date: '2026-09-20' reviewer: codex genes: - gene_file: genes/DESRO/K9IJK6/K9IJK6-ai-review.yaml status: awaiting_adjudication scope: full_gene annotation_count: 12 reviewed_annotation_indices: - 0 - 1 - 2 - 3 - 4 - 5 - 6 - 7 - 8 - 9 - 10 - 11 source_fields_preserved: true outcome: Kringle-specific warning corrected; six catalytic assertions restored and four distinct signaling/response claims remain uncertain. changes: - annotation_index: 0 term: GO:0014909 from: REMOVE to: UNDECIDED - annotation_index: 1 term: GO:0031639 from: UNDECIDED to: ACCEPT - annotation_index: 2 term: GO:0048008 from: REMOVE to: UNDECIDED - annotation_index: 3 term: GO:0004252 from: UNDECIDED to: ACCEPT - annotation_index: 6 term: GO:0006508 from: UNDECIDED to: ACCEPT - annotation_index: 7 term: GO:0008233 from: UNDECIDED to: ACCEPT - annotation_index: 8 term: GO:0008236 from: UNDECIDED to: ACCEPT - annotation_index: 9 term: GO:0016787 from: UNDECIDED to: ACCEPT - annotation_index: 10 term: GO:0071396 from: REMOVE to: UNDECIDED - annotation_index: 11 term: GO:1901701 from: REMOVE to: UNDECIDED evidence: primary_sources_reviewed: - PMID:23411029 - PROSITE:PRU00121 primary_notes: genes/DESRO/K9IJK6/K9IJK6-notes.md lineage_artifact: genes/DESRO/K9IJK6/K9IJK6-paint-lineage.json reference_tree_target_leaf_recovered: false original_node: PTN000667065 actual_node_lineage: - PTN001208002 - PTN004684475 - PTN008399132 - PTN008611593 - PTN008611594 - PTN008399133 - PTN008611595 - PTN008399134 - PTN002799995 - PTN008611606 - PTN000667062 - PTN000667063 - PTN000667064 - PTN000667065 adjudication: status: gated_request terms: - GO:0014909 - GO:0048008 - GO:0071396 - GO:1901701 cache_check: Substantive repository and global provider query/report search completed; existing reports read and assessed. No duplicated focused run. reason: Root-authorized focused request registered and launcher started; local state confirms waiting_for_submission_slot, not remote submission. slug: dspa-gamma-signaling-and-cell-response-capacities launcher_session: 13709 state_file: projects/IBA_REVIEW/rereview-2026-09-20/adjudication-runs/DESRO--K9IJK6--dspa-gamma-signaling-and-cell-response-capacities.json validation: gene: passed history: passed source_fields: all original rows unchanged warning_scope: No deep-research citation where those reports conflate target proteins/isoforms; primary evidence and critical report assessment are recorded in notes. history_file: history/genes/DESRO/K9IJK6/2026-09-21T040505Z-codex-49c9a9.yaml - gene_file: genes/PSEPK/ydiJ/ydiJ-ai-review.yaml status: reviewed scope: full_gene annotation_count: 8 reviewed_annotation_indices: - 0 - 1 - 2 - 3 - 4 - 5 - 6 - 7 source_fields_preserved: true outcome: Three broad catalytic/cofactor calls restored; lactate MODIFY decisions retained on new direct negative donor-subfamily assays. changes: - annotation_index: 0 term: GO:0003824 from: MARK_AS_OVER_ANNOTATED to: ACCEPT - annotation_index: 3 term: GO:0050660 from: MARK_AS_OVER_ANNOTATED to: ACCEPT - annotation_index: 5 term: GO:0071949 from: MARK_AS_OVER_ANNOTATED to: ACCEPT evidence: primary_sources_reviewed: - PMID:31064836 - PMID:36144368 primary_notes: genes/PSEPK/ydiJ/ydiJ-notes.md lineage_artifact: genes/PSEPK/ydiJ/ydiJ-paint-lineage.json reference_tree_target_leaf_recovered: false original_node: PTN001714929 actual_node_lineage: - PTN007534471 - PTN000202298 - PTN002621911 - PTN000922846 - PTN000202393 - PTN001714929 decisive_excerpt: there was no detectable activity on L-2-hydroxyglutarate, L-malate, D-malate, L-lactate, D-lactate, L-tartrate, D-tartrate, L-glycerate, D-glycerate, glutarate, or pyruvate at final concentrations of 5–10 mM. adjudication: status: existing_report_incorporated terms: [] cache_check: Substantive repository and global provider query/report search completed; existing reports read and assessed. No duplicated focused run. existing_report: /Users/cjm/.deep_research_cache/openscientist-commissioned-modulepathwaytaxo-43e91d7b.json incorporation: Read full Dav-module report; PP_4493 downstream placement is a module boundary, not evidence against lysine catabolism or an assay of lactate specificity. No new run needed after full donor specificity primary. validation: gene: passed history: passed source_fields: all original rows unchanged warning_scope: No warnings. history_file: history/genes/PSEPK/ydiJ/2026-09-21T040508Z-codex-0429bc.yaml - gene_file: genes/PYROR/PoMZ_10221/PoMZ_10221-ai-review.yaml status: reviewed scope: full_gene annotation_count: 6 reviewed_annotation_indices: - 0 - 1 - 2 - 3 - 4 - 5 source_fields_preserved: true outcome: Full focused report incorporated with disagreement; three direct sugar-enzyme rows ACCEPT and three MAT-related rows UNDECIDED. No source action changed during incorporation. changes: - annotation_index: 0 term: GO:0006556 from: PENDING to: UNDECIDED - annotation_index: 1 term: GO:0048269 from: PENDING to: UNDECIDED - annotation_index: 2 term: GO:0048270 from: PENDING to: UNDECIDED - annotation_index: 3 term: GO:0010489 from: PENDING to: ACCEPT - annotation_index: 4 term: GO:0010490 from: PENDING to: ACCEPT - annotation_index: 5 term: GO:0019300 from: PENDING to: ACCEPT evidence: primary_sources_reviewed: - PMID:22102281 - PMID:25075345 primary_notes: genes/PYROR/PoMZ_10221/PoMZ_10221-notes.md lineage_artifact: genes/PYROR/PoMZ_10221/PoMZ_10221-paint-lineage.json reference_tree_target_leaf_recovered: false original_node: PTN008946252 actual_node_lineage: - PTN000051874 - PTN000051875 - PTN008500101 - PTN008946251 - PTN008946252 report_errors: - Local OpenAI report describes unrelated DHODH/PoPYR4. - Global Perplexity report 70b8d6b9 describes unrelated bacterial PyrR. - Absence of MAT assays in a sugar-enzyme paper is not refutation. - A separate SAM catalytic enzyme does not exclude a regulatory subunit. - Mammalian MAT2B literature and low pairwise identity do not establish target-specific loss. - Reported alignment code/outputs were not delivered with HTML/PDF. access_limit: 'Cached full-text flag is misleading: Methods/Results omitted. Primary publisher/PMC indexed Results checked; ordinary PMC and publisher opens failed. No negative IDA decision based on incomplete access.' interface_check: projects/TREEGRAFTER/rereview-2026-09-20/pomz-mat-report-evidence.json adjudication: status: incorporated_with_disagreement terms: - GO:0006556 - GO:0048269 - GO:0048270 cache_check: Substantive repository and global provider query/report search completed; existing reports read and assessed. No duplicated focused run. slug: rhamnose-enzyme-and-mat-regulatory-capacity launcher_session: 66998 state_file: projects/IBA_REVIEW/rereview-2026-09-20/adjudication-runs/PYROR--PoMZ_10221--rhamnose-enzyme-and-mat-regulatory-capacity.json report: file:PYROR/PoMZ_10221/PoMZ_10221-hypotheses/rhamnose-enzyme-and-mat-regulatory-capacity/openscientist.md incorporated: '2026-09-21' remaining_uncertainty: Exact historical graft/regulator propagation and target-specific MAT interaction remain unresolved; no duplicate research request. validation: gene: passed history: passed source_fields: all original rows unchanged warning_scope: No deep-research citation where those reports conflate target proteins/isoforms; primary evidence and critical report assessment are recorded in notes. history_file: history/genes/PYROR/PoMZ_10221/2026-09-21T040509Z-codex-3da7b8.yaml report_incorporation_history: history/genes/PYROR/PoMZ_10221/2026-09-21T071242Z-codex-8ba7c3.yaml - gene_file: genes/STABO/mdr/mdr-ai-review.yaml status: awaiting_adjudication scope: full_gene annotation_count: 10 reviewed_annotation_indices: - 0 - 1 - 2 - 3 - 4 - 5 - 6 - 7 - 8 - 9 source_fields_preserved: true outcome: Broad ATP/nucleotide/membrane calls restored; three narrow mitochondrial-peptide claims unresolved. changes: - annotation_index: 0 term: GO:0005743 from: REMOVE to: UNDECIDED - annotation_index: 1 term: GO:0015421 from: MODIFY to: UNDECIDED - annotation_index: 2 term: GO:0090374 from: REMOVE to: UNDECIDED - annotation_index: 3 term: GO:0000166 from: KEEP_AS_NON_CORE to: ACCEPT - annotation_index: 4 term: GO:0005524 from: KEEP_AS_NON_CORE to: ACCEPT - annotation_index: 6 term: GO:0016020 from: KEEP_AS_NON_CORE to: ACCEPT evidence: primary_sources_reviewed: - PMID:23516968 - PMID:23964782 - PMID:34998388 primary_notes: genes/STABO/mdr/mdr-notes.md lineage_artifact: genes/STABO/mdr/mdr-paint-lineage.json reference_tree_target_leaf_recovered: false original_node: PTN008681462 actual_node_lineage: - PTN009169590 - PTN002459074 - PTN008681400 - PTN009169591 - PTN008681402 - PTN002459076 - PTN008107465 - PTN008450928 - PTN008681429 - PTN008681460 - PTN008681461 - PTN008681462 adjudication: status: gated_request terms: - GO:0005743 - GO:0015421 - GO:0090374 cache_check: Substantive repository and global provider query/report search completed; existing reports read and assessed. No duplicated focused run. slug: sophorolipid-export-and-mitochondrial-peptide-capacity launcher_session: 66998 state_file: projects/IBA_REVIEW/rereview-2026-09-20/adjudication-runs/STABO--mdr--sophorolipid-export-and-mitochondrial-peptide-capacity.json validation: gene: passed history: passed source_fields: all original rows unchanged warning_scope: No deep-research citation where those reports conflate target proteins/isoforms; primary evidence and critical report assessment are recorded in notes. history_file: history/genes/STABO/mdr/2026-09-21T040510Z-codex-ef21c4.yaml