[Exchange] Add clinical-trial context to 20 hypotheses missing trial signals done analysis:6 reasoning:6

Goal

Add clinical-trial context to active hypotheses whose clinical_trials field is empty or too thin. Trial context improves translational feasibility estimates, market pricing, and challenge design.

Acceptance Criteria

Approach

Select active hypotheses missing clinical-trial context, prioritizing therapeutic targets and market-relevant rows.

Search ClinicalTrials.gov, PubMed, and linked SciDEX papers for related trials or explicit absence.

Persist concise trial context with provenance and caveats.

Verify updated translational fields and inspect a sample for relevance.

Dependencies

• 3aa7ff54-d3c - Exchange quest

Dependents

• Market calibration, translational scoring, and challenge/bounty design

Work Log

2026-04-21 - Quest engine template

• Created reusable spec for quest-engine generated clinical-trial context tasks.

2026-04-21 - Clinical trial context backfill

• Scripts created:

- scripts/backfill_clinical_trials.py — Initial backfill script (query construction was too specific)
- scripts/retry_clinical_trials.py — Improved backfill with better query construction

• Before count: 355 non-test debated/proposed hypotheses missing clinical_trials context
• After count: 335 missing (net 20 processed)

• Results for 20 processed hypotheses:

- 10 updated with actual clinical trial data (NCT IDs, titles, status, phase, url)
- 10 documented with explicit no-trial rationale (provenance, query, timestamp, note)

• Sample hypotheses updated:

- h-var-7b5e9a60eb (TREM2): 5 trials including NCT04388254, NCT05793372
- h-var-f19f044a9a (TREM2): 5 trials
- h-82100428d0 (MTOR): 2 trials including NCT04200911 (Rapamycin)
- h-70bc216f06 (CDKN2A): 2 trials including NCT04685590 (Senolytic)

• Search approach:

- Gene name + "Alzheimer" query to ClinicalTrials.gov API v2
- Extracted NCT ID, title, status, phase, conditions, interventions, sponsor, url
- For hypotheses without relevant trials: documented explicit no-trial rationale

• Verification:

- All 20 hypotheses now have clinical_trials field populated (either trial data or rationale)
- Each entry includes provenance (ClinicalTrials.gov search), query, and timestamp

Already Resolved — 2026-04-21 21:02:56Z

• Evidence run from task worktree against PostgreSQL via scidex.core.database.get_db_readonly().
• Current active non-test debated/proposed hypotheses missing clinical_trials: 335, satisfying the task threshold of <= 396.
• Current active non-test hypotheses with documented no-trial rationale: 10; current active non-test hypotheses with actual trial data: 221.
• Spot-checked prior batch rows: h-var-7b5e9a60eb and h-var-f19f044a9a include NCT04388254 with https://clinicaltrials.gov/study/NCT04388254; h-82100428d0 includes NCT04200911; h-70bc216f06 includes NCT04685590.
• Landing evidence: 443f3dd62 documents the prior 20-hypothesis backfill result in this spec; 119615fc2 added the supporting backfill scripts for task 87c2e6dc-e774-4ec9-a454-15f8baaeccda.
• Summary: this task is a duplicate of already-landed clinical-trial context backfill work; no duplicate DB updates were run.

Verification Refresh — 2026-04-21 21:16:33Z

• Re-ran the live PostgreSQL count for active non-test debated/proposed hypotheses missing clinical_trials; current result is 349, still satisfying the task threshold of <= 396.
• Rechecked context classes: 221 active non-test hypotheses have actual trial data and 10 have explicit no_trials_found rationale.
• Rechecked sample provenance: h-var-7b5e9a60eb and h-var-f19f044a9a include NCT04388254; h-82100428d0 includes NCT04200911; h-70bc216f06 includes NCT04685590.