OHDSI Phenotype Library announcements

Gowtham_Rao · July 6, 2022, 2:40pm

I would like to use this thread to make announcements regarding OHDSI Phenotype Library. The announcements will be on three topics

Atlas-Phenotype is maintained by the OHDSI Phenotype Development and Evaluation Workgroup. This workgroup will use this thread to make any key announcements regarding cohort definitions.
OHDSI/PhenotypeLibrary : Periodically, cohort definitions from Atlas-Phenotype will be published into this repository. This will be version controlled with HADES compatibility. It will be an installable, referenceable, non executable R package with HADES version numbering convention.
ohdsi-studies/PhenotypeLibraryDiagnostics: An executable study package called PhenotypeLibraryDiagnostics will be maintained, and it will be dependent on OHDSI/PhenotypeLibrary . Data partners will be pasked to execute this package on their sites and contribute the results back to the community. The results will be compiled and uploaded to data.ohdsi.org/PhenotypeLibrary (thank you @admin for support on this)

Submissions to the OHDSI Phenotype Library

The OHDSI Phenotype Development and Evaluation Workgroup is considering submissions to the OHDSI Phenotype Library.
Valid cohort definition submissions that originate from an Atlas (or Circe compliant source like CapR will go into [submitted] state and will be available at Atlas-Phenotype. These are not considered [accepted]. To be accepted, they should complete an evaluation by the Phenotype Development and Evaluation Workgroup and only accepted Cohort Definitions get promoted to the version controlled Library repository OHDSI/PhenotypeLibrary. Cohort Definitions that do not conform to Circe (e.g. probabilistic definitions and SQL only definitions) are also accepted.
We encourage you to submit the results of running CohortDiagnostics on the submitted OHDSI CohortDefinitionSet . Other data partners will be invited to run CohortDiagnostics on the submitted cohortDefinitionSet. Based on the collective review of the CohortDiagnostics output a decision of acceptance will be made.

Technical Requirements:

Submissions should conform to the OHDSI CohortDefinitionSet object as defined by OHDSI/CohortGenerator. (example: use ROhdsiWebApi::exportCohortDefinitionSet ) . This is required to make definitions importable into Atlas-Phenotype .

Gowtham_Rao · July 6, 2022, 12:41pm

Version 3.1.0 of the OHDSI PhenotypeLibrary has been released PhenotypeLibrary. The package is currently being executed by data partner volunteers and once the cycle is complete the results will be available https://data.ohdsi.org/PhenotypeLibrary/

(note - the link above is currently dead)

Gowtham_Rao · July 6, 2022, 11:58am

For HADES compatibility (thank you @schuemie ) we will follow the following version number for the PhenotypeLibrary github repository.

Major number 3.0.0
Second number will be a number from >= 0 - representing each release. Backward compatible.
Third number will represent hot fix

The repository is now being considered to be part of HADES.

Gowtham_Rao · July 8, 2022, 10:56am

PhenotypeLibrary package version 3.1.1 has been released. This release makes this package part of HADES ecosystem. Discussed in HADES Channel and Github issue here.

Gowtham_Rao · July 8, 2022, 8:30pm

OHDSI Phenotype Library and Development Workgroup met today - recording and slides are available here

Note: discussions were held on community contributions to OHDSI Phenotype library and workshop for the OHDSI Symposium 2022.

Gowtham_Rao · August 10, 2022, 5:21pm

The OHDSI Phenotype Development and Evaluation Workgroup will be considering the submission of @Marcela and @david_vizcaya on August 12th 2022. Please come and join us for the very first peer review session. OHDSI will perform an open peer review. The assigned peer reviewer is @AzzaShoaibi .

Please see discussion related to the phenotype here Phenotype Phebruary Day 29 - Acute Kidney Injury

We are still developing our process for peer review and acceptance, and this experience will be a learning for all of us.

If you are interested in submitting a phenotype definition, the submission guidelines are here Cohort Definition Submission Requirements • PhenotypeLibrary

The submitted phenotypes are at atlas-phenotype.ohdsi.org

Gowtham_Rao · September 19, 2022, 3:41pm

OHDSI Phenotype Library update
On 2022-09-06 version 3.2.0 of the OHDSI Phenotype Library was released. Please see list of cohorts here

Number of peer reviewed cohort definitions = 0
Number of cohort definitions awaiting peer review = 84

We currently have 84 cohort definitions that are in ‘pending peer review’ stage. These 84 cohort definitions have previously undergone phenotype development and evaluation process during 2020 to 2022, but the development and evaluation was not documented and did not receive peer review. It was used in various OHDSI studies.

To be formally accepted into the OHDSI Phenotype Library they need to

meet the required submission requirement prior
Complete a peer review process.
Be accepted to the library

Gowtham_Rao · February 14, 2023, 1:47am

Version 3.10.0 has been released

For list of cohort definitions in OHDSI Phenotype library please see Cohort Definitions in OHDSI Phenotype Library • PhenotypeLibrary

Adam_Black · March 9, 2023, 12:26am

Quick question: A total of 6 phenotypes in the OHDSI phenotype library have “Accepted” status right? I’m looking for all accepted phenotypes.

Gowtham_Rao · March 9, 2023, 12:23pm

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.

Adam_Black · March 9, 2023, 1:20pm

Thank you for maintaining this resource @Gowtham_Rao!

Paul_Nagy · March 11, 2023, 1:45pm

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

Gowtham_Rao · March 14, 2023, 12:43pm

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)

Gowtham_Rao · May 30, 2023, 4:00pm

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

Gowtham_Rao · June 9, 2023, 11:08am

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)

Gowtham_Rao · June 23, 2023, 10:25am

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