OHDSI Phenotype Phebruary and workgroup updates

General
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Phenotype Phebruary 2025 Office Hours – February 14, 2025

1. Project Overview & Code Definition Process

  • Context & Deadline:
    The team is under a strict February 14 deadline to finalize and extract core phenotype definitions. These definitions are being reviewed, renamed, and packaged as JSON files for deployment (e.g., in Strategus) and diagnostic testing by Johnson and Johnson. Outputs will eventually be shared on results.ohdsi.org for broader community access.

  • Key Steps:

    • Review and properly name existing code definitions (likely developed within Atlas).
    • Extract definitions and run diagnostic tests.
    • Update the progress tracker and coordinate next actions.

  • Speaker Highlights:

    • Gowtham Rao: Sets clear objectives to “grab all the core definitions.”
    • Anna Ostropolets: Confirms the deadline and extraction process.
    • Team Input: Supports and clarifies immediate next steps.

  • Assumptions & Gaps:

    • Assumes familiarity with current definitions and processes.
    • Lacks discussion on technical challenges during JSON extraction.

2. Rheumatic Disease Phenotyping

  • Overview:
    The team is finalizing phenotype definitions for rheumatic diseases, focusing on patient identification and medication outcomes. While most definitions are near-final, some (especially those involving steroid use) require further review and expert input.

  • Key Actions:

    • Refine definitions with feedback from clinical experts across infectious disease, ophthalmology, and rheumatology.
    • Address complexities in cases involving steroids and cancer outcomes.

  • Speaker Highlights:

    • Christopher Mecoli: Provides status updates and notes that only select cases need further input.
    • Clinical Experts: Their input will be integrated to ensure accuracy and clinical relevance.

  • Assumptions & Gaps:

    • Assumes that the majority of definitions are robust.
    • Specific strategies for addressing complex cases remain to be detailed.

3. Vision Screening Phenotyping & Analysis

  • Overview:
    For pediatric vision screening, the team is defining a cohort using well-child visits as a proxy, while considering stratification by age and calendar periods despite some data limitations (e.g., for children under one).

  • Key Actions:

    • Determine whether to use well-child visits exclusively or a broader set of outpatient visits.
    • Incorporate age restrictions and temporal stratification to facilitate trend analysis.

  • Speaker Highlights:

    • Michelle Hribar: Raises questions on cohort definition and data limitations.
    • Gowtham Rao & Anna Ostropolets: Guide on structuring the phenotype and refining concept sets.

  • Assumptions & Gaps:

    • Assumes well-child visits are a reliable proxy despite potential data capture challenges.
    • Lacks a clear validation plan against actual vision screening records.

4. Osteoporosis Phenotyping & Criteria

  • Overview:
    The osteoporosis phenotype is being refined using a “two out of three” logic based on diagnosis, medication, and fragility fractures—ensuring traumatic fractures (especially in patients under 50) are excluded.

  • Key Actions:

    • Establish nested logic that includes any two of the three criteria.
    • Align the clinical description with the operational model in Atlas.

  • Speaker Highlights:

    • Chen Yanover: Questions the clarity of the “two out of three” approach.
    • Gowtham Rao & Anna Ostropolets: Emphasize logical clarity and proper exclusion of traumatic fractures.

  • Assumptions & Gaps:

    • Assumes current definitions and concept sets are robust.
    • More detail is needed on handling borderline cases and potential data inconsistencies.

5. Medication Concept Set Challenges

  • Overview:
    The team is refining medication concept sets for the osteoporosis phenotype by addressing classification challenges—favoring RxNorm ingredients over SPL for capturing oral residronic acid formulations and ensuring clear differentiation between monotherapy and combination therapies.

  • Key Actions:

    • Reassess the medication grouping logic to align with clinical intent.
    • Validate that all descendant concepts (various formulations) are appropriately captured without over-specification.

  • Speaker Highlights:

    • Anna Ostropolets: Recommends against using SPL and advocates for RxNorm-based classification.
    • Chen Yanover & Gowtham Rao: Stress the need for streamlined logic that matches the intended clinical grouping.

  • Assumptions & Gaps:

    • Assumes current mappings between classification systems are robust.
    • More discussion is needed on reconciling data differences across sites.

6. Operational Next Steps & Diagnostics

  • Overview:
    The team is transitioning to operational readiness by finalizing core phenotype definitions, updating the progress tracker, and standardizing cohort naming. Upcoming steps include running diagnostic tests internally and with Johnson and Johnson.

  • Key Actions:

    • Extract definitions as JSON files and update the progress tracker.
    • Standardize naming conventions (using square brackets with study abbreviations).
    • Coordinate diagnostic runs and follow-up meetings to address any data inconsistencies.

  • Speaker Highlights:

    • Gowtham Rao: Urges quick finalization and execution of diagnostic tests.
    • Anna Ostropolets: Highlights the importance of consistent naming and data validation.
    • Oleg Zhuk & Evan Minty: Ensure operational steps are practical given the current infrastructure.

  • Assumptions & Gaps:

    • Assumes the progress tracker accurately reflects the status of each definition.
    • Does not elaborate contingency plans for unexpected diagnostic discrepancies.