realmarcin · Sep 29, 2026 · Sep 29, 2026 · Sep 29, 2026 · Sep 29, 2026 · Sep 29, 2026
diff --git a/docs/reviews/bacdive-ec-substrate-corrections-1249-1250.md b/docs/reviews/bacdive-ec-substrate-corrections-1249-1250.md
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+# Four finite BacDive EC/substrate corrections (#1249, #1250)
+
+These corrections address four complete historical mapping rows, not a global
+CHEBI:54684 replacement, a CAS identity export, or the complete #286 backlog.
+Raw `bacdive_mappings.tsv` remains unchanged. The canonical policy retains all
+eight original cells, including the trailing space in the glucoside name.
+Actual matching uses complete cells, not historical physical line numbers.
+
+| Original source line (reviewed snapshot) | Exact source assay | Target | Scope |
+|---|---|---|---|
+|119|API_ID32E_alpha GLU|CHEBI:91122|alpha-D-glucopyranoside / EC:3.2.1.20|
+|28|API_rID32A_alpha GAL|CHEBI:546840|alpha-D-galactoside / EC:3.2.1.22|
+|120|API_ID32E_alpha GAL|CHEBI:546840|same molecule; contradictory KEGG cell is audit-only|
+|271|API_rID32STR_alpha GAL|CHEBI:546840|alpha-D-galactoside / EC:3.2.1.22|
+
+The immutable test fixture retains complete original rows, complete native
+ChEBI records and incident edges, selected native TSV rows, primary structural
+facts/URLs, and scientific input hashes. Native CHEBI:91122's exact IUPAC
+synonym and full InChI match [manufacturer 487506](https://www.sigmaaldrich.com/US/en/product/mm/487506),
+which identifies alpha-glucosidase substrate use. Native CHEBI:546840's distinct
+stereostructure matches [manufacturer N0877](https://www.sigmaaldrich.com/US/en/product/sigma/n0877).
+The two stereospecific InChIKeys differ; equal formulas and CAS annotations alone
+would not establish this identity. Official EC nomenclature corroborates
+[alpha-glucosidase](https://iubmb.qmul.ac.uk/enzyme/EC3/2/1/20.html) and
+[alpha-galactosidase](https://iubmb.qmul.ac.uk/enzyme/EC3/2/1/22.html).
+
+Evidence caveats remain explicit: the glucoside ChEBI prose mentions beta-D-
+glucopyranose despite its exact IUPAC name, parent, stereostructure and supplier
+evidence agreeing on alpha glucoside. N0877's marketing subtitle names
+alpha-glucosidase, while its formal product/application sections and EC authority
+support alpha-galactosidase. The original conflicting text is documented, not
+used as corroboration. Supplier records do not prove which commercial batch an
+API kit used or substrate specificity of every enzyme in an EC class.
+
+Line120's original [KEGG:C01083](https://www.kegg.jp/entry/C01083) denotes
+trehalose, not nitrophenyl galactoside. `withheld_source_fields=KEGG_ID` clears
+only that cell in the corrected in-memory row; its complete original claim
+remains in the raw file, curated rule, immutable fixture and audit. No KEGG or
+CAS identity edge, assay-to-reagent assertion, or taxon phenotype is introduced.
+
+The selected native export does not declare CHEBI:54684 or an official alias/
+replacement. Native absence is not proof of historical obsolescence, and digit
+similarity to CHEBI:546840 is not the correction's basis. The raw ontology SHA
+is `a5d40380ab78bde0e8b5a704dbee3cba2bcaa7608be46eebc2f4a92932516c9b`;
+the reviewed legacy source SHA is
+`f39e9753fe2879877b2cba51c9896f44515f3a5785e790deb0d0bd5ca02c9379`.
+These are review witnesses, not runtime pins forcing future source snapshots.
+
+## Producer boundary
+
+The real run consumes the finite canonical policy and legacy mapping through
+immutable snapshots before opening graph outputs. Malformed/duplicate policy
+fields fail; changes within a recognized reviewed scope require new review.
+Exact already-corrected rows are idempotent, and an absent cohort is normal.
+Unrelated old-ID uses do not acquire either reviewed target. Source row
+multiplicity is retained through correction, before ordinary graph deduplication.
+
+`ec_substrate_corrections.tsv` is mandatory producer audit output. It retains
+each original complete source row, actual physical ordinal, original and emitted
+seven-field edge claims, reason, primary evidence URLs, source/policy locations
+and original read hashes. The producer's final input guards verify the same
+admission, including symlink targets; finalization and merge enforce the original
+audit bytes through existing producer-audit hooks. Even an empty cohort writes
+a header-only audit and binds both required consumed roles.
+
+The existing EC edge predicate, relation and provenance tier are unchanged.
+Ontology dependencies and ordinary finalization still govern native endpoint
+closure. No unified artifact, immutable supported MIM table, release pin, raw
+record, or shared finalizer is edited. A fresh real source rebuild and graph
+reviews remain necessary; focused fixture tests are not production acceptance.
diff --git a/docs/reviews/combined-material-scope-20260929/PROMOTION.md b/docs/reviews/combined-material-scope-20260929/PROMOTION.md
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+# Combined material-scope candidate: isolated staging, 2026-09-29
+
+Status: the accepted derived unified artifact and reviewed native-pair test are
+staged in the isolated combined-materials worktree, after source integration at
+`620c9c9ea9c5d3e5ab777cb635ab85f9438cd550`. The coordinator preserved the
+production checkout and its mapping artifact, archive and user statistics.
+The 19 native paired-artifact/predicate tests and 584 broader source-integration
+tests passed after staging. Actual combined source replay/comparison, final
+repository gates and CI remain pending at this checkpoint. This is not release
+acceptance or evidence of fresh production transforms.
+
+## Exact paired artifacts
+
+| Role | SHA-256 |
+| --- | --- |
+| Previous Potato-only unified baseline | `09c44642ab13b234e89ce113f7510aa9efb56969e4b539cb7843b43dcb425ba7` |
+| Staged unified candidate, 13,374,300 bytes | `67c48e1bf6bed1f1fef03a0da1d7d1b56af9fc72374dddd703c222fb36df3cd4` |
+| Unchanged supported MIM table | `6b52b30e018b369aa322d41dfd4e81fcfae0e895e34d7fe48900abf5835815fb` |
+| Unchanged reviewed MIM release pin | `f082c05656a0910c85176eec7b41deeb77c27967aecb80393fddc262819b6d97` |
+| Unchanged identity-only writer | `257fe4d8bf16f92eb78d5e375065e030ea56d7c1174d859fecd2baa80ac18c27` |
+| Identity-policy fingerprint | `4670cbb9255bdac7e9654fc415c9bfd35e55955fea5f27865a74e55849810b4c` |
+| Applied native paired-artifact test | `e77a1c342549097e94542dc8fcc4e424bb475eb94ddff0c47f6a781ff47bc7ad` |
+
+Upstream remains immutable MIM commit
+`1848b0fe521bc2462f165912fcf92d09ad9a8cec`, manifest
+`9bb29d5605d93dea351be9624d99c5d8ada57d4b9831b22764957b784bd685af`:
+1,747 supported exact mappings and 1,696 names. This is not a new upstream
+release, repin or supported-MIM rewrite. The policy fingerprint binds the
+curated exclusions plus the shared identity and CAS implementations.
+
+## Completed candidate checks
+
+The complete streaming delta removed exactly three generic CHEBI:86658 claims
+(two exact, one close) and changed only `object_label` on four retained native
+structural-synonym rows. All other row bytes/order and unrelated metadata stayed
+identical. Only the description's policy fingerprint changed; the writer,
+assertion dates, historical unified version and legacy predicate semantics did
+not. The seven original complete rows and native synonym witness remain in the
+[immutable P3556 fixture](../../../tests/resources/mediadive/p3556_scope.json),
+SHA-256 `7c06f4e2179356ddf1d917a6938cba5e3bdf6669f42a29019b93963e4a70646c`.
+
+The candidate contains **591,946 rows**, **120,183 distinct targets**,
+**336,048 exact** and **255,898 close** matches, with no broad/narrow rows.
+The coordinator independently confirmed these counts by a full gzip/CSV stream
+under unchanged before/after candidate hashes.
+
+Three serial native consumer phases completed with exit zero and settled
+process groups: a second identity-only export and fresh reader processes with
+synonyms enabled and disabled. The second export removed/relabelled zero rows
+and reproduced the exact compressed candidate bytes. Both reader modes passed
+their finite native controls. Generic lexical phosphatidylcholine can still
+reach a class in synonym mode; that is not approval to assign the whole P3556
+product to that class. The source-qualified local guard and real source replay
+remain necessary.
+
+The completed checks ran at frozen pre-BacDive-integration head
+`b8f18b838f5797c9dc4f4a64451c27298713e7ef`; they are not represented as new
+execution at the subsequent integrated/staged head. Local evidence resides in
+the primary checkout under
+`data/issue1224-quarantine-20260929.xjuS9H/combined-identity-candidate.9eHuMu/`:
+
+- [Finite delta receipt](../../../data/issue1224-quarantine-20260929.xjuS9H/combined-identity-candidate.9eHuMu/review-delta-01/result.json):
+  `a4ec8a0c7a3d30d46208a16ac034301bdb1dae8209cbb951681856b596f0af5d`.
+- [Complete original/changed-row ledger](../../../data/issue1224-quarantine-20260929.xjuS9H/combined-identity-candidate.9eHuMu/review-delta-01/complete-row-delta.json):
+  `13fbefd64155d220a75731dfecfd9e5ab64df3f29e42e561c705d266aad6e50c`.
+- [Completed consumer receipt](../../../data/issue1224-quarantine-20260929.xjuS9H/combined-identity-candidate.9eHuMu/consumer-review-01/result.json):
+  `fa785548ca557e87057acf2d19b4e543437d3e39e28e7b160641617dd90f1100`,
+  status `PASS_FINITE_CANDIDATE_CONSUMER_CHECKS_ONLY`.
+
+These project-relative evidence links refer to retained local data, not files
+duplicated into the isolated worktree or a published release.
+
+## Separate source changes and remaining acceptance
+
+The seven-row mapping delta must not be conflated with recipe/assay changes:
+
+- [P3556](../mediadive-p3556-scope-1241.md) retains the qualified whole product
+  on its existing local ID and preserves full imported candidate evidence.
+- [Qualified mixed Sugar](../mediadive-sugar-context-1245.md) uses its exact
+  source-context decision. Generic supported MIM Sugar remains unchanged.
+- [Two finite peptone holds](../mediadive-peptone-scope-1248.md) reject only the
+  reviewed name/CID combinations; independent alternative targets are not
+  globally banned. Their [26 original occurrences](../../../tests/resources/mediadive/peptone_scope.json)
+  and all original matching legacy claims remain preserved.
+- [Tetramethyl ammonium chloride](../tetramethylammonium-chloride-20260929.md)
+  gains its finite existing-name route; unqualified tetramethylammonium is not
+  the salt.
+- [BacDive EC/substrate corrections](../bacdive-ec-substrate-corrections-1249-1250.md)
+  match four complete original rows and preserve their full mandatory audit,
+  including the withheld contradictory KEGG cell. They do not change this
+  unified artifact or establish a global identifier replacement.
+
+The [historical Potato promotion](../mediadive-potato-scope-20260929/PROMOTION.md)
+and earlier MIM promotion records are unchanged. No historical receipt is
+restamped as current acceptance. The updated paired-artifact test preserves
+their CAS, Potato, native-provenance and generic Sugar/Mucin controls.
+
+Next require approved real source replay/comparison with full
+raw/quantity/provenance preservation and manual
+node-delta review. Replay may precede or accompany frozen-head repository gates.
+All four full gates, green exact-head CI and independent review are required
+before PR merge. A fresh all-15-source transform batch, candidate-only merge,
+source-to-merged evidence retention and final KG reviews remain separate release
+requirements. This checkpoint does not close the broader #286 backlog.
diff --git a/docs/reviews/mediadive-p3556-scope-1241.md b/docs/reviews/mediadive-p3556-scope-1241.md
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+# Source-qualified Sigma P3556 material scope (#1241)
+
+## Evidence and scientific limit
+
+The saved MediaDive observation `mediadive.solution:629#recipe/1` names
+`L-α-Phosphatidylcholine`, compound 2082, and explicitly supplies
+`attribute: SIGMA P3556`. Its amount is 5 mg and its source `g_l` value is 5.
+Those original values are retained, not recalculated or silently corrected.
+The source does **not** assert a CAS identifier.
+
+The [supplier product sheet](https://www.sigmaaldrich.com/deepweb/assets/sigmaaldrich/product/documents/152/475/p3556pis.pdf)
+describes an egg-yolk material with several fatty-acid constituents, not one
+pure acyl species. The supplier's [drug-delivery brochure](https://b2b.sigmaaldrich.com/deepweb/assets/sigmaaldrich/marketing/global/documents/709/352/polymeric-drug-delivery-techniques-web.pdf)
+also depicts variable fatty-acid residues for P3556 (PDF page index 18,
+printed page 17). The [product page](https://www.sigmaaldrich.com/US/en/product/sigma/p3556)
+additionally supplies a fixed structure. That catalog structure is not proof
+of whole-product molecular purity; its stereolayer differs from the native
+ChEBI witness. These primary documents were read online. Local PDF downloads
+failed, so no local PDF checksum is claimed.
+
+Native `CHEBI:86658` has a generic preferred label but explicit synonyms,
+SMILES and InChI identifying a particular 16:0/(9E,12E)-18:2 structure.
+The immutable fixture `tests/resources/mediadive/p3556_scope.json` preserves
+that structured witness, all eight selected full original mapping rows,
+the exact raw occurrence, and hashes of the original raw/mapping inputs.
+The error is assigning the **whole product quantity** to that molecule.
+This is not a claim that the molecule cannot occur in the material.
+
+## Transform and mapping behavior
+
+- Two finite existing-policy exclusions reject generic `L-alpha`/`L-α`
+  phosphatidylcholine names and the exact `MIM:L-alpha-Phosphatidylcholine`
+  pair for `CHEBI:86658`. The policy authority label is an actual native
+  structured synonym, not the misleadingly generic preferred label.
+- The explicit source qualifier `SIGMA P3556` (case and whitespace only)
+  keeps a recipe occurrence on its existing MediaDive ingredient/solution
+  ID before unified, legacy or embedded identity selection. The current
+  observation therefore remains `mediadive.ingredient:2082` with its raw
+  source record, assertion ID, quantities and observation/manual provenance.
+  Neither ingredient number, recipe number, a generic name nor a fuzzy
+  catalog-code match triggers this product decision.
+- A supplied occurrence, including `{}`, never inherits another recipe's
+  embedded product qualifier. Direct calls without an occurrence can use an
+  explicit qualifier in the embedded source compound record.
+- Local category remains the existing broad `biolink:ChemicalEntity` for
+  the current source name. This change does not assert new native mixture
+  typing, a replacement ChEBI charge/class, CAS or other molecular identity.
+- Explicitly structured native molecular routes and unrelated generic
+  phosphatidylcholine classification claims remain eligible. There is no
+  global ban on `CHEBI:86658`, `CHEBI:16110`, `CHEBI:49183` or CAS 8002-43-5.
+  Eligibility alone is not new identity approval.
+
+## Reversible candidate evidence
+
+The existing required producer sidecar
+`mediadive_material_scope_quarantine.tsv` retains available candidate rows
+separately from graph identity. Its schema, producer-time byte snapshot,
+source-finalization copying and public-admission checks are unchanged.
+Potato/extract and P3556 candidates are separate finite profiles.
+
+For a P3556 observation, the audit preserves applicable current unified and
+legacy rows (matching the actual occurrence spelling), the original exact
+generic MIM claim, and actual embedded identifiers when present. Duplicate
+input rows have separate locators. Full original row columns, raw record,
+source/candidate path and hash, retained local target, qualifier, authority
+URI and reason are retained. A contradictory structure-specific display
+name cannot override the product qualifier; its applicable mapping claims
+are still auditable. These rows are **available candidates**, not assertions
+that every lookup was attempted, and are never fabricated raw CAS claims.
+
+Review #1243 corrected canonical object-label coverage: eligible identity,
+attribute, canonical-name and synonym rows can supply the reader's object
+label; synonym rows additionally supply the subject label. A row matching
+both fields is retained once per original locator, while duplicate physical
+rows remain distinct. Broader, hydrate and annotation rows do not become
+grounding candidates. The old fixture's four structured-synonym rows also
+carry the generic object label, so they remain auditable until a reviewed
+derived export relabels that metadata. Audit row counts are not historical
+constants.
+
+Conditional consumed-input role `material_scope_supported` binds the
+canonical unchanged `mappings/ingredient_mappings.sssom.tsv` only when the
+selected source contains P3556. It is audit evidence, not an active grounding
+source. It preserves the complete original imported assertion after a future
+derived unified export removes the held pair. The supported MIM table and
+release pin remain immutable. Empty source cohorts or removed candidates
+are valid; a genuinely empty audit retains its header.
+
+## Verification and deployment boundary
+
+Hermetic tests cover native reader/direct-pair denial, explicit structure
+controls, legacy and bounded/conservative regeneration, all occurrence
+fallbacks, raw quantities, duplicate full-row audit evidence, profile
+isolation, input-origin/drift protection, and real source finalization/reuse/
+public admission. The tiny identity-only refresh removes three generic rows
+and replaces the misleading object label on four retained structural rows;
+its second cycle is byte-identical. Conservative regeneration preserves full
+quarantined originals and multiplicity.
+
+This source change alone is not a rebuilt graph or release acceptance.
+A separate reviewed derived-mapping candidate, source replay, transform
+freshness checks and merged-graph reviews remain required. No immutable
+supported MIM release, production raw data or production archive is modified
+by this implementation stage.