OHDSI / OHDSI/StudyAgent

Add review-gated prior-event exclusion support to phenotype_make_computable

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enhancement
Dominant language
Python
Stars
12
Forks
7
Avg merge
2m
Merged PRs (30d)
12

Description

Summary

Extend phenotype_make_computable with a typed, review-gated negative temporal criterion that can express an index event with no earlier event from a separately reviewed concept set.

Motivating designs

  • New canagliflozin exposure with no prior SGLT2 inhibitor exposure.
  • An index event with no specified Condition occurrence in a defined pre-index or near-index window.

The current supporting_condition_occurrence mode is positive-only and therefore cannot represent either design. temporal_followup also cannot: its Drug mode uses a Condition trigger and its clean window applies to the index drug and trigger condition, rather than a separate drug-class exclusion set.

Proposed scope

Add a typed scope object such as prior_event_exclusion, with:

  • an index concept set and separately named, human-reviewed exclusion concept set;
  • explicit OMOP domain(s), including Drug and Condition;
  • explicit start and end bounds (for example, -365 through -1);
  • explicit index-day policy; and
  • an explicit distinction between a finite clean-window new-user definition and the non-provable claim of no recorded event ever.

The deterministic emitter should produce an attrition criterion requiring zero qualifying exclusion events in the confirmed interval. Preserve existing concept-set policy review, durable review/approval artifacts, validation, and fail-closed behavior. Do not infer the interval, class concept policy, or exclusion policy.

Acceptance considerations

  • A reviewed canagliflozin index set plus reviewed SGLT2 inhibitor class set can emit a valid definition for a declared clean-window new-user cohort.
  • A direct entry event plus reviewed Condition exclusion set can emit a valid no-prior-condition cohort.
  • Positive supporting-condition and post-exposure temporal-followup behavior remain unchanged.
  • Invalid/incomplete exclusion scope is rejected before emission.
  • Tests cover typed validation, Capr/Circe output, and review-gated provenance.

Cross-repository coordination

The enhancement needs corresponding shell and ACP-client handoff work in OHDSI/SlashOhdsiStrategusAssistant and OHDSI/SlashOhdsiAcpClient; linked issues will track those changes.

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First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start at the phenotype_make_computable entry point and trace the existing supporting_condition_occurrence and temporal_followup modes through validation and the deterministic emitter. Review how Capr/Circe output and concept-set approval provenance are tested, then define the typed exclusion scope, interval and index-day policy before adding coverage for valid and rejected definitions.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
data
Issue type
Feature
Difficulty
5/5
Estimated time
Over a week
Activity status
Active
Clarity
Mostly clear
Newbie friendliness
35/100

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