Phenotype Pheburary 2025

General
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Recording Youtube Playlist Phenotype Phebruary 2025

Kicking Off 2025 Phenotype Phebruary!

Dear OHDSI Community,

We are beyond excited to launch 2025 Phenotype Phebruary! For the past three years, February has been one of the most thrilling times for our community—a month where we come together to focus on the crucial science of phenotype development and evaluation.

Looking back, the past three Phebruaries have brought remarkable achievements:

:white_check_mark: Dozens of new phenotypes added to our library
:white_check_mark: Over 50 new collaborators joining our mission
:white_check_mark: Two peer-reviewed publications advancing the field
:white_check_mark: Key clinical insights into critical health conditions
:white_check_mark: Tens of educational sessions and engaging community calls ️
:white_check_mark: A deeper understanding of the challenges and opportunities in phenotype science

Now, as we step into February 2025, we’re fueled by our past successes, inspired by the magic of OHDSI, and more motivated than ever to push boundaries. We recognize the challenges ahead, but we also believe that the sky is the limit when this incredible community comes together!

Let’s make 2025 Phenotype Phebruary our best one yet! :rocket::sparkles:

Building on the momentum from Dry January, we are excited to continue our journey of tackling the 14 critical evidence gaps—questions where our observational data can provide valuable insights! Addressing these questions starts with building high-quality phenotypes for the exposures, indications (patient populations), and outcomes specified in each research question. Our primary goal this Phebruary is to develop these phenotypes, make them analysis-ready, and ensure they are available in the OHDSI Phenotype Library for future reuse.

How We’ll Achieve This :mag:

We’ll structure the month by aligning each week with a key step in the phenotype development and evaluation process:

:pushpin: Week 1 – Writing clinical descriptions & reviewing prior work
:pushpin: Week 2 – Developing cohort definitions
:pushpin: Week 3 – Evaluating cohorts using CohortDiagnostics
:pushpin: Week 4 – Iterating on cohort definitions & evaluating with additional OHDSI tools

Rather than discussing these steps in the abstract, we will work hands-on using real phenotypes needed for the 14 studies, engaging both study leads and the broader OHDSI community to collaborate at each stage.

Get Involved! :handshake:

:white_check_mark: Weekly instructions will be posted in the forums
:white_check_mark: Discussions will take place in our community calls
:white_check_mark: Support will be available in Phenotype WG weekly meetings

Our collective mission is to track our progress and finalize as many phenotypes as possible for these studies, ensuring they are ready for analysis and available in the OHDSI Phenotype Library for broader community use.

Together, let’s make 2025 Phenotype Phebruary a milestone for phenotype development! :rocket::sparkles:

Your fellow Phebruarians
@Azza_Shoaibi @aostropolets @Gowtham_Rao

(Thank you to our artificial intelligence friend for the cheese writing style)

Phenotype Phebruary 2025 discussions are here

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January 31st 2025, Planning call:
(AI Generated)
Recording Youtube Playlist Phenotype Phebruary 2025

Recording MS Teams Join conversation

Working location
Phenotype Phebruary 2025

2025 Planning

Overview:
The working group has established a structured four-week process dedicated to phenotype development. The overall goal is to produce ready-to-use phenotypes by the end of February, providing a clear framework that the community can build upon.

Development Process:

  1. Clinical Description (Week 1):
    • Utilize Gen AI prompts and conduct literature searches to create detailed clinical descriptions.
  2. Concept Set and Logic Building (Week 2):
    • Develop concept sets and construct logical frameworks for the phenotypes.
  3. Evaluation and Iteration (Weeks 3–4):
    • Employ diagnostic tools (e.g., cohort diagnostics) to evaluate and refine the phenotypes through iterative feedback.

The team emphasized the value of reusing existing phenotype templates where possible and discussed criteria for when new definitions are necessary. This approach balances standardized procedures with the flexibility required to address complex or unique cases.

Coordination and Tracking:

  • A master tracker (Excel-based tool) will be created to consolidate and monitor progress for each phenotype. Phenotype Phebruary 2025
  • The tracker will record key milestones, including the completion of clinical descriptions, cohort development steps, and the assignment of final cohort IDs.
  • Discussions also covered the best folder structure within Microsoft Teams—whether to organize by study or by phenotype—to ensure all study leads and contributors have the required access.
  • This robust tracking framework is intended to streamline progress and facilitate the migration of completed phenotypes into a centralized library.

Contributor Engagement and Task Allocation:

  • A sign-up form will be launched to collect details from interested members, including their skills, time commitment, and data access.
  • This structured approach is designed to build a diverse pool of contributors who will support various stages of the process, while study leads maintain overall responsibility for their respective projects.
  • Clear role delineation is key to preventing overlap and ensuring effective collaboration.

Meeting Scheduling and Communication Protocols:

  • A detailed meeting schedule has been established with recurring sessions on Tuesday, Wednesday, and Friday:
    • Tuesday: Demos and process overviews
    • Wednesday: Study lead coordination and task assignment
    • Friday: Broader working group discussions
  • Microsoft Teams will be used to create recurring invitations with shared links to essential documents, ensuring that all study leads and contributors are well informed.

Q&A and Process Adjustments:

  • The team addressed concerns about phenotype specificity, timeline rigidity, and adjustments for complex definitions (e.g., “major surgery”).
  • While the official deadline for phenotype completion is set at the end of February, the group acknowledged that iterative improvements can continue post-deadline.
  • This balanced approach reinforces the importance of structured progress while accommodating real-world complexities, ensuring all contributors understand expectations and can collaborate effectively.

To-Do List

  1. Clinical Description Phase:

    • Prepare and distribute Gen AI prompts for clinical descriptions.
    • Schedule literature review sessions and assign topics to contributors.

  2. Concept Set and Logic Building:

    • Organize a tutorial/demo on concept set construction.
    • Identify phenotypes that can be templated versus those needing new development.

  3. Evaluation and Iteration:

    • Execute, Set up access to cohort diagnostic tools.
    • Define criteria for evaluating phenotype readiness.
    • Plan a feedback loop for iterative improvements.

  4. Master Tracker and Folder Structure:

    • Create the master tracker (Excel sheet) with key milestones.
    • Decide on and implement the optimal folder structure in Teams (by study or phenotype).
    • Verify that all study leads and contributors have proper access.

  5. Contributor Engagement:

    • Develop and launch the volunteer sign-up form.
    • Define and communicate specific roles and tasks for study leads and contributors.

  6. Meeting Coordination:

    • Finalize recurring meeting times and invite all participants via Microsoft Teams.
    • Ensure shared links and documents are attached to meeting invitations.
    • Confirm schedule details with all study leads and adjust if necessary.

  7. Communication and Follow-Up:

    • Publish the online forum announcement with the detailed process overview.
    • Set reminders for each phase’s key milestones.
    • Plan a post-February review session to discuss iterative improvements.
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Read more

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Thank you @Gowtham_Rao ! For next steps:

  1. all Clinical Guideline Opportunities study leads watch your inbox for an email from @aostropolets and please follow the instructions of the email.
  2. everyone interested in participating on this year phenotype pheburary- please attend this Tuesday community call where we will go over the plan circulate a form for all of you sign up
  3. on Tuesday community call @Gowtham_Rao will go over step one: developing a clinical description.
    Can’t wait to collaborate with the amazing members of this community!!!
1 Like
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We are seeking volunteers to assist in reformatting a dataset for the 2025 Guideline-driven Evidence Phenotype initiative. The task involves converting the existing wide-format spreadsheet into a long-format structure, and tracking the progress. Please DM me if interested.

See full details here OHDSI Phenotype Phebruary and workgroup updates - #70 by Gowtham_Rao

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Full details posted here : OHDSI Phenotype Phebruary and workgroup updates - #71 by Gowtham_Rao

Youtube https://youtu.be/vmRWfCBb6OQ

Executive summary:

During the February 5th Phenotype Phebruary 2025 Office Hours, participants focused on five main areas of collaboration and methodological refinement. First, they confirmed that all current study materials must be stored in the Teams Phenotype Workgroup folder for easy access, eventually transferring finalized cohorts and code to GitHub for broader community use. Next, the group discussed methods for searching and reusing existing phenotype definitions, including the OHDSI Phenotype Library, Shiny-based cohort diagnostics, VA’s Cipher platform, and external resources such as Darwin and Sentinel. They stressed verifying definitions for suitability and converting them into Atlas-compatible formats when necessary.

Participants then reviewed best practices for phenotype development and validation, emphasizing both qualitative (clinical expertise) and quantitative (cohort diagnostics) measures, along with tools like PheValuator and Keeper. This stepwise, iterative approach aims to ensure robust, multi-site applicability. A detailed discussion on pediatric vision screening illustrated the complexities of defining non-disease phenotypes: it requires procedure-based logic, complementary comparator cohorts (e.g., well-child visits), and careful attention to data capture inconsistencies. Finally, the conversation turned to Kevin’s progress on Ulcerative Colitis and Crohn’s Disease phenotypes, which will incorporate “enhanced” treatment pathway analyses (e.g., switching behaviors, durations). These will soon transition from the J&J Library to OHDSI’s Library, aligning with network standards and improving cross-site comparability.

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Phenotype Phebruary 2025 Office Hours Phebruary 7th 2025

Youtube https://youtu.be/3_hvmbIZa5Q

Full details OHDSI Phenotype Phebruary and workgroup updates - #72 by Gowtham_Rao

Executive Summary
During the February 7, 2025 Phenotype Phebruary Office Hours, the group focused on ensuring that 14 ongoing studies finalize their clinical descriptions and record them in a centralized progress tracker. Organizers emphasized prompt engineering for ChatGPT-based drafting, recognizing both the tool’s usefulness and the need for expert review. Several leads shared their experiences—highlighting successes and limitations in adapting ChatGPT outputs for conditions, drug exposures, or procedures.

Participants also discussed leveraging existing resources (e.g., the OHDSI Phenotype Library, PubMed) for validated algorithms, while acknowledging the challenges in converting older ICD-9-based definitions to ICD-10. Attention turned to cohort construction in Atlas Demo, where record counts in the OHDSI Evidence Network inform concept set choices. With Tuesday’s community call approaching, the group agreed on final deadlines for uploading clinical descriptions and setting up concept sets. Two volunteers (Tatsiana and Kevin) will demonstrate live how they develop phenotypes—one focusing on first-episode psychosis, the other adapting inflammatory bowel disease definitions—showcasing the detailed steps, sharing lessons, and clarifying best practices for building robust, reproducible cohorts.

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See post from @Azza_Shoaibi

“team, here is a the log of the phenotype library cohorts- if you want to look for a phenotype in the library OHDSIpLCohorts.xlsx”

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Phenotype Phebruary 2025 Office Hours Phebruary 12th 2025

Youtube https://youtu.be/17UXeDIJWos

Full details OHDSI Phenotype Phebruary and workgroup updates - #73 by Gowtham_Rao

Executive Summary:

  1. Type 2 Diabetes Phenotype Development:
    The group debated whether to define type 2 diabetes using diagnosis codes alone or by incorporating lab values and medication data. Emphasis was placed on balancing sensitivity (to capture as many cases as possible) with specificity (to avoid misclassification), particularly in relation to insulin use and alternate entry criteria. Multiple phenotype variants will be developed and compared using cohort diagnostics to determine the optimal approach.

  2. Diabetic Retinopathy Screening Cohort Design:
    Discussion centered on designing a cohort that reflects the recurrent nature of diabetic retinopathy screening (typically recommended annually). The team weighed the benefits of indexing on the earliest screening event versus capturing all screening events over time. Key challenges include managing variable provider specialty data, reliance on specific CPT codes, and the potential need for custom SQL to integrate washout periods effectively.

  3. Antipsychotic Treatment Cohort and Censoring Strategy:
    Strategies were discussed to isolate a monotherapy cohort by excluding patients with prior exposure to other antipsychotics and censoring those who switch treatments post-index. Although this approach helps maintain a clean cohort, concerns were raised about the risk of informative censoring, where treatment changes driven by clinical factors could bias the results.

  4. Technical Implementation in Atlas and Query Logic:
    The technical discussion emphasized using the visit start date as the index for cohort entry, with conditions required to occur within the visit window. Given that condition end dates are often missing, the query logic defaults to using the condition start date. The group acknowledged that while standard Atlas functionality covers most needs, complex scenarios may require custom SQL adjustments.

  5. Naming Conventions and Infrastructure for the Phenotype Library:
    To enhance consistency and discoverability, the group proposed standard naming conventions (e.g., prefixes like PP25 or F-25) for phenotype definitions. Integration with the Odyssey forums and GitHub was recommended to ensure clear clinical descriptions, facilitate collaboration, and maintain version control across the phenotype library.

  6. Project Coordination, Communication, and Next Steps:
    The meeting concluded with plans for robust progress tracking through scheduled office hours and proactive outreach to study leads. Emphasis was placed on volunteer engagement, standardization of outputs, and ensuring that phenotype definitions are well-documented and aligned with the established infrastructure.

Overall, the workgroup’s collaborative effort aims to refine phenotype development by testing multiple definitions, addressing technical challenges, and ensuring clear communication and coordination among study leads and volunteers.

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Youtube: https://youtu.be/BPfKjNHoh9g
Full details OHDSI Phenotype Phebruary and workgroup updates - #76 by Gowtham_Rao

Executive Summary

On February 14, 2025, the team convened to advance and refine key phenotype definitions critical to upcoming diagnostic evaluations and broader research deployment. The discussion centered on six primary areas:

  • Project Overview & Code Definition:
    The team is on a tight deadline to finalize and extract core phenotype definitions, converting them into JSON files for diagnostic testing by Johnson and Johnson. Clear objectives were set for reviewing, naming, and packaging these definitions, with a progress tracker guiding the next steps.

  • Rheumatic Disease Phenotyping:
    Focus was placed on refining phenotype definitions for rheumatic diseases. While most definitions are nearly complete, further expert input is needed—especially for cases involving complex scenarios like steroid usage—to ensure clinical accuracy.

  • Vision Screening Phenotyping:
    The team is developing a pediatric vision screening phenotype using well-child visits as a proxy. They are addressing challenges related to data granularity and stratification by age and time, aiming to validate the approach against real-world screening records.

  • Osteoporosis Phenotyping:
    An iterative “two out of three” logic is being implemented for osteoporosis, combining diagnosis codes, medication records, and fragility fracture data. Discussions emphasized the need to exclude traumatic fractures and to ensure that the operational criteria align with clinical descriptions.

  • Medication Concept Set Challenges:
    The refinement of medication groupings, particularly for osteoporosis treatments, is underway. The team is moving away from SPL classifications in favor of RxNorm ingredients to more accurately capture relevant drug formulations and distinguish between monotherapy and combination therapies.

  • Operational Next Steps & Diagnostics:
    Final steps include updating the progress tracker, standardizing cohort naming conventions, and scheduling diagnostic tests both internally and with external partners. These actions will help identify and resolve any data inconsistencies before broader deployment.

This meeting set the stage for ensuring that phenotype definitions are both clinically robust and operationally ready, supporting the ongoing effort to standardize and validate these definitions across different data sources.