OHDSI Home | Forums | Wiki | Github

OHDSI Phenotype Library announcements

#1

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

  1. 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.
  2. 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.
  3. 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

  1. The OHDSI Phenotype Development and Evaluation Workgroup is considering submissions to the OHDSI Phenotype Library.
  2. 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.
  3. 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:

1 Like
Status of the OHDSI phenotype library and associated resources
Brainstorming on how to build the OHDSI Phenotype Library as a community resource
#2

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)

3 Likes
#3

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.

#4

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.

#5

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.

#6

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

1 Like
#7

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

  1. meet the required submission requirement prior
  2. Complete a peer review process.
  3. Be accepted to the library
#8

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

image
image875×603 37.7 KB

1 Like
#9

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

image
image1864×770 55 KB

#10

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.

1 Like
#11

Thank you for maintaining this resource @Gowtham_Rao!

#12

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
1 Like
#13

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)
t