Separate vitamin, PET, catalyst and plant-protection causal evidence (batch80)

[realmarcin]

Scope

Closes #1660.
Closes #1661.
Closes #1662.
Closes #1663.
Research #1664/#1665 and non-graph #1666 stay OPEN after graph-repair merge.

• Preserve positive bacterial rescue and its persistence contribution with partial thiamine-rescue limits.; Preserve reciprocal niacin/biotin/pABA complementation and distinguish supplemented ratio assays.; Preserve serial persistence while removing the mismatched reverse arrow and qualifying exact-ratio regulation.
• Preserve complementary extracellular hydrolysis and both product-supply arrows without Bacillus nutrient-uptake claims.; Replace misassigned film evidence with direct TPA consumption and correct Results timing.; Preserve EG utilization while separating BHET nonaccumulation, PET intermediates and partial mediation.; Preserve experimental medium/inoculum control without long-term coexistence claims.; Preserve23.2%seven-day optimized37C film loss and correct four-member versus three-species scope.
• Preserve observed column Al leaching without inferred PGM exposure and correct elemental label.; Preserve separate biogenic-thiosulfate Pd result with synthetic-support, phase and processing limits.; Preserve actual uncrushed-column Ni/Al/Mo/V outcomes without cross-study PGM or industrial claims.
• Preserve all six individual positive hits and assay units without a mixed-community or colonization claim.; Preserve quantified CF313 confirmation relative to heat shock and thermopriming; remove workflow arrow.; Preserve live/killed/supernatant contrast while explicitly qualifying physical contact and pathway inference.

Adversarial Review

• Pre-paper both-root baseline and whole-record reads preceded curation. Every17original node and10arrow has a retained/removed decision. Three protocol nodes removed,14biological-result nodes and6arrows retained; no new causal topology or provider spend.
• Vitamin complementation is experimentally demonstrated in both directions. Preserve cobalamin rescue, partial thiamine rescue and algal support of niacin/biotin/pABA needs. Do not downgrade physiological mutualism merely because transport and secretion flux were not measured.
• Vitamin ratio dynamics supplied thiamine/biotin, unlike the all-vitamin-omission experiment. Serial persistence and approximate1:1ratios survive; addback and convergence do not exclude competition for other nutrients or establish active regulation. Remove the fixed-carbon/persistence-to-vitamin arrow; the biologically motivated reciprocal rescue-to-persistence extension remains1664pending workflow.
• PET uses four strains in three species, with distinct canonical Bs_PETase and Bs_MHETase preferred names sharing1423. Extracellular enzyme division is not itself nutrient uptake by the MHETase producer. Both hydrolysis-product supply arrows remain.
• PET exogenous inhibition, standalone RHA1TPA consumption and consortium degradation are positive experiments. Replace31.2%film loss as a TPA-utilization quote with the28h standalone assay; use7days from Results rather than conflicting3day abstract. Preserve contribution to degradation with quantitative/mediator limits.
• KT2440EG utilization and EG inhibition are real, but BHET product nonaccumulation is not PET mass balance; PETTPA transiently increases. Different media/inocula and lower four-member film loss do not isolate EG-mediated improvement. No complete mineralization or zero-intermediate claim.
• Rich-medium P.putida dominance motivates Wn/inoculum control. Preserve23.2%seven-day optimized37C film loss and same-medium two-member comparison, not durable coexistence or unique resource-competition mediation.37C is actually supported for the community, not automatically preculture-only.
• PGM source identity matters: PMID31059950=DOI10.1016/j.jenvman.2019.04.081is one uncrushed refinery-column paper. Its Ni82.9%,Al33.4%,Mo22.7%at315h and V53.6%at105h are not Pd/Pt/Rh recovery or a two-step PGM exposure cascade. Abstract-only access is not proof that unseen experiments are absent.
• The complete thiosulfate paper prepares synthetic metallic Pd on alpha-alumina. Separate activated-sludge thiosulfate is concentrated100C/filtered before60C,pH8leaching.93.22%solid depletion differs from63.53%dissolved recovery with precipitation; no exact unique complex stoichiometry or benign industrial viability asserted. Preserve prior605 taxon removals and correct aluminium elemental label without inventing ionic state.
• Variovorax six hits are individually tested, not a co-inoculated consortium. Preserve CF31317%chlorophyll loss versus20.4%mock and9.3%thermopriming. Wells are experimental units; approximately10seedlings per well are pooled, not independent treatment replicates. Removed establishment/calibration/screen nodes preserve methods in surviving prose. Adversarial follow-up explicitly grounds the six-hit panel and limits both CF313 nodes to its exact canonical preferred name despite shared genus34072;17affected checks rerun with prior outputs retained.
• Live/killed/filtered-supernatant controls support a live-cell benefit, not a physically isolated contact requirement. The author contact inference remainsPARTIAL; ongoing/unstable/host-induced signals remain alternatives. ACC/ethylene is proposed, not tested. Prior workflow removals retained and final confirmation-to-contact workflow arrow removed.
• Three fresh main texts, thiosulfate tables/captions and cached vitamin main manuscript/captions read. Column abstract plus climate-source identity/abstract inspected; climate source is not used for graph support. No supplemental figures, raw data or original figure pixels audited. Truncated combined reads do not support negative conclusions; bounded source reads supply the science.
• Twenty-five literal graph quotations checked;22independent fresh-primary matches and3cached vitamin matches. All920caches,456other records and raw non-graph blocks unchanged. Four append-only histories. No canonical membership or auditor-rule change. Metadata1666remains open, coordinated with broader573/615.
• One9032character vitamin Edison dry run, zero provider submissions/credits; scoped question unanswered. Research1664/1665and metadata1666stay open after repair merge. Repair1660-1663stay open until protected-main merge. Self-adversarial COMMENT is not independent approval.
• Actual schema/strict/term/reference/snippet/history outputs, full related regressions, both-root network/inventory/rank and deterministic render checks are hash-bound. The first participant rerun found the explicit-users registry needed the intentional241st record; the unchanged measured census justified adding only this record, not weakening the guard or changing bounds. Eighteen superseded outputs include that715pass/1failure result. Exact description checks across456pages are not browser screenshots. Postcommit docs-current and exact remote head COMMENT are separate publication checks; do not delete parent branches before moving dependents.

Verification And Output Records

716 passed in 223.25s (0:03:43); ten new focused tests. All four schema, strict, term, full-record reference, snippet and history gates passed. All four full-record reference validators exit0. CLI Total checks counts issues, not executed checks. Twenty-five graph quotations match primary content and unchanged caches;22also match fresh retrievals, while3vitamin quotations use the existing accepted-manuscript cache. Literal matching is not entailment or full provenance certification. No recertification of every cache/non-graph field.

All17 original nodes and10arrows reviewed;14nodes6arrows remain. Four records repaired; three protocol nodes and four unsupported arrows removed. Preserve reciprocal vitamin rescue, PET inhibition/consumption/degradation, separate metal extraction and individual Variovorax plant protection with actual assay boundaries. Reciprocal vitamin topology and authorized refinery-column full-text review remain #1664/#1665; metadata #1666 stays OPEN.

All456 other records,920 caches and raw non-graph blocks verified unchanged. Canonical taxa and auditor rules unchanged. Zero structural defects;44 baseline warnings and connectivity census unchanged. Repeat renders deterministic; exact descriptions parsed across456 pages, not browser screenshots.

Postcommit just check-docs-current passed with clean tree; log SHA256 c7f5305e5630a28bdb95403e8b6f6a275f210968a57e6411c3d48cf284113c6c. Every-node/every-arrow decisions,40 actual check outputs/digests and source-based self-adversarial review committed under reports/causal_graph_review, batch80. Final focused rerun:19 passed. Corpus:254 reviewed,172 pending,34 needs_research. One Ostreococcus Edison dry run; zero paid submissions/credits, scoped question unanswered. Not independent approval or corpus completion.

Source Limits

• Fresh pre-paper baseline covers460 records and920 caches across both roots, including ignored/hidden files. Every17existing node and10arrow reviewed;14nodes6arrows remain, three protocol nodes/four unsupported arrows removed. Four guarded repairs/history events;456other records and920caches unchanged.
• Three fresh complete primary main bodies read: PET, thiosulfate and Variovorax. Thiosulfate embedded tables and all main captions read. Ostreococcus fresh abstract plus existing cached accepted-manuscript main text/captions read; cached full text is not an independent fresh retrieval. Column abstract read; full-text publisher403 respected. Populus climate source acquired but only abstract/identity inspected, not used for graph claims. No original figure pixels, separate supplements or raw data audited.
• Twenty-five graph quotations match primary content and unchanged caches;22also independently match fresh primary extraction. Vitamin cache has PDF line-number/extraction artifacts. Literal matching does not prove entailment. Oversized graph/cache searches were truncated; whole records and cited main texts were separately read in bounded chunks, and no absence finding depends on truncated output.
• Vitamin complementation and serial persistence are real positive findings. Partial thiamine rescue and supplemented ratio-dynamics conditions are distinguished from all-vitamin omission; exact1:1 active regulation and transport mechanisms are unresolved. One mismatched reverse arrow removed, bacterial-rescue arrow preserved; reciprocal rescue-to-persistence topology remains1664.
• PET preserves positive inhibition perturbations, product utilization and film weight loss, with five existing biochemical/contribution arrows. Three-member31.2%is7days in Results despite3days in abstract. BHET nonaccumulation is not a PET-film carbon balance;37C optimized four-member growth is supported, not automatically a preculture-only condition. Four members are three species. EG-specific mediation and durable coexistence are not independently demonstrated.
• PGM separates uncrushed spent-refinery Ni/V/Mo/Al from synthetic Pd/alpha-alumina. Pd93.22%solid depletion differs from63.53%dissolved recovery. Concentration100C/filtration precedes60C chemical leaching; no combined column cascade, invented supporting taxa, Pt/Rh outcome, exact complex stoichiometry or benign industrial proof retained. PMID31059950 and DOIalias are one source.
• Variovorax preserves six individual hits, CF313 confirmation and live/killed/supernatant contrast. Three method-only nodes and remaining workflow arrow removed. Assay units are wells, not independently treated seedlings; no mixed six-strain consortium, colonization facilitation, isolated contact requirement or tested ACC/ethylene mediation asserted.
• One9032character Ostreococcus Edison LITERATURE dry run; zero provider submissions/credits. Scoped paid question unanswered. Prior denied/pending scopes unchanged. Research1664/1665 and metadata1666 stay OPEN after repair merge;1660-1663remain OPEN until protected-main merge.
• Dedup searched940all-state issue titles/bodies and72ignored/hidden-inclusive local matching files excluding git/docs/site/reference-cache. All10matched issue bodies plus605/529/573read. No exhaustive historical PR-comment audit. Canonical membership/raw non-graph blocks preserved, not certified. Self-review is not independent approval or corpus completion.
• Adversarial follow-up gives the six-hit panel explicit canonical participants and restricts both CF313 follow-ups to its exact preferred name despite shared NCBITaxon34072. No taxonomy, node/arrow or scope change. Affected checks rerun; prior outputs retained as superseded.
• Intentional241st participating_taxa user was missing from explicit registry; measured census unchanged. Only this record added to USERS; no guard or bounds weakened. The caught715pass/1failure result is retained; final validation must pass after the registry update.

Dependency

Draft depends on #1659. Do not merge into the topic parent. Require eligible exact-head CI and protected main queue after the parent merges. Move dependents before deleting parent branches.

[realmarcin]

Source-based self-adversarial review at exact head 7ec537d; not independent approval.

Repairs #1660-#1663 addressed; non-graph #1666 unresolved.

• Preserve positive bacterial rescue and its persistence contribution with partial thiamine-rescue limits.; Preserve reciprocal niacin/biotin/pABA complementation and distinguish supplemented ratio assays.; Preserve serial persistence while removing the mismatched reverse arrow and qualifying exact-ratio regulation.

• Preserve complementary extracellular hydrolysis and both product-supply arrows without Bacillus nutrient-uptake claims.; Replace misassigned film evidence with direct TPA consumption and correct Results timing.; Preserve EG utilization while separating BHET nonaccumulation, PET intermediates and partial mediation.; Preserve experimental medium/inoculum control without long-term coexistence claims.; Preserve23.2%seven-day optimized37C film loss and correct four-member versus three-species scope.

• Preserve observed column Al leaching without inferred PGM exposure and correct elemental label.; Preserve separate biogenic-thiosulfate Pd result with synthetic-support, phase and processing limits.; Preserve actual uncrushed-column Ni/Al/Mo/V outcomes without cross-study PGM or industrial claims.

• Preserve all six individual positive hits and assay units without a mixed-community or colonization claim.; Preserve quantified CF313 confirmation relative to heat shock and thermopriming; remove workflow arrow.; Preserve live/killed/supernatant contrast while explicitly qualifying physical contact and pathway inference.

• Pre-paper both-root baseline and whole-record reads preceded curation. Every17original node and10arrow has a retained/removed decision. Three protocol nodes removed,14biological-result nodes and6arrows retained; no new causal topology or provider spend.

• Vitamin complementation is experimentally demonstrated in both directions. Preserve cobalamin rescue, partial thiamine rescue and algal support of niacin/biotin/pABA needs. Do not downgrade physiological mutualism merely because transport and secretion flux were not measured.

• Vitamin ratio dynamics supplied thiamine/biotin, unlike the all-vitamin-omission experiment. Serial persistence and approximate1:1ratios survive; addback and convergence do not exclude competition for other nutrients or establish active regulation. Remove the fixed-carbon/persistence-to-vitamin arrow; the biologically motivated reciprocal rescue-to-persistence extension remains1664pending workflow.

• PET uses four strains in three species, with distinct canonical Bs_PETase and Bs_MHETase preferred names sharing1423. Extracellular enzyme division is not itself nutrient uptake by the MHETase producer. Both hydrolysis-product supply arrows remain.

• PET exogenous inhibition, standalone RHA1TPA consumption and consortium degradation are positive experiments. Replace31.2%film loss as a TPA-utilization quote with the28h standalone assay; use7days from Results rather than conflicting3day abstract. Preserve contribution to degradation with quantitative/mediator limits.

• KT2440EG utilization and EG inhibition are real, but BHET product nonaccumulation is not PET mass balance; PETTPA transiently increases. Different media/inocula and lower four-member film loss do not isolate EG-mediated improvement. No complete mineralization or zero-intermediate claim.

• Rich-medium P.putida dominance motivates Wn/inoculum control. Preserve23.2%seven-day optimized37C film loss and same-medium two-member comparison, not durable coexistence or unique resource-competition mediation.37C is actually supported for the community, not automatically preculture-only.

• PGM source identity matters: PMID31059950=DOI10.1016/j.jenvman.2019.04.081is one uncrushed refinery-column paper. Its Ni82.9%,Al33.4%,Mo22.7%at315h and V53.6%at105h are not Pd/Pt/Rh recovery or a two-step PGM exposure cascade. Abstract-only access is not proof that unseen experiments are absent.

• The complete thiosulfate paper prepares synthetic metallic Pd on alpha-alumina. Separate activated-sludge thiosulfate is concentrated100C/filtered before60C,pH8leaching.93.22%solid depletion differs from63.53%dissolved recovery with precipitation; no exact unique complex stoichiometry or benign industrial viability asserted. Preserve prior605 taxon removals and correct aluminium elemental label without inventing ionic state.

• Variovorax six hits are individually tested, not a co-inoculated consortium. Preserve CF31317%chlorophyll loss versus20.4%mock and9.3%thermopriming. Wells are experimental units; approximately10seedlings per well are pooled, not independent treatment replicates. Removed establishment/calibration/screen nodes preserve methods in surviving prose. Adversarial follow-up explicitly grounds the six-hit panel and limits both CF313 nodes to its exact canonical preferred name despite shared genus34072;17affected checks rerun with prior outputs retained.

• Live/killed/filtered-supernatant controls support a live-cell benefit, not a physically isolated contact requirement. The author contact inference remainsPARTIAL; ongoing/unstable/host-induced signals remain alternatives. ACC/ethylene is proposed, not tested. Prior workflow removals retained and final confirmation-to-contact workflow arrow removed.

• Three fresh main texts, thiosulfate tables/captions and cached vitamin main manuscript/captions read. Column abstract plus climate-source identity/abstract inspected; climate source is not used for graph support. No supplemental figures, raw data or original figure pixels audited. Truncated combined reads do not support negative conclusions; bounded source reads supply the science.

• Twenty-five literal graph quotations checked;22independent fresh-primary matches and3cached vitamin matches. All920caches,456other records and raw non-graph blocks unchanged. Four append-only histories. No canonical membership or auditor-rule change. Metadata1666remains open, coordinated with broader573/615.

• One9032character vitamin Edison dry run, zero provider submissions/credits; scoped question unanswered. Research1664/1665and metadata1666stay open after repair merge. Repair1660-1663stay open until protected-main merge. Self-adversarial COMMENT is not independent approval.

• Actual schema/strict/term/reference/snippet/history outputs, full related regressions, both-root network/inventory/rank and deterministic render checks are hash-bound. The first participant rerun found the explicit-users registry needed the intentional241st record; the unchanged measured census justified adding only this record, not weakening the guard or changing bounds. Eighteen superseded outputs include that715pass/1failure result. Exact description checks across456pages are not browser screenshots. Postcommit docs-current and exact remote head COMMENT are separate publication checks; do not delete parent branches before moving dependents.

716 passed in 223.25s (0:03:43); ten new focused tests. All four schema, strict, term, full-record reference, snippet and history gates passed. All four full-record reference validators exit0. CLI Total checks counts issues, not executed checks. Twenty-five graph quotations match primary content and unchanged caches;22also match fresh retrievals, while3vitamin quotations use the existing accepted-manuscript cache. Literal matching is not entailment or full provenance certification. No recertification of every cache/non-graph field.

All17 original nodes and10arrows reviewed;14nodes6arrows remain. Four records repaired; three protocol nodes and four unsupported arrows removed. Preserve reciprocal vitamin rescue, PET inhibition/consumption/degradation, separate metal extraction and individual Variovorax plant protection with actual assay boundaries. Reciprocal vitamin topology and authorized refinery-column full-text review remain #1664/#1665; metadata #1666 stays OPEN.

All456 other records,920 caches and raw non-graph blocks verified unchanged. Canonical taxa and auditor rules unchanged. Zero structural defects;44 baseline warnings and connectivity census unchanged. Repeat renders deterministic; exact descriptions parsed across456 pages, not browser screenshots.

Postcommit just check-docs-current passed with clean tree; log SHA256 c7f5305e5630a28bdb95403e8b6f6a275f210968a57e6411c3d48cf284113c6c. Every-node/every-arrow decisions,40 actual check outputs/digests and source-based self-adversarial review committed under reports/causal_graph_review, batch80. Final focused rerun:19 passed. Corpus:254 reviewed,172 pending,34 needs_research. One Ostreococcus Edison dry run; zero paid submissions/credits, scoped question unanswered. Not independent approval or corpus completion.

Protected-main merge pending.

[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, 44 warning across 16 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)

GLBRC_UFMP_Fermentation_Community
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'RUG023 sp. (MAG SPH2)' has no interactions

Total: 1 issues (0 error, 1 warning)

KBase_Models_for_Zahmeeth_Original_PLOS
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Klebsiella' has no interactions
  [warning] DISCONNECTED: Taxon 'Pseudomonas fluorescens' has no interactions

Total: 2 issues (0 error, 2 warning)

Lake_Washington_Methane_Oxygen_Methylotroph_Community
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Methylosarcina' has no interactions

Total: 1 issues (0 error, 1 warning)

Lotus_LjSC3
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Burkholderiaceae bacterium' has no interactions
  [warning] DISCONNECTED: Taxon 'Mesorhizobium sp. LjNodule210' has no interactions
  [warning] DISCONNECTED: Taxon 'Mesorhizobium sp. LjNodule215' has no interactions
  [warning] DISCONNECTED: Taxon 'Mesorhizobium sp. LjNodule218' has no interactions
  [warning] DISCONNECTED: Taxon 'Microbacteriaceae bacterium' has no interactions
  [warning] DISCONNECTED: Taxon 'Oxalobacteriaceae bacterium' has no interactions
  [warning] DISCONNECTED: Taxon 'Phyllobacteriaceae bacterium' has no interactions
  [warning] DISCONNECTED: Taxon 'Pseudomonadaceae bacterium' has no interactions
  [warning] DISCONNECTED: Taxon 'Rhizobiaceae bacterium' has no interactions

Total: 9 issues (0 error, 9 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 integration review at exact head eadf5954e338ea462ee514ae898c0bd2ca843caa. Not independent approval.

Integrated already-merged schema prerequisite #1692 (67603e192525899fae75420e2c19e8212b16afc9). Compared with the prior reviewed head 7ec537d56ef438e86391971c9237d7df47bd7486, 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 150c3db9f209525503a30c49974ea6dd51b098b8bc548c22be6b34bf702c8a32). 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 21c7feaa328faa397c7999193bc311a660e57248
after protected main merge of #1361. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 4a88bfdba1eb68ff3bb621df1ddbd852957b5f6b.
The batch-owned binary patch is byte-identical
(SHA-256 150c3db9f209525503a30c49974ea6dd51b098b8bc548c22be6b34bf702c8a32); 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 a24d395764c87444a22b8aab29a1fee770e92a1a. This is a COMMENT, not independent approval.

Integrated already-merged main PR #1730 (fe1752572a688051e8105e5b89d3099fe2202c63). Compared with prior reviewed head 21c7feaa328faa397c7999193bc311a660e57248, 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 150c3db9f209525503a30c49974ea6dd51b098b8bc548c22be6b34bf702c8a32). 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 bad7e3e642f2f4fddc6d221e2749493e3d045dc0.
COMMENT, not independent approval.

The batch-owned binary patch remains byte-identical:
SHA-256 150c3db9f209525503a30c49974ea6dd51b098b8bc548c22be6b34bf702c8a32.
Tree 43ae3adc804394da44495a6a5d3db4562a4ec9b3 matches the independently computed clean merge.
Compared with historical tree 6ba240d90dd01c75cbf99e8f9784a9fcf60a3a49, 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 ff03de75237a80f09cd900b1c3f878ba645ab57f 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.