SciDEX — Task: [Exchange] Enrich top hypotheses with PubMed citat

## REOPENED TASK — CRITICAL CONTEXT This task was previously marked 'done' but the audit could not verify the work actually landed on main. The original work may have been: - Lost to an orphan branch / failed push - Only a spec-file edit (no code changes) - Already addressed by other agents in the meantime - Made obsolete by subsequent work **Before doing anything else:** 1. **Re-evaluate the task in light of CURRENT main state.** Read the spec and the relevant files on origin/main NOW. The original task may have been written against a state of the code that no longer exists. 2. **Verify the task still advances SciDEX's aims.** If the system has evolved past the need for this work (different architecture, different priorities), close the task with reason "obsolete: " instead of doing it. 3. **Check if it's already done.** Run `git log --grep=''` and read the related commits. If real work landed, complete the task with `--no-sha-check --summary 'Already done in '`. 4. **Make sure your changes don't regress recent functionality.** Many agents have been working on this codebase. Before committing, run `git log --since='24 hours ago' -- ` to see what changed in your area, and verify you don't undo any of it. 5. **Stay scoped.** Only do what this specific task asks for. Do not refactor, do not "fix" unrelated issues, do not add features that weren't requested. Scope creep at this point is regression risk. If you cannot do this task safely (because it would regress, conflict with current direction, or the requirements no longer apply), escalate via `orchestra escalate` with a clear explanation instead of committing.

Completion Notes

Auto-completed by supervisor after successful deploy to main

Git Commits (2)

Squash merge: orchestra/task/e881d7bb-enrich-top-hypotheses-with-pubmed-citati (6 commits)2026-04-16

[Exchange] Enrich 16 zero-citation hypotheses with PubMed evidence [task:e881d7bb-9f71-4f02-af2c-bbfbdab1def3]2026-04-02

Spec File

[Exchange] Enrich top hypotheses with PubMed citations — batch 2 (0-citation high-scorers)

ID: e881d7bb-9f7 Priority: 92 Type: one_shot Status: open

Goal

[Exchange] Enrich top hypotheses with PubMed citations — batch 2 (0-citation high-scorers)

Acceptance Criteria

☐ Concrete deliverables created

☐ Work log updated with timestamped entry

Work Log

2026-04-15 11:30 PT — Slot 0

Processed 30 top-scoring 0-citation hypotheses
Added 130 new citation entries across 17 successfully enriched hypotheses
13 hypotheses had no PubMed papers found (very specific/compound names)
Zero-citation count reduced: 124 → 107 (17 enriched, 13 skipped)
Script ran to completion without errors

2026-04-15 14:30 PT — Slot 0

Processed 30 more 0-citation hypotheses (composite_score 0.485-0.675)
Added 76 new citation entries across 30 hypotheses
9 hypotheses skipped (no papers found for very specific/compound names)
Zero-citation count reduced: 107 → 93
Total coverage: 436/529 hypotheses now have citations (82.4%)

2026-04-15 16:00 PT — Slot 0

Committed script improvements: better hypothesis filtering (excludes archived/invalid titles), exponential backoff retry for PubMed rate limits, improved LLM classification JSON parsing, comma-separated gene splitting for targeted queries
Script runs correctly (verified via dry-run)

2026-04-15 10:00 PT — Slot 0

Found 144 hypotheses with citations_count=0
Created scripts/enrich_hypotheses_pubmed_citations.py with PubMed search + Haiku LLM classification
Fixed NoneType bug in build_search_queries when disease field is null
Ran enrichment on top 20 hypotheses: added 76 citation entries
Remaining: 124 hypotheses still have 0 citations (many lack gene/disease metadata)
Committed script: 71d4d1286

2026-04-02T15:30 — Slot 16

Identified 16 hypotheses with citations_count=0, composite scores 0.57–0.80
Created enrich_batch2_citations.py with targeted PubMed queries (2 for + 2 against per hypothesis)
Ran enrichment: added 38 new evidence items across all 16 hypotheses
Updated citations_count for all 16 (range: 5–22 citations each)
All 199/199 hypotheses now enriched (100% coverage)

Payload JSON

{
  "requirements": {
    "analysis": 7,
    "reasoning": 6
  },
  "completion_shas": [
    "9a09ab7be9ad3f6d0e6fefe8b9649ebf4f525501"
  ],
  "completion_shas_checked_at": "2026-04-16T07:26:43.681590+00:00"
}