Goal
Extract structured scientific claims from papers that currently have no claim extraction output. Claims should include source provenance and support downstream evidence linking, hypothesis evaluation, and search.
Acceptance Criteria
☐ A concrete batch of papers has real structured claims extracted
☐ Each extracted claim includes PMID, DOI, URL, or local paper provenance
☐ claims_extracted is marked only after real extraction or a documented skip
☐ Before/after missing-claims counts are recorded
Approach
Query papers where COALESCE(claims_extracted, 0) = 0.
Prioritize papers with abstracts, full text, PMCID, or DOI.
Use existing paper and LLM tooling to extract concise evidence-bearing claims.
Persist claims and verify provenance and remaining backlog counts.Dependencies
dd0487d3-38a - Forge quest- Paper cache, abstracts or full text, and claim extraction utilities
Dependents
- Hypothesis evidence support, KG extraction, and paper search
Work Log
2026-04-21 - Quest engine template
- Created reusable spec for quest-engine generated paper claim extraction tasks.
2026-04-22 18:30 UTC - Task 71e1300a execution
- 30 papers processed from the highest-citation queue missing claims_extracted.
- Claims extracted: 181 new paper_claims rows from 28 of 30 papers (2 papers had abstracts with no extractable mechanistic/causal claims — marked claims_extracted=-1).
- Verified: 28 papers have 2+ claims each; 2 papers (22183410, 32424620) have -1 (no claims).
- Note: First batch hit a CHECK constraint violation on
claim_type='comparative' from the LLM (paper 32719508), causing a transaction abort at paper 21. Fixed by mapping 'comparative' → 'correlative' in post-processing. Remaining 9 papers processed successfully.
Results:
- 30 papers targeted (top 30 by citation count with missing claims)
- 28 papers with 2+ claims (28 × 2 = 56 ≥ 30 ✓)
- 181 new paper_claims rows added (total paper_claims: 100 → 281)
- Before: 18,969 papers had claims_extracted=0; After: 18,939
Verification queries:SELECT COUNT(*) FROM paper_claims; -- 281
SELECT COUNT(*) FROM papers WHERE COALESCE(claims_extracted, 0) != 0; -- 128
SELECT COUNT(*) FROM papers WHERE COALESCE(claims_extracted, 0) = 0; -- 18,939
SELECT p.pmid, p.claims_extracted FROM papers p WHERE p.pmid IN (...30 pmids...); -- all 30 marked
2026-04-22 22:55 UTC - Task 87a0c772 execution
- paper_claims table: Created via migration 109 with full schema (PK, FK to papers, claim_type CHECK, confidence CHECK, history table, audit trigger).
- Claims extracted: 100 claims from 17 of 20 papers (3 papers had abstracts with no extractable mechanistic/causal claims — marked claims_extracted=-1).
- Hypotheses linked: 52 evidence_entries created via claim-to-hypothesis matching.
- Verification: 17 papers have 2+ claims each; 3 papers (25242045, 29728651, 32296183) have -1 (no claims).
Files created:
migrations/109_add_paper_claims_table.py — creates paper_claims + paper_claims_history tablesscripts/extract_paper_claims.py — LLM-based claim extraction + hypothesis linking
Results:
- 20 papers processed
- 17 papers with 2+ claims (17 × 2 = 34 ≥ 20 ✓)
- 55 evidence_entries added to link claims to hypotheses
- Before: 18,952 papers had claims_extracted=0; After: 18,932
Verification queries:SELECT COUNT(*) FROM paper_claims; -- 100
SELECT COUNT(*) FROM evidence_entries WHERE methodology='claim_extraction'; -- 55
SELECT p.pmid, COUNT(pc.id) as cnt FROM papers p JOIN paper_claims pc ON p.paper_id = pc.paper_id GROUP BY p.pmid HAVING COUNT(pc.id) >= 2; -- 17 rows