Bound dental and East River causal graphs to measured evidence (batch 35)

[realmarcin]

Scope

Three existing-graph reviews: early dental five-species biofilm, East River floodplain core and East River hillslope-riparian transect. Corpus: 147 reviewed / 306 pending / 7 needs_research across 460 records in both roots.

Closes #1417. Closes #1418. Closes #1419. Non-graph #1420/#1421/#1422 remain open.

Changes

Ten nodes retained; four unsupported arrows removed and three qualified. No new causal structure or Edison job/charge.

Dental planktonic coaggregation is not demonstrated colonization benefit or a mediator of collective glucose-induced acidification. Remove the two assay-order arrows and categorical niche-partitioning claim; preserve five canonical participants.

Floodplain core capacity is not a cause of its own constituent functions or a predictor of one-time transcription. Remove both arrows. The 2016 RNA snapshot is limited to floodplain L, despite broader abstract wording; transcripts are not flux. Core/low-carbon participants exclude non-core Acidobacteriota and the Nitrospirae-to-Nitrospira rank mismatch. Higher-level groups are partial participants, not universal pathway assignments.

Hillslope environmental drivers remain HYPOTHESIZED. DNA gene abundances are potential, not RNA activity or measured flux. Distinguish non-CPR depth enrichment, CPR distributions with hillslope exceptions, and untested host dependency. SrdA is selenate-reduction potential, not demonstrated selenium removal or water-quality improvement. Preserve distinct compartment labels despite shared broad IDs.

Verification And Output Records

384 passed in 164.84s (0:02:44); eight new regression tests. Schema, strict, terms, independent snippets and history checks passed. Three reference-validator commands exit 0 but perform zero checks: no-op, not evidence validation. Textual matching is not scientific support.

Zero structural errors. All 31 baseline warnings exactly preserved; two DISCONNECTED warnings exposed for the floodplain members above, tracked by #1418/#1421. No invented links to suppress them. Participant registry 180 to 183 adds only these three records; broad census, taxonomy, algorithms and numeric bounds unchanged.

Three guarded writes, append-only histories and llm-assisted events. Non-graph raw blocks, 457 other records and 920 caches preserved. Repeated renders deterministic; exact descriptions checked across 456 pages. Actual post-commit docs-current passed with clean tree.

Committed decision ledger, validation output and adversarial-review records are under reports/causal_graph_review, dated 20261006, batch35. Actual pre-research baseline included. Cached primary main-body text reviewed at recorded access scope, not visual figures, raw data or external supplements. Source-based self-adversarial review, not independent approval.

Dependency

Draft depends on #1416; do not merge into the topic parent. Require protected exact-head checks and main merge queue after parents merge. Move dependents before branch deletion. Full-corpus completion is not claimed.

[realmarcin]

Source-based self-adversarial review at exact head 54ce25c; not independent approval.

Addressed #1417/#1418/#1419 after primary-text and actual diff review. Ten nodes retained, four unsupported arrows removed, three qualified. Dental coaggregation is not acidification mediation. Floodplain core capacity and one-time L-only RNA remain distinct; source abstract/Methods scope conflict disclosed. Partial participants do not propagate wrong-rank Nitrospira or non-core Acidobacteriota into unsupported functions. Hillslope DNA potential, candidate-phylum/CPR distinctions, unknown hosts and srdA limits remain explicit; shared-ID compartments retain distinct labels.

384 passed in 164.84s (0:02:44); eight new tests. Focused schema/strict/terms/snippets/history passed, deterministic renders and exact descriptions verified across 456 pages, and actual post-commit docs-current passed. Reference-validator did zero checks despite exit 0; no-op is not evidence validation. Zero structural errors; 31 prior warnings unchanged and two newly exposed DISCONNECTED warnings disclosed under #1418/#1421. Registry adds three records without changing taxonomy, algorithms or numeric bounds. Non-graph raw blocks, 457 other records and 920 caches preserved.

#1420/#1421/#1422 remain OPEN. Committed decision, validation and adversarial output records include limitations and actual pre-research baseline. No new structure/provider job/charge, visual figures, raw data, browser screenshots or external supplement review claimed. Protected main merge and full-corpus completion not asserted.

[github-actions]

Network integrity findings

Warnings only — a member with no interaction yet, or a participant matched by ontology id rather than by name, or one on a community-level interaction that resolves to no member. Reported, but does not fail the build.

Network Integrity Audit Report
================================================================================

0 error, 33 warning across 13 records with findings
Only error-severity findings fail the build.

Algal_Methanotroph_Biogas_Valorization_Coculture
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Leptolyngbya' has no interactions

Total: 1 issues (0 error, 1 warning)

At_RSPHERE_SynCom
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Flavobacterium sp.' has no interactions
  [warning] DISCONNECTED: Taxon 'Pseudomonas sp.' has no interactions
  [warning] DISCONNECTED: Taxon 'Rhodococcus sp.' has no interactions
  [warning] DISCONNECTED: Taxon 'Streptomyces sp.' has no interactions
  [warning] DISCONNECTED: Taxon 'Variovorax sp.' has no interactions

Total: 5 issues (0 error, 5 warning)

Australian_Lead_Zinc_Polymetallic
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Acidithiobacillus ferrooxidans' has no interactions
  [warning] DISCONNECTED: Taxon 'Leptospirillum ferriphilum' has no interactions

Total: 2 issues (0 error, 2 warning)

Bacillus_G12_Y4_X25_Tobacco_Biocontrol_SynCom
--------------------------------------------------------------------------------
  [warning] UNKNOWN_TARGET: Target taxon 'tobacco' not found in taxonomy section (community-level scope)
  [warning] UNKNOWN_TARGET: Target taxon 'tobacco' not found in taxonomy section (community-level scope)

Total: 2 issues (0 error, 2 warning)

Bacillus_siamensis_vallismortis_HT_Masson_Pine_SynCom
--------------------------------------------------------------------------------
  [warning] UNKNOWN_TARGET: Target taxon 'Fusarium oxysporum' not found in taxonomy section (community-level scope)
  [warning] UNKNOWN_TARGET: Target taxon 'Pinus massoniana' not found in taxonomy section (community-level scope)
  [warning] UNKNOWN_TARGET: Target taxon 'Pinus massoniana' not found in taxonomy section (community-level scope)

Total: 3 issues (0 error, 3 warning)

Brocadia_Low_Nitrogen_Anammox_Consortium
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Ca. Kuenenia early-acclimation lineage' has no interactions

Total: 1 issues (0 error, 1 warning)

Dangl_SynComm_35
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Escherichia coli DH5α' has no interactions
  [warning] DISCONNECTED: Taxon 'Flavobacterium species' has no interactions
  [warning] DISCONNECTED: Taxon 'Microbacterium species' has no interactions
  [warning] DISCONNECTED: Taxon 'Stenotrophomonas species' has no interactions
  [warning] DISCONNECTED: Taxon 'Xanthomonadales members' has no interactions

Total: 5 issues (0 error, 5 warning)

Deepwater_Horizon_Deep_Sea_Oil_Plume_Succession
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Methylophaga' has no interactions

Total: 1 issues (0 error, 1 warning)

East_River_Floodplain_Core_Microbiome
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Acidobacteriota floodplain representatives' has no interactions
  [warning] DISCONNECTED: Taxon 'Nitrospirae core floodplain members' has no interactions

Total: 2 issues (0 error, 2 warning)

Mangrove_Benzene_MFC_Bioanode_Consortium
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Pelobacter' has no interactions
  [warning] DISCONNECTED: Taxon 'Pseudomonas' has no interactions

Total: 2 issues (0 error, 2 warning)

Nitrifying_Wastewater_Ammonia_Oxidizing_Consortium
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Legionella MAGs' has no interactions

Total: 1 issues (0 error, 1 warning)

Sclerotinia_Sclerotia_12Strain_Biocontrol_SynCom
--------------------------------------------------------------------------------
  [warning] UNKNOWN_TARGET: Target taxon 'Sclerotinia sclerotiorum' not found in taxonomy section (community-level scope)
  [warning] UNKNOWN_TARGET: Target taxon 'Sclerotinia sclerotiorum' not found in taxonomy section (community-level scope)

Total: 2 issues (0 error, 2 warning)

Space_Habitat_SevenMember_Stress_Tolerance_SynCom
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Acinetobacter radioresistens 50V1' has no interactions
  [warning] DISCONNECTED: Taxon 'Micrococcus luteus W4-Al-K1' has no interactions
  [warning] DISCONNECTED: Taxon 'Propionibacterium cyclohexanicum TA-12T' has no interactions
  [warning] DISCONNECTED: Taxon 'Pseudomonas antarctica CMS 35T' has no interactions
  [warning] DISCONNECTED: Taxon 'Staphylococcus capitis K1-2-2-23' has no interactions
  [warning] DISCONNECTED: Taxon 'Streptococcus halotolerans HTS9T' has no interactions

Total: 6 issues (0 error, 6 warning)

The full report is attached to the workflow run as an artifact.

[realmarcin]

Self-adversarial review refreshed at exact head caa8c96c3af9ddbec45c258e676f74523104bef8
after protected main merge of #1315. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 254290bd77b3009f858019ea4ce274d0e9ba20e5.
The batch-owned binary patch is byte-identical
(SHA-256 e194f5aec4f210418241841fedbe9a7ca3ef36917a9646cbeb9932b746380ed9); only ancestry changed.
Scientific records, caches, source-review output, histories, regression tests, and generated pages
are unchanged. Historical validation results and recorded source/access limitations therefore
remain applicable, but required CI must pass at this new head. No new source review or local test
rerun is claimed by this ancestry-only update.

The protected main queue remains mandatory. Keep dependents on their reviewed parent until that
parent is confirmed merged; move dependents before deleting merged branches.

[realmarcin]

Self-adversarial review refreshed at exact head f45b2af710bb3550af47eb52ac11d211aa4ed69c
after protected main merge of #1318. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 254290bd77b3009f858019ea4ce274d0e9ba20e5.
The batch-owned binary patch is byte-identical
(SHA-256 e194f5aec4f210418241841fedbe9a7ca3ef36917a9646cbeb9932b746380ed9); only ancestry changed.
Scientific records, caches, source-review output, histories, regression tests, and generated pages
are unchanged. Historical validation results and recorded source/access limitations therefore
remain applicable, but required CI must pass at this new head. No new source review or local test
rerun is claimed by this ancestry-only update.

The protected main queue remains mandatory. Keep dependents on their reviewed parent until that
parent is confirmed merged; move dependents before deleting merged branches.

[realmarcin]

Reference-counter correction (#1469)

The earlier statement that linkml-reference-validator 0.1.7's Total checks: 0 means zero executed checks or a no-op is incorrect and withdrawn. The installed CLI prints the number of validation issues, not checks performed. Existing positive/negative and field-discovery canaries pass; EvidenceItem snippets are genuinely checked. SupportingReference coverage remains incomplete under #476. Text matching is not scientific support or independent source provenance.

The source-backed correction and historical candidate inventory are committed in #1470 at 22b5b12c2386a949d1ec4ddb1f79ee288085bd1c, under reports/causal_graph_review/README.md and reference-validator-correction-20261006-batch42.json. Earlier raw command output, source review, biological decisions and tested bytes are preserved; this notice does not claim a rerun of this PR's validation or change its biological findings. The older CLI counter is not a coverage metric.

The new Fucoidan batch separately retains 14 baseline reference-CLI failures and 15 baseline snippet-audit mismatches for supplement-sidecar excerpts. Those are not failures attributed to this older PR. This correction is self-review, not independent approval or merge authorization beyond the existing protected workflow.

[realmarcin]

Self-adversarial review refreshed at exact head e6e6da273d6ac0e1b94cc902f2d3aa6bb103ba3c
after protected main merge of #1323. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 254290bd77b3009f858019ea4ce274d0e9ba20e5.
The batch-owned binary patch is byte-identical
(SHA-256 e194f5aec4f210418241841fedbe9a7ca3ef36917a9646cbeb9932b746380ed9); only ancestry changed.
Scientific records, caches, source-review output, histories, regression tests, and generated pages
are unchanged. Historical validation results and recorded source/access limitations therefore
remain applicable, but required CI must pass at this new head. No new source review or local test
rerun is claimed by this ancestry-only update.

The protected main queue remains mandatory. Keep dependents on their reviewed parent until that
parent is confirmed merged; move dependents before deleting merged branches.

[realmarcin]

Self-adversarial review refreshed at exact head 4565d99a0745e89a3e02443f8d147e81f3efac2e
after protected main merge of #1328. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 254290bd77b3009f858019ea4ce274d0e9ba20e5.
The batch-owned binary patch is byte-identical
(SHA-256 e194f5aec4f210418241841fedbe9a7ca3ef36917a9646cbeb9932b746380ed9); only ancestry changed.
Scientific records, caches, source-review output, histories, regression tests, and generated pages
are unchanged. Historical validation results and recorded source/access limitations therefore
remain applicable, but required CI must pass at this new head. No new source review or local test
rerun is claimed by this ancestry-only update.

The protected main queue remains mandatory. Keep dependents on their reviewed parent until that
parent is confirmed merged; move dependents before deleting merged branches.

[realmarcin]

Self-adversarial review refreshed at exact head d00d603867ee0adfc1298f5960fd56a3ff6a486e
after protected main merge of #1334. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 254290bd77b3009f858019ea4ce274d0e9ba20e5.
The batch-owned binary patch is byte-identical
(SHA-256 e194f5aec4f210418241841fedbe9a7ca3ef36917a9646cbeb9932b746380ed9); only ancestry changed.
Scientific records, caches, source-review output, histories, regression tests, and generated pages
are unchanged. Historical validation results and recorded source/access limitations therefore
remain applicable, but required CI must pass at this new head. No new source review or local test
rerun is claimed by this ancestry-only update.

The protected main queue remains mandatory. Keep dependents on their reviewed parent until that
parent is confirmed merged; move dependents before deleting merged branches.

[realmarcin]

Self-adversarial review refreshed at exact head c8d24c1a99932ff4b622cd6e21ac43217b380416
after protected main merge of #1339. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 254290bd77b3009f858019ea4ce274d0e9ba20e5.
The batch-owned binary patch is byte-identical
(SHA-256 e194f5aec4f210418241841fedbe9a7ca3ef36917a9646cbeb9932b746380ed9); only ancestry changed.
Scientific records, caches, source-review output, histories, regression tests, and generated pages
are unchanged. Historical validation results and recorded source/access limitations therefore
remain applicable, but required CI must pass at this new head. No new source review or local test
rerun is claimed by this ancestry-only update.

The protected main queue remains mandatory. Keep dependents on their reviewed parent until that
parent is confirmed merged; move dependents before deleting merged branches.

[realmarcin]

Self-adversarial review refreshed at exact head 9c0c1faf92e2cbe50a4934d73d0c02b214d9d3d1
after protected main merge of #1346. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 254290bd77b3009f858019ea4ce274d0e9ba20e5.
The batch-owned binary patch is byte-identical
(SHA-256 e194f5aec4f210418241841fedbe9a7ca3ef36917a9646cbeb9932b746380ed9); only ancestry changed.
Scientific records, caches, source-review output, histories, regression tests, and generated pages
are unchanged. Historical validation results and recorded source/access limitations therefore
remain applicable, but required CI must pass at this new head. No new source review or local test
rerun is claimed by this ancestry-only update.

The protected main queue remains mandatory. Keep dependents on their reviewed parent until that
parent is confirmed merged; move dependents before deleting merged branches.

[realmarcin]

Self-adversarial review refreshed at exact head b1d90b07b3935af3ae5b423577d4509e4de86216
after protected main merge of #1350. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 254290bd77b3009f858019ea4ce274d0e9ba20e5.
The batch-owned binary patch is byte-identical
(SHA-256 e194f5aec4f210418241841fedbe9a7ca3ef36917a9646cbeb9932b746380ed9); only ancestry changed.
Scientific records, caches, source-review output, histories, regression tests, and generated pages
are unchanged. Historical validation results and recorded source/access limitations therefore
remain applicable, but required CI must pass at this new head. No new source review or local test
rerun is claimed by this ancestry-only update.

The protected main queue remains mandatory. Keep dependents on their reviewed parent until that
parent is confirmed merged; move dependents before deleting merged branches.

[realmarcin]

Self-adversarial review refreshed at exact head e3bcef7c02146fd3271fc5b1f9bd1e1ef944bcab
after protected main merge of #1355. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 254290bd77b3009f858019ea4ce274d0e9ba20e5.
The batch-owned binary patch is byte-identical
(SHA-256 e194f5aec4f210418241841fedbe9a7ca3ef36917a9646cbeb9932b746380ed9); only ancestry changed.
Scientific records, caches, source-review output, histories, regression tests, and generated pages
are unchanged. Historical validation results and recorded source/access limitations therefore
remain applicable, but required CI must pass at this new head. No new source review or local test
rerun is claimed by this ancestry-only update.

The protected main queue remains mandatory. Keep dependents on their reviewed parent until that
parent is confirmed merged; move dependents before deleting merged branches.

[realmarcin]

Self-adversarial integration review at exact head fa49a29b05590e0747835f6c6e220fdfdaf09ad5. Not independent approval.

Integrated already-merged schema prerequisite #1692 (67603e192525899fae75420e2c19e8212b16afc9). Compared with the prior reviewed head e3bcef7c02146fd3271fc5b1f9bd1e1ef944bcab, the only changes are the canonical schema pin, shared schema and generated datamodel from that main commit. Every other tracked file is identical; the batch-owned binary patch remains byte-identical (SHA-256 e194f5aec4f210418241841fedbe9a7ca3ef36917a9646cbeb9932b746380ed9). All 60 published batch patches were checked this way. No scientific assertion, reference cache, history, decision ledger or generated page was edited by this integration.

Adversarial checks: no inherited schema-file edits lost; generated CrossCorpusLink remains standalone and does not add a causal claim; normal strict validation passed all 460 records; required CrossCorpusLink fields enforced. Fresh broad regression runs on both ends of the stack: 302 passed in 172.77s (0:02:52); 756 passed in 255.55s (0:04:15). Docs-current passed clean at batches25/84, and vendored-sync passed. The 58 intermediate combinations were not independently retested. Existing primary-source review limitations and unresolved research issues remain applicable; historic validation receipts are not rewritten as new scientific reviews.

An additional generated-datamodel loading check FAILED and is retained in the integration receipt. Differential testing found exactly the same failures on all 460 paths before and after this integration:417 unhashable TaxonDescriptor and43 unhashable CultureCollectionEnum exceptions, with linkml-runtime1.11.1. Existing tests explicitly use plain YAML instead of this loader. Pre-existing defect #1703 remains OPEN; no datamodel-loader success is claimed. Normal strict schema validation is a separate passing path, not a relabeling of that failure.

Required CI must pass on this exact head and the protected merge-queue candidate. No manual workflow dispatch, artificial status, administrative merge or protection bypass. Dependents stay draft until their parent is confirmed merged; move dependents before branch deletion.

[realmarcin]

Self-adversarial review refreshed at exact head ec9500f392e639b193270dbeada930bb80d2d887
after protected main merge of #1361. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 3f545bcf6ada9c71a6ad56a89702a625aba2bd48.
The batch-owned binary patch is byte-identical
(SHA-256 e194f5aec4f210418241841fedbe9a7ca3ef36917a9646cbeb9932b746380ed9); only ancestry changed.
Scientific records, caches, source-review output, histories, regression tests, and generated pages
are unchanged. Historical validation results and recorded source/access limitations therefore
remain applicable, but required CI must pass at this new head. No new source review or local test
rerun is claimed by this ancestry-only update.

The protected main queue remains mandatory. Keep dependents on their reviewed parent until that
parent is confirmed merged; move dependents before deleting merged branches.

[realmarcin]

Self-adversarial governance integration review at exact head dfe7d5014ad6f65559ac9e26bd5aa657b394cd43. This is a COMMENT, not independent approval.

Integrated already-merged main PR #1730 (fe1752572a688051e8105e5b89d3099fe2202c63). Compared with prior reviewed head ec9500f392e639b193270dbeada930bb80d2d887, exactly two files changed: scripts/.vendored_canon_ref and tests/test_id_label_empty_adapter.py. Each resulting tree differs from its old tree by the exact binary patch from main, and each batch-owned binary patch remains byte-identical (SHA-256 e194f5aec4f210418241841fedbe9a7ca3ef36917a9646cbeb9932b746380ed9). These invariants passed on all 74 published branches. Original heads are retained in local archive refs/archive/communitymech-pre-governance-20261007. No scientific record, source cache, history, decision ledger, schema, runtime code or generated page changed in this integration.

Adversarial inspection: the adapter regression still checks the empty sentinel and case-insensitive caching, now with an isolated fake oaklib module and a one-call selector assertion. No validation threshold or runtime behavior was relaxed. Fresh regressions at both stack ends: 337 passed in 214.19s (0:03:34); 917 passed in 402.58s (0:06:42). Docs-current and pinned vendored-sync passed at batches26/99. The 72 intermediate combinations were checked by tree/patch hashes, not independently retested. Historical source-review limitations and unresolved issues, including loader #1703 and cache #1091, remain applicable. This is not new paper review, independent approval, or a claim that those outstanding issues are fixed.

Digest-bound integration receipt/logs: /private/tmp/communitymech-governance-integration-20261007/receipt.json. Prior output/review records in reports/causal_graph_review/ remain unchanged. The prior lifecycle receipt is archived and will be updated only after all exact-head comments are verified.

Required CI and independent review must pass for the exact head and protected merge-queue candidate. No CI rerun, manual dispatch, fabricated status, admin merge or protection bypass. Dependents remain draft; move them before deleting a merged parent branch.

[realmarcin]

Exact-head self-adversarial restack review at 8e7d2a6bb522ee35e52b91693119fc9a21e5f092.
COMMENT, not independent approval.

The batch-owned binary patch remains byte-identical:
SHA-256 e194f5aec4f210418241841fedbe9a7ca3ef36917a9646cbeb9932b746380ed9.
Tree 414b5da27e9abd13e9aefadbf0a8d2dbbaf7c713 matches the independently computed clean merge.
Compared with historical tree 6467e88ac9437b4cb62e3d9f23ab63959b30755f, only scripts/.vendored_canon_ref
changes, incorporating main PR #1834's pin 849f336e025510316a5f235eb0af8547b8bd50cc.
All curated records, source caches, review outputs, histories, regression tests, and rendered
pages remain unchanged. No new primary-source review or local scientific-test rerun is claimed.

This PR is now part of native stack #1973, rooted at #1363 on main. No protected merge
has occurred. Fresh eligible PR/merge-group CI remains mandatory. No rule bypass, fabricated
status, merge into a topic parent, or premature branch deletion.

[realmarcin]

Superseded by the protected cumulative merge #1975 at 42959bef2549f9a42c3e3303a0e10fd5be99f30e. This PR's reviewed source head a02b315efa4bd40644f8aebf98bcfda5344d7530 was included in the cumulative branch; the final squash tree matches the reviewed integration tree exactly, and all seven required merge-group checks passed.

Patch-inclusion receipt. Existing issue-closing links were transferred to #1975; unresolved research and non-graph gaps are not closed by this action. This PR is being closed as superseded, not represented as individually merged. Archival provenance tags retain source commits; cleanup removes branch refs only and preserves worktree files.