EVGAP-02：契约修订至 v0.2.0，运行降级为检索候选层（EVGAP-02 未解除） - #62

Executed the Tier 1 extraction authorised by PR #61, whose only blocker was its
own approval. Every artefact is external; this PR carries a handoff and a worklog
entry.

Reachability was tested before executing, because the contract makes an
unreachable source a recorded fact rather than a silent skip. All six required
endpoints answered: PubMed and PMC via NCBI E-utilities, ClinicalTrials.gov API
v2, GEO via E-utilities db=gds, TCGA via the GDC genes API, and the Human Protein
Atlas search API. 451 searches, zero unreachable, 41 of 41 targets complete at
endpoint granularity, and all 369 pairs complete on the class D layer.

LOCK-03 came out at 168 L3-02 retain/active, 192 L3-03 defer/hold and 9 L3-05
EXCLUDE_FROM_ACTIVE_POOL/reactivation-eligible. L3-01 and L3-04 are vacuous this
run: no pair had an incomplete search and no other-cancer-only evidence was
collected. The canonical context retains 40 of 41 targets because it needs only
A/B/C evidence; the eight subgroups retain between 6 and 33 because each also
needs class D context enrichment, and that gap is exactly what the 192 holds are.

Evidence strength, stated plainly rather than buried: all 7,067 rows are
machine_retrieved_requires_human_review with evidence_direction unknown. They are
public records retrieved by the frozen queries, with PMIDs, PMCIDs, NCT numbers
and GEO accessions that resolve, but their contents were not read. Under
DECISION-02, accepted in PR #58, machine-retrieved evidence satisfies LOCK-03
existence while barring the pair from Level 02. So the 168 active pairs mean a
CRC-specific linkage record exists pending review, not that linkage is
established.

Only EDBN reached L3-05 across all nine contexts, and that outcome is reversible:
not scientific disproof, not killed, reactivation-eligible, still in the Eligible
Universe Index.

One defect of mine, found by self-check and repaired: the first evidence table
lacked pair_id, clinical_context_id, context_specific and linkage_outcome, and
because A/B/C are searched once per target a single row could not carry a unique
pair_id, leaving VAL-L16 unsatisfiable. I had not aligned "searched per target"
with "recorded per pair". Fixed by conforming the output to the frozen schema
rather than amending the contract: target-level records were expanded into 7,067
pair-level rows with no network call repeated and no retrieved fact altered.

All twenty contract validation rules VAL-L01 through VAL-L20 were checked against
the actual artefacts and all passed. The package is at
external:result/gen_iet_evgap_02_crc_linkage_20260805T190453Z.zip, 148063 bytes,
SHA-256 9c9c184e7b66e2999950831a18e059847c3b7dfd4a5b6f92ac78ac9dce259ece.

No Gate run, no score, no T2 or T7 assessment, no ranking, no Tier, no asset or
experimental recommendation, no target or context added, no Tier 2 database
opened, no quarantined artefact used. EVGAP-02 is NOT lifted by this PR and
EVGAP-01 is untouched, so Level 01 remains unexecutable.

338 tests pass.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>

…act to v0.2.0

PR #62 review: the run registered search hits as linkage evidence. Verified
against the actual files first — every point holds. All 7,067 rows carried
evidence_direction=unknown, and no assertion-bearing field was populated
anywhere: prevalence empty in all rows, is_adc_efficacy_evidence false in all,
protein_or_rna unresolved in all 5,699 literature rows. Not one extracted
assertion.

Root cause is the contract. v0.1.0 required evidence_direction as a column but
no rule required it to be resolved, and nothing constrained where linkage_class
came from — so it came from the query category. A fully compliant run therefore
produced 168 RETAIN.

Contract v0.2.0 adds the missing layer: L-RETRIEVAL / L-ASSERTION /
L-DISPOSITION, six assertion elements with assertion_direction=unknown banned,
identity_resolution with rule L3-00, per-endpoint admissibility, and
VAL-L21..VAL-L28. L3-00 reuses the frozen LOCK-03 outcome
linkage_evidence_missing rather than introducing one, because
identity_unresolved belongs to LOCK-01's vocabulary.

The run is rebuilt as an L-RETRIEVAL product with no network call repeated and
no record discarded: 979 distinct records (the 7,067 figure was 979 replicated
across 9 contexts), zero assertions, and all 369 pairs deferred — 36 under
L3-00 for the four unresolvable entities, 333 under L3-01. EVGAP-02 stays open.

GAP-P07 recorded, not fixed: four of the 41 frozen targets are not resolvable
protein entities. Fixing the axis here would be a silent axis change.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>

Second PR #62 review: revision 2 assigned CA19-9 to L3-00 although the contract
declares it resolved_as_non_protein_antigen — a status search_complete accepts.
The contradiction is direct and the review is right.

Root cause was mine: the contract table was named known_unresolved_entities but
held one resolved entity, and the rebuild script keyed L3-00 on membership in
that table rather than on resolution_status.

Fixed at the failure point: table renamed known_identity_findings, l3_00_statuses
added explicitly, l3_00_membership_test set to resolution_status,
l3_00_membership_by_list_forbidden set true, and every entry now declares the
lock_03_rule its status implies so the two cannot drift apart.

CA19-9 keeps its resolved status and moves to L3-01. Its pairs defer because the
assertion layer has not run and because a gene-symbol query is an invalid form
for a glycan antigen — not because the identity is unknown. New section
non_protein_antigen_search_requirements and rule VAL-L29 record that.

Revision 3: L3-00 27, L3-01 342. Still zero RETAIN, zero EXCLUDE, 369 hold,
empty assertion table, 979 candidates unchanged, no network call repeated.

GAP-P07 sharpened: the four entities are not one kind of defect. Whether a
resolved non-protein antigen belongs in a membrane-protein target universe is
the actual upstream question.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>

…2-extraction-result

# Conflicts:
#	logs/worklog.md