Bound Ferroplasma and Fomitopsis claims; record lung graph gap (batch 41)

[realmarcin]

Scope

Bounded existing-graph repairs and an explicit missing-graph research record. Corpus: 162 reviewed / 288 pending / 10 needs_research across 460 records in both roots.

Closes #1459. Closes #1460. Graph research #1461 and non-graph #1462/#1463 remain open.

Changes

Six existing nodes retained, one HYPOTHESIZED arrow retained and one unsupported mechanism-to-reciprocal-assay arrow removed. Five existing nodes renamed. No new causal structure.

Ferroplasma: restore the primary abstract's hypothesis qualifier for organic supply/consumption and detoxification. Reciprocal filtered-medium growth does not identify mediators or prove obligate syntrophy; FBA inputs are not independent flux measurements. Keep Y(T) and isolated rusticyanin results separate from BRL-115 coculture, and remove unsupported oxygen niche partitioning and process annotations.

Fomitopsis: distinguish liquid glucose depletion, fungal biomass and transcription from agar bacterial inhibition. Putative metabolite identities and acid mediation remain qualified; BGC expression is not active-product identification. Preserve two nodes and zero arrows, previous cache-support fixes and the removed natural-partner caveat.

Lung model: public primary main body now read, but the record still has no graph. Record source-backed candidates and readout/assay limits; keep needs_research under #1461. A one-community Edison dry run is retained with query hash. Specific credit authorization requested, no provider job or spend. Hypothesized exchanges and challenge organisms are not new curated structure.

Verification And Output Records

431 passed in 170.84s (0:02:50); eight new regression tests. Focused schema, strict, term, snippet and history checks passed. All 42 snippets MATCH cached text, which is not scientific validation. Reference validator 0.1.7 exits 0 with zero effective checks: explicitly a no-op.

Zero structural defects; all 33 baseline network warnings exactly preserved. Participant registry remains 187 with unchanged connectivity census and numeric bounds. Guarded writes and append-only histories; non-graph raw blocks, 457 other records and 920 caches byte-preserved. Repeat renders deterministic and exact published descriptions checked across 456 pages.

Actual post-commit just check-docs-current exited 0 with a clean tree; output SHA256 03c181d4dc23381862d0201c97c4bffb3dcc3386139a2a8a292a6da24f234b92. Committed decisions, actual validation outputs/baseline/digests and source-based self-adversarial review are under reports/causal_graph_review, dated 20261006, batch41. The pre-paper baseline commit is preserved; its content-identical ancestry restack is documented. Initial no-graph helper dry-run failure is disclosed, not presented as a pass.

Source limits: Ferroplasma abstracts only; Fomitopsis selected preprint excerpts (full PDF returned HTTP 429); lung public primary main body, tables and captions. No figure images, equation rendering, separate supplements or raw data reviewed. No rate-control bypass, no full-text cache addition. Source-based self-adversarial review is not independent approval.

Dependency

Draft depends on #1458; do not merge into the topic parent. Require eligible exact-head checks and the protected main merge queue after parent merges. Move dependents before deleting branches. Full-corpus completion is not claimed.

[realmarcin]

Source-based self-adversarial review at exact head 12c0771; not independent approval.

Existing-graph defects #1459/#1460 addressed after source and complete diff review. New graph #1461 remains research-pending, not closed by documenting a gap.

Six existing nodes retained, one HYPOTHESIZED arrow retained and one unsupported mechanism-to-reciprocal-assay arrow removed. Five existing nodes renamed. No new causal structure.

Ferroplasma: restore the primary abstract's hypothesis qualifier for organic supply/consumption and detoxification. Reciprocal filtered-medium growth does not identify mediators or prove obligate syntrophy; FBA inputs are not independent flux measurements. Keep Y(T) and isolated rusticyanin results separate from BRL-115 coculture, and remove unsupported oxygen niche partitioning and process annotations.

Fomitopsis: distinguish liquid glucose depletion, fungal biomass and transcription from agar bacterial inhibition. Putative metabolite identities and acid mediation remain qualified; BGC expression is not active-product identification. Preserve two nodes and zero arrows, previous cache-support fixes and the removed natural-partner caveat.

Lung model: public primary main body now read, but the record still has no graph. Record source-backed candidates and readout/assay limits; keep needs_research under #1461. A one-community Edison dry run is retained with query hash. Specific credit authorization requested, no provider job or spend. Hypothesized exchanges and challenge organisms are not new curated structure.

431 passed in 170.84s (0:02:50); eight new regression tests. Focused schema, strict, term, snippet and history checks passed. All 42 snippets MATCH cached text, which is not scientific validation. Reference validator 0.1.7 exits 0 with zero effective checks: explicitly a no-op.

Zero structural defects; all 33 baseline network warnings exactly preserved. Participant registry remains 187 with unchanged connectivity census and numeric bounds. Guarded writes and append-only histories; non-graph raw blocks, 457 other records and 920 caches byte-preserved. Repeat renders deterministic and exact published descriptions checked across 456 pages.

Actual post-commit just check-docs-current exited 0 with a clean tree; output SHA256 03c181d4dc23381862d0201c97c4bffb3dcc3386139a2a8a292a6da24f234b92. Committed decisions, actual validation outputs/baseline/digests and source-based self-adversarial review are under reports/causal_graph_review, dated 20261006, batch41. The pre-paper baseline commit is preserved; its content-identical ancestry restack is documented. Initial no-graph helper dry-run failure is disclosed, not presented as a pass.

Source limits: Ferroplasma abstracts only; Fomitopsis selected preprint excerpts (full PDF returned HTTP 429); lung public primary main body, tables and captions. No figure images, equation rendering, separate supplements or raw data reviewed. No rate-control bypass, no full-text cache addition. Source-based self-adversarial review is not independent approval.

#1461/#1462/#1463 remain OPEN. Protected main merge and full-corpus completion are 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]

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 12c9301c7205188b924d54f772ee0fdaba5b5a33
after protected main merge of #1323. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree d6664ec28961715038f08b1565bcbffc98383a50.
The batch-owned binary patch is byte-identical
(SHA-256 21835bd9151b04bbad68693c5bd79e665745eb66c4ec997523d40286a94c66c7); 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 b47d72566b30576e4f709625346075b99a0053c5
after protected main merge of #1328. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree d6664ec28961715038f08b1565bcbffc98383a50.
The batch-owned binary patch is byte-identical
(SHA-256 21835bd9151b04bbad68693c5bd79e665745eb66c4ec997523d40286a94c66c7); 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 489b149b11e371356925c43aaf44a83df4f29d5d
after protected main merge of #1334. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree d6664ec28961715038f08b1565bcbffc98383a50.
The batch-owned binary patch is byte-identical
(SHA-256 21835bd9151b04bbad68693c5bd79e665745eb66c4ec997523d40286a94c66c7); 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 d18f5bbc7a879b06903e73c40aac3c0123d873c7
after protected main merge of #1339. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree d6664ec28961715038f08b1565bcbffc98383a50.
The batch-owned binary patch is byte-identical
(SHA-256 21835bd9151b04bbad68693c5bd79e665745eb66c4ec997523d40286a94c66c7); 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 47383f07b28a8f73a748a5c5e9867b46ff870f3c
after protected main merge of #1346. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree d6664ec28961715038f08b1565bcbffc98383a50.
The batch-owned binary patch is byte-identical
(SHA-256 21835bd9151b04bbad68693c5bd79e665745eb66c4ec997523d40286a94c66c7); 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 a4a941861208a2d3566df533e4e83043b29d0964
after protected main merge of #1350. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree d6664ec28961715038f08b1565bcbffc98383a50.
The batch-owned binary patch is byte-identical
(SHA-256 21835bd9151b04bbad68693c5bd79e665745eb66c4ec997523d40286a94c66c7); 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 5eb7272dd99a56386464134e6e3abd0811eefdd6
after protected main merge of #1355. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree d6664ec28961715038f08b1565bcbffc98383a50.
The batch-owned binary patch is byte-identical
(SHA-256 21835bd9151b04bbad68693c5bd79e665745eb66c4ec997523d40286a94c66c7); 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 7ad970662d1dbc916ee837738b9d6fc08da091a2. Not independent approval.

Integrated already-merged schema prerequisite #1692 (67603e192525899fae75420e2c19e8212b16afc9). Compared with the prior reviewed head 5eb7272dd99a56386464134e6e3abd0811eefdd6, 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 21835bd9151b04bbad68693c5bd79e665745eb66c4ec997523d40286a94c66c7). 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 972246afc5a7390d25004549215fd6b43006aa26
after protected main merge of #1361. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree da57c9dacaff868573849657593b21966a2c92cb.
The batch-owned binary patch is byte-identical
(SHA-256 21835bd9151b04bbad68693c5bd79e665745eb66c4ec997523d40286a94c66c7); 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 e0d957608ce0e9439719a176b2278e96df633698. This is a COMMENT, not independent approval.

Integrated already-merged main PR #1730 (fe1752572a688051e8105e5b89d3099fe2202c63). Compared with prior reviewed head 972246afc5a7390d25004549215fd6b43006aa26, 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 21835bd9151b04bbad68693c5bd79e665745eb66c4ec997523d40286a94c66c7). 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 26a2022963140afe87eedc2fc0170c9e640ded8f.
COMMENT, not independent approval.

The batch-owned binary patch remains byte-identical:
SHA-256 21835bd9151b04bbad68693c5bd79e665745eb66c4ec997523d40286a94c66c7.
Tree 7abb42c2f6c47cde7879cc929bd074929eb024d4 matches the independently computed clean merge.
Compared with historical tree d6b40aa1dc1ba9178028a4f6fe793f19cd3579ec, 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 5a3e7ec6251a997c33a76371cd6ca7f9fd7a62ec 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.