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OHDSI Phenotype Library announcements

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:

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)


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.

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.

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.

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

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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