{ "snapshot_date": "2026-10-25", "base_commit": "18649bf0031ae143b8dd4a0b8c776c470c3dcec6", "module_count": 777, "notes": [ "Structural triage only; declared COMPLETE, citation presence, family presence and PR overlap do not establish successful audit.", "PR overlap from 239 open PRs; paginated full file list used for broad PR 5076. Other PR file lists may be truncated by GitHub; recheck exact paths before edits.", "All modules require manual literature, taxon, family/exemplar, member-review and merged-PR verification.", "Initial snapshot contained 702 modules. Refreshed against origin/main at 10fd59941fcea227d9d157251e61a9b54f039aed on 2026-10-26; 12 additions bring current coverage to 714 modules. At that refresh the additions were unaudited; subsequent progress is recorded in each row; no removals or renames were observed. Recheck upstream before final completion.", "Universe refresh against 3dd6e1dba91d22efd7bed30faeb9fbe6813925f8: adds only chaperone_mediated_autophagy (upstream b646a26364/PR5562), bringing coverage to 715 modules. Existing rows and historical evidence are retained; the new module remains NOT_STARTED.", "2026-10-26 canonical checkpoint: verified merged content for PR5563, PR5568, PR5569 and PR5586 brings completion to 17 of 715 modules. Eight open PRs plus audits 26 and 27 remain active; 688 are NOT_STARTED. The Asp/Asn shared GO-CAM index exception is an exact clean union with upstream threonine updates, not lost approved content. Explicit requested-review states and queue membership are retained independently of auto-merge flags. Audit28 remains NOT_STARTED pending scope approval.", "BCR PR5584 subsequently merged at 17:21:03Z as 67e246011a: independent comparison confirms all 340 scoped approved blobs unchanged. Completion is now 18 of 715, with nine active and 688 NOT_STARTED. This newer verified completion supersedes the immediately preceding 17-completion checkpoint narrative.", "Audit26 full validation subsequently passed (session70329: 9,145 reviews, zero errors, 30,059 advisory warnings, 54 pathway files). Root then authorized audit28 IN_PROGRESS after its 15-member/258-row/30-raw baseline was captured; this supersedes the previous not-started gate. Counts are 18 complete, ten active and 687 NOT_STARTED out of 715. Audit27 session77356 remains live.", "Audit26 published as PR5591 at 886264d5442163b6a3fc69a69eb5ac7224e13dd3 after terminal full validation; review/CI pending. This moves one active audit from IN_PROGRESS to PR_OPEN, without changing aggregate completion counts.", "2026-10-26 late checkpoint: 715 identities retained, including the canonical-only chaperone_mediated_autophagy row absent from the incoming 714-row main tracker. Exact-head and merge-content verification adds anti-CRISPR PR5555, alginate PR5552 and arginase PR5566 to COMPLETE. Counts are 21 complete, 8 active and 686 not started. Apoptosis remains open. Audit27 is published with terminal full PASS; audit28 full validation remains live; audit29 research foundation has started. The arginase final row count is corrected to359 (357 original plus2 authored matrix proposals). All other canonical rows and incoming historical notes are preserved. The new acetylcholine integration requires renewed review and CI.", "2026-10-29 polar integration: only auxin_polar_transport is refreshed against a pinned GitHub snapshot. Other rows retain their incoming dated evidence and are not represented as freshly checked live statuses. The inventory counts describe this ledger, not a new repository-wide survey.", "2026-11-05 reconciliation: original nitrate audit PR5740 was merged on 2026-10-30 but omitted from the current ledger. Verified 209 scoped merged blobs and 21 COMPLETE reviews; restored COMPLETE with retained proof. Later family-review PR5928 is a separate overlap." ], "modules": [ { "module": "2_aminoethylphosphonate_degradation", "path": "modules/2_aminoethylphosphonate_degradation.yaml", "declared_status": "DRAFT", "audit_status": "COMPLETE", "related_open_prs": [], "annotons": 2, "annotons_with_family": 2, "annotons_with_direct_evidence": 2, "representative_accessions": [ "UniProtKB:Q88KT0", "UniProtKB:Q88KT1" ], "has_root_taxon_context": false, "audit_evidence": { "module": "modules/2_aminoethylphosphonate_degradation.yaml", "notes": "modules/2_aminoethylphosphonate_degradation-notes.md", "member_reviews": [ "genes/PSEPK/phnW/phnW-ai-review.yaml", "genes/PSEPK/phnX/phnX-ai-review.yaml", "genes/SALTY/phnW/phnW-ai-review.yaml", "genes/SALTY/phnX/phnX-ai-review.yaml", "genes/BACCE/phnW/phnW-ai-review.yaml", "genes/BACCE/phnX/phnX-ai-review.yaml" ], "targeted_validation": "passed; module zero warnings, PSEPK genes each one advisory uncited-deep-research warning", "merge_commit": "7d28f887b2dbbab34afee940716ba660efc3a173", "ci": "Required checks passed and approved head merged through queue at 2026-10-25T22:48:55Z. Merged notes and source-specific module/member evidence rechecked against the six audit requirements.", "head_commit": "80884c9365d106f85b0bc498cb8f1ba49c74592f", "review_decision": "APPROVED", "merged_at": "2026-10-25T22:48:55Z", "completion_verification": "Merged curated module, gene and history content byte-compared with approved head: 32 files identical. Literature, step and edge support, taxon limitations, family and member evidence inspected; required checks passed." }, "audit_pr": "https://github.com/ai4curation/ai-gene-review/pull/5538" }, { "module": "abscisic_acid_signaling", "path": "modules/abscisic_acid_signaling.yaml", "declared_status": "DRAFT", "audit_status": "COMPLETE", "related_open_prs": [], "annotons": 7, "annotons_with_family": 5, "annotons_with_direct_evidence": 7, "representative_accessions": [ "UniProtKB:O49686", "UniProtKB:P49597", "UniProtKB:Q39192", "UniProtKB:Q39193", "UniProtKB:Q940H6", "UniProtKB:Q9M7Q4", "UniProtKB:Q9SJN0" ], "has_root_taxon_context": true, "audit_pr": "https://github.com/ai4curation/ai-gene-review/pull/5540", "audit_evidence": { "module": "modules/abscisic_acid_signaling.yaml", "notes": "modules/abscisic_acid_signaling-notes.md", "branch": "cmungall/aigr-aba-taxon-audit", "head": "a02939ec5453612eb9a7b0d69e7ff5353311e618", "reviewed_members": 19, "reviewed_annotation_rows": 524, "curated_references": 26, "targeted_validation": "All 19 gene reviews pass; final module passes with three documented advisories; histories validated.", "repository_validation": "Passed full just validate-all; final review fixes passed targeted validation.", "merge_commit": "d4ae4f02f7ab9759d41d104d7cd7af0ec66abb16", "ci": "Approved; all required head checks passed; merged through the normal queue.", "full_validation": "just validate-all completed successfully; full run overlapped review fixes, which also passed targeted validation.", "head_commit": "a02939ec5453612eb9a7b0d69e7ff5353311e618", "review_decision": "APPROVED", "merged_at": "2026-10-25T23:26:17Z", "completion_verification": "Merged curated module, gene and history content byte-compared with approved head: 100 files identical. Literature, step and edge support, taxon limitations, family and member evidence inspected; required checks passed." } }, { "module": "acetylcholine_signaling", "path": "modules/acetylcholine_signaling.yaml", "declared_status": "COMPLETE", "audit_status": "COMPLETE", "related_open_prs": [], "overlap_check": "NOT_YET_CHECKED", "annotons": 38, "annotons_with_family": 38, "annotons_with_direct_evidence": 38, "representative_accessions": [ "UniProtKB:O14775", "UniProtKB:O95837", "UniProtKB:P02708", "UniProtKB:P04899", "UniProtKB:P07510", "UniProtKB:P08172", "UniProtKB:P08173", "UniProtKB:P08912", "UniProtKB:P09471", "UniProtKB:P11229", "UniProtKB:P11230", "UniProtKB:P17787", "UniProtKB:P20309", "UniProtKB:P22303", "UniProtKB:P25098", "UniProtKB:P28329", "UniProtKB:P29992", "UniProtKB:P30532", "UniProtKB:P30926", "UniProtKB:P32297", "UniProtKB:P34947", "UniProtKB:P36544", "UniProtKB:P41220", "UniProtKB:P43144", "UniProtKB:P43681", "UniProtKB:P49758", "UniProtKB:P49798", "UniProtKB:P50148", "UniProtKB:P62881", "UniProtKB:P63096", "UniProtKB:Q04844", "UniProtKB:Q05901", "UniProtKB:Q07001", "UniProtKB:Q15822", "UniProtKB:Q15825", "UniProtKB:Q9ERZ4", "UniProtKB:Q9GZV3", "UniProtKB:Q9GZZ6", "UniProtKB:Q9I8C7", "UniProtKB:Q9JLB5", "UniProtKB:Q9PTS8", "UniProtKB:Q9UGM1", "UniProtKB:Q9Z2H2" ], "has_root_taxon_context": true, "inventory_added_at": "2026-10-26", "inventory_source_commit": "10fd59941fcea227d9d157251e61a9b54f039aed", "audit_evidence": { "branch": "cmungall/aigr-acetylcholine-taxon-audit", "worktree": "/Users/cjm/orca/workspaces/ai-gene-review/aigr-acetylcholine-taxon-audit", "members_in_scope": 44, "members_reviewed": 44, "phase": "Merged PR #5582 at e145466d152df2f67b82bbe3f775c7a4b43040ce after approval of 00eb524d6e and passing required checks. Verified 722 scoped paths against the approved head; 44 member reviews, 2786 original annotation rows and 88 raw sources are preserved.", "progress": "Merged PR #5582 at e145466d152df2f67b82bbe3f775c7a4b43040ce after approval of 00eb524d6e and passing required checks. Verified 722 scoped paths against the approved head; 44 member reviews, 2786 original annotation rows and 88 raw sources are preserved.", "worktree_provenance": "Tracked-file APFS clonefile checkout with independent index; verified clean at main 10fd59941f, uv sync passed. No ordinary full checkout or external agent launch.", "members_foundation": 36, "members_comparative_additions": 8, "foundation_annotation_rows": 2456, "foundation_seed_validation": "All 44 review identifiers, primary UniProt accessions and taxa verified; all seven preexisting reviews preserved by normal fetch. Authoritative prereview payload snapshot contains 2,786 rows.", "original_annotation_rows": 2786, "curated_references": 38, "module_qa": "PASS: all 44 focused member checks; 39 route cases (18 receptor assembly and 21 signaling); all 672 replacement terms have the correct GO aspect. All retained connections have source-specific evidence; native and comparative assay limits are preserved.", "provider_attempts": "All 44 actual Falcon/fallback attempts failed authentication or quota; normal publication acquisition and documented manual source assessment used. No fabricated provider outputs.", "member_review_status": "COMPLETE", "annotation_rows_reviewed": 2786, "new_proposals": 0, "inherited_proposals": 1, "head_commit": "00eb524d6ecb1307fac668a68a592d33c1e04aa1", "science_commits": 3, "actions": { "MODIFY": 640, "ACCEPT": 1327, "MARK_AS_OVER_ANNOTATED": 19, "KEEP_AS_NON_CORE": 425, "UNDECIDED": 104, "REMOVE": 270, "NEW": 1 }, "full_validation": "PASS: follow-up session 32917 terminal exit zero; 9,103 reviews and 54 pathway files.", "push_status": "Approved content merged and independently verified", "review_decision": "APPROVED", "ci": "Required validation, suite, test and scientific-review checks passed for approved merged head.", "review_followup": "Merged PR #5582 at e145466d152df2f67b82bbe3f775c7a4b43040ce after approval of 00eb524d6e and passing required checks. Verified 722 scoped paths against the approved head; 44 member reviews, 2786 original annotation rows and 88 raw sources are preserved.", "merge_state": "MERGED", "connections_reviewed": 15, "member_reviews": [ "genes/CHICK/CHRNA10/CHRNA10-ai-review.yaml", "genes/CHICK/CHRNA9/CHRNA9-ai-review.yaml", "genes/human/ACHE/ACHE-ai-review.yaml", "genes/human/CHAT/CHAT-ai-review.yaml", "genes/human/CHRM1/CHRM1-ai-review.yaml", "genes/human/CHRM2/CHRM2-ai-review.yaml", "genes/human/CHRM3/CHRM3-ai-review.yaml", "genes/human/CHRM4/CHRM4-ai-review.yaml", "genes/human/CHRM5/CHRM5-ai-review.yaml", "genes/human/CHRNA1/CHRNA1-ai-review.yaml", "genes/human/CHRNA10/CHRNA10-ai-review.yaml", "genes/human/CHRNA2/CHRNA2-ai-review.yaml", "genes/human/CHRNA3/CHRNA3-ai-review.yaml", "genes/human/CHRNA4/CHRNA4-ai-review.yaml", "genes/human/CHRNA5/CHRNA5-ai-review.yaml", "genes/human/CHRNA6/CHRNA6-ai-review.yaml", "genes/human/CHRNA7/CHRNA7-ai-review.yaml", "genes/human/CHRNA9/CHRNA9-ai-review.yaml", "genes/human/CHRNB1/CHRNB1-ai-review.yaml", "genes/human/CHRNB2/CHRNB2-ai-review.yaml", "genes/human/CHRNB3/CHRNB3-ai-review.yaml", "genes/human/CHRNB4/CHRNB4-ai-review.yaml", "genes/human/CHRND/CHRND-ai-review.yaml", "genes/human/CHRNE/CHRNE-ai-review.yaml", "genes/human/CHRNG/CHRNG-ai-review.yaml", "genes/human/GNA11/GNA11-ai-review.yaml", "genes/human/GNA14/GNA14-ai-review.yaml", "genes/human/GNAI1/GNAI1-ai-review.yaml", "genes/human/GNAI2/GNAI2-ai-review.yaml", "genes/human/GNAO1/GNAO1-ai-review.yaml", "genes/human/GNAQ/GNAQ-ai-review.yaml", "genes/human/GNB5/GNB5-ai-review.yaml", "genes/human/GRK2/GRK2-ai-review.yaml", "genes/human/GRK5/GRK5-ai-review.yaml", "genes/human/RGS2/RGS2-ai-review.yaml", "genes/human/RGS4/RGS4-ai-review.yaml", "genes/human/RGS6/RGS6-ai-review.yaml", "genes/human/SLC18A3/SLC18A3-ai-review.yaml", "genes/human/SLC5A7/SLC5A7-ai-review.yaml", "genes/mouse/Chrm2/Chrm2-ai-review.yaml", "genes/mouse/Gnb5/Gnb5-ai-review.yaml", "genes/mouse/Rgs6/Rgs6-ai-review.yaml", "genes/rat/Chrna10/Chrna10-ai-review.yaml", "genes/rat/Chrna9/Chrna9-ai-review.yaml" ], "structural_metrics_source": "Pinned 9a873125b88e3ec4763b2b0a77da58ef51f44b25: 38 module activities, 43 exact representative accessions, 38 references and 15 connections; 44 parsed member reviews contain 2786 annotation rows.", "tracker_integration": "Current checkpoint preserves canonical identities, current lifecycle facts and all approved scientific content; historical integration details remain in dated notes.", "github_snapshot_at": "2026-10-27T15:35:23.328938+00:00", "auto_merge_enabled": true, "publication_state": "MERGED", "current_head_checks": [ { "__typename": "CheckRun", "completedAt": "2026-10-26T17:48:05Z", "conclusion": "SKIPPED", "detailsUrl": "https://github.com/ai4curation/ai-gene-review/actions/runs/40372007960/job/121744910644", "name": "claude", "startedAt": "2026-10-26T17:48:06Z", "status": "COMPLETED", "workflowName": "Claude Code" }, { "__typename": "CheckRun", "completedAt": "2026-10-26T17:57:43Z", "conclusion": "SUCCESS", "detailsUrl": "https://github.com/ai4curation/ai-gene-review/actions/runs/40369579749/job/121736379992", "name": "validation (3.12)", "startedAt": "2026-10-26T17:35:04Z", "status": "COMPLETED", "workflowName": "Build and test" }, { "__typename": "CheckRun", "completedAt": "2026-10-26T17:49:01Z", "conclusion": "SUCCESS", "detailsUrl": "https://github.com/ai4curation/ai-gene-review/actions/runs/40369579451/job/121736379024", "name": "claude-review", "startedAt": "2026-10-26T17:34:46Z", "status": "COMPLETED", "workflowName": "Claude Code Review" }, { "__typename": "CheckRun", "completedAt": "2026-10-26T17:49:17Z", "conclusion": "SUCCESS", "detailsUrl": "https://github.com/ai4curation/ai-gene-review/actions/runs/40369579749/job/121736380509", "name": "suite (3.12)", "startedAt": "2026-10-26T17:34:49Z", "status": "COMPLETED", "workflowName": "Build and test" }, { "__typename": "CheckRun", "completedAt": "2026-10-26T17:57:49Z", "conclusion": "SUCCESS", "detailsUrl": "https://github.com/ai4curation/ai-gene-review/actions/runs/40369579749/job/121750143699", "name": "test (3.12)", "startedAt": "2026-10-26T17:57:46Z", "status": "COMPLETED", "workflowName": "Build and test" } ], "latest_submitted_review": { "id": 5656517905, "state": "APPROVED", "commit_id": "b4760e897b053857339c94f1e7bce75eed9cdb4c", "submitted_at": "2026-10-26T17:48:01Z", "html_url": "https://github.com/ai4curation/ai-gene-review/pull/5582#pullrequestreview-5656517905" }, "integration_pending": null, "merge_commit": "e145466d152df2f67b82bbe3f775c7a4b43040ce", "merged_at": "2026-10-26T19:43:47Z", "merged_content_verification": { "verified_at": "2026-10-27T15:30:36.181509+00:00", "scoped_paths_equal": 722, "shared_three_way_unions": [], "member_reviews": 44, "original_rows": 2786, "raw_files": 88 } }, "audit_pr": "https://github.com/ai4curation/ai-gene-review/pull/5582" }, { "module": "activin_receptor_signaling", "path": "modules/activin_receptor_signaling.yaml", "declared_status": "DRAFT", "audit_status": "COMPLETE", "related_open_prs": [], "annotons": 7, "annotons_with_family": 1, "annotons_with_direct_evidence": 0, "representative_accessions": [ "UniProtKB:P08476" ], "has_root_taxon_context": true, "audit_evidence": { "branch": "cmungall/aigr-activin-taxon-audit", "worktree": "aigr-activin-taxon-audit", "notes": "modules/activin_receptor_signaling-notes.md", "merge_commit": "aff0030d3689b50ae9f6d147fc8334a0b942f0a7", "head_commit": "8937ae9e6b37b4b23d0fab87c6da60d4bb684539", "curated_references": 29, "reviewed_members": 11, "adjudicated_annotation_rows": 1658, "undecided_rows": 50, "targeted_validation": "Eleven member reviews pass; module schema and scoped validation pass with zero warnings; seventeen histories validated.", "full_validation": "Full just validate-all passed; four final review follow-ups passed targeted validation.", "review": "Approved after rendered-page update; auto-merge enabled; current validation CI running.", "review_decision": "APPROVED", "merged_at": "2026-10-25T23:21:39Z", "render": "Module HTML generated and committed.", "ci": "Approved; all required head checks passed; merged through the normal queue.", "completion_verification": "Merged curated module, gene and history content byte-compared with approved head: 64 files identical. Literature, step and edge support, taxon limitations, family and member evidence inspected; required checks passed." }, "audit_pr": "https://github.com/ai4curation/ai-gene-review/pull/5541" }, { "module": "adp_heptose_biosynthesis", "path": "modules/adp_heptose_biosynthesis.yaml", "declared_status": "DRAFT", "audit_status": "COMPLETE", "related_open_prs": [ 5076 ], "annotons": 5, "annotons_with_family": 5, "annotons_with_direct_evidence": 5, "representative_accessions": [ "UniProtKB:P63228", "UniProtKB:P76658", "UniProtKB:Q88D93", "UniProtKB:Q88N89", "UniProtKB:Q88RS0", "UniProtKB:Q9HVZ0", "UniProtKB:Q9HYQ8" ], "has_root_taxon_context": false, "audit_branch": "cmungall/aigr-adp-heptose-taxon-audit", "audit_evidence": { "module": "modules/adp_heptose_biosynthesis.yaml", "notes": "modules/adp_heptose_biosynthesis-notes.md", "curated_references": 12, "reviewed_members": 16, "adjudicated_annotation_rows": 107, "undecided_rows": 7, "new_annotation_rows": 2, "taxon_scope": "Bacteria and Archaea as non-universal complete-route envelopes; partial viral/eukaryotic enzyme complements distinguished.", "targeted_validation": "All sixteen members pass; module schema/scoped checks pass with zero warnings; twenty-six histories validated. Four empty-GOA archaeal reviews retain core-coverage advisories.", "merge_commit": "8954a5dc480f1311f440eb4e50f5cefca5931980", "full_validation": "Full just validate-all completed successfully; final three-gene evidence/ancestry follow-up also passed targeted validation.", "head_commit": "19f3d2568d5abc426c7e75d7c284e6656639629d", "identity_caveat": "Only the archaeal kinase matches a published construct exactly; other three archived DSM2067 exemplars are qualified family/domain and genomic-context assignments.", "review_decision": "APPROVED", "merged_at": "2026-10-25T23:26:33Z", "review": "Requested changes and four suggestions addressed; prior follow-up approved. Two optional accuracy points corrected on latest head; fresh review/CI pending. PR ready.", "render": "Module HTML generated and committed.", "ci": "Approved; normal merge queue awaiting integration checks as of 2026-10-25 23:10 UTC.", "completion_verification": "Merged curated module, gene and history content byte-compared with approved head: 100 files identical. Literature, step and edge support, taxon limitations, family and member evidence inspected; required checks passed." }, "audit_pr": "https://github.com/ai4curation/ai-gene-review/pull/5542" }, { "module": "adrenal_steroidogenesis", "path": "modules/adrenal_steroidogenesis.yaml", "declared_status": "DRAFT", "audit_status": "COMPLETE", "related_open_prs": [ 5076 ], "annotons": 7, "annotons_with_family": 7, "annotons_with_direct_evidence": 7, "representative_accessions": [ "UniProtKB:P05093", "UniProtKB:P05108", "UniProtKB:P08686", "UniProtKB:P15538", "UniProtKB:P19099", "UniProtKB:P26439", "UniProtKB:P49675" ], "has_root_taxon_context": false, "audit_branch": "cmungall/aigr-adrenal-taxon-audit", "audit_evidence": { "notes": "modules/adrenal_steroidogenesis-notes.md", "curated_references": 26, "review": "Thirteen gene reviews complete: eleven native pathway representatives and two fish comparators; 434 original annotations preserved and adjudicated, no NEW rows.", "taxon_scope": "Vertebrate adrenal/interrenal branches distinguish rodent corticosterone, fish CYP17/CYP11 divergence, and independently evolved CYP11B duplications.", "merge_commit": "38c2b634f063c40c1e957bde87be87050daed719", "head_commit": "74e860184b3357abf6cb64e828f4097cc3b7ae1c", "review_decision": "APPROVED", "merged_at": "2026-10-26T13:06:33Z", "reviewed_members": 13, "adjudicated_annotation_rows": 434, "reaction_nodes": 14, "annotons": 17, "targeted_validation": "All thirteen reviews pass locally; module has eighteen documented family-source/conformance advisories. Fifteen initial histories validated.", "full_validation": "PASS: corrective-state just validate-all reached terminal exit zero before PR creation.", "ci": "Required checks passed before merge.", "render": "Module HTML generated and committed.", "repository_validation": "Full just validate-all passed; targeted follow-up checks pass.", "review_followup": "All requested corrections reviewed and merged; scoped merged content verified.", "history_records": 25, "completion_verification": "Merged as `38c2b634f063c40c1e957bde87be87050daed719` after approval and passing checks. All 31 scoped curation, history and source files match approved head `74e860184b`. The corrective merge retains 22 supported organelle assertions across seven genes and preserves all 320 affected rows; the full module audit covers thirteen members.", "retrospective_policy_audit": "Corrective merge verified; supported root-organelle assertions retained.", "progress": "Merged as `38c2b634f063c40c1e957bde87be87050daed719` after approval and passing checks. All 31 scoped curation, history and source files match approved head `74e860184b`. The corrective merge retains 22 supported organelle assertions across seven genes and preserves all 320 affected rows; the full module audit covers thirteen members.", "corrective_branch": "cmungall/aigr-adrenal-organelle-followup", "corrective_head": "74e860184b", "corrective_pr": "https://github.com/ai4curation/ai-gene-review/pull/5571", "phase": "Merged as `38c2b634f063c40c1e957bde87be87050daed719` after approval and passing checks. All 31 scoped curation, history and source files match approved head `74e860184b`. The corrective merge retains 22 supported organelle assertions across seven genes and preserves all 320 affected rows; the full module audit covers thirteen members.", "review_service_status": "Scientific review completed; prior service quota failures are historical.", "initial_merge_commit": "72b4d12be1a4b1dbbd1e4abd526ecfd4e06b7a3f", "merged_content_verified": true, "verified_scope_files": 31, "resolved_reopening_reason": "Prior merged review is retained as provenance, but the explicit root-organelle retention invariant is not satisfied. A module-specific corrective follow-up is required." }, "audit_pr": "https://github.com/ai4curation/ai-gene-review/pull/5571" }, { "module": "aerobic_nicotinate_degradation", "path": "modules/aerobic_nicotinate_degradation.yaml", "declared_status": "DRAFT", "audit_status": "COMPLETE", "related_open_prs": [], "annotons": 6, "annotons_with_family": 0, "annotons_with_direct_evidence": 6, "representative_accessions": [], "has_root_taxon_context": true, "audit_pr": "https://github.com/ai4curation/ai-gene-review/pull/5544", "audit_evidence": { "head_commit": "6bb8654d436d38c917629bc880703b03bcc8b7cb", "merge_commit": "94a80ada9f7143d2fb1b38b5e97a5301859c0a7c", "review_decision": "APPROVED", "merged_at": "2026-10-26T00:46:43Z", "branch": "cmungall/aigr-nicotinate-taxon-audit", "notes": "modules/aerobic_nicotinate_degradation-notes.md", "curated_references": 12, "reviewed_members": 12, "adjudicated_annotation_rows": 42, "new_annotation_rows": 0, "reaction_nodes": 6, "family_roles": 7, "panther_subfamilies": 8, "representative_members": 9, "comparators": 3, "taxon_scope": "Pseudomonadota as non-universal evidence envelope; documented two-component NicAB implementation, with qualified Bordetella and S16 comparators.", "targeted_validation": "All twelve genes pass; all pre-existing fields preserved. Module schema/reference/biological/family-member checks pass, with nine documented ontology-conformance/DOI advisories; fourteen histories validated.", "full_validation": "Running; schema passed, term validation underway.", "render": "Module HTML generated and committed.", "ci": "Merged after approval and successful required checks; audit-ledger supersession records evidence-bounded NicD UNDECIDED localization.", "head": "90df36ce72", "reviewed_annotation_rows": 43, "history_records": 27, "review_followup": "MaiA tetramer transfer removed; NicD localization left unresolved with irrelevant evidence removed; one NicC NEW process row after comparator/parent/participation checks. All 42 original rows retained.", "repository_validation": "Full just validate-all passed; PR ready with all targeted follow-up checks passing.", "completion_verification": "All 64 scoped module, gene and history files byte-compared between approved head and merge; identical. Twelve curated references, twelve member reviews and source-specific taxon/chemistry/family decisions inspected. Required checks and merge-group checks passed." } }, { "module": "alcoholic_fermentation", "path": "modules/alcoholic_fermentation.yaml", "declared_status": "DRAFT", "audit_status": "COMPLETE", "related_open_prs": [], "annotons": 7, "annotons_with_family": 7, "annotons_with_direct_evidence": 5, "representative_accessions": [ "UniProtKB:O42873", "UniProtKB:O82647", "UniProtKB:P00330", "UniProtKB:P00332", "UniProtKB:P06169", "UniProtKB:P06525", "UniProtKB:P06672", "UniProtKB:P0DJA2", "UniProtKB:P10127", "UniProtKB:P16467", "UniProtKB:P26263", "UniProtKB:P39714", "UniProtKB:Q04777", "UniProtKB:Q04789", "UniProtKB:Q09669", "UniProtKB:Q09737", "UniProtKB:Q92345", "UniProtKB:Q9P7P6" ], "has_root_taxon_context": true, "audit_evidence": { "module": "modules/alcoholic_fermentation.yaml", "notes": "modules/alcoholic_fermentation-notes.md", "branch": "cmungall/aigr-alcoholic-fermentation-taxon-audit", "reviewed_members": 23, "reviewed_annotation_rows": 487, "curated_references": 34, "targeted_validation": "All 23 gene reviews pass; module biological/reference/membership checks pass with ten free-text-function advisories and three explicitly ungrounded narrower functional subsets.", "repository_validation": "Full just validate-all and targeted follow-ups passed.", "merge_commit": "fe302bb372e476d4c1d6911c825e33bb49c23eac", "head_commit": "337db24a4f26c8a47596c1bcefeb2770ddb59a11", "full_validation": "PASS: corrective-state just validate-all reached terminal exit zero before PR creation.", "review_decision": "APPROVED", "ci": "Required checks passed before merge.", "merged_at": "2026-10-26T13:06:34Z", "completion_verification": "Merged as `fe302bb372e476d4c1d6911c825e33bb49c23eac` after approval and passing checks. All 6 scoped curation, history and source files match approved head `337db24a4f`. The corrective merge retains both SCHPO adh4 mitochondrial assertions beside matrix assertions and preserves all fifteen affected rows.", "retrospective_policy_audit": "Corrective merge verified; supported root-organelle assertions retained.", "progress": "Merged as `fe302bb372e476d4c1d6911c825e33bb49c23eac` after approval and passing checks. All 6 scoped curation, history and source files match approved head `337db24a4f`. The corrective merge retains both SCHPO adh4 mitochondrial assertions beside matrix assertions and preserves all fifteen affected rows.", "corrective_branch": "cmungall/aigr-fermentation-organelle-followup", "corrective_head": "337db24a4f", "review_followup": "All requested corrections reviewed and merged; scoped merged content verified.", "corrective_pr": "https://github.com/ai4curation/ai-gene-review/pull/5572", "phase": "Merged as `fe302bb372e476d4c1d6911c825e33bb49c23eac` after approval and passing checks. All 6 scoped curation, history and source files match approved head `337db24a4f`. The corrective merge retains both SCHPO adh4 mitochondrial assertions beside matrix assertions and preserves all fifteen affected rows.", "review_service_status": "Scientific review completed; prior service quota failures are historical.", "initial_merge_commit": "16bffd8e632185a8be7f5d9936d01c18017d33f7", "merged_content_verified": true, "verified_scope_files": 6, "resolved_reopening_reason": "Prior merged review is retained as provenance, but the explicit root-organelle retention invariant is not satisfied. A module-specific corrective follow-up is required." }, "audit_pr": "https://github.com/ai4curation/ai-gene-review/pull/5572" }, { "module": "alginate_o_acetylation", "path": "modules/alginate_o_acetylation.yaml", "declared_status": "DRAFT", "audit_status": "COMPLETE", "related_open_prs": [], "annotons": 4, "annotons_with_family": 4, "annotons_with_direct_evidence": 2, "representative_accessions": [ "UniProtKB:O52194", "UniProtKB:O52196", "UniProtKB:O52197", "UniProtKB:P70799", "UniProtKB:Q06062", "UniProtKB:Q51372", "UniProtKB:Q51392", "UniProtKB:Q51393", "UniProtKB:Q88ND0", "UniProtKB:Q88ND2", "UniProtKB:Q88ND3", "UniProtKB:Q88ND4" ], "has_root_taxon_context": true, "audit_evidence": { "module": "modules/alginate_o_acetylation.yaml", "notes": "modules/alginate_o_acetylation-notes.md", "branch": "cmungall/aigr-alginate-acetylation-taxon-audit", "curated_references": 15, "member_review_plan": "All 12 verified Pseudomonas aeruginosa, P. putida and Azotobacter vinelandii member reviews are complete.", "taxon_scope": "Pseudomonadaceae evidence envelope, not universal retention.", "mechanistic_limits": "AlgI acyl shuttle and AlgJ-to-AlgX handoff remain proposed; AlgF interaction role distinguished from enzymatic transfer. AlgJ/AlgX InterPro domains are not mislabeled as full-length family identifiers.", "merge_commit": "47f648bb3d97f15c19051afb270c527728b17e51", "reviewed_members": 12, "reviewed_annotation_rows": 52, "original_goa_rows": 42, "retained_prior_proposals": 4, "new_proposals": 6, "removed_redundant_prior_proposals": 2, "targeted_validation": "All 12 targeted reviews and QA follow-ups, module/schema/render checks and module/member histories pass; one manually checked InterPro-prefix advisory.", "full_validation": "Full just validate-all passed; later curation corrections passed targeted checks.", "head_commit": "f15f9ec44b34c91ede77efb94608de2183c638f1", "ci": "Merged as `47f648bb3d97f15c19051afb270c527728b17e51` after current-head approval and passing required checks. All 83 scoped curation/history files match approved head `f15f9ec44b`; 12 reviews, 52 rows and 15 references are verified.", "reviewed_rows": 52, "history_scope": "Module/member provenance and project-progress records are distinct; PR-delta totals change as shared project history merges into main.", "nomenclature": "The alias algV is deliberately used for Azotobacter O52197 (UniProt primary name algJ) to distinguish it from historical export AlgJ Q44497, now algE.", "review_followup": "Four metadata-only conflicts were resolved with all 83 reviewed curated/history paths unchanged. Focused checks and all build CI pass. Current-head automated review failed before assessment; approval remains required.", "review_service_status": "Scientific review completed; prior service quota failures are historical.", "progress": "Merged as `47f648bb3d97f15c19051afb270c527728b17e51` after current-head approval and passing required checks. All 83 scoped curation/history files match approved head `f15f9ec44b`; 12 reviews, 52 rows and 15 references are verified.", "review_decision": "APPROVED", "phase": "Merged as `47f648bb3d97f15c19051afb270c527728b17e51` after current-head approval and passing required checks. All 83 scoped curation/history files match approved head `f15f9ec44b`; 12 reviews, 52 rows and 15 references are verified.", "merged_content_verified": true, "verified_scope_files": 83 }, "audit_pr": "https://github.com/ai4curation/ai-gene-review/pull/5546" }, { "module": "alginate_polymerization_export", "path": "modules/alginate_polymerization_export.yaml", "declared_status": "DRAFT", "audit_status": "COMPLETE", "related_open_prs": [], "annotons": 6, "annotons_with_family": 5, "annotons_with_direct_evidence": 4, "representative_accessions": [ "UniProtKB:P18895", "UniProtKB:P96956", "UniProtKB:Q06749", "UniProtKB:Q51371", "UniProtKB:Q88NC6", "UniProtKB:Q88NC7", "UniProtKB:Q88NC8", "UniProtKB:Q88NC9", "UniProtKB:Q88ND1", "UniProtKB:Q9HY69" ], "has_root_taxon_context": false, "audit_evidence": { "module": "modules/alginate_polymerization_export.yaml", "notes": "modules/alginate_polymerization_export-notes.md", "branch": "cmungall/aigr-alginate-polymerization-taxon-audit", "member_review_plan": "18 new/audited reviews across PSEPK, PSEAE and AZOVI plus reuse of 3 AlgX reviews after acetylationPR merge", "literature": "Comparative bacterial and Azotobacter reviews plus primary AlgKX, AlgL, AlgG, AlgE and 2026 MucD evidence; source/strain identity checked.", "reviewed_members": 18, "reviewed_annotation_rows": 98, "curated_references": 23, "targeted_validation": "All 18 gene reviews, module checks and histories pass; independent biological QA completed; six existing gene pages regenerated.", "full_validation": "Full just validate-all passed. Draft PR #5552 awaits upstream PR #5546 AlgX reviews before rebase/readiness.", "head_commit": "efc62375b8ac2974d47ea2aaac0cdf8b9e920907", "history_records": 26, "reviewed_rows": 98, "ci": "Approved head merged; scoped content verified.", "annotation_rows_reviewed": 99, "review_followup": "Merged PR #5552 as 2bb4ff1c018298e73c1ebd054a6e02949a2cd163 at 2026-10-26T17:25:41Z, after exact-head approval of efc62375b8ac2974d47ea2aaac0cdf8b9e920907. All 142 scoped approved science/source/history blobs match the actual merge; 21 reviews, 116 final rows, 42 raw sources verified. Three approved reviewer-authored ISS proposal source corrections are recorded separately from unchanged machine payloads; all 116 rows remain present.", "progress": "Merged PR #5552 as 2bb4ff1c018298e73c1ebd054a6e02949a2cd163 at 2026-10-26T17:25:41Z, after exact-head approval of efc62375b8ac2974d47ea2aaac0cdf8b9e920907. All 142 scoped approved science/source/history blobs match the actual merge; 21 reviews, 116 final rows, 42 raw sources verified. Three approved reviewer-authored ISS proposal source corrections are recorded separately from unchanged machine payloads; all 116 rows remain present.", "review_decision": "APPROVED", "phase": "Merged PR #5552 as 2bb4ff1c018298e73c1ebd054a6e02949a2cd163 at 2026-10-26T17:25:41Z, after exact-head approval of efc62375b8ac2974d47ea2aaac0cdf8b9e920907. All 142 scoped approved science/source/history blobs match the actual merge; 21 reviews, 116 final rows, 42 raw sources verified. Three approved reviewer-authored ISS proposal source corrections are recorded separately from unchanged machine payloads; all 116 rows remain present.", "merge_state": "UNKNOWN", "github_snapshot_at": "2026-10-26T18:05:00.077112+00:00", "push_status": "Published remote head verified at snapshot", "auto_merge_enabled": false, "publication_state": "MERGED", "current_head_checks": [ { "__typename": "CheckRun", "completedAt": "2026-10-26T16:47:45Z", "conclusion": "SKIPPED", "detailsUrl": "https://github.com/ai4curation/ai-gene-review/actions/runs/40362529628/job/121711472263", "name": "claude", "startedAt": "2026-10-26T16:47:45Z", "status": "COMPLETED", "workflowName": "Claude Code" }, { "__typename": "CheckRun", "completedAt": "2026-10-26T17:02:52Z", "conclusion": "SUCCESS", "detailsUrl": "https://github.com/ai4curation/ai-gene-review/actions/runs/40361319276/job/121707223602", "name": "validation (3.12)", "startedAt": "2026-10-26T16:45:30Z", "status": "COMPLETED", "workflowName": "Build and test" }, { "__typename": "CheckRun", "completedAt": "2026-10-26T16:47:57Z", "conclusion": "SUCCESS", "detailsUrl": "https://github.com/ai4curation/ai-gene-review/actions/runs/40361319377/job/121707225919", "name": "claude-review", "startedAt": "2026-10-26T16:40:45Z", "status": "COMPLETED", "workflowName": "Claude Code Review" }, { "__typename": "CheckRun", "completedAt": "2026-10-26T16:47:32Z", "conclusion": "SUCCESS", "detailsUrl": "https://github.com/ai4curation/ai-gene-review/actions/runs/40361319276/job/121707223159", "name": "suite (3.12)", "startedAt": "2026-10-26T16:44:34Z", "status": "COMPLETED", "workflowName": "Build and test" }, { "__typename": "CheckRun", "completedAt": "2026-10-26T17:02:58Z", "conclusion": "SUCCESS", "detailsUrl": "https://github.com/ai4curation/ai-gene-review/actions/runs/40361319276/job/121719920782", "name": "test (3.12)", "startedAt": "2026-10-26T17:02:54Z", "status": "COMPLETED", "workflowName": "Build and test" } ], "latest_submitted_review": { "id": 5655741336, "state": "APPROVED", "commit_id": "efc62375b8ac2974d47ea2aaac0cdf8b9e920907", "submitted_at": "2026-10-26T16:47:41Z", "html_url": "https://github.com/ai4curation/ai-gene-review/pull/5552#pullrequestreview-5655741336" }, "merge_commit": "2bb4ff1c018298e73c1ebd054a6e02949a2cd163", "merged_at": "2026-10-26T17:25:41Z", "completion_verification": "All 142 scoped approved science/source/history blobs match the actual merge; 21 reviews, 116 final rows, 42 raw sources verified.", "completion_proof": ".cache/module-audit-logs/merged-audits-20261026-late/5552-proof.json" }, "audit_pr": "https://github.com/ai4curation/ai-gene-review/pull/5552" }, { "module": "aliphatic_glucosinolate_myrosinase_defense", "path": "modules/aliphatic_glucosinolate_myrosinase_defense.yaml", "declared_status": "DRAFT", "audit_status": "COMPLETE", "related_open_prs": [ 5076 ], "annotons": 18, "annotons_with_family": 18, "annotons_with_direct_evidence": 18, "representative_accessions": [ "UniProtKB:A0AAU9RDZ2", "UniProtKB:A0AAU9RP64", "UniProtKB:A0AAU9RX80", "UniProtKB:A0AAU9S298", "UniProtKB:A0AAU9SEL1", "UniProtKB:A0AAU9SYX6", "UniProtKB:A0AAU9T3M3", "UniProtKB:A0AAU9T4X1", "UniProtKB:G1FNI6", "UniProtKB:P37702", "UniProtKB:P48421", "UniProtKB:Q8L7C9", "UniProtKB:Q8RY71", "UniProtKB:Q945B5", "UniProtKB:Q949U1", "UniProtKB:Q94AR8", "UniProtKB:Q96324", "UniProtKB:Q9C5C2", "UniProtKB:Q9C9C9", "UniProtKB:Q9FG67", "UniProtKB:Q9FMT1", "UniProtKB:Q9FN52", "UniProtKB:Q9FUY7", "UniProtKB:Q9FZ80", "UniProtKB:Q9LE06", "UniProtKB:Q9LYT7", "UniProtKB:Q9M0A7", "UniProtKB:Q9M401", "UniProtKB:Q9SDM9", "UniProtKB:Q9SIV0", "UniProtKB:Q9SKC1", "UniProtKB:Q9SS04" ], "has_root_taxon_context": true, "audit_evidence": { "worktree": "aigr-glucosinolate-defense-taxon-audit", "module": "modules/aliphatic_glucosinolate_myrosinase_defense.yaml", "notes": "modules/aliphatic_glucosinolate_myrosinase_defense-notes.md", "progress": "Thirty-one curated references and 35 member reviews (453 rows); full repository validation passed. PR review follow-up restores direct evidence and resolves adjudicable localization claims; source-specific unavailable cases remain explicit.", "family_qa": "Verified dual P450 placements preserved; MAM family boundary corrected for directly assayed BjMAM1-A outside SF60.", "head_commit": "9115b56b952469501717d9d089bc3c70ebf9cfb8", "ci": "Renewed scientific review approved all requested corrections; required head checks passed and normal merge-queue checks are running.", "full_validation": "Full just validate-all passed; targeted follow-up checks for fourteen edited member reviews pass.", "merge_commit": "75d569bf94a697ed142f0f1397736819563b8d74", "merged_at": "2026-10-26T03:31:08Z", "review_decision": "APPROVED", "completion_verification": "All 208 PR paths enumerated with pagination; 187 module/gene/source/family/history files byte-identical between approved head and merge commit. Literature, steps, taxon, verified families and 35 member reviews inspected; normal checks/queue passed." }, "audit_pr": "https://github.com/ai4curation/ai-gene-review/pull/5550" }, { "module": "ampk_energy_sensing", "path": "modules/ampk_energy_sensing.yaml", "declared_status": "DRAFT", "audit_status": "NOT_STARTED", "related_open_prs": [], "annotons": 10, "annotons_with_family": 1, "annotons_with_direct_evidence": 10, "representative_accessions": [ "UniProtKB:O43741", "UniProtKB:O95685", "UniProtKB:P0DP23", "UniProtKB:P0DP24", "UniProtKB:P0DP25", "UniProtKB:P49593", "UniProtKB:P49815", "UniProtKB:P54619", "UniProtKB:P54646", "UniProtKB:P62136", "UniProtKB:P62140", "UniProtKB:P67775", "UniProtKB:Q13131", "UniProtKB:Q15831", "UniProtKB:Q7RTN6", "UniProtKB:Q8N5S9", "UniProtKB:Q8WY54", "UniProtKB:Q92574", "UniProtKB:Q96RR4", "UniProtKB:Q9UGI9", "UniProtKB:Q9UGJ0", "UniProtKB:Q9Y376", "UniProtKB:Q9Y478" ], "has_root_taxon_context": true, "audit_evidence": { "phase": "Newly discovered in the 2026-11-05 universe refresh; PR overlaps and biology not yet audited." } }, { "module": "androgen_receptor_signaling", "path": "modules/androgen_receptor_signaling.yaml", "declared_status": "DRAFT", "audit_status": "COMPLETE", "related_open_prs": [], "annotons": 10, "annotons_with_family": 10, "annotons_with_direct_evidence": 10, "representative_accessions": [ "UniProtKB:A4GT83", "UniProtKB:D0VX34", "UniProtKB:D1MV72", "UniProtKB:D1MV73", "UniProtKB:O75376", "UniProtKB:P07900", "UniProtKB:P10275", "UniProtKB:P19091", "UniProtKB:P30416", "UniProtKB:Q02790", "UniProtKB:Q13451", "UniProtKB:Q15185", "UniProtKB:Q15596", "UniProtKB:Q15788", "UniProtKB:Q64378" ], "has_root_taxon_context": true, "audit_evidence": { "worktree": "aigr-androgen-receptor-taxon-audit", "progress": "Merged PR #5554 as 70a5964a22d14e7972cfb43fe02095aa4cb8a7c1 at 2026-10-26T15:23:25Z after current-head approval and successful queue checks. All 270 scoped science, source and history blobs match approved head 93ce23a1a7d136ce286372b29b6e3174abc45979. Fifteen reviews and 1,683 original rows are preserved.", "reviewed_members": 15, "reviewed_annotation_rows": 1683, "curated_references": 26, "head_commit": "93ce23a1a7d136ce286372b29b6e3174abc45979", "full_validation": "Full just validate-all passed; all fifteen focused reviews, module checks, histories and renders pass.", "ci": "PR-head and merge-group validation, suite and required aggregate checks passed before normal queue merge.", "review_followup": "All requested scientific and prose follow-ups were completed and approved; both addressed review threads were resolved before the normal queue merge.", "review_service_status": "Scientific review completed; prior service quota failures are historical.", "review_decision": "APPROVED", "phase": "Merged PR #5554 as 70a5964a22d14e7972cfb43fe02095aa4cb8a7c1 at 2026-10-26T15:23:25Z after current-head approval and successful queue checks. All 270 scoped science, source and history blobs match approved head 93ce23a1a7d136ce286372b29b6e3174abc45979. Fifteen reviews and 1,683 original rows are preserved.", "merge_state": "MERGED", "merge_commit": "70a5964a22d14e7972cfb43fe02095aa4cb8a7c1", "merged_at": "2026-10-26T15:23:25Z", "merge_blob_proof": { "scoped_files": 270, "all_identical": true, "approved_head": "93ce23a1a7d136ce286372b29b6e3174abc45979", "merge_commit": "70a5964a22d14e7972cfb43fe02095aa4cb8a7c1" }, "annotons": 10, "connections_reviewed": 12 }, "audit_pr": "https://github.com/ai4curation/ai-gene-review/pull/5554" }, { "module": "angiotensin_ii_receptor_signaling", "path": "modules/angiotensin_ii_receptor_signaling.yaml", "declared_status": "DRAFT", "audit_status": "NOT_STARTED", "related_open_prs": [], "annotons": 21, "annotons_with_family": 0, "annotons_with_direct_evidence": 16, "representative_accessions": [ "UniProtKB:O60674", "UniProtKB:P01019", "UniProtKB:P04899", "UniProtKB:P08754", "UniProtKB:P25098", "UniProtKB:P28562", "UniProtKB:P29350", "UniProtKB:P29597", "UniProtKB:P29992", "UniProtKB:P30556", "UniProtKB:P32121", "UniProtKB:P34947", "UniProtKB:P35626", "UniProtKB:P43250", "UniProtKB:P49407", "UniProtKB:P50052", "UniProtKB:P50148", "UniProtKB:Q05516", "UniProtKB:Q6RW13", "UniProtKB:Q96P48", "UniProtKB:Q9ULD2" ], "has_root_taxon_context": true, "audit_evidence": { "phase": "Newly discovered in the 2026-11-05 universe refresh; PR overlaps and biology not yet audited." } }, { "module": "anti_crispr_suppression", "path": "modules/anti_crispr_suppression.yaml", "declared_status": "DRAFT", "audit_status": "COMPLETE", "related_open_prs": [], "annotons": 9, "annotons_with_family": 8, "annotons_with_direct_evidence": 9, "representative_accessions": [ "UniProtKB:A0A247D711", "UniProtKB:A0A2D0TCG3", "UniProtKB:A0A5H1ZR47", "UniProtKB:H9C180", "UniProtKB:H9C181", "UniProtKB:L7P7R7", "UniProtKB:Q6TM72", "UniProtKB:Q8QL27" ], "has_root_taxon_context": true, "audit_branch": "cmungall/aigr-anti-crispr-taxon-audit", "audit_evidence": { "worktree": "aigr-anti-crispr-taxon-audit", "progress": "Merged PR #5555 as aa66b5213685b58a3a8c3d5503aa1c44411c9b5e at 2026-10-26T17:25:40Z, after exact-head approval of 76b0361126d8dbe5cf7c170acf34d289426c9c2e. All 114 scoped approved science/source/history blobs match the actual merge; 13 reviews, 42 final rows, 26 raw sources verified.", "module": "modules/anti_crispr_suppression.yaml", "head_commit": "76b0361126d8dbe5cf7c170acf34d289426c9c2e", "reviewed_members": 13, "reviewed_annotation_rows": 42, "full_validation": "PASS: session 1434 terminal exit 0; anti-crispr-final-followup-validate-all.log ends All validations passed. 9,092 valid reviews, zero errors; all 54 pathway PMID checks pass. Repository-wide advisory warnings remain.", "ci": "Approved head merged; scoped content verified.", "review_followup": "Merged PR #5555 as aa66b5213685b58a3a8c3d5503aa1c44411c9b5e at 2026-10-26T17:25:40Z, after exact-head approval of 76b0361126d8dbe5cf7c170acf34d289426c9c2e. All 114 scoped approved science/source/history blobs match the actual merge; 13 reviews, 42 final rows, 26 raw sources verified.", "review_decision": "APPROVED", "phase": "Merged PR #5555 as aa66b5213685b58a3a8c3d5503aa1c44411c9b5e at 2026-10-26T17:25:40Z, after exact-head approval of 76b0361126d8dbe5cf7c170acf34d289426c9c2e. All 114 scoped approved science/source/history blobs match the actual merge; 13 reviews, 42 final rows, 26 raw sources verified.", "merge_state": "UNKNOWN", "github_snapshot_at": "2026-10-26T18:05:00.077112+00:00", "push_status": "Published remote head verified at snapshot", "auto_merge_enabled": false, "publication_state": "MERGED", "current_head_checks": [ { "__typename": "CheckRun", "completedAt": "2026-10-26T16:49:05Z", "conclusion": "SKIPPED", "detailsUrl": "https://github.com/ai4curation/ai-gene-review/actions/runs/40362738152/job/121712219940", "name": "claude", "startedAt": "2026-10-26T16:49:05Z", "status": "COMPLETED", "workflowName": "Claude Code" }, { "__typename": "CheckRun", "completedAt": "2026-10-26T16:57:25Z", "conclusion": "SUCCESS", "detailsUrl": "https://github.com/ai4curation/ai-gene-review/actions/runs/40360859146/job/121705569633", "name": "validation (3.12)", "startedAt": "2026-10-26T16:38:53Z", "status": "COMPLETED", "workflowName": "Build and test" }, { "__typename": "CheckRun", "completedAt": "2026-10-26T16:49:16Z", "conclusion": "SUCCESS", "detailsUrl": "https://github.com/ai4curation/ai-gene-review/actions/runs/40360859231/job/121705570327", "name": "claude-review", "startedAt": "2026-10-26T16:43:22Z", "status": "COMPLETED", "workflowName": "Claude Code Review" }, { "__typename": "CheckRun", "completedAt": "2026-10-26T16:40:42Z", "conclusion": "SUCCESS", "detailsUrl": "https://github.com/ai4curation/ai-gene-review/actions/runs/40360859146/job/121705569022", "name": "suite (3.12)", "startedAt": "2026-10-26T16:37:55Z", "status": "COMPLETED", "workflowName": "Build and test" }, { "__typename": "CheckRun", "completedAt": "2026-10-26T16:58:00Z", "conclusion": "SUCCESS", "detailsUrl": "https://github.com/ai4curation/ai-gene-review/actions/runs/40360859146/job/121716857345", "name": "test (3.12)", "startedAt": "2026-10-26T16:57:57Z", "status": "COMPLETED", "workflowName": "Build and test" } ], "latest_submitted_review": { "id": 5655759311, "state": "APPROVED", "commit_id": "76b0361126d8dbe5cf7c170acf34d289426c9c2e", "submitted_at": "2026-10-26T16:49:01Z", "html_url": "https://github.com/ai4curation/ai-gene-review/pull/5555#pullrequestreview-5655759311" }, "merge_commit": "aa66b5213685b58a3a8c3d5503aa1c44411c9b5e", "merged_at": "2026-10-26T17:25:40Z", "completion_verification": "All 114 scoped approved science/source/history blobs match the actual merge; 13 reviews, 42 final rows, 26 raw sources verified.", "completion_proof": ".cache/module-audit-logs/merged-audits-20261026-late/5555-proof.json" }, "audit_pr": "https://github.com/ai4curation/ai-gene-review/pull/5555" }, { "module": "apoptotic_execution_phase", "path": "modules/apoptotic_execution_phase.yaml", "declared_status": "DRAFT", "audit_status": "COMPLETE", "related_open_prs": [], "annotons": 10, "annotons_with_family": 10, "annotons_with_direct_evidence": 10, "representative_accessions": [ "UniProtKB:O00273", "UniProtKB:O08738", "UniProtKB:O54786", "UniProtKB:O54788", "UniProtKB:O76075", "UniProtKB:O95831", "UniProtKB:P42574", "UniProtKB:P55210", "UniProtKB:P55212", "UniProtKB:P70677", "UniProtKB:P97864", "UniProtKB:P98170", "UniProtKB:Q60989", "UniProtKB:Q9JIQ3", "UniProtKB:Q9NR28", "UniProtKB:Q9UKV3" ], "has_root_taxon_context": true, "audit_evidence": { "branch": "cmungall/aigr-apoptotic-execution-taxon-audit", "notes": "modules/apoptotic_execution_phase-notes.md", "member_review_plan": "Sixteen human/mouse reviews completed; 1608 annotation rows reviewed with original machine payloads preserved. Six new mouse seeds fetched normally.", "curated_references": 35, "taxon_scope": "Mammalian template with qualified human/mouse exemplars and nonmammalian boundary comparisons.", "mechanistic_limits": "Separate CASP3/6/7; XIAP restraint scoped to CASP3/7; ICAD folding distinct from inhibition; contextual Acinus activity not equated to RNA binding; AIF not universally downstream of CASP3.", "full_validation": "PASS: full-validation session 37836 exited zero. Root inspected the terminal log: All validations passed; 9,094 reviews, zero errors, 29,664 corpus warnings and 54 pathway checks passed. This integration did not restart validation.", "members_in_scope": 16, "annotation_rows_in_scope": 1608, "members_reviewed": 16, "annotation_rows_reviewed": 1608, "connections_reviewed": 10, "source_quotes_checked": 28, "actions": { "ACCEPT": 607, "KEEP_AS_NON_CORE": 230, "MARK_AS_OVER_ANNOTATED": 2, "MODIFY": 254, "NEW": 2, "REMOVE": 426, "UNDECIDED": 87 }, "head_commit": "0786e694fbf3d2e2cb6f224397efa88607ddb927", "ci": "Pinned GitHub snapshot 2026-10-27T16:02:16.235792+00:00 for head 0786e694fbf3d2e2cb6f224397efa88607ddb927. See current_head_checks for exact states; queued or running checks are not counted as passed. Later follow-up commits require fresh CI.", "logic_validation": "PASS: 54 module-logic tests after requiring CASP3 or CASP7 while preserving optional context. CI restarts on the corrected head.", "progress": "PR #5558 and DIABLO follow-up #6124 merged. All 16 member reviews are COMPLETE with 1,608 reviewed rows and no PENDING. The sole later module delta is the precomposed inhibitor-term decomposition from merged #5565; existing process context and all other parsed module content are preserved. The scoped module audit is complete; unresolved scientific questions remain represented explicitly.", "review_followup": "Sixteen member reviews preserve 1,608 original annotation rows and 32 raw sources. All 174 scoped scientific/source/history paths remain unchanged by this tracker repair; the earlier apoptosis-specific quote-baseline union is retained. Pinned GitHub snapshot 2026-10-27T16:02:16.235792+00:00: PR #5558 is OPEN at 0786e694fbf3d2e2cb6f224397efa88607ddb927; latest submitted review 5670099085 is APPROVED on 0786e694fbf3d2e2cb6f224397efa88607ddb927 at 2026-10-27T15:49:35Z. CI is recorded for that same observed head. The tracker follow-up prepared here has not yet received remote review or CI; those checks remain pending after publication.", "review_decision": "APPROVED", "phase": "PR #5558 and DIABLO follow-up #6124 merged. All 16 member reviews are COMPLETE with 1,608 reviewed rows and no PENDING. The sole later module delta is the precomposed inhibitor-term decomposition from merged #5565; existing process context and all other parsed module content are preserved. The scoped module audit is complete; unresolved scientific questions remain represented explicitly.", "source_followup_commit": "5c0c9cf686", "focused_validation": "Human CASP3 and mouse Casp3 strict schema, term, source and consistency checks: both PASS, zero errors and zero warnings; history/backfill/render and full-panel payload/raw-source proof PASS.", "module_graph": "Unchanged by the 36-review-object source follow-up; current module has 10 family-backed activities with evidence, 10 connections and 35 references. CASP3-or-CASP7 execution requirement remains intact.", "tracker_reconciliation": "Rebuilt from origin/main fe302bb372e476d4c1d6911c825e33bb49c23eac; only this existing audit row was replaced. Twelve missing module rows were imported verbatim from canonical 3c93882525: eleven NOT_STARTED and the active acetylcholine audit with its PR evidence. All 701 other main rows and unrelated upstream prose are preserved.", "merge_state": "MERGED", "member_reviews": 16, "structural_metrics_source": "Pinned a7496544eff7cbe3cb844be911bf05ae635b0e91: 10 module activities, 16 exact representative accessions, 35 references and 10 connections; 16 parsed member reviews contain 1608 annotation rows.", "tracker_integration": "Current checkpoint preserves canonical identities, current lifecycle facts and all approved scientific content; historical integration details remain in dated notes.", "github_snapshot_at": "2026-10-27T16:02:16.235792+00:00", "push_status": "Published head observed at the pinned snapshot; this snapshot is not a claim about a later push.", "auto_merge_enabled": true, "publication_state": "MERGED", "current_head_checks": [ { "__typename": "CheckRun", "completedAt": "0001-01-01T00:00:00Z", "conclusion": "", "detailsUrl": "https://github.com/ai4curation/ai-gene-review/actions/runs/40533190743/job/122291287525", "name": "validation (3.12)", "startedAt": "2026-10-27T15:39:48Z", "status": "IN_PROGRESS", "workflowName": "Build and test" }, { "__typename": "CheckRun", "completedAt": "2026-10-27T15:49:39Z", "conclusion": "SKIPPED", "detailsUrl": "https://github.com/ai4curation/ai-gene-review/actions/runs/40534829620/job/122297137630", "name": "claude", "startedAt": "2026-10-27T15:49:40Z", "status": "COMPLETED", "workflowName": "Claude Code" }, { "__typename": "CheckRun", "completedAt": "2026-10-27T15:49:54Z", "conclusion": "SUCCESS", "detailsUrl": "https://github.com/ai4curation/ai-gene-review/actions/runs/40533190746/job/122291288818", "name": "claude-review", "startedAt": "2026-10-27T15:39:49Z", "status": "COMPLETED", "workflowName": "Claude Code Review" }, { "__typename": "CheckRun", "completedAt": "2026-10-27T16:00:50Z", "conclusion": "SUCCESS", "detailsUrl": "https://github.com/ai4curation/ai-gene-review/actions/runs/40533190743/job/122291288189", "name": "suite (3.12)", "startedAt": "2026-10-27T15:39:48Z", "status": "COMPLETED", "workflowName": "Build and test" } ], "latest_submitted_review": { "id": 5670099085, "state": "APPROVED", "commit_id": "0786e694fbf3d2e2cb6f224397efa88607ddb927", "submitted_at": "2026-10-27T15:49:35Z", "html_url": "https://github.com/ai4curation/ai-gene-review/pull/5558#pullrequestreview-5670099085" }, "integration_pending": null, "ci_head_commit": "0786e694fbf3d2e2cb6f224397efa88607ddb927", "pr": 5558, "pr_url": "https://github.com/ai4curation/ai-gene-review/pull/5558", "merged_at": "2026-10-27T18:54:34Z", "merge_commit": "6cea7bd0a5c9ed4fa53bd44e7c9cafd4185e338a", "approved_head": "de31e9f06c9105812e17a17c118fa3a4705678a1", "scoped_blobs_verified": 185, "ci_status": "Head validation, suite, test and review checks succeeded", "merged_content_proof": "projects/MODULE_TAXON_AUDIT/proofs/pr5558-merged-content.json", "previous_status_snapshot": { "phase": "Merged content verified against the approved head and all decisions resolved, but human DIABLO retains DRAFT metadata and requires a scoped follow-up before marking the audit COMPLETE.", "progress": "Sixteen member reviews preserve 1,608 original annotation rows and 32 raw sources. All 174 scoped scientific/source/history paths remain unchanged by this tracker repair; the earlier apoptosis-specific quote-baseline union is retained. Pinned GitHub snapshot 2026-10-27T16:02:16.235792+00:00: PR #5558 is OPEN at 0786e694fbf3d2e2cb6f224397efa88607ddb927; latest submitted review 5670099085 is APPROVED on 0786e694fbf3d2e2cb6f224397efa88607ddb927 at 2026-10-27T15:49:35Z. CI is recorded for that same observed head. The tracker follow-up prepared here has not yet received remote review or CI; those checks remain pending after publication.", "merge_state": "OPEN at the pinned snapshot; review and CI for subsequent follow-up commits remain pending.", "publication_state": "OPEN", "integration_pending": { "snapshot_head": "0786e694fbf3d2e2cb6f224397efa88607ddb927", "snapshot_at": "2026-10-27T16:02:16.235792+00:00", "followup_review": "PENDING", "followup_checks": "PENDING", "scope": "tracker correction prepared here" } }, "completion": "PR #5558 and DIABLO follow-up #6124 merged. All 16 member reviews are COMPLETE with 1,608 reviewed rows and no PENDING. The sole later module delta is the precomposed inhibitor-term decomposition from merged #5565; existing process context and all other parsed module content are preserved. The scoped module audit is complete; unresolved scientific questions remain represented explicitly.", "completion_verified_at": "2026-11-06T16:19:44.202889+00:00", "completion_main_commit": "1970e159b929a11ec02b0bc86e64cebae7cf4c9e", "completion_merge_proof": "projects/MODULE_TAXON_AUDIT/proofs/pr6124-merged-content.json", "completion_merge_commit": "fd782f231a5593f3aa27e21150286d650a7f6def", "completion_pr": 6124, "completion_panel_proof": "projects/MODULE_TAXON_AUDIT/proofs/apoptotic-execution-completion-panel.json", "followup_pr": 6124 }, "audit_pr": "https://github.com/ai4curation/ai-gene-review/pull/5558", "audit_phase": "PR #5558 and DIABLO follow-up #6124 merged. All 16 member reviews are COMPLETE with 1,608 reviewed rows and no PENDING. The sole later module delta is the precomposed inhibitor-term decomposition from merged #5565; existing process context and all other parsed module content are preserved. The scoped module audit is complete; unresolved scientific questions remain represented explicitly." }, { "module": "aps_dependent_assimilatory_sulfate_reduction", "path": "modules/aps_dependent_assimilatory_sulfate_reduction.yaml", "declared_status": "DRAFT", "audit_status": "COMPLETE", "related_open_prs": [ 5076 ], "annotons": 10, "annotons_with_family": 7, "annotons_with_direct_evidence": 4, "representative_accessions": [ "UniProtKB:O05927", "UniProtKB:O14463", "UniProtKB:P08536", "UniProtKB:P0A6J1", "UniProtKB:P17854", "UniProtKB:P18408", "UniProtKB:P22217", "UniProtKB:P22803", "UniProtKB:P78937", "UniProtKB:P9WJ02", "UniProtKB:Q02196", "UniProtKB:Q10270", "UniProtKB:Q88KB9", "UniProtKB:Q88KG2", "UniProtKB:Q88MD5", "UniProtKB:Q9P7G9" ], "has_root_taxon_context": false, "audit_evidence": { "branch": "cmungall/aigr-sulfate-assimilation-taxon-audit", "notes": "modules/aps_dependent_assimilatory_sulfate_reduction-notes.md", "member_review_plan": "All 29 reviews complete and independently integrated; exact H37Rv SirA P9WJ03 replaces the mislabeled CDC1551 exemplar. All focused checks pass, two existing unused-provider advisories remain.", "members_in_scope": 29, "literature_findings": "Plant APR1 GSH-dependent fused redox domain differs from bacterial thioredoxin-fed APR; Pseudomonas FprA genetics do not resolve the immediate CysI donor.", "overlap": "PR #5076 remains open with older broad family-grounding work; this independent module audit preserves verified source identity and checks current main.", "curated_references": 28, "connections_reviewed": 5, "members_reviewed": 29, "annotation_rows_reviewed": 496, "full_validation": "PASS: terminal exit zero, all validations passed. Current main integrated with all 197 scoped files byte-identical.", "annotation_rows_in_scope": 496, "actions": { "ACCEPT": 351, "MODIFY": 58, "REMOVE": 28, "UNDECIDED": 16, "KEEP_AS_NON_CORE": 33, "MARK_AS_OVER_ANNOTATED": 3, "NEW": 4, "TOO_GENERAL": 3 }, "module_qa": "Independent comparative QA passes schema, family/source/term grounding and render. Eleven explicit advisories preserve honest mixed-family scope, unresolved Pseudomonas donor and contributes-to complex activities.", "head_commit": "8553f16ce504ba93baa73707e210112b389092a9", "pr": 5560, "ci": "Required checks passed before merge.", "progress": "Merged as `6349c3ef3ea2c8604949502686281dde0c0aaa7a` after approval and passing checks. All 226 scoped curation, history and source files match approved head `8553f16ce5`. The audit covers 29 member reviews, 496 rows, 28 curated references and five qualified connections.", "review_followup": "All requested corrections reviewed and merged; scoped merged content verified.", "review_decision": "APPROVED", "phase": "Merged as `6349c3ef3ea2c8604949502686281dde0c0aaa7a` after approval and passing checks. All 226 scoped curation, history and source files match approved head `8553f16ce5`. The audit covers 29 member reviews, 496 rows, 28 curated references and five qualified connections.", "review_service_status": "Scientific review completed; prior service quota failures are historical.", "merge_commit": "6349c3ef3ea2c8604949502686281dde0c0aaa7a", "merged_at": "2026-10-26T13:06:32Z", "merged_content_verified": true, "verified_scope_files": 226, "completion_verification": "Merged as `6349c3ef3ea2c8604949502686281dde0c0aaa7a` after approval and passing checks. All 226 scoped curation, history and source files match approved head `8553f16ce5`. The audit covers 29 member reviews, 496 rows, 28 curated references and five qualified connections." }, "audit_pr": "https://github.com/ai4curation/ai-gene-review/pull/5560" }, { "module": "arginine_biosynthesis", "path": "modules/arginine_biosynthesis.yaml", "declared_status": "DRAFT", "audit_status": "COMPLETE", "related_open_prs": [ 5076 ], "annotons": 16, "annotons_with_family": 16, "annotons_with_direct_evidence": 16, "representative_accessions": [ "UniProtKB:O33289", "UniProtKB:O60060", "UniProtKB:O74548", "UniProtKB:O94313", "UniProtKB:O94330", "UniProtKB:O94346", "UniProtKB:O94354", "UniProtKB:P03965", "UniProtKB:P04076", "UniProtKB:P05150", "UniProtKB:P07258", "UniProtKB:P0A0Z9", "UniProtKB:P0A6C5", "UniProtKB:P0A6C8", "UniProtKB:P11446", "UniProtKB:P11447", "UniProtKB:P18544", "UniProtKB:P22768", "UniProtKB:P23908", "UniProtKB:P31317", "UniProtKB:P31318", "UniProtKB:P36843", "UniProtKB:P40360", "UniProtKB:P40369", "UniProtKB:P50514", "UniProtKB:P54894", "UniProtKB:P59300", "UniProtKB:P59308", "UniProtKB:P59604", "UniProtKB:P59612", "UniProtKB:P59618", "UniProtKB:P73133", "UniProtKB:P77973", "UniProtKB:P9WIT9", "UniProtKB:Q01217", "UniProtKB:Q04728", "UniProtKB:Q57645", "UniProtKB:Q88CJ5", "UniProtKB:Q88NX4", "UniProtKB:Q88QQ6", "UniProtKB:Q88QW2", "UniProtKB:Q9M8M7", "UniProtKB:Q9SCL7" ], "has_root_taxon_context": true, "audit_evidence": { "branch": "cmungall/aigr-arginine-biosynthesis-taxon-audit", "notes": "modules/arginine_biosynthesis-notes.md", "members_in_original_panel": 39, "member_review_plan": "All 43 reviews are complete: 19 fungi, 10 PSEPK, 10 other original bacteria and 4 added architecture/taxon exemplars (METJA ArgJ, ARATH NAGK/WIN1 and MYCTU short ArgA). The 555 rows include 2 inherited proposals; original annotation payloads are preserved.", "literature": "Comparative reviews PMID:17347518, PMID:26284079, PMID:16122935, PMID:37358082 and PMID:19720555 were assessed alongside primary donor-specific ArgJ, fungal metabolon, plant and short-NAGS evidence; the module contains 22 assessed references.", "mechanistic_limits": "Separate acetyl-CoA initiation from ArgJ acetylornithine recycling, short-NAGS weak glutamate activity from glutamine kinetics, and Arg7 pre-import processing from Arg5,6 import-dependent processing. Bacteria, Archaea, Fungi and Viridiplantae form an occurrence envelope, not a claim of one universal architecture, compartment or complete pathway.", "members_in_scope": 43, "members_reviewed": 43, "annotation_rows_in_scope": 555, "annotation_rows_reviewed": 555, "actions": { "ACCEPT": 404, "KEEP_AS_NON_CORE": 20, "MARK_AS_OVER_ANNOTATED": 1, "MODIFY": 102, "NEW": 2, "REMOVE": 16, "UNDECIDED": 10 }, "full_validation": "PASS: repository-wide just validate-all terminal exit zero; 46 module-logic tests pass.", "module_qa": "PASS: independent source, family, taxon and compartment QA; all 43 representative placements match actual UniProt classifications and cached GO-CAM claims were checked. Schema/grounding/render pass; remaining advisory classes are documented.", "gene_commit": "6ff6782a7b", "curated_references": 22, "connections_reviewed": 9, "head_commit": "b4971234e3c94371d017b6ea69791c636e4b730f", "pr": 5563, "progress": "PR #5563 merged as bfd5d651c11e41f1c509f167bb15a003c2da4bc3 at 2026-10-26T16:46:07Z, after approval of b4971234e3c94371d017b6ea69791c636e4b730f. All 276 scoped approved science, source and history blobs are identical in the merge. The module has 43 reviewed members and 555 annotation rows; the shared CAR1 comparator is included in the wider content proof.", "ci": "Captured remote-head check rollup: SUCCESS; see named checks. Review, checks, queue state and verified merged content are distinct gates.", "review_followup": "PR #5563 merged as bfd5d651c11e41f1c509f167bb15a003c2da4bc3 at 2026-10-26T16:46:07Z, after approval of b4971234e3c94371d017b6ea69791c636e4b730f. All 276 scoped approved science, source and history blobs are identical in the merge. The module has 43 reviewed members and 555 annotation rows; the shared CAR1 comparator is included in the wider content proof.", "review_decision": "APPROVED", "phase": "PR #5563 merged as bfd5d651c11e41f1c509f167bb15a003c2da4bc3 at 2026-10-26T16:46:07Z, after approval of b4971234e3c94371d017b6ea69791c636e4b730f. All 276 scoped approved science, source and history blobs are identical in the merge. The module has 43 reviewed members and 555 annotation rows; the shared CAR1 comparator is included in the wider content proof.", "taxon_context": [ { "preferred_term": "Bacteria", "term": { "id": "NCBITaxon:2", "label": "Bacteria" } }, { "preferred_term": "Archaea", "term": { "id": "NCBITaxon:2157", "label": "Archaea" } }, { "preferred_term": "Fungi", "term": { "id": "NCBITaxon:4751", "label": "Fungi" } }, { "preferred_term": "Viridiplantae", "term": { "id": "NCBITaxon:33090", "label": "Viridiplantae" } } ], "structural_metrics_source": "Pinned 0c9ac5952cd3411c4bbf1abc1b337c5a5a7599ac: 16 module activities, 43 exact representative accessions, 22 references and 9 connections; 43 parsed member reviews contain 555 annotation rows.", "tracker_restoration": "Restored this row from the canonical acetylcholine-worktree tracker, reconciled against the actual current module and all 43 gene reviews; all 701 other pre-existing rows are unchanged.", "merge_state": "UNKNOWN", "member_reviews": [ "genes/ARATH/NAGK/NAGK-ai-review.yaml", "genes/ARATH/WIN1/WIN1-ai-review.yaml", "genes/BACSU/argJ/argJ-ai-review.yaml", "genes/ECOLI/argA/argA-ai-review.yaml", "genes/ECOLI/argB/argB-ai-review.yaml", "genes/ECOLI/argC/argC-ai-review.yaml", "genes/ECOLI/argE/argE-ai-review.yaml", "genes/ECOLI/argH/argH-ai-review.yaml", "genes/METJA/argJ/argJ-ai-review.yaml", "genes/MYCTU/argA/argA-ai-review.yaml", "genes/MYCTU/argF/argF-ai-review.yaml", "genes/NOSS1/argC2/argC2-ai-review.yaml", "genes/PSEPK/argA/argA-ai-review.yaml", "genes/PSEPK/argB/argB-ai-review.yaml", "genes/PSEPK/argC1/argC1-ai-review.yaml", "genes/PSEPK/argC2/argC2-ai-review.yaml", "genes/PSEPK/argE/argE-ai-review.yaml", "genes/PSEPK/argF/argF-ai-review.yaml", "genes/PSEPK/argG/argG-ai-review.yaml", "genes/PSEPK/argH/argH-ai-review.yaml", "genes/PSEPK/argJ/argJ-ai-review.yaml", "genes/PSEPK/aruC/aruC-ai-review.yaml", "genes/SCHPO/aga1/aga1-ai-review.yaml", "genes/SCHPO/arg1/arg1-ai-review.yaml", "genes/SCHPO/arg11/arg11-ai-review.yaml", "genes/SCHPO/arg12/arg12-ai-review.yaml", "genes/SCHPO/arg3/arg3-ai-review.yaml", "genes/SCHPO/arg4/arg4-ai-review.yaml", "genes/SCHPO/arg41/arg41-ai-review.yaml", "genes/SCHPO/arg5/arg5-ai-review.yaml", "genes/SCHPO/arg6/arg6-ai-review.yaml", "genes/SCHPO/arg7/arg7-ai-review.yaml", "genes/SYNY3/argD/argD-ai-review.yaml", "genes/SYNY3/argG/argG-ai-review.yaml", "genes/yeast/ARG1/ARG1-ai-review.yaml", "genes/yeast/ARG2/ARG2-ai-review.yaml", "genes/yeast/ARG3/ARG3-ai-review.yaml", "genes/yeast/ARG4/ARG4-ai-review.yaml", "genes/yeast/ARG5,6/ARG5,6-ai-review.yaml", "genes/yeast/ARG7/ARG7-ai-review.yaml", "genes/yeast/ARG8/ARG8-ai-review.yaml", "genes/yeast/CPA1/CPA1-ai-review.yaml", "genes/yeast/CPA2/CPA2-ai-review.yaml" ], "tracker_integration": "Published merge with pinned main 77121ffa32 and semantic canonical tracker union; scoped science, raw-source and local-file proofs passed.", "github_snapshot_at": "2026-10-26T17:23:37.591323+00:00", "push_status": "Current follow-up head is published; merge/CI status is recorded separately.", "merge_queue": { "state": "MERGED" }, "auto_merge_enabled": false, "publication_state": "MERGED", "current_head_checks": { "state": "SUCCESS", "contexts": { "nodes": [ { "name": "claude", "conclusion": "SKIPPED", "status": "COMPLETED", "detailsUrl": "https://github.com/ai4curation/ai-gene-review/actions/runs/40347057212/job/121656740467" }, { "name": "validation (3.12)", "conclusion": "SUCCESS", "status": "COMPLETED", "detailsUrl": "https://github.com/ai4curation/ai-gene-review/actions/runs/40345616842/job/121651624567" }, { "name": "claude-review", "conclusion": "SUCCESS", "status": "COMPLETED", "detailsUrl": "https://github.com/ai4curation/ai-gene-review/actions/runs/40345618750/job/121651711271" }, { "name": "suite (3.12)", "conclusion": "SUCCESS", "status": "COMPLETED", "detailsUrl": "https://github.com/ai4curation/ai-gene-review/actions/runs/40345616842/job/121651624938" }, { "name": "test (3.12)", "conclusion": "SUCCESS", "status": "COMPLETED", "detailsUrl": "https://github.com/ai4curation/ai-gene-review/actions/runs/40345616842/job/121664175809" } ] } }, "latest_opinionated_reviews": [ { "author": { "login": "ai4c-reviewer" }, "state": "APPROVED", "submittedAt": "2026-10-26T15:12:32Z", "commit": { "oid": "b4971234e3c94371d017b6ea69791c636e4b730f" } } ], "merge_commit": "bfd5d651c11e41f1c509f167bb15a003c2da4bc3", "merged_at": "2026-10-26T16:46:07Z", "completion_verification": "All 276 scoped approved science, source and history blobs are identical in the merge. The module has 43 reviewed members and 555 annotation rows; the shared CAR1 comparator is included in the wider content proof." }, "audit_pr": "https://github.com/ai4curation/ai-gene-review/pull/5563" }, { "module": "arginine_catabolism_arginase_pathway", "path": "modules/arginine_catabolism_arginase_pathway.yaml", "declared_status": "DRAFT", "audit_status": "COMPLETE", "related_open_prs": [ 5076, 5566 ], "annotons": 9, "annotons_with_family": 9, "annotons_with_direct_evidence": 9, "representative_accessions": [ "UniProtKB:O74524", "UniProtKB:O74766", "UniProtKB:P00812", "UniProtKB:P04181", "UniProtKB:P07275", "UniProtKB:P07991", "UniProtKB:P09368", "UniProtKB:P30038", "UniProtKB:P32263", "UniProtKB:P37818", "UniProtKB:P46637", "UniProtKB:P78540", "UniProtKB:Q10066", "UniProtKB:Q8VZC3", "UniProtKB:Q9FNK4", "UniProtKB:Q9P7L5", "UniProtKB:Q9P7Y7", "UniProtKB:Q9ZPF5" ], "has_root_taxon_context": true, "audit_evidence": { "branch": "cmungall/aigr-arginase-catabolism-taxon-audit", "notes": "modules/arginine_catabolism_arginase_pathway-notes.md", "members_in_original_panel": 16, "members_in_scope": 18, "members_reviewed": 18, "annotation_rows_reviewed": 359, "member_review_plan": "All 18 reviews preserve 357 original annotation payloads. The organelle-policy follow-up added two ARGAH1/ARGAH2 matrix proposals, yielding 359 current rows; the original panel already included one NEW proposal.", "literature": "Five comparative reviews assessed among 34 curated source entries; four evidence-backed connections.", "mechanistic_limits": "Budding-yeast shuttle evidence is not generalized to all fungi; fission-yeast arginine re-synthesis is retained; plant agmatinase activity and heterologous localization are distinct from native arginine-catabolic flux.", "module_qa": "PASS: independent source/family/taxon/GO-CAM assessment; schema, grounding, quotes, 46 corpus logic tests and 14 route cases pass. Two broad plant-family adjudication advisories remain. Global family/gene crosscheck: 734 families, zero conflicts.", "annotation_rows_in_scope": 359, "actions": { "ACCEPT": 235, "MODIFY": 44, "UNDECIDED": 16, "KEEP_AS_NON_CORE": 48, "NEW": 3, "REMOVE": 12, "MARK_AS_OVER_ANNOTATED": 1 }, "gene_commit": "bfdb0069d7", "curated_references": 34, "connections_reviewed": 4, "full_validation": "PASS: repository-wide just validate-all terminal exit zero, including references, best practices and pathway references.", "pr": 5566, "head_commit": "90bdd63dec857b055c5f9f9a03fd5a15c7209bec", "review_followup": "Merged PR #5566 as bb5f066dbaf3d5d968bde928c8852ea0d4062408 at 2026-10-26T17:52:57Z, after exact-head approval of 90bdd63dec857b055c5f9f9a03fd5a15c7209bec. All 144 scoped approved science/source/history blobs match the actual merge; 18 reviews, 359 final rows, 36 raw sources verified. The correct total is 357 original rows plus two supported ARGAH matrix proposals, giving 359 final rows.", "progress": "Merged PR #5566 as bb5f066dbaf3d5d968bde928c8852ea0d4062408 at 2026-10-26T17:52:57Z, after exact-head approval of 90bdd63dec857b055c5f9f9a03fd5a15c7209bec. All 144 scoped approved science/source/history blobs match the actual merge; 18 reviews, 359 final rows, 36 raw sources verified. The correct total is 357 original rows plus two supported ARGAH matrix proposals, giving 359 final rows.", "original_annotation_rows_preserved": 357, "ci": "Approved head merged; scoped content verified.", "review_decision": "APPROVED", "phase": "Merged PR #5566 as bb5f066dbaf3d5d968bde928c8852ea0d4062408 at 2026-10-26T17:52:57Z, after exact-head approval of 90bdd63dec857b055c5f9f9a03fd5a15c7209bec. All 144 scoped approved science/source/history blobs match the actual merge; 18 reviews, 359 final rows, 36 raw sources verified. The correct total is 357 original rows plus two supported ARGAH matrix proposals, giving 359 final rows.", "new_annotation_rows_added": 2, "taxon_context": [ { "preferred_term": "Eukaryota", "term": { "id": "NCBITaxon:2759", "label": "Eukaryota" }, "description": "Characterized fungal, plant and animal implementations; this envelope does not assert universal presence, one location, or the same physiological direction in every eukaryote." } ], "merge_state": "UNKNOWN", "member_reviews": [ "genes/ARATH/ALDH12A1/ALDH12A1-ai-review.yaml", "genes/ARATH/ARGAH1/ARGAH1-ai-review.yaml", "genes/ARATH/ARGAH2/ARGAH2-ai-review.yaml", "genes/ARATH/DELTA-OAT/DELTA-OAT-ai-review.yaml", "genes/SCHPO/aru1/aru1-ai-review.yaml", "genes/SCHPO/car1/car1-ai-review.yaml", "genes/SCHPO/car2/car2-ai-review.yaml", "genes/SCHPO/pro3/pro3-ai-review.yaml", "genes/SCHPO/put1/put1-ai-review.yaml", "genes/SCHPO/put2/put2-ai-review.yaml", "genes/human/ALDH4A1/ALDH4A1-ai-review.yaml", "genes/human/ARG2/ARG2-ai-review.yaml", "genes/human/OAT/OAT-ai-review.yaml", "genes/yeast/CAR1/CAR1-ai-review.yaml", "genes/yeast/CAR2/CAR2-ai-review.yaml", "genes/yeast/PRO3/PRO3-ai-review.yaml", "genes/yeast/PUT1/PUT1-ai-review.yaml", "genes/yeast/PUT2/PUT2-ai-review.yaml" ], "structural_metrics_source": "Pinned 8e521a8612471b7aa0db46c542e7eb5006764660: 9 module activities, 18 exact representative accessions, 34 references and 4 connections; 18 parsed member reviews contain 359 annotation rows.", "tracker_integration": "Current checkpoint preserves canonical identities, current lifecycle facts and all approved scientific content; historical integration details remain in dated notes.", "github_snapshot_at": "2026-10-26T18:05:00.077112+00:00", "push_status": "Published remote head verified at snapshot", "auto_merge_enabled": false, "publication_state": "MERGED", "current_head_checks": [ { "__typename": "CheckRun", "completedAt": "2026-10-26T17:17:54Z", "conclusion": "SKIPPED", "detailsUrl": "https://github.com/ai4curation/ai-gene-review/actions/runs/40367289757/job/121728316854", "name": "claude", "startedAt": "2026-10-26T17:17:55Z", "status": "COMPLETED", "workflowName": "Claude Code" }, { "__typename": "CheckRun", "completedAt": "2026-10-26T17:26:06Z", "conclusion": "SUCCESS", "detailsUrl": "https://github.com/ai4curation/ai-gene-review/actions/runs/40365451302/job/121721783645", "name": "validation (3.12)", "startedAt": "2026-10-26T17:06:13Z", "status": "COMPLETED", "workflowName": "Build and test" }, { "__typename": "CheckRun", "completedAt": "2026-10-26T17:18:18Z", "conclusion": "SUCCESS", "detailsUrl": "https://github.com/ai4curation/ai-gene-review/actions/runs/40365451490/job/121721783983", "name": "claude-review", "startedAt": "2026-10-26T17:06:13Z", "status": "COMPLETED", "workflowName": "Claude Code Review" }, { "__typename": "CheckRun", "completedAt": "2026-10-26T17:27:29Z", "conclusion": "SUCCESS", "detailsUrl": "https://github.com/ai4curation/ai-gene-review/actions/runs/40365451302/job/121721783653", "name": "suite (3.12)", "startedAt": "2026-10-26T17:06:13Z", "status": "COMPLETED", "workflowName": "Build and test" }, { "__typename": "CheckRun", "completedAt": "2026-10-26T17:27:34Z", "conclusion": "SUCCESS", "detailsUrl": "https://github.com/ai4curation/ai-gene-review/actions/runs/40365451302/job/121733611436", "name": "test (3.12)", "startedAt": "2026-10-26T17:27:32Z", "status": "COMPLETED", "workflowName": "Build and test" } ], "latest_submitted_review": { "id": 5656139826, "state": "APPROVED", "commit_id": "90bdd63dec857b055c5f9f9a03fd5a15c7209bec", "submitted_at": "2026-10-26T17:17:51Z", "html_url": "https://github.com/ai4curation/ai-gene-review/pull/5566#pullrequestreview-5656139826" }, "merge_commit": "bb5f066dbaf3d5d968bde928c8852ea0d4062408", "merged_at": "2026-10-26T17:52:57Z", "completion_verification": "All 144 scoped approved science/source/history blobs match the actual merge; 18 reviews, 359 final rows, 36 raw sources verified.", "completion_proof": ".cache/module-audit-logs/merged-audits-20261026-late/5566-proof.json" }, "audit_pr": "https://github.com/ai4curation/ai-gene-review/pull/5566" }, { "module": "asgr_galnac_hepatocyte_delivery", "path": "modules/asgr_galnac_hepatocyte_delivery.yaml", "declared_status": "DRAFT", "audit_status": "NOT_STARTED", "related_open_prs": [], "annotons": 10, "annotons_with_family": 10, "annotons_with_direct_evidence": 0, "representative_accessions": [ "UniProtKB:P07306", "UniProtKB:P07307", "UniProtKB:P07339", "UniProtKB:P35603", "UniProtKB:P38606", "UniProtKB:P50570", "UniProtKB:P51149", "UniProtKB:P51150", "UniProtKB:Q00610", "UniProtKB:Q96CW1", "UniProtKB:Q99816", "UniProtKB:Q9H4M9" ], "has_root_taxon_context": false, "audit_evidence": { "phase": "Newly discovered in the 2026-11-05 universe refresh; PR overlaps and biology not yet audited." } }, { "module": "aspartate_asparagine_metabolism", "path": "modules/aspartate_asparagine_metabolism.yaml", "declared_status": "DRAFT", "audit_status": "COMPLETE", "related_open_prs": [ 5076 ], "annotons": 6, "annotons_with_family": 6, "annotons_with_direct_evidence": 4, "representative_accessions": [ "UniProtKB:O42652", "UniProtKB:O94320", "UniProtKB:P00505", "UniProtKB:P00805", "UniProtKB:P08243", "UniProtKB:P0A962", "UniProtKB:P0CX77", "UniProtKB:P0CX78", "UniProtKB:P0CX79", "UniProtKB:P0CZ17", "UniProtKB:P17174", "UniProtKB:P23542", "UniProtKB:P24298", "UniProtKB:P38986", "UniProtKB:P49089", "UniProtKB:P49090", "UniProtKB:P52893", "UniProtKB:P78753", "UniProtKB:Q01802", "UniProtKB:Q10334", "UniProtKB:Q8TD30" ], "has_root_taxon_context": false, "audit_evidence": { "branch": "cmungall/aigr-aspartate-asparagine-taxon-audit", "notes": "modules/aspartate_asparagine_metabolism-notes.md", "members_in_original_panel": 21, "members_in_scope": 27, "member_review_plan": "Complete: 14 fungi, 5 human, 6Arabidopsis exemplars plus 2E.coli comparator reviews. No NEW/PENDING rows; original annotation payloads preserved.", "literature": "Comparative reviews PMID:33624365, 34258001, 35697072, 31998641 and recent aminotransferase study PMID:40940428 normally cached. Primary fungal and plant evidence under review.", "mechanistic_limits": "Separate glutamate-linked transamination, glutamine-amide-dependent amidation and asparagine hydrolysis; taxonomic labels of asparaginase structural classes do not delimit taxa. Test ASP3 horizontal-transfer assertion against 2022 phylogeny/synteny.", "members_reviewed": 27, "module_representatives": 25, "biochemical_comparator_reviews": 2, "annotation_rows_in_scope": 548, "annotation_rows_reviewed": 548, "actions": { "MODIFY": 88, "ACCEPT": 345, "REMOVE": 20, "KEEP_AS_NON_CORE": 65, "UNDECIDED": 25, "MARK_AS_OVER_ANNOTATED": 5 }, "curated_source_entries": 44, "assessed_references": 6, "connections_reviewed": 2, "module_qa": "PASS: independent chemistry/taxon/family/source review; 9 family labels, 25 member placements, 12 activity links across 5 models. All 46 corpus logic tests and 13 route cases pass. Existing PAT/asparaginase classification discrepancies explicitly retained.", "full_validation": "PASS: session 3814 terminal exit 0; aspartate-second-followup-validate-all.log ends All validations passed. 9,098 valid reviews, zero errors; all 54 pathway PMID checks pass. Repository-wide advisory warnings remain.", "head_commit": "2c004eaaf8eab6febfe5abceb00f2f9ebce37b71", "progress": "PR #5568 merged as 551ec0d1221116c8753105bed861739daf5a6479 at 2026-10-26T17:07:11Z, after approval of 2c004eaaf8eab6febfe5abceb00f2f9ebce37b71. 406 of 407 scoped blobs are identical to the approved head. The sole exception is the shared GO-CAM index: a clean three-way merge with the independently merged threonine update reproduces the final index byte-for-byte. All 27 reviews, 548 annotation rows and 54 raw sources are preserved.", "organelle_followup": "All 22 root-organelle corrections complete; six focused checks, renders and added histories pass, all 140 payloads preserved.", "ci": "Captured remote-head check rollup: SUCCESS; see named checks. Review, checks, queue state and verified merged content are distinct gates.", "review_followup": "PR #5568 merged as 551ec0d1221116c8753105bed861739daf5a6479 at 2026-10-26T17:07:11Z, after approval of 2c004eaaf8eab6febfe5abceb00f2f9ebce37b71. 406 of 407 scoped blobs are identical to the approved head. The sole exception is the shared GO-CAM index: a clean three-way merge with the independently merged threonine update reproduces the final index byte-for-byte. All 27 reviews, 548 annotation rows and 54 raw sources are preserved.", "review_decision": "APPROVED", "phase": "PR #5568 merged as 551ec0d1221116c8753105bed861739daf5a6479 at 2026-10-26T17:07:11Z, after approval of 2c004eaaf8eab6febfe5abceb00f2f9ebce37b71. 406 of 407 scoped blobs are identical to the approved head. The sole exception is the shared GO-CAM index: a clean three-way merge with the independently merged threonine update reproduces the final index byte-for-byte. All 27 reviews, 548 annotation rows and 54 raw sources are preserved.", "merge_state": "UNKNOWN", "github_snapshot_at": "2026-10-26T17:23:37.591323+00:00", "push_status": "Current follow-up head is published; merge/CI status is recorded separately.", "merge_queue": { "state": "MERGED" }, "auto_merge_enabled": false, "publication_state": "MERGED", "current_head_checks": { "state": "SUCCESS", "contexts": { "nodes": [ { "name": "claude", "conclusion": "SKIPPED", "status": "COMPLETED", "detailsUrl": "https://github.com/ai4curation/ai-gene-review/actions/runs/40355404892/job/121686394741" }, { "name": "validation (3.12)", "conclusion": "SUCCESS", "status": "COMPLETED", "detailsUrl": "https://github.com/ai4curation/ai-gene-review/actions/runs/40353872881/job/121680974843" }, { "name": "claude-review", "conclusion": "SUCCESS", "status": "COMPLETED", "detailsUrl": "https://github.com/ai4curation/ai-gene-review/actions/runs/40353872851/job/121680976263" }, { "name": "suite (3.12)", "conclusion": "SUCCESS", "status": "COMPLETED", "detailsUrl": "https://github.com/ai4curation/ai-gene-review/actions/runs/40353872881/job/121680975633" }, { "name": "test (3.12)", "conclusion": "SUCCESS", "status": "COMPLETED", "detailsUrl": "https://github.com/ai4curation/ai-gene-review/actions/runs/40353872881/job/121691116713" } ] } }, "latest_opinionated_reviews": [ { "author": { "login": "ai4c-reviewer" }, "state": "APPROVED", "submittedAt": "2026-10-26T16:03:29Z", "commit": { "oid": "2c004eaaf8eab6febfe5abceb00f2f9ebce37b71" } } ], "merge_commit": "551ec0d1221116c8753105bed861739daf5a6479", "merged_at": "2026-10-26T17:07:11Z", "completion_verification": "406 of 407 scoped blobs are identical to the approved head. The sole exception is the shared GO-CAM index: a clean three-way merge with the independently merged threonine update reproduces the final index byte-for-byte. All 27 reviews, 548 annotation rows and 54 raw sources are preserved." }, "audit_pr": "https://github.com/ai4curation/ai-gene-review/pull/5568" }, { "module": "aspartate_family_threonine_biosynthesis", "path": "modules/aspartate_family_threonine_biosynthesis.yaml", "declared_status": "DRAFT", "audit_status": "COMPLETE", "related_open_prs": [ 5076 ], "annotons": 8, "annotons_with_family": 8, "annotons_with_direct_evidence": 5, "representative_accessions": [ "UniProtKB:O43056", "UniProtKB:O60163", "UniProtKB:O94671", "UniProtKB:P00547", "UniProtKB:P00561", "UniProtKB:P00562", "UniProtKB:P00934", "UniProtKB:P08660", "UniProtKB:P0A9Q9", "UniProtKB:P10869", "UniProtKB:P13663", "UniProtKB:P16120", "UniProtKB:P17423", "UniProtKB:P31116", "UniProtKB:P78780", "UniProtKB:Q42598", "UniProtKB:Q8L7R2", "UniProtKB:Q9S7B5", "UniProtKB:Q9SA18" ], "has_root_taxon_context": false, "audit_evidence": { "branch": "cmungall/aigr-threonine-biosynthesis-taxon-audit", "notes": "modules/aspartate_family_threonine_biosynthesis-notes.md", "members_in_original_panel": 19, "members_in_scope": 24, "member_review_plan": "All three panels complete; all original payloads preserved. One new Arabidopsis ASAD stroma CC is supported by the exact proteomic supplement. Focused validation, histories and renders pass.", "mechanistic_limits": "Direct plant ASAD evidence recovered; explicit phosphoserine-dependent ThrH alternative and plant branch point under module integration. Native archaeal step evidence does not prove a complete route.", "literature": "Comparative reviews and primary sources normally cached; full Arabidopsis review recovered, with a wrong HSK locus noted against primary evidence. Current source GO-CAMs are being refreshed.", "progress": "PR #5569 merged as 3dd6e1dba91d22efd7bed30faeb9fbe6813925f8 at 2026-10-26T17:00:27Z, after approval of e12e959a11f41f682bfd71e9c567e227fee875b6. All 315 scoped approved science, source and history blobs are identical in the merge, including 24 reviews, 439 annotation rows and 48 raw files.", "members_reviewed": 24, "annotation_rows_in_scope": 438, "annotation_rows_reviewed": 439, "actions": { "ACCEPT": 325, "MODIFY": 77, "KEEP_AS_NON_CORE": 14, "REMOVE": 12, "UNDECIDED": 8, "MARK_AS_OVER_ANNOTATED": 2, "NEW": 1 }, "negation_qa": "The single original negative row, ThrH NOT ATP kinase, is ACCEPT after source-based correction. Positive phosphotransferase remains separate; all machine flags preserved.", "head_commit": "e12e959a11f41f682bfd71e9c567e227fee875b6", "curated_references": 27, "connections_reviewed": 4, "module_qa": "PASS: independent scientific QA; nine leaves, 24 member placements, 15 GO-CAM activity links, 18 route cases and 46 logic tests. Two family-coverage advisories retained.", "full_validation": "PASS: session 56949 terminal exit 0; threonine-second-followup-validate-all.log ends All validations passed. 9,102 valid reviews, zero errors; all 54 pathway PMID checks pass. Repository-wide advisory warnings remain.", "ci": "Captured remote-head check rollup: SUCCESS; see named checks. Review, checks, queue state and verified merged content are distinct gates.", "review_followup": "PR #5569 merged as 3dd6e1dba91d22efd7bed30faeb9fbe6813925f8 at 2026-10-26T17:00:27Z, after approval of e12e959a11f41f682bfd71e9c567e227fee875b6. All 315 scoped approved science, source and history blobs are identical in the merge, including 24 reviews, 439 annotation rows and 48 raw files.", "review_decision": "APPROVED", "phase": "PR #5569 merged as 3dd6e1dba91d22efd7bed30faeb9fbe6813925f8 at 2026-10-26T17:00:27Z, after approval of e12e959a11f41f682bfd71e9c567e227fee875b6. All 315 scoped approved science, source and history blobs are identical in the merge, including 24 reviews, 439 annotation rows and 48 raw files.", "merge_state": "UNKNOWN", "github_snapshot_at": "2026-10-26T17:23:37.591323+00:00", "push_status": "Current follow-up head is published; merge/CI status is recorded separately.", "merge_queue": { "state": "MERGED" }, "auto_merge_enabled": false, "publication_state": "MERGED", "current_head_checks": { "state": "SUCCESS", "contexts": { "nodes": [ { "name": "claude", "conclusion": "SKIPPED", "status": "COMPLETED", "detailsUrl": "https://github.com/ai4curation/ai-gene-review/actions/runs/40354762674/job/121684153489" }, { "name": "validation (3.12)", "conclusion": "SUCCESS", "status": "COMPLETED", "detailsUrl": "https://github.com/ai4curation/ai-gene-review/actions/runs/40353704221/job/121680380380" }, { "name": "claude-review", "conclusion": "SUCCESS", "status": "COMPLETED", "detailsUrl": "https://github.com/ai4curation/ai-gene-review/actions/runs/40353704181/job/121680368410" }, { "name": "suite (3.12)", "conclusion": "SUCCESS", "status": "COMPLETED", "detailsUrl": "https://github.com/ai4curation/ai-gene-review/actions/runs/40353704221/job/121680379729" }, { "name": "test (3.12)", "conclusion": "SUCCESS", "status": "COMPLETED", "detailsUrl": "https://github.com/ai4curation/ai-gene-review/actions/runs/40353704221/job/121690352793" } ] } }, "latest_opinionated_reviews": [ { "author": { "login": "ai4c-reviewer" }, "state": "APPROVED", "submittedAt": "2026-10-26T15:59:35Z", "commit": { "oid": "e12e959a11f41f682bfd71e9c567e227fee875b6" } } ], "merge_commit": "3dd6e1dba91d22efd7bed30faeb9fbe6813925f8", "merged_at": "2026-10-26T17:00:27Z", "completion_verification": "All 315 scoped approved science, source and history blobs are identical in the merge, including 24 reviews, 439 annotation rows and 48 raw files." }, "audit_pr": "https://github.com/ai4curation/ai-gene-review/pull/5569" }, { "module": "atm_dsb_signaling", "path": "modules/atm_dsb_signaling.yaml", "declared_status": "DRAFT", "audit_status": "NOT_STARTED", "related_open_prs": [], "annotons": 34, "annotons_with_family": 0, "annotons_with_direct_evidence": 34, "representative_accessions": [ "UniProtKB:O00743", "UniProtKB:O15297", "UniProtKB:O60934", "UniProtKB:O75150", "UniProtKB:O75164", "UniProtKB:O75925", "UniProtKB:O76064", "UniProtKB:O95071", "UniProtKB:P16104", "UniProtKB:P38398", "UniProtKB:P46736", "UniProtKB:P49959", "UniProtKB:P53041", "UniProtKB:P55072", "UniProtKB:P60510", "UniProtKB:P61088", "UniProtKB:P67775", "UniProtKB:P78317", "UniProtKB:Q12888", "UniProtKB:Q13315", "UniProtKB:Q14669", "UniProtKB:Q14676", "UniProtKB:Q5UIP0", "UniProtKB:Q5VTR2", "UniProtKB:Q6UWZ7", "UniProtKB:Q8IYW5", "UniProtKB:Q8N2W9", "UniProtKB:Q92878", "UniProtKB:Q92993", "UniProtKB:Q96FW1", "UniProtKB:Q96RL1", "UniProtKB:Q99502", "UniProtKB:Q99504", "UniProtKB:Q99728", "UniProtKB:Q9H0E7", "UniProtKB:Q9NWV8", "UniProtKB:Q9NXR7", "UniProtKB:Q9UIG0", "UniProtKB:Q9Y468", "UniProtKB:Q9Y5T5", "UniProtKB:Q9Y6I4" ], "has_root_taxon_context": true, "audit_evidence": { "phase": "Newly discovered in the 2026-11-05 universe refresh; PR overlaps and biology not yet audited." } }, { "module": "autonomous_flowering_pathway", "path": "modules/autonomous_flowering_pathway.yaml", "declared_status": "COMPLETE", "audit_status": "COMPLETE", "related_open_prs": [], "annotons": 13, "annotons_with_family": 13, "annotons_with_direct_evidence": 13, "representative_accessions": [], "has_root_taxon_context": true, "audit_evidence": { "progress": "Merged PR #5574 at 9c626393756af403d2700b57f66374fae6a1331f after approval and passing checks. All 153 branch-scoped files, and the entire committed tree, match approved head b483aad33dd72e8ac687827a21834d161740077e. Fifteen reviews, 304 rows, 34 assessed references and ten connections are preserved.", "branch": "cmungall/aigr-autonomous-flowering-taxon-audit", "worktree": "/Users/cjm/orca/workspaces/ai-gene-review/aigr-modules-taxon", "phase": "Merged PR #5574 at 9c626393756af403d2700b57f66374fae6a1331f after approval and passing checks. All 153 branch-scoped files, and the entire committed tree, match approved head b483aad33dd72e8ac687827a21834d161740077e. Fifteen reviews, 304 rows, 34 assessed references and ten connections are preserved.", "members_reviewed": 15, "review_followup": "All requested follow-up corrections are included in the approved and merged content.", "ci": "All checks passed; merge and all 153 scoped files independently verified.", "native_members": 13, "comparative_members": 2, "original_annotation_rows_preserved": 302, "annotation_rows_reviewed": 304, "actions": { "ACCEPT": 141, "MODIFY": 54, "KEEP_AS_NON_CORE": 32, "UNDECIDED": 17, "REMOVE": 44, "MARK_AS_OVER_ANNOTATED": 5, "NEW": 11 }, "taxon_scope": "Arabidopsis thaliana native circuit; rice FCA and OsFY are comparative evidence only", "curated_references": 34, "connections_reviewed": 10, "module_qa": "PASS: schema/source/term/member/gene-function checks, 12 route cases and 46 corpus logic tests. Two family-function coverage advisories remain; all 11 asserted GO functions match member cores.", "full_validation": "PASS: flowering-followup-validate-all.log ended All validations passed; all 153 branch-scoped files preserved by subsequent rebase.", "head_commit": "b483aad33dd72e8ac687827a21834d161740077e", "review_decision": "APPROVED", "review_service_status": "Scientific review completed; prior service quota failures are historical.", "merge_commit": "9c626393756af403d2700b57f66374fae6a1331f", "merged_at": "2026-10-26T14:08:15Z" }, "audit_pr": "https://github.com/ai4curation/ai-gene-review/pull/5574" }, { "module": "auxin_nuclear_signaling", "path": "modules/auxin_nuclear_signaling.yaml", "declared_status": "COMPLETE", "audit_status": "COMPLETE", "related_open_prs": [ 5076 ], "annotons": 19, "annotons_with_family": 19, "annotons_with_direct_evidence": 19, "representative_accessions": [ "UniProtKB:A0A0G3FGV9", "UniProtKB:A0A0G3FH20", "UniProtKB:A0A0G3FLP1", "UniProtKB:A0A0G3FNI9", "UniProtKB:A0A0K2QW32", "UniProtKB:O24409", "UniProtKB:P93022", "UniProtKB:P93024", "UniProtKB:P93830", "UniProtKB:Q38830", "UniProtKB:Q570C0", "UniProtKB:Q8RYC8", "UniProtKB:Q94AI7", "UniProtKB:Q9LW29" ], "has_root_taxon_context": true, "audit_evidence": { "progress": "Merged PR #5576 as 77121ffa32de060d9b717476356f41f2fabef3e3 at 2026-10-26T14:17:11Z after approval and passing checks. All 133 scoped science/history files match approved head c2b52875f38fa802ce967fbe9541025bc9652976. Fourteen reviews, 633 current rows, 29 references and thirteen connections remain verified.", "review_followup": "Current-head scientific approval and required checks completed; merged content verified against the approved head.", "ci": "Merged PR #5576 as 77121ffa32de060d9b717476356f41f2fabef3e3 at 2026-10-26T14:17:11Z after approval and passing checks. All 133 scoped science/history files match approved head c2b52875f38fa802ce967fbe9541025bc9652976. Fourteen reviews, 633 current rows, 29 references and thirteen connections remain verified.", "branch": "cmungall/aigr-auxin-nuclear-taxon-audit", "worktree": "/Users/cjm/orca/workspaces/ai-gene-review/aigr-auxin-nuclear-taxon-audit", "members_in_scope": 14, "members_reviewed": 14, "annotation_rows_in_scope": 632, "phase": "Merged PR #5576 as 77121ffa32de060d9b717476356f41f2fabef3e3 at 2026-10-26T14:17:11Z after approval and passing checks. All 133 scoped science/history files match approved head c2b52875f38fa802ce967fbe9541025bc9652976. Fourteen reviews, 633 current rows, 29 references and thirteen connections remain verified.", "research": "Recent comparative reviews and primary papers normally cached, including recovered full 40265222; native Marchantia constructs and correction PMID:26901620 are assessed explicitly. Provider attempts failed authentication; manual source research is documented.", "head_commit": "c2b52875f38fa802ce967fbe9541025bc9652976", "annotation_rows_reviewed": 633, "actions": { "ACCEPT": 104, "MODIFY": 244, "KEEP_AS_NON_CORE": 43, "NEW": 8, "UNDECIDED": 2, "REMOVE": 232 }, "curated_references": 29, "connections_reviewed": 13, "module_qa": "PASS: zero module-validator warnings, 22 route cases, 46 existing logic tests and independent scientific QA. Original payloads preserved; source closure 120 local paths.", "full_validation": "PASS: session 77464 terminal exit zero; 9,071 gene reviews and 54 pathway files.", "pr": 5576, "review_service_status": "Scientific review completed; prior service quota failures are historical.", "review_decision": "APPROVED", "merge_state": "MERGED", "merge_commit": "77121ffa32de060d9b717476356f41f2fabef3e3", "merged_at": "2026-10-26T14:17:11Z", "merged_content_verified": true, "completion_verification": "Direct approved-head versus merge comparison: all 133 scoped science/history files identical; root pr5576-merge-proof.json inspected. Required checks and approval verified before merge." }, "audit_pr": "https://github.com/ai4curation/ai-gene-review/pull/5576" }, { "module": "auxin_polar_transport", "path": "modules/auxin_polar_transport.yaml", "declared_status": "COMPLETE", "audit_status": "COMPLETE", "related_open_prs": [], "annotons": 20, "annotons_with_family": 20, "annotons_with_direct_evidence": 20, "representative_accessions": [ "UniProtKB:A0A2R6WHW5", "UniProtKB:A9RN82", "UniProtKB:O64682", "UniProtKB:O80725", "UniProtKB:Q05085", "UniProtKB:Q5N892", "UniProtKB:Q5TK28", "UniProtKB:Q651V6", "UniProtKB:Q96247", "UniProtKB:Q9C6B8", "UniProtKB:Q9CA25", "UniProtKB:Q9FG74", "UniProtKB:Q9LDC0", "UniProtKB:Q9LJX0", "UniProtKB:Q9LU77", "UniProtKB:Q9S7Z8", "UniProtKB:Q9ZR72" ], "has_root_taxon_context": true, "audit_evidence": { "branch": "cmungall/aigr-auxin-polar-transport-taxon-audit", "worktree": "/Users/cjm/orca/workspaces/ai-gene-review/aigr-auxin-polar-transport-taxon-audit", "members_in_scope": 17, "members_reviewed": 17, "annotation_rows_in_scope": 483, "phase": "Merged content verified against the approved head; all member reviews COMPLETE.", "progress": "Seventeen member reviews contain 484 active rows, preserving 483 original annotation payloads; 34 raw sources and the NRT1.1 consolidation of Q05085 are preserved. All 224 scoped scientific/source/history paths are unchanged by this integration. Pinned GitHub snapshot 2026-10-29T14:51:06.922623+00:00: PR #5579 is OPEN at 30a3cf7f6644f25698db78ec16c2779dd8867292, with APPROVED review 5670621005 submitted at 2026-10-27T16:23:33Z and successful required checks on that head. The merge of main bb749eff8b133cccae14d5b91f202f5b03167630 prepared here requires fresh review and CI after publication; the prior approval does not cover the integration commit.", "worktree_provenance": "Orca creation failed runtime recovery and rolled back. A normal full Git checkout then exhausted disk and rolled back. APFS clonefile of tracked paths, an independent refreshed index and reset to main 10fd59941f produced a verified clean isolated worktree without duplicated file data.", "literature": "41 assessed references include transporter structure, regulation, comparative evolution, native transport contexts and direct primary assays. Abstract-only source limits and source-specific comparative findings are retained in the module.", "annotation_rows_reviewed": 484, "head_commit": "30a3cf7f6644f25698db78ec16c2779dd8867292", "actions": { "ACCEPT": 209, "KEEP_AS_NON_CORE": 128, "MARK_AS_OVER_ANNOTATED": 18, "MODIFY": 66, "NEW": 6, "REMOVE": 33, "UNDECIDED": 24 }, "curated_references": 41, "connections_reviewed": 7, "full_validation": "PASS: session 42896 terminal exit zero; 9,076 gene reviews and 54 pathway files.", "module_qa": "Independent scientific PASS, 22 route cases and 46 logic tests PASS; one documented NPF family-function coverage advisory.", "source_closure": "191 local source paths and 208 declared IDs for the 17-member audit; 200 original science paths plus 3 CHL1 quote-only companion paths.", "ci": "Pinned GitHub snapshot 2026-10-29T14:51:06.922623+00:00 for head 30a3cf7f6644f25698db78ec16c2779dd8867292; checks are recorded in current_head_checks. The integration commit requires fresh CI.", "pr": 5579, "review_decision": "APPROVED", "original_annotation_rows": 483, "member_reviews": 17, "nomenclature": "Q05085 is consolidated to the single NRT1.1 review, with CHL1 and NPF6.3 retained as aliases and durable legacy provenance.", "mechanistic_limits": "Six native Arabidopsis multiactivity implementations are distinct from optional rice influx/efflux segments and moss/Marchantia exporter comparisons. Carrier biochemistry alone does not establish polarized tissue transport or a conserved complete circuit.", "tracker_refresh_source": "bb749eff8b133cccae14d5b91f202f5b03167630", "merge_state": "OPEN at the pinned snapshot; review and CI for the integration commit remain pending.", "structural_metrics_source": "Pinned f75fa24d36b9332d2eea1f0ebb3028991903dbbb: 20 module activities, 17 exact representative accessions, 41 references and 7 connections; 17 parsed member reviews contain 484 annotation rows.", "tracker_integration": "Only the polar row is refreshed here; all 714 other incoming inventory rows and all historical tracker journal blocks are preserved.", "review_followup": "Seventeen member reviews contain 484 active rows, preserving 483 original annotation payloads; 34 raw sources and the NRT1.1 consolidation of Q05085 are preserved. All 224 scoped scientific/source/history paths are unchanged by this integration. Pinned GitHub snapshot 2026-10-29T14:51:06.922623+00:00: PR #5579 is OPEN at 30a3cf7f6644f25698db78ec16c2779dd8867292, with APPROVED review 5670621005 submitted at 2026-10-27T16:23:33Z and successful required checks on that head. The merge of main bb749eff8b133cccae14d5b91f202f5b03167630 prepared here requires fresh review and CI after publication; the prior approval does not cover the integration commit.", "github_snapshot_at": "2026-10-29T14:51:06.922623+00:00", "push_status": "Published head observed at the pinned snapshot; this snapshot is not a claim about a later push.", "auto_merge_enabled": false, "publication_state": "OPEN", "current_head_checks": [ { "__typename": "CheckRun", "completedAt": "2026-10-27T16:23:37Z", "conclusion": "SKIPPED", "detailsUrl": "https://github.com/ai4curation/ai-gene-review/actions/runs/40540459185/job/122317125763", "name": "claude", "startedAt": "2026-10-27T16:23:38Z", "status": "COMPLETED", "workflowName": "Claude Code" }, { "__typename": "CheckRun", "completedAt": "2026-10-27T16:25:56Z", "conclusion": "SUCCESS", "detailsUrl": "https://github.com/ai4curation/ai-gene-review/actions/runs/40538344309/job/122309607629", "name": "validation (3.12)", "startedAt": "2026-10-27T16:10:51Z", "status": "COMPLETED", "workflowName": "Build and test" }, { "__typename": "CheckRun", "completedAt": "2026-10-27T16:23:54Z", "conclusion": "SUCCESS", "detailsUrl": "https://github.com/ai4curation/ai-gene-review/actions/runs/40538359341/job/122309661238", "name": "claude-review", "startedAt": "2026-10-27T16:10:57Z", "status": "COMPLETED", "workflowName": "Claude Code Review" }, { "__typename": "CheckRun", "completedAt": "2026-10-27T16:29:30Z", "conclusion": "SUCCESS", "detailsUrl": "https://github.com/ai4curation/ai-gene-review/actions/runs/40538344309/job/122309607159", "name": "suite (3.12)", "startedAt": "2026-10-27T16:10:51Z", "status": "COMPLETED", "workflowName": "Build and test" }, { "__typename": "CheckRun", "completedAt": "2026-10-27T16:29:35Z", "conclusion": "SUCCESS", "detailsUrl": "https://github.com/ai4curation/ai-gene-review/actions/runs/40538344309/job/122320516521", "name": "test (3.12)", "startedAt": "2026-10-27T16:29:32Z", "status": "COMPLETED", "workflowName": "Build and test" } ], "latest_submitted_review": { "id": 5670621005, "state": "APPROVED", "commit_id": "30a3cf7f6644f25698db78ec16c2779dd8867292", "submitted_at": "2026-10-27T16:23:33Z", "html_url": "https://github.com/ai4curation/ai-gene-review/pull/5579#pullrequestreview-5670621005" }, "integration_pending": { "snapshot_head": "30a3cf7f6644f25698db78ec16c2779dd8867292", "snapshot_at": "2026-10-29T14:51:06.922623+00:00", "followup_review": "PENDING", "followup_checks": "PENDING", "scope": "merge of published main bb749eff8b133cccae14d5b91f202f5b03167630" }, "ci_head_commit": "30a3cf7f6644f25698db78ec16c2779dd8867292", "pr_url": "https://github.com/ai4curation/ai-gene-review/pull/5579", "merged_at": "2026-10-29T15:36:36Z", "merge_commit": "414b8d6a53e252e5aacc8fd7d45e1ad259ac0f6f", "approved_head": "56067df160def39432912d507de90e11fa4cadc8", "scoped_blobs_verified": 229, "ci_status": "Head validation, suite, test and review checks succeeded", "merged_content_proof": "projects/MODULE_TAXON_AUDIT/proofs/pr5579-merged-content.json" }, "audit_pr": "https://github.com/ai4curation/ai-gene-review/pull/5579" }, { "module": "b_cell_receptor_signaling", "path": "modules/b_cell_receptor_signaling.yaml", "declared_status": "DRAFT", "audit_status": "COMPLETE", "related_open_prs": [ 5584 ], "annotons": 20, "annotons_with_family": 20, "annotons_with_direct_evidence": 20, "representative_accessions": [ "UniProtKB:F1N9Y5", "UniProtKB:O00329", "UniProtKB:O35904", "UniProtKB:P07948", "UniProtKB:P11911", "UniProtKB:P11912", "UniProtKB:P15391", "UniProtKB:P15530", "UniProtKB:P16885", "UniProtKB:P27986", "UniProtKB:P35991", "UniProtKB:P40259", "UniProtKB:P43405", "UniProtKB:P48025", "UniProtKB:P48736", "UniProtKB:Q06187", "UniProtKB:Q6ZUJ8", "UniProtKB:Q8CIH5", "UniProtKB:Q8JH64", "UniProtKB:Q8WV28", "UniProtKB:Q9QUN3", "UniProtKB:Q9YGC1" ], "has_root_taxon_context": true, "preliminary_survey": "Preliminary research is complete; the full audit is published as PR #5584.", "audit_evidence": { "branch": "cmungall/aigr-b-cell-receptor-taxon-audit", "worktree": "/Users/cjm/orca/workspaces/ai-gene-review/aigr-b-cell-receptor-taxon-audit", "base_commit": "6fb9e79b44d53f248675021c9a25f2183a9ec757", "worktree_provenance": "Tracked-file APFS copy-on-write checkout verified clean at stated base; uv sync session 17849 completed successfully.", "phase": "PR #5584 merged as 67e246011a263eeb00e61ef5219ee2fb8720d069 at 2026-10-26T17:21:03Z from approved head 49a03553b5d92f4e5162fb6514d4d26ba52b5ccc. Independent verification proves all 340 scoped gene, module, source and history blobs identical, with no exceptions. All 22 reviews and 2,645 original annotation payloads, including two inherited proposals, are preserved.", "members_original": 7, "members_in_scope": 22, "members_reviewed": 22, "planned_human_members": 12, "planned_mouse_members": 7, "planned_chicken_members": 3, "progress": "PR #5584 merged as 67e246011a263eeb00e61ef5219ee2fb8720d069 at 2026-10-26T17:21:03Z from approved head 49a03553b5d92f4e5162fb6514d4d26ba52b5ccc. Independent verification proves all 340 scoped gene, module, source and history blobs identical, with no exceptions. All 22 reviews and 2,645 original annotation payloads, including two inherited proposals, are preserved.", "scientific_scope": "Reassess PIK3CG as the default BCR PI3K exemplar versus class IA/p110-delta, place PI3K lipid production upstream of BTK recruitment, distinguish CD79 signal transducers from immunoglobulin antigen recognition, and define exact taxon implementations. No complete conserved circuit is asserted from the comparative panel.", "survey_path": ".cache/module-audit-logs/b-cell-preliminary-survey.md", "full_validation": "PASS: session 61187 terminal exit 0; b-cell-validate-all.log ends All validations passed. 9,100 valid reviews, zero errors; 54 pathway PMID checks pass. Repository-wide advisory warnings remain.", "original_annotation_rows": 2645, "preexisting_annotation_rows": 1715, "inherited_proposals": 2, "provider_attempts": "18 actual Falcon/fallback failures; four substantive existing reports reused. No fabricated provider outputs.", "source_acquisition": "COMPLETE: 749 unique PMIDs cached, none missing; four recent review papers fetched subsequently.", "review_decision": "APPROVED", "ci": "Captured remote-head check rollup: SUCCESS; see named checks. 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The scoped module audit is complete; unresolved scientific questions remain represented explicitly.", "checked_at": "2026-11-06T11:27:50.981625+00:00", "full_validation_proof": "analysis/module_audits/bacterial_cysteine_biosynthesis_via_o_acetylserine/preexisting-reference-failures.yaml", "round1_full_validation": { "status": "TERMINAL_PREEXISTING_REFERENCE_ERRORS_ONLY", "exit_code": 1, "validated_science_commit": "e90f3048306da3250ee664f74119fb5974a36ed7", "full_log_sha256": "e110e00dfdb918846877ffae1fb3a7903ff1c662ae3a76e8bc15906098d9f89e", "reference": { "Input files": 10544, "Files validated": 10544, "Snippets checked": 277258, "Snippets skipped": 118671, "Snippets unavailable": 15, "Titles checked": 108103, "Issues found": 69, "blocking_errors": 17, "advisories": 52, "affected_error_reviews": 16 }, "best_practices": { "Total files": 10544, "Valid": 10544, "Invalid": 0, "Files with warnings": 5037, "Total errors": 0, "Total warnings": 27995 }, "pathways": { "checked": 81, "with_PMID_references": 54, "passed": 54 }, "proof": "analysis/module_audits/bacterial_cysteine_biosynthesis_via_o_acetylserine/round1-fullrun-terminal.json" }, "previous_status_snapshot": { "phase": "Full validation terminal with base-identical unrelated reference errors; publication and actual merge pending" }, "progress": "PR #6120 merged; all 152 scoped changed files match the reviewed head and remain unchanged at main 1970e159b9. 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The scoped module audit is complete; unresolved scientific questions remain represented explicitly." }, { "module": "bacterial_cytochrome_c_maturation_system_i", "path": "modules/bacterial_cytochrome_c_maturation_system_i.yaml", "declared_status": "COMPLETE", "audit_status": "PR_OPEN", "related_open_prs": [ 6121 ], "annotons": 16, "annotons_with_family": 16, "annotons_with_direct_evidence": 16, "representative_accessions": [ "UniProtKB:A0A140FWM3", "UniProtKB:A0A140FWM4", "UniProtKB:D5ALI6", "UniProtKB:F9XXF9", "UniProtKB:P0AA86", "UniProtKB:P0ABL8", "UniProtKB:P0ABM1", "UniProtKB:P0ABM5", "UniProtKB:P0ABM9", "UniProtKB:P33927", "UniProtKB:P33931", "UniProtKB:P36893", "UniProtKB:P69490", "UniProtKB:Q00500", "UniProtKB:Q00501", "UniProtKB:Q311W9", "UniProtKB:Q311X0", "UniProtKB:Q311X1", "UniProtKB:Q311X2", "UniProtKB:Q311X3", "UniProtKB:Q311X4", "UniProtKB:Q88EX5", "UniProtKB:Q88EX6", "UniProtKB:Q88EX7", "UniProtKB:Q88EX8", "UniProtKB:Q88EX9", "UniProtKB:Q88EY0", "UniProtKB:Q88EY1", "UniProtKB:Q8EK41" ], "has_root_taxon_context": true, "audit_evidence": { "status": "FULL_VALIDATION_PASS_PENDING_PUBLICATION", "updated_at": "2026-11-06T12:02:15.857047+00:00", "base_commit": "4460e9d2b7cc2470f3ab0fc1243a51c08a68c44b", "prior_module_pr": { "number": 5362, "state": "MERGED", "merge_commit": "310e7cdaaa924d05af08b8f20dd9da4d5f84bca1" }, "module_status": "COMPLETE", "reviews_complete": 29, "historical_rows": 227, "historical_machine_rows": 224, "inherited_NEW": 3, "genuinely_added_NEW": 6, "current_rows": 233, "raw_sources_preserved": 58, "provider_artifacts_preserved": 6, "module_references": 24, "curated_findings": 55, "annotons": 16, "annotons_with_direct_evidence": 16, "families_corrected": 7, "capacity_cases": 151, "full_corpus": { "status": "TERMINAL", "head": "072461b9b27dce869d81fb5bcef43bf7ce698d9f", "manifest_files": 374, "started_at": "2026-11-06T23:37:46.116738+00:00", "log": ".cache/module-audit-logs/cytochrome-20261106/round3-provenance/validate-all.log", "exit_code": 0, "finished_at": "2026-11-07T00:46:15.674910+00:00", "log_sha256": "0b48d15bea476e9ca5b81b295c6197a65178bf0224e9ac15fca3f58ba9115fa7", "result": "PASS", "review_count": 10722, "schema": "PASS", "ontology_errors": 0, "ontology_label_advisories": 115, "reference_errors": 0, "reference_advisories": 53, "best_practice_errors": 0, "best_practice_warnings": 27784, "pathway_checks": 54, "frozen_inputs_verified": 374, "verified_at": "2026-11-07T00:51:05.569497+00:00", "limits": "Full gene-corpus pass on recorded head; separate focused gene/module/history/render checks and151 coverage cases passed before the run. Current-head review, CI and merge pending." }, "publication": "FOLLOWUP_PENDING", "review_CI": "PENDING_NEW_HEAD", "merge": "NOT_VERIFIED", "next": "Publish follow-up, fresh independent review/CI and actual merge verification", "audit_directory": "analysis/module_audits/bacterial_cytochrome_c_maturation_system_i", "module": "modules/bacterial_cytochrome_c_maturation_system_i.yaml", "family_selectors": "15 direct family leaves plus one complex with two family active units; optional G20 CcmI uses an intentionally unassigned family id", "prior_full_corpus_state": "NOT_STARTED", "full_validation": { "status": "TERMINAL", "head": "072461b9b27dce869d81fb5bcef43bf7ce698d9f", "manifest_files": 374, "started_at": "2026-11-06T23:37:46.116738+00:00", "log": ".cache/module-audit-logs/cytochrome-20261106/round3-provenance/validate-all.log", "exit_code": 0, "finished_at": "2026-11-07T00:46:15.674910+00:00", "log_sha256": "0b48d15bea476e9ca5b81b295c6197a65178bf0224e9ac15fca3f58ba9115fa7", "result": "PASS", "review_count": 10722, "schema": "PASS", "ontology_errors": 0, "ontology_label_advisories": 115, "reference_errors": 0, "reference_advisories": 53, "best_practice_errors": 0, "best_practice_warnings": 27784, "pathway_checks": 54, "frozen_inputs_verified": 374, "verified_at": "2026-11-07T00:51:05.569497+00:00", "limits": "Full gene-corpus pass on recorded head; separate focused gene/module/history/render checks and151 coverage cases passed before the run. Current-head review, CI and merge pending." }, "metadata_closure_histories": { "module-bacterial_cytochrome_c_maturation_system_i": { "path": "history/modules/bacterial_cytochrome_c_maturation_system_i/2026-11-06T120214Z-codex-150201.yaml", "validation_exit_code": 0 }, "project-MODULE_TAXON_AUDIT": { "path": "history/projects/MODULE_TAXON_AUDIT/2026-11-06T120215Z-codex-16bca5.yaml", "validation_exit_code": 0 } }, "round1_followup": { "status": "FOCUSED_CHECKS_PASS_FULL_CORPUS_PENDING", "prior_head": "95122d628add088ad1e67c5c58027753374320ee", "changed_gene_reviews": 13, "action_changes": 9, "new_annotation_rows": 0, "reference_finding_corrections": 7, "focused_validations": 13, "supplemental_validations": 5, "new_gene_histories": 18, "checker_cases": 151, "module_conformance_advisories": 1, "gene_advisories": 4, "gene_assessment": "analysis/module_audits/bacterial_cytochrome_c_maturation_system_i/round1-gene-assessment.yaml", "reference_corrections": "analysis/module_audits/bacterial_cytochrome_c_maturation_system_i/round1-reference-finding-supplement.yaml", "full_corpus": { "status": "NOT_STARTED", "command": "just validate-all", "reason": "New full-corpus run required after reviewed scientific corrections" }, "unresolved_nonblocking": [ "Historical ECOLI ccmE NEW GO0018063 retained without deleting frozen payload", "RHOCB ccl2 protein-substrate specificity refinement deferred; no invented net-direction distinction", "Module process terms remain broader contexts than some gene refinements; no conformance conflict" ] }, "prior_full_corpus": { "status": "TERMINAL_PREEXISTING_REFERENCE_ERRORS_ONLY", "validated_science_commit": "4c2bbabe93147e918eac550662546f6de9d537e7", "base_commit": "4460e9d2b7cc2470f3ab0fc1243a51c08a68c44b", "session_id": 7109, "exit_code": 1, "review_count": 10548, "schema": "PASS", "ontology": "PASS; 115 advisory issues in 109 files", "reference": { "blocking_errors": 17, "advisories": 52, "affected_error_reviews": 16, "unchanged_inputs": 22, "proof": "analysis/module_audits/bacterial_cytochrome_c_maturation_system_i/fullrun-terminal.json" }, "best_practices": { "errors": 0, "warnings": 28001, "files_with_warnings": 5042 }, "pathways": "PASS; 54 PMID-bearing files out of 81", "log_sha256": "27ac6031e1ba458511a909b5d9f85bfd2450a47655177aac8d67d82bcf9eb03c", "publication_manifest_files_verified_before_metadata": 264 }, "prior_full_validation": { "status": "TERMINAL_PREEXISTING_REFERENCE_ERRORS_ONLY", "validated_science_commit": "4c2bbabe93147e918eac550662546f6de9d537e7", "base_commit": "4460e9d2b7cc2470f3ab0fc1243a51c08a68c44b", "session_id": 7109, "exit_code": 1, "review_count": 10548, "schema": "PASS", "ontology": "PASS; 115 advisory issues in 109 files", "reference": { "blocking_errors": 17, "advisories": 52, "affected_error_reviews": 16, "unchanged_inputs": 22, "proof": "analysis/module_audits/bacterial_cytochrome_c_maturation_system_i/fullrun-terminal.json" }, "best_practices": { "errors": 0, "warnings": 28001, "files_with_warnings": 5042 }, "pathways": "PASS; 54 PMID-bearing files out of 81", "log_sha256": "27ac6031e1ba458511a909b5d9f85bfd2450a47655177aac8d67d82bcf9eb03c", "publication_manifest_files_verified_before_metadata": 264 }, "round1_full_validation": { "status": "TERMINAL_PREEXISTING_REFERENCE_ERRORS_ONLY", "exit_code": 1, "validated_science_commit": "6b9e19aa58271a05c09964839266abb6b1ccf5b7", "full_log_sha256": "dd079be8e4bf67481fe79962fe3e8ea022184ecbfefafc5018b89b8ce969a33e", "reference": { "Input files": 10548, "Files validated": 10548, "Snippets checked": 277299, "Snippets skipped": 118687, "Snippets unavailable": 15, "Titles checked": 108143, "Issues found": 69, "blocking_errors": 17, "advisories": 52, "affected_error_reviews": 16 }, "best_practices": { "Total files": 10548, "Valid": 10548, "Invalid": 0, "Files with warnings": 5043, "Total errors": 0, "Total warnings": 28002 }, "pathways": { "checked": 81, "with_PMID_references": 54, "passed": 54 }, "proof": "analysis/module_audits/bacterial_cytochrome_c_maturation_system_i/round1-fullrun-terminal.json" }, "phase": "PR #6121 provenance/CcmE follow-up passes full validation on 072461b9b2: 10,722 reviews, zero blocking errors and 374 frozen inputs verified. Fresh review, CI and actual merge pending." }, "audit_phase": "PR #6121 provenance/CcmE follow-up passes full validation on 072461b9b2: 10,722 reviews, zero blocking errors and 374 frozen inputs verified. Fresh review, CI and actual merge pending.", "round2_followup": { "head": "7641af14dc93ed09a1b7e0b5c24ff7d7802c8bc0", "status": "Full validation classified; follow-up publication and renewed review/CI pending", "fullrun_proof": "analysis/module_audits/bacterial_cytochrome_c_maturation_system_i/round2-fullrun-terminal.json" }, "round3_followup": { "status": "PR #6121 provenance/CcmE follow-up passes full validation on 072461b9b2: 10,722 reviews, zero blocking errors and 374 frozen inputs verified. Fresh review, CI and actual merge pending.", "fullrun_proof": "analysis/module_audits/bacterial_cytochrome_c_maturation_system_i/round3-full-validation.json" } }, { "module": "bacterial_dimethylglycine_sarcosine_catabolism", "path": "modules/bacterial_dimethylglycine_sarcosine_catabolism.yaml", "declared_status": "DRAFT", "audit_status": "NOT_STARTED", "related_open_prs": [ 5076 ], "annotons": 4, "annotons_with_family": 1, "annotons_with_direct_evidence": 0, "representative_accessions": [ "UniProtKB:P40873" ], "has_root_taxon_context": true }, { "module": "bacterial_divisome_peptidoglycan_transpeptidation", "path": "modules/bacterial_divisome_peptidoglycan_transpeptidation.yaml", "declared_status": "COMPLETE", "audit_status": "COMPLETE", "related_open_prs": [], "annotons": 10, "annotons_with_family": 10, "annotons_with_direct_evidence": 10, "representative_accessions": [ "O07639", "P0ABG4", "P0AD68", "P42971", "Q07868", "Q2FZ94", "Q2G2C2", "Q5M2U8", "Q5M5I9" ], "has_root_taxon_context": true, "audit_phase": "PR #6123 merged; all 125 scoped changed files match the reviewed head and remain unchanged at main 1970e159b9. The scoped module audit is complete; unresolved scientific questions remain represented explicitly.", "audit_evidence": { "member_review_count": 9, "original_annotation_rows": 160, "current_rows": 164, "curated_reference_count": 14, "review_reference_count": 3, "mined_findings": 10, "capacity_cases": 56, "primary_evidence_controls": 1, "completion": "PR #6123 merged; all 125 scoped changed files match the reviewed head and remain unchanged at main 1970e159b9. The scoped module audit is complete; unresolved scientific questions remain represented explicitly.", "snapshot_date": "2026-11-06", "initial_full_validation": { "status": "TERMINAL_PREEXISTING_REFERENCE_ERRORS_ONLY", "exit_code": 1, "validated_science_commit": "579fdd34fec0c49c471e899244dcb6abf4473a83", "full_log_sha256": "67bc6e5bd479abbad360959dae9bd0675160952c9716e23a0c407af528c444b2", "schema": "PASS", "term": { "blocking_errors": 0, "advisory_issues": 115, "files_with_advisories": 109, "total_files": 10555 }, "reference": { "Input files": 10555, "Files validated": 10555, "Snippets checked": 277675, "Snippets skipped": 119197, "Snippets unavailable": 15, "Titles checked": 108198, "Issues found": 69, "blocking_errors": 17, "advisories": 52, "affected_error_reviews": 16 }, "best_practices": { "Total files": 10555, "Valid": 10555, "Invalid": 0, "Files with warnings": 4926, "Total errors": 0, "Total warnings": 27705 }, "pathways": { "checked": 81, "with_PMID_references": 54, "passed": 54 }, "proof": "analysis/module_audits/bacterial_divisome_peptidoglycan_transpeptidation/fullrun-terminal.json", "base_identical_error_inputs": 22 }, "full_validation": { "status": "TERMINAL_PREEXISTING_REFERENCE_ERRORS_ONLY", "proof": "analysis/module_audits/bacterial_divisome_peptidoglycan_transpeptidation/round1-fullrun-terminal.json", "validated_science_commit": "ab9b9b9ea919d6c8efa9e541bdade882f0207741", "review_files": 10555, "reference_errors": 17, "base_identical_inputs": 22, "best_practices_errors": 0, "best_practices_warnings": 27715, "pathways_passed": 54 }, "previous_status_snapshot": { "completion": "PR #6123 open; independent review, CI and actual merge pending." }, "phase": "PR #6123 merged; all 125 scoped changed files match the reviewed head and remain unchanged at main 1970e159b9. The scoped module audit is complete; unresolved scientific questions remain represented explicitly.", "progress": "PR #6123 merged; all 125 scoped changed files match the reviewed head and remain unchanged at main 1970e159b9. The scoped module audit is complete; unresolved scientific questions remain represented explicitly.", "merge_state": "MERGED", "publication_state": "MERGED", "integration_pending": null, "completion_verified_at": "2026-11-06T16:19:44.202490+00:00", "completion_main_commit": "1970e159b929a11ec02b0bc86e64cebae7cf4c9e", "completion_merge_proof": "projects/MODULE_TAXON_AUDIT/proofs/pr6123-merged-content.json", "completion_merge_commit": "1970e159b929a11ec02b0bc86e64cebae7cf4c9e", "completion_pr": 6123, "merged_at": "2026-11-06T15:47:31Z", "merge_commit": "1970e159b929a11ec02b0bc86e64cebae7cf4c9e", "pr": 6123, "pr_url": "https://github.com/ai4curation/ai-gene-review/pull/6123", "merged_content_proof": "projects/MODULE_TAXON_AUDIT/proofs/pr6123-merged-content.json", "completion_panel": "All 9 changed member reviews independently checked COMPLETE with no PENDING." } }, { "module": "bacterial_dnak_dnaj_refolding_cycle", "path": "modules/bacterial_dnak_dnaj_refolding_cycle.yaml", "declared_status": "DRAFT", "audit_status": "NOT_STARTED", "related_open_prs": [], "annotons": 3, "annotons_with_family": 0, "annotons_with_direct_evidence": 0, "representative_accessions": [], "has_root_taxon_context": true }, { "module": "bacterial_dsbab_oxidative_folding", "path": "modules/bacterial_dsbab_oxidative_folding.yaml", "declared_status": "COMPLETE", "audit_status": "PR_OPEN", "related_open_prs": [], "annotons": 10, "annotons_with_family": 10, "annotons_with_direct_evidence": 10, "representative_accessions": [ "UniProtKB:A0A0H2ZG77", "UniProtKB:A0A1J6PBD5", "UniProtKB:A0A1J6UFJ6", "UniProtKB:A8FLS4", "UniProtKB:O32217", "UniProtKB:O32218", "UniProtKB:P0A6M2", "UniProtKB:P0AEG4", "UniProtKB:P59344", "UniProtKB:P59345", "UniProtKB:Q02DM0", "UniProtKB:Q02EA7", "UniProtKB:Q02TM7", "UniProtKB:Q88RK2" ], "has_root_taxon_context": true, "audit_phase": "Round1 scientific follow-up fully validated; renewed independent review/CI and actual merge pending", "audit_evidence": { "members": 14, "original_rows": 78, "current_rows": 92, "raw_sources": 28, "explicit_archive_preserved": true, "references": 14, "review_articles": 4, "findings": 24, "capacity_cases": 75, "phase": "Round1 scientific follow-up fully validated; renewed independent review/CI and actual merge pending", "snapshot_date": "2026-11-06", "full_validation": { "status": "TERMINAL_PREEXISTING_REFERENCE_ERRORS_ONLY", "proof": "analysis/module_audits/bacterial_dsbab_oxidative_folding/round1-fullrun-terminal.json", "validated_science_commit": "2edeb4ad9169dbc9b8fde193d8748624aadf92cf", "review_files": 10627, "reference_errors": 17, "base_identical_inputs": 22, "best_practices_errors": 0, "best_practices_warnings": 27700, "pathways_passed": 54, "scoped_files_verified": 190 } }, "pr": 6129 }, { "module": "bacterial_ethanolamine_uptake_catabolism", "path": "modules/bacterial_ethanolamine_uptake_catabolism.yaml", "declared_status": "COMPLETE", "audit_status": "IN_PROGRESS", "related_open_prs": [ 5970 ], "annotons": 10, "annotons_with_family": 9, "annotons_with_direct_evidence": 10, "representative_accessions": [ "UniProtKB:A0A0H3GBB1", "UniProtKB:A0A0H3GFM0", "UniProtKB:A0A0H3GFN0", "UniProtKB:P0AEJ6", "UniProtKB:P19264", "UniProtKB:P19265", "UniProtKB:P19636", "UniProtKB:P41790", "UniProtKB:P41793", "UniProtKB:P41795", "UniProtKB:P41796", "UniProtKB:Q88QF0", "UniProtKB:Q88QF1", "UniProtKB:Q88QF2", "UniProtKB:Q9HX02", "UniProtKB:Q9HX03", "UniProtKB:Q9HX05", "UniProtKB:Q9ZAA1", "UniProtKB:Q9ZFV2", "UniProtKB:Q9ZFV5" ], "has_root_taxon_context": true, "audit_phase": "Comparative audit and full validation complete locally; adopted PR5970 update, renewed review, CI and actual merge pending", "pr": 5970, "audit_evidence": { "completed_reviews": 22, "original_rows": 224, "current_rows": 226, "raw_provider_sources": 47, "references": 22, "review_articles": 3, "findings": 58, "capacity_cases": 79, "mutation_cases": 8, "complex_with_family_units": 1, "phase": "Comparative audit and full validation complete locally; adopted PR5970 update, renewed review, CI and actual merge pending", "snapshot_date": "2026-11-06", "full_validation": { "status": "TERMINAL_PREEXISTING_REFERENCE_ERRORS_ONLY", "proof": "analysis/module_audits/bacterial_ethanolamine_uptake_catabolism/fullrun-terminal.json", "validated_science_commit": "60b72729693b2b7c74ca1e1bb982cee1b9d94666", "review_files": 10637, "reference_errors": 17, "base_identical_inputs": 22, "best_practices_errors": 0, "best_practices_warnings": 27701, "pathways_passed": 54 } } }, { "module": "bacterial_fatty_acid_beta_oxidation", "path": "modules/bacterial_fatty_acid_beta_oxidation.yaml", "declared_status": "COMPLETE", "audit_status": "PR_OPEN", "related_open_prs": [ 6136 ], "annotons": 10, "annotons_with_family": 10, "annotons_with_direct_evidence": 10, "representative_accessions": [ "UniProtKB:O32176", "UniProtKB:O32177", "UniProtKB:O32178", "UniProtKB:O53871", "UniProtKB:O53872", "UniProtKB:P0A2H7", "UniProtKB:P21151", "UniProtKB:P21177", "UniProtKB:P28790", "UniProtKB:P28793", "UniProtKB:P94549", "UniProtKB:Q47146", "UniProtKB:Q88L01", "UniProtKB:Q88L02", "UniProtKB:Q88LN6", "UniProtKB:Q8ZRJ7", "UniProtKB:Q9I610", "UniProtKB:Q9I612", "UniProtKB:Q9L6L5" ], "has_root_taxon_context": true, "audit_phase": "PR6136 review corrections prepared; renewed focused/full validation and review/CI/merge pending", "audit_evidence": { "completed_reviews": 19, "original_rows": 211, "current_rows": 217, "inherited_NEW": 2, "added_NEW": 6, "raw_provider_files": 40, "references": 17, "review_articles": 4, "findings": 21, "family_reviews": 8, "capacity_cases": 54, "mutation_cases": 12, "parts": 4, "annotons": 10, "taxon": "NCBITaxon:2", "snapshot_date": "2026-11-06", "full_validation": { "head": "79f177e6497c4cb7c31d4478509c4e9910c868db", "exit_code": 0, "reviews": 10688, "proof": "analysis/module_audits/bacterial_fatty_acid_beta_oxidation/full-validation.json" } }, "audit_pr": 6136, "audit_notes": "Round1 corrections validated by just validate-all on f063b332b1c5aa1ff7b1ac043f43586bd51819a4 (10688 reviews; zero blocking errors); 290 frozen files unchanged. All 217 current annotation payloads and 40 raw/provider sources preserved. Renewed external review, CI and merge pending for PR6136." }, { "module": "bacterial_flagellar_assembly_export", "path": "modules/bacterial_flagellar_assembly_export.yaml", "declared_status": "COMPLETE", "audit_status": "PR_OPEN", "related_open_prs": [ 5076, 6138 ], "annotons": 31, "annotons_with_family": 31, "annotons_with_direct_evidence": 31, "representative_accessions": [ "UniProtKB:O06873", "UniProtKB:O06874", "UniProtKB:P0A1J1", "UniProtKB:P0A1K1", "UniProtKB:P26416", "UniProtKB:P26465", "UniProtKB:P26477", "UniProtKB:P40729", "UniProtKB:P52612", "UniProtKB:Q88DC2", "UniProtKB:Q88DC3", "UniProtKB:Q88EQ8", "UniProtKB:Q88ER2", "UniProtKB:Q88ER3", "UniProtKB:Q88ER4", "UniProtKB:Q88ER5", "UniProtKB:Q88ER7", "UniProtKB:Q88ER8", "UniProtKB:Q88ES2", "UniProtKB:Q88ES3", "UniProtKB:Q88ES5", "UniProtKB:Q88ES7", "UniProtKB:Q88ET4", "UniProtKB:Q88ET5", "UniProtKB:Q88ET6", "UniProtKB:Q88ET7", "UniProtKB:Q88ET8", "UniProtKB:Q88EU2", "UniProtKB:Q88EU5", "UniProtKB:Q88EU6", "UniProtKB:Q88EU8", "UniProtKB:Q88EU9", "UniProtKB:Q88EV0", "UniProtKB:Q88EV1", "UniProtKB:Q88EV8", "UniProtKB:Q88EW1", "UniProtKB:Q88EW6", "UniProtKB:Q88EW7" ], "has_root_taxon_context": true, "audit_phase": "PR #6138: main ac30fe31cf integrated at 5bb074ac23; 316 branch-specific files retain their exact pre-integration Git blob ids. 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Current review and CI govern merge readiness; earlier full-corpus results remain scoped to their recorded commits.", "latest_main_integration_proof": "analysis/module_audits/bacterial_flagellar_assembly_export/resume-round4-20261111/integration-proof.json" }, "round1_evidence": { "revised_reviews": 17, "preserved_rows": 254, "protected_sources": 131, "adjudication": "analysis/module_audits/bacterial_flagellar_assembly_export/round1-source-adjudication.md" }, "progress": "PR #6138: main ac30fe31cf integrated at 5bb074ac23; 316 branch-specific files retain their exact pre-integration Git blob ids. Current review and CI govern merge readiness; earlier full-corpus results remain scoped to their recorded commits.", "audit_pr": "https://github.com/ai4curation/ai-gene-review/pull/6138" }, { "module": "bacterial_flavonoid_degradation", "path": "modules/bacterial_flavonoid_degradation.yaml", "declared_status": "COMPLETE", "audit_status": "PR_OPEN", "related_open_prs": [ 6140 ], "annotons": 8, "annotons_with_family": 8, "annotons_with_direct_evidence": 8, "representative_accessions": [ "UniProtKB:D8J0W6", "UniProtKB:D8J0W7", "UniProtKB:D8J0W8", "UniProtKB:D8J0W9", "UniProtKB:D8J0X2", "UniProtKB:D8J0X3", "UniProtKB:D8J0X4", "UniProtKB:Q88HZ6", "UniProtKB:Q88HZ7", "UniProtKB:Q88HZ8", "UniProtKB:Q88I03", "UniProtKB:Q88I04", "UniProtKB:Q88I05", "UniProtKB:Q88I07", "UniProtKB:Q89GB7", "UniProtKB:Q89GB8", "UniProtKB:Q89GB9", "UniProtKB:Q89GC0", "UniProtKB:Q89GC2", "UniProtKB:Q89GC3", "UniProtKB:Q89GC4" ], "has_root_taxon_context": true, "audit_phase": "PR6140 revised science passes full validation on 9e1e860ce0: 10,717 reviews, zero blocking errors and 300 frozen inputs verified. Nine inherited process proposals are retired in place; seven remain active. Fresh review, CI and actual merge pending.", "audit_evidence": { "branch": "cmungall/aigr-flavonoid-taxon-audit", "baseline_reviews": 14, "baseline_rows": 34, "protected_source_files": 34, "scope_snapshot": "analysis/module_audits/bacterial_flavonoid_degradation/taxonomy-snapshot.json", "notes": "modules/bacterial_flavonoid_degradation-notes.md", "member_reviews": 21, "references": 9, "review_articles": 3, "primary_articles": 6, "preservation": "analysis/module_audits/bacterial_flavonoid_degradation/panel-preservation.json", "endpoint_contract": "analysis/module_audits/bacterial_flavonoid_degradation/endpoint-contract.json", "full_validation": { "status": "TERMINAL", "head": "ee4222b667d93d9587aa0502d028d3b1b78dabf7", "manifest_files": 367, "started_at": "2026-11-07T02:45:54.182385+00:00", "log": ".cache/module-audit-logs/flavonoid-20261107/round3/validate-all.log", "exit_code": 0, "finished_at": "2026-11-07T03:45:55.154893+00:00", "log_sha256": "d68836335f74438b99b806313f13f54f430ea9c5246b052e102ca45640b09bfc", "review_count": 10754, "ontology_label_advisories": 115, "reference_advisories": 53, "best_practice_warnings": 27629, "result": "PASS", "blocking_errors": 0, "pathway_checks": 54, "frozen_inputs_verified": 367, "verified_at": "2026-11-07T03:48:35.455987+00:00", "limits": "Full gene-corpus validation on the recorded science head. Separate focused module/family/member/history/render checks precede this run. Main integration and subsequent review/CI are separately reported." }, "pr": 6140, "pr_url": "https://github.com/ai4curation/ai-gene-review/pull/6140", "integration_proof": "analysis/module_audits/bacterial_flavonoid_degradation/validated-head-integration.json", "round1_preservation": "analysis/module_audits/bacterial_flavonoid_degradation/round1-preservation.json", "round1_root_verification": "analysis/module_audits/bacterial_flavonoid_degradation/round1-root-verification.json", "round1_consultation": "analysis/module_audits/bacterial_flavonoid_degradation/round1-consultation.md", "round1_validation": "analysis/module_audits/bacterial_flavonoid_degradation/round1-validation.json", "reviewed_rows": 46, "historical_proposal_rows": 16, "retired_proposals": 9, "active_new_rows": 7, "round1_protected_source_files": 85, "module_advisories": 20, "capacity_checks": 44, "mutations_rejected": 4, "full_validation_status": "PR6140 revised science passes full validation on 9e1e860ce0: 10,717 reviews, zero blocking errors and 300 frozen inputs verified. Nine inherited process proposals are retired in place; seven remain active. Fresh review, CI and actual merge pending.", "round1_full_validation": { "status": "TERMINAL", "head": "9e1e860ce07284f7c728ee53ee155973f471575f", "manifest_files": 300, "started_at": "2026-11-06T23:27:20.253228+00:00", "log": ".cache/module-audit-logs/flavonoid-20261106/round1/validate-all.log", "exit_code": 0, "finished_at": "2026-11-07T00:33:18.559950+00:00", "log_sha256": "89e75df56498da4e4783a6fdfc88e335f1128d02d0b829e15a5d00f082842e12", "result": "PASS", "review_count": 10717, "schema": "PASS", "ontology_errors": 0, "ontology_label_advisories": 115, "reference_errors": 0, "reference_advisories": 53, "best_practice_errors": 0, "best_practice_warnings": 27789, "pathway_checks": 54, "frozen_inputs_verified": 300, "verified_at": "2026-11-07T00:35:29.114110+00:00", "limits": "Full gene-corpus validation. Focused module validation retained 20 conformance advisories; 44 coverage cases and four mutations test candidate-model logic, not complete native flux. Fresh review, CI and actual merge remain pending." }, "phase": "PR #6140 scientific review follow-up passes full validation on ee4222b667; main 5b68ef3aac is integrated with 361 frozen nonshared inputs preserved. Fresh review, CI and actual merge remain pending.", "fullrun_proof": "analysis/module_audits/bacterial_flavonoid_degradation/round3-full-run.json" }, "audit_notes": "PR #5076 is the older broad family-grounding PR; #6140 is this dedicated comparative audit. Historical full validation and original baseline counts remain recorded separately from this review follow-up.", "round2_followup": { "phase": "PR #6140 round-2 follow-up: nine retired proposals use explicit withdrawal actions; three FdeB orthologs retain supported broad hydrolase core inference while substrate and catalytic geometry remain unresolved. Two speculative reaction terms moved to questions. Ten focused gene checks, 44 coverage cases and four mutations pass; fresh full validation and publication pending.", "root_proof": "analysis/module_audits/bacterial_flavonoid_degradation/round2-root-verification.json", "full_validation": "PENDING", "annotation_payloads_preserved": 46, "protected_sources": 91 }, "audit_pr": 6140 }, { "module": "bacterial_fructose_pts_catabolism", "path": "modules/bacterial_fructose_pts_catabolism.yaml", "declared_status": "COMPLETE", "audit_status": "PR_OPEN", "related_open_prs": [ 5076, 6144 ], "annotons": 4, "annotons_with_family": 4, "annotons_with_direct_evidence": 4, "representative_accessions": [ "UniProtKB:A0A0P0ES92", "UniProtKB:A0A0P0F764", "UniProtKB:A0A0P0F8C9", "UniProtKB:P0AEW9", "UniProtKB:P20966", "UniProtKB:P23354", "UniProtKB:P23355", "UniProtKB:P23386", "UniProtKB:P23387", "UniProtKB:P23388", "UniProtKB:P45597", "UniProtKB:Q88PQ3", "UniProtKB:Q88PQ4", "UniProtKB:Q88PQ5", "UniProtKB:Q9RZP6", "UniProtKB:Q9RZP7" ], "has_root_taxon_context": true, "audit_notes": "Sixteen COMPLETE member reviews; all 148 original/seed rows and 34 raw/provider files preserved. Fused relay and transporter architecture, substrate specificity and same-system evidence are separate from family membership. Deinococcus historical ATP-dependent transport and restored FruB reading frame are distinguished; no native PEP-dependent uptake is inferred solely from that sequence. Related PR #5076 remains the earlier broad family-grounding change; PR #6144 is this dedicated comparative module audit.", "audit_phase": "PR #6144 label/evidence follow-up passes focused validation and 49 coverage cases; current QuickGO label retained; review, CI and actual merge pending", "audit_evidence": { "member_reviews": 16, "references": 11, "review_articles": 2, "primary_articles": 9, "family_reviews": 3, "preservation": "analysis/module_audits/bacterial_fructose_pts_catabolism/final-panel-preservation.json", "endpoint_contract": "analysis/module_audits/bacterial_fructose_pts_catabolism/endpoint-contract.json", "full_validation": "analysis/module_audits/bacterial_fructose_pts_catabolism/full-validation.json", "integrated_main": "577501df51a3742542ac9522dbe663a60f55ba78", "integration_proof": "analysis/module_audits/bacterial_fructose_pts_catabolism/validated-head-integration.json", "capacity_cases": 49, "mechanism_mutations_rejected": 7, "historical_outcome_regression": "PASS: existing test_treegrafter_rereview_outcomes.py, one test", "round1": { "response": "analysis/module_audits/bacterial_fructose_pts_catabolism/round1-review-response.md", "preservation": "analysis/module_audits/bacterial_fructose_pts_catabolism/round1-preservation.yaml", "validation": "analysis/module_audits/bacterial_fructose_pts_catabolism/round1-validation.yaml", "scope": "Source names, evidence specificity and ontology-request placement; 148 rows/actions and mechanism preserved", "full_validation": "No new full-corpus run; earlier recorded combined-stage result remains historical" }, "phase": "PR #6144 approved at c0fcd8377d; main 0a807fc555 integrated at 55d1cd6d66 with 224 approved nonshared files preserved. Focused integration checks pass. Historical full-corpus validation remains scoped to its recorded head; fresh review, CI and actual merge are pending.", "latest_main_integration_head": "55d1cd6d6681988461ee5a004fc5093cfdfee208", "latest_incoming_main": "0a807fc55576d0371b2dfacb482f8d695992535b", "latest_main_integration": "analysis/module_audits/bacterial_fructose_pts_catabolism/approved-main5-integration-proof.json" }, "pr": 6144, "progress": "PR #6144 approved at c0fcd8377d; main 0a807fc555 integrated at 55d1cd6d66 with 224 approved nonshared files preserved. Focused integration checks pass. Historical full-corpus validation remains scoped to its recorded head; fresh review, CI and actual merge are pending." }, { "module": "bacterial_fused_puta_proline_catabolism", "path": "modules/bacterial_fused_puta_proline_catabolism.yaml", "declared_status": "DRAFT", "audit_status": "NOT_STARTED", "related_open_prs": [], "annotons": 3, "annotons_with_family": 1, "annotons_with_direct_evidence": 3, "representative_accessions": [ "UniProtKB:Q88D81" ], "has_root_taxon_context": true }, { "module": "bacterial_gallate_catabolism", "path": "modules/bacterial_gallate_catabolism.yaml", "declared_status": "DRAFT", "audit_status": "NOT_STARTED", "related_open_prs": [ 5076, 5353 ], "annotons": 5, "annotons_with_family": 5, "annotons_with_direct_evidence": 4, "representative_accessions": [ "UniProtKB:Q88JX5", "UniProtKB:Q88JX6", "UniProtKB:Q88JX8", "UniProtKB:Q88JX9", "UniProtKB:Q88JY0" ], "has_root_taxon_context": true }, { "module": "bacterial_glutamate_to_p5c_biosynthesis", "path": "modules/bacterial_glutamate_to_p5c_biosynthesis.yaml", "declared_status": "COMPLETE", "audit_status": "PR_OPEN", "related_open_prs": [ 6160 ], "annotons": 2, "annotons_with_family": 2, "annotons_with_direct_evidence": 2, "representative_accessions": [ "UniProtKB:O07509", "UniProtKB:P07004", "UniProtKB:P0A7B5", "UniProtKB:P0C1E0", "UniProtKB:P0C1E2", "UniProtKB:P39820", "UniProtKB:P39821", "UniProtKB:Q88DL4", "UniProtKB:Q88Q07" ], "has_root_taxon_context": true, "audit_evidence": { "base_commit": "0f30fca1c9c7dbe4d545d6fba1c42ab48c14825d", "phase": "PR #6160: main 0ca78c07ea integrated at 049188ba91; 207 branch-specific files were verified unchanged at that integration. Subsequent review fixes are separately recorded. Fresh current-head review and CI govern merge readiness; historical full-corpus results retain their recorded scope.", "completed_gene_reviews": 9, "bounded_comparator_edits": 2, "module_references": 7, "comparative_reviews": 2, "mined_findings": 14, "coverage_cases_passed": 33, "preserved_annotation_rows": 123, "added_annotation_rows": 0, "proof": "analysis/module_audits/bacterial_glutamate_to_p5c_biosynthesis/root-verification.json", "full_validation": { "status": "TERMINAL", "head": "dea61b999950240d98a37193e419ef8b9c25299f", "manifest_files": 162, "started_at": "2026-11-07T02:36:22.404140+00:00", "log": ".cache/module-audit-logs/glutamate-p5c-20261107/round1/validate-all.log", "exit_code": 0, "finished_at": "2026-11-07T03:37:37.345827+00:00", "log_sha256": "5f50e12d0baaa48b31dfd26efbac57f708778a223e1ae86fa958a6b285005635", "review_count": 10740, "ontology_label_advisories": 115, "reference_advisories": 53, "best_practice_warnings": 27613, "result": "PASS", "blocking_errors": 0, "pathway_checks": 54, "frozen_inputs_verified": 162, "verified_at": "2026-11-07T03:39:10.365801+00:00", "limits": "Full gene-corpus validation on the recorded science head. Separate focused module/family/member/history/render checks precede this run. Main integration and subsequent review/CI are separately reported." }, "fullrun_proof": "analysis/module_audits/bacterial_glutamate_to_p5c_biosynthesis/round1-full-run.json", "pr": 6160, "pr_url": "https://github.com/ai4curation/ai-gene-review/pull/6160", "latest_main_integration": "analysis/module_audits/bacterial_glutamate_to_p5c_biosynthesis/resume-round5-20261111/integration-proof.json", "latest_incoming_main": "0ca78c07ea0a7ee0ce4760193cc5b22848471d21", "progress": "PR #6160: main 0ca78c07ea integrated at 049188ba91; 207 branch-specific files were verified unchanged at that integration. Subsequent review fixes are separately recorded. Fresh current-head review and CI govern merge readiness; historical full-corpus results retain their recorded scope.", "provenance_correction": "analysis/module_audits/bacterial_glutamate_to_p5c_biosynthesis/provenance-correction-20261107.json", "preserved_files_in_correction": 176, "latest_main_integration_head": "049188ba911bca7f67555509249b90a72d551199", "publication_closeout": "analysis/module_audits/bacterial_glutamate_to_p5c_biosynthesis/approved-main-20261107-1356-closeout.json", "review_followup": "analysis/module_audits/bacterial_glutamate_to_p5c_biosynthesis/proa-root-ready-20261107.json", "current_full_validation": "NOT_RUN_PROA_LOCALIZATION_CORRECTION", "latest_main_integration_proof": "analysis/module_audits/bacterial_glutamate_to_p5c_biosynthesis/resume-round5-20261111/integration-proof.json" }, "progress": "PR #6160: main 0ca78c07ea integrated at 049188ba91; 207 branch-specific files were verified unchanged at that integration. 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