: [P][R] Osteoporosis
457: [P][R] Rheumatoid arthritis
458: [P][R] Ulcerative colitis
459: [P][R] Urinary tract infectious disease
460: [P][R] Psoriasis with arthropathy
461: [P][R] Erythema multiforme
462: [P][R] Lichen planus
463: [P][R] Sepsis
464: [P][R] Myelofibrosis
465: [P][R] Thyroiditis
466: [P][R] Atopic dermatitis
467: [P][R] Systemic sclerosis
468: [P][R] Pityriasis rubra pilaris
469: [P][R] Jaundice
470: [P][R] Chronic lymphoid leukemia, disease
471: [P][R] Vitiligo
472: [P][R] Myelodysplastic syndrome (clinical)
473: [P][R] Acute transverse myelitis
474: [P][R] Pemphigoid
475: [P][R] Psoriasis
476: [P][R] Acute myeloid leukemia, disease
477: [P][R] Hypothyroidism
478: [P][R] Malignant melanoma of skin
479: [P][R] Chilblains
480: [P][R] Alopecia areata
481: [P][R] Renal failure syndrome
482: [P][R] Gastrointestinal hemorrhage
483: [P][R] Biliary cirrhosis
484: [P][R] End-stage renal disease
485: [P][R] Low back pain
486: [P][R] Premature rupture of membranes
487: [P][R] Celiac disease
488: [P][R] Diarrhea
489: [P][R] Acute renal failure syndrome
490: [P][R] Viral hepatitis C
491: [P][R] Malignant tumor of urinary bladder
492: [P][R] Cardiogenic shock
493: [P][R] Malignant tumor of cervix
494: [P][R] Primary malignant neoplasm of kidney
495: [P][R] Acute pancreatitis
496: [P][R] Abdominal pain
497: [P][R] Autoimmune hepatitis
498: [P][R] Toxic shock syndrome
499: [P][R] Type 1 diabetes mellitus
500: [P][R] Gastritis
501: [P][R] Crohn's disease
502: [P][R] Kidney stone
503: [P][R] Type 2 diabetes mellitus
504: [P][R] Sj?gren's syndrome
505: [P][R] Cough
506: [P][R] Chronic obstructive lung disease
507: [P][R] Pneumonia
508: [P][R] Allergic rhinitis
509: [P][R] Systemic lupus erythematosus
510: [P][R] Acute myocardial infarction
511: [P][R] Dyspnea
512: [P][R] Thromboangiitis obliterans
513: [P][R] Atrial fibrillation
514: [P][R] Granulomatosis with polyangiitis
515: [P][R] Sleep apnea
516: [P][R] Thrombotic microangiopathy
517: [P][R] Acute febrile mucocutaneous lymph node syndrome
518: [P][R] Myocarditis
519: [P][R] Heart failure
520: [P][R] Hypertensive disorder
521: [P][R] Asthma
522: [P][R] Coronary arteriosclerosis
523: [P][R] Arteriosclerotic vascular disease
524: [P][R] Migraine
525: [P][R] Gastroesophageal reflux disease
526: [P][R] Orthostatic hypotension
527: [P][R] Acute respiratory failure
528: [P][R] Polyarteritis nodosa
529: [P][R] Cardiac arrest
530: [P][R] Peripheral vascular disease
531: [P][R] Angina pectoris
532: [P][R] Heart disease
533: [P][R] Otitis media
534: [P][R] Transient cerebral ischemia
535: [P][R] Acute disseminated encephalomyelitis
536: [P][R] Age related macular degeneration
537: [P][R] Sensorineural hearing loss
538: [P][R] Paralytic syndrome
539: [P][R] Multiple sclerosis
540: [P][R] Optic neuritis
541: [P][R] Idiopathic peripheral neuropathy
542: [P][R] Cerebral hemorrhage
543: [P][R] Seizure
544: [P][R] Encephalitis
545: [P][R] Headache
546: [P][R] Retinal detachment
547: [P][R] Retinal disorder
549: [P][R] Epilepsy
550: [P][R] Chronic inflammatory demyelinating polyradiculoneuropathy
551: [P][R] Microcephalus
552: [P][R] Parkinson's disease
553: [P][R] Cerebrovascular accident
554: [P][R] Cerebrovascular disease
555: [P][R] Blood coagulation disorder
556: [P][R] Amyloidosis
557: [P][R] Angioedema
558: [P][R] Hyperlipidemia
559: [P][R] Thrombocytopenic disorder
560: [P][R] Pancytopenia
561: [P][R] Myasthenic syndrome due to another disorder
562: [P][R] Edema
563: [P][R] Obesity
564: [P][R] Hidradenitis
565: [P][R] Tuberculosis
566: [P][R] Kaposi's sarcoma (clinical)
567: [P][R] B-cell lymphoma (clinical)
568: [P][R] Hyperkalemia
569: [P][R] Systemic inflammatory response syndrome
570: [P][R] Leukopenia
571: [P][R] Schizophrenia
572: [P][R] Psychotic disorder
573: [P][R] Chronic pain
574: [P][R] Narcolepsy
575: [P][R] Behcet's syndrome
576: [P][R] Bipolar disorder
577: [P][R] Posttraumatic stress disorder
578: [P][R] Insomnia
579: [P][R] Ankylosing spondylitis
580: [P][R] Respiratory syncytial virus infection
581: [P][R] Multiple myeloma
582: [P][R] Bleeding
583: [P][R] Glaucoma
584: [P][R] Fever
585: [P][R] Hypokalemia
586: [P][R] Opioid dependence
587: [P][R] Opioid abuse
588: [P][R] Attention deficit hyperactivity disorder
589: [P][R] Pre-eclampsia
590: [P][R] Human immunodeficiency virus infection
591: [P][R] Autism spectrum disorder
592: [P][R] Anemia
593: [P][R] Paralysis
594: [P][R] Depressive disorder
595: [P][R] Pulmonary embolism
596: [P][R] Gout
597: [P][R] Takayasu's disease
598: [P][R] Methicillin resistant Staphylococcus aureus infection
599: [P][R] Anaphylaxis
600: [P][R] Open-angle glaucoma
601: [P][R] Vomiting
602: [P][R] Anxiety
603: [P][R] Human papilloma virus infection
604: [P][R] Cranial nerve disorder
605: [P][R] Muscle pain
606: [P][R] Stillbirth
607: [P][R] Malignant tumor of stomach
608: [P][R] Malignant neoplastic disease
609: [P][R] Cerebral infarction
610: [P][R] Eclampsia
611: [P][R] Diabetic ketoacidosis
612: [P][R] Acute tubular necrosis
613: [P][R] Tachycardia
614: [P][R] Venous thrombosis
615: [P][R] Herpes simplex
616: [P][R] Acute arthritis
617: [P][R] Monoclonal gammopathy (clinical)
618: [P][R] Pulmonary arterial hypertension
619: [P][R] Gestational diabetes mellitus
620: [P][R] Uveitis
621: [P][R] Renal impairment
622: [P][R] Non-Hodgkin's lymphoma (clinical)
623: [P][R] Motor neuropathy with multiple conduction block
624: [P][R] Primary sclerosing cholangitis
625: [P][R] Pustular psoriasis
626: [P][R] Cirrhosis of liver
627: [P][R] Miscarriage
628: [P][R] Fisher's syndrome
629: [P][R] Inflammatory bowel disease
630: [P][R] Facial palsy
631: [P][R] Livebirth
632: [P][R] Antiphospholipid syndrome
633: [P][R] Waldenstr?m macroglobulinemia
634: [P][R] Immunoglobulin A vasculitis
635: [P][R] Ventricular tachycardia
636: [P][R] Malignant tumor of breast
637: [P][R] Peripheral ischemia
638: [P][R] Neoplasm of thyroid gland
639: [P][R] Deep venous thrombosis
640: [P][R] Vasculitis
641: [P][R] Pericarditis
642: [P][R] Immune reconstitution syndrome
643: [P][R] Follicular non-Hodgkin's lymphoma
644: [P][R] Malignant tumor of prostate
645: [P][R] Guillain-Barr? syndrome
646: [P][R] Bradycardia
647: [P][R] Retinopathy due to diabetes mellitus
648: [P][R] Malignant tumor of colon
649: [P][R] Malignant tumor of esophagus
650: [P][R] Malignant tumor of ovary
651: [P][R] Dementia
652: [P][R] Vasculitis of the skin
653: [P][R] Loss of sense of smell
654: [P][R] Ischemic heart disease
655: [P][R] Aseptic meningitis
656: [P][R] Fatigue
657: [P][R] Paresthesia
658: [P][R] Hepatic failure
659: [P][R] Malignant neoplasm of liver
660: [P][R] Juvenile rheumatoid arthritis
661: [P][R] Respiratory failure
662: [P][R] Diverticulitis of large intestine
663: [P][R] Influenza
664: [P][R] Malaise
665: [P][R] Suicidal thoughts
666: [P][R] Type B viral hepatitis
667: [P][R] Guttate psoriasis
668: [P][R] SLE glomerulonephritis syndrome
669: [P][R] Schizoaffective disorder
670: [P][R] Temporal arteritis
671: [P][R] Pregnant
672: [P][R] Sense of smell impaired
673: [P][R] Primary malignant neoplasm of respiratory tract
674: [P][R] Degeneration of retina
675: [P][R] Pulmonary hypertension
676: [P][R] Microscopic polyarteritis nodosa
677: [P][R] Preterm labor with preterm delivery
678: [P][R] COVID-19
679: [P][R] Takotsubo cardiomyopathy
680: [P][R] Mantle cell lymphoma
681: [P][R] Malignant neoplasm of anorectum
682: [P][R] Marginal zone lymphoma
683: [P][R] Antineutrophil cytoplasmic antibody positive vasculitis
684: [P][R] Sensory disorder of smell and/or taste
685: [P][R] Cardiac arrhythmia
686: [P][R] Fracture of bone of hip region
687: [P][R] Chronic kidney disease
688: [P][R] Death
689: [P][R] Newborn death
690: [P][R] Suicide
695: [P][R] Optic nerve glioma
696: [P][R] Neurofibromatosis type 2
697: [P][R] Neurofibromatosis type 1
698: [P][R] Neurofibromatosis syndrome
699: [P][R] Major Depressive Disorder
Accepted Cohorts: No cohorts were accepted in this release. Four new cohorts have been added. These are minor modifications of previously published cohorts.
691: Transverse myelitis or symptoms indexed on symptoms or diagnosis
692: Transverse myelitis indexed on diagnosis
693: Acquired Neutropenia or unspecified leukopenia
694: Appendicitis during Inpatient visit
PhenotypeLibrary 3.17.0
Accepted Cohorts: No cohorts were accepted in this release.
New Cohorts: 39 were added.
701: [P][R] Ascites
702: [P] Alanine aminotransferase (ALT) elevated
703: [P] Aspartate aminotransferase (AST) elevated
705: [P] Total Bilirubin elevated
706: [P] Prothrombin time (PT) elevated
707: Inpatient Hospitalization (0Pe, 1Era)
708: [P] International normalized ratio (INR) elevated
709: [P][R] Chronic liver disease
710: [P] Cirrhosis of liver or its sequela
711: [P][R] Transplanted liver present
712: [P] Viral hepatitis including history of
713: [P] Alcoholic hepatitis or alcohol liver disorder
714: [P][R] Endometriosis (clinical)
715: [P] Hepatic fibrosis
716: [P] Acute Hepatic Injury
717: [P] Portal hypertension or esophageal varices
719: [P] Acute Hepatic Injury or jaundice while inpatient with no cooccurring certain liver disease
720: [P] Aplastic Anemia
721: [P] Sudden New Onset Blindness
722: [P] Endometriosis indexed on procedure with two or more diagnosis among females 15 to 49
723: [P] First Acute Hepatic Failure with no known severe liver disease
724: [P] First Acute Hepatic Failure with no known liver disease
725: [P] All events of Acute Kidney Injury (AKI), with a washout period of 30 days
726: [P] All events of Anaphylaxis, Mini-Sentinel
727: [P] All events of Angioedema, with a washout period of 180 days
728: [P] Autoimmune hemolytic anemia events not including evans syndrome
729: [P] Autoimmune hepatitis, with a washout period of 365 days
730: [P] Acute pancreatitis, indexed on visit with NO chronic or hereditary pancreatitis
731: [P] Sudden Hearing Loss, No congenital anomaly or middle or inner ear conditions
732: [P] Severe Cutaneous Adverse Reaction (SCAR = SJS+TEN+DRESS) with clean window
733: [P] Drug Rash with Eosinophilia and Systemic Symptoms (DRESS) with clean window
734: [P] Drug Rash with Eosinophilia and Systemic Symptoms (DRESS)
735: [P] Acute Liver Injury indexed on diagnosis or symptoms with no chronic hepatic failure
736: [P] Acute Liver Injury NO viral, alcoholic, chronic hepatic failure
737: [P] Neutropenic Fever, Inpatient or ER, indexed on fever or Infection, 90 days era
738: [P] Autoimmune hemolytic anemia
739: [P] All events of Isolated Immune Thrombocytopenia (ITP), with a washout period of 365 days
740: [P] Earliest event of Pulmonary arterial hypertension (PAH)
741: [P] Earliest event of Thrombotic microangiopathy (TMA) or Microangiopathic hemolytic anemia (MAHA)
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.