{"atlas_id":"pmmr-mucinous-colon","claim_ceiling":"deterministic cross-file status compilation only; source evidence classes and claim ceilings are preserved, and no binding, site, action, candidate-promotion, clinical, safety, efficacy, or therapeutic claim is added","compiled_at":"2026-09-05","compiler":{"deterministic":true,"name":"compile_science_handoff.py","network_calls":0},"coverage_counts":{"action_matrix_target_count":50,"actionable_site_records":14,"discovery_total":601,"excluded_targets":334,"extracellular_determinant_concepts":6,"intervention_records":766,"intervention_symbol_mediated_assignments_matching_retained_targets":114,"intervention_target_assignments":140,"measured_known_compound_interactions":57,"molecular_library_records":44,"opportunity_records":7,"retained_extracellular_determinants":0,"retained_surface_targets":185,"rows_not_site_evaluated_in_demo_tier":38,"rows_requiring_site_discovery":30,"rows_without_measured_compound_coverage":40,"screening_result_records":58,"screening_site_count":2,"screening_target_count":2,"structure_records":16,"tier_scoped_site_coverage_targets":50,"unresolved_discovery_entities":82,"unresolved_extracellular_determinants":6},"execution_outcomes":{"campaigns":[{"campaign_id":"fap-6y0f-smina-chargeaware-v1","execution_state":"complete"},{"campaign_id":"nt5e-9r0g-smina-v1","execution_state":"complete"},{"campaign_id":"8tcg-itgav-itgb6-geometry-recovery","execution_state":"complete"},{"campaign_id":"ceacam5-8bw0-multigenerator","execution_state":"failed"},{"campaign_id":"ceacam5-8bw0-three-arm-checkpoint","execution_state":"complete"},{"campaign_id":"ceacam5-8bw0-paired-fv-context-diagnostic","execution_state":"complete"},{"campaign_id":"ceacam5-8bw0-replacement-generators-20260904","execution_state":"complete"}],"defined_pocket_screening":{"claim_ceiling":"computational-screening-hypothesis","completed_molecule_count":58,"execution_complete":true,"failed_molecule_count":0,"failed_seed_count":0,"requested_molecule_count":58,"requested_seed_count":110,"run_count":2,"successful_seed_count":110},"flagship_closeout":{"campaign_count":7,"execution_state":"failed"}},"schema_version":"codex-surface-science-campaign-handoff/v0.1","source_artifacts":[{"bytes":11622,"path_scope":"atlas-directory","schema_version":"codex-surface-search-ledger/v0.1","sha256":"9e8b8abad54d024a15554078ac9aacc6d7cee15a27a80f7a43f0e42200cdda32"},{"bytes":1945084,"path_scope":"atlas-directory","record_count":601,"schema_version":"codex-surface-discovered-entity-collection/v0.1","sha256":"ca456767c2ef85c60f6bd266d96c131c8943e09c7179ba616286f2be50756927"},{"bytes":2563163,"path_scope":"atlas-directory","record_count":185,"schema_version":"codex-surface-target-collection/v0.1","sha256":"c6e20ca44b161b182f2c298dde20afcfb384e382a71d0926f21461aec3fd29a4"},{"bytes":478026,"path_scope":"atlas-directory","record_count":334,"schema_version":"codex-surface-exclusion-collection/v0.1","sha256":"2c1b4ba20df8f33ba49084a293f7fba725d775f8c3eeae8bb3d1d003a25975da"},{"bytes":416015,"path_scope":"atlas-directory","record_count":6,"schema_version":"codex-surface-extracellular-determinant-discovery/v0.1","sha256":"fa64cb7a9b627c6eceb19482d24745f2f5ae36f896931c48e5408c6653669498"},{"bytes":228650,"path_scope":"atlas-directory","record_count":16,"schema_version":"codex-surface-structure-collection/v0.1","sha256":"42015660cf5e51fb59cf5159077b29a3daae6012fca9fde8307e9487815ab72d"},{"bytes":272569,"path_scope":"atlas-directory","record_count":14,"schema_version":"codex-surface-actionable-site-library/v0.1","sha256":"07f5d2921fdf8345e0540003b0cb9ad50d8d42c349c95b2ae1dc26b2763d2897"},{"bytes":1935155,"path_scope":"atlas-directory","record_count":766,"schema_version":"codex-surface-intervention-collection/v0.1","sha256":"e7935e91eee2054a968d34ed0c38104ae37343e790aa9ae0cc08c30f20586ed7"},{"bytes":240108,"path_scope":"atlas-directory","record_count":57,"schema_version":"codex-surface-known-compound-interaction-collection/v0.1","sha256":"26aaa2e132443759fd200931f372de154e56b370d6ecd291299684383a3ce627"},{"bytes":101508,"path_scope":"atlas-directory","record_count":44,"schema_version":"codex-surface-molecular-library/v0.1","sha256":"670cede98177a0d11b6ac666750b9c5fd131d020e852927baf3ec7e4e800cb0c"},{"bytes":758843,"path_scope":"atlas-directory","record_count":58,"schema_version":"codex-surface-screening-result-collection/v0.1","sha256":"a5a56bc3fb954cf011c9ac5c69b8a532d555ea3dc1dc257a10dcb01dcfe193b9"},{"bytes":420416,"path_scope":"atlas-directory","record_count":50,"schema_version":"codex-surface-target-action-modality-matrix/v0.1","sha256":"8f466368b83b5509e78d6a41a060651fc9f88fbdd29a3fe760d573d0db6d3ebc"},{"bytes":19192,"path_scope":"atlas-directory","record_count":7,"schema_version":"codex-surface-opportunity-collection/v0.1","sha256":"edcd492b57337024f6ed6d753791ef7c566f8d512b1753b6399b7c63af3a95b7"},{"bytes":175526,"path_scope":"atlas-directory","schema_version":"surface-atlas-campaign-execution-closeout/v1","sha256":"ebdffc8a31820dd968cbd6afe4fa0be7d863225b34bec01daa93679994d87c4f"},{"bytes":5120,"path_scope":"atlas-directory","schema_version":"codex-surface-molecular-library-amendment/v1","sha256":"e7a00ce50be26511098af79d72e4627773c506989d09e56af34bda829f2704ab"},{"bytes":109084,"path_scope":"demo-directory","sha256":"f37633562eff1beee3e7809796e90111c4b7986b980049fb29c83b1bf73edbf2"}],"source_claim_ceilings":{"actionable_sites":{"claim_ceiling":"deposited contact geometry and explicit tier coverage state; no therapeutic action, affinity, selectivity, normal-tissue safety, or efficacy claim","state":"collection-level"},"extracellular_determinants":{"claim_ceiling":"deterministic registration and lexical leads only; no validated extracellular determinant or therapeutic opportunity","state":"collection-level"},"known_compound_interactions":{"claim_ceiling":"bounded measured and curated database evidence at protein-target level; no record is promoted to deposited extracellular-site binding, therapeutic action, selectivity, normal-tissue safety, or efficacy without separate evidence","state":"collection-level"},"screening_results":{"claim_ceiling":"computational-screening-hypothesis","state":"collection-and-record-level"},"structures":{"claim_ceilings":["hash-bound target preparation and observed deposited interface geometry","verified deposited experimental structure"],"state":"record-level"},"target_action_modality_matrix":{"claim_ceiling":"cross-collection evidence routing for tiered targets only; observed deposited contacts, intervention labels, and target-level measured compound records remain within their source claim ceilings. This matrix does not assert approval status, extracellular site localization of an intervention or compound, mechanism, affinity, efficacy, selectivity, safety, candidate quality, promotion, or patient-specific applicability.","state":"collection-level"}},"stage_truth_table":[{"basis":"partition-complete within the recorded source universe: retained, excluded, and unresolved identities exactly partition the normalized discovery records and match the search ledger; this is not an exhaustive biological discovery claim","stage_id":"discovery-and-surface-triage","state":"complete/current-scope"},{"basis":"registered determinant concepts retain explicit resolved/unresolved dispositions and claim ceilings","stage_id":"extracellular-determinant-resolution","state":"partial"},{"basis":"tier-scoped targets have explicit deposited-site or unresolved/not-evaluated coverage states","stage_id":"structure-and-actionable-site-coverage","state":"partial"},{"basis":"registry interventions and measured target-level compound records are retained without site promotion","stage_id":"intervention-and-known-compound-evidence","state":"partial"},{"basis":"executed-run completeness only: screening records are linked directly to molecular-library and target records for 2 of 50 matrix targets; actionable-site linkage is indirect through the corresponding opportunity handoffs; 1 molecular-library identity remains unresolved; all screen outcomes remain computational hypotheses","stage_id":"molecular-library-and-defined-pocket-screening","state":"complete/current-scope"},{"basis":"representation-complete for 50/50 structure-a/b/c targets against current hash-bound science inputs; 30 rows require site discovery, 38 were not site-evaluated in this demo tier, and 40 lack measured compound coverage","stage_id":"target-action-modality-matrix","state":"complete/current-scope"},{"basis":"No designed binder was promoted. Campaign results record the completed computations and stop decisions.","stage_id":"flagship-campaign-execution-and-promotion","state":"not-qualified"}],"zero_promotion_status":{"claim_ceiling":"explicit source-recorded promotion counts only; zero promotions is not evidence that the targets or modalities are infeasible","observations":[{"opportunity_id":"O-ITGB6-8TCG-REFERENCE-RECOVERY","promoted_count":0,"source_field":"result_ingestion.promoted_candidate_count"},{"opportunity_id":"O-FAP-6Y0F-DEFINED-POCKET-SCREEN-HANDOFF","promoted_count":0,"source_field":"screen_handoff.binder_promotions"},{"opportunity_id":"O-NT5E-9R0G-DEFINED-POCKET-SCREEN-HANDOFF","promoted_count":0,"source_field":"screen_handoff.binder_promotions"},{"opportunity_id":"O-CEACAM5-8BW0-THREE-ARM-CHECKPOINT-HANDOFF","promoted_count":0,"source_field":"checkpoint_handoff.binder_promotions"},{"opportunity_id":"O-CEACAM5-8BW0-FOUR-ARM-OUTCOME","promoted_count":0,"source_field":"campaign_handoff.binder_promotions"},{"opportunity_id":"O-CEACAM5-8BW0-PAIRED-FV-DIAGNOSTIC","promoted_count":0,"source_field":"diagnostic_handoff.binder_promotions"},{"opportunity_id":"O-CEACAM5-8BW0-REPLACEMENT-GENERATOR-OUTCOME","promoted_count":0,"source_field":"campaign_handoff.binder_promotions"}],"opportunity_count":7,"promoted_candidate_count":0,"state":"confirmed-zero-across-opportunity-handoffs"}}
