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Bound endpoint and mechanism claims in four community graphs (batch105) - #1828
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Source-based self-adversarial review at exact head 20d6692; not independent approval.
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Retain reduced B. subtilis colony recovery and its canonical participant; remove categorical competition and distinguish cultivability from definitive viability loss.
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Retain positive lettuce-pot PHE outcomes with IN_VIVO provenance and no inferred exchange.; Retain carbon-content measurements and qualify modeled drivers; remove carbon-dioxide/fixation annotations not established by stock endpoints.
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Retain designed pairwise cleavage/conversion coupling and its existing direction as HYPOTHESIZED/PARTIAL; remove the background-study quotation and categorical cross-feeding.; Preserve muconate conversion separately from gallate potential across source systems; correct the graph gallate identity using the existing local descriptor.; Retain reported dimer substrate coverage; remove niche-partitioning classification and the product restatement arrow.
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Retain tested broth-density comparison without universal stability or reciprocal-benefit claims.; Preserve positive maize-pot endpoints and the water-control dry-matter comparator without inferred mediator arrows.; Restrict the transcript observation to canonical Ensifer S2-8-1 and distinguish it from protein activity, flux or causal mediation.
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Whole original targets and all changed graph/discussion diffs reviewed. All9 original nodes and2 directions have dispositions: retain9nodes and1 qualified existing direction, remove1 substrate-range restatement arrow, rename3nodes. No new topology or provider spend.
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Challenge removal versus lost evidence: retain positive colony-recovery, phenanthrene removal, soil carbon-content, lignin-conversion, broth-density, maize-pot and transcript observations. Removing categorical mechanism labels does not reject the source results.
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Space habitat: reduced B. subtilis CFU is cultivability, not definitive viability loss or reciprocal negative effects. The canonical B. subtilis participant remains. Genomic potential is not confirmed metabolite activity. Prior accession repair771 preserved; no new survival, stress-tolerance, biofilm, resistance, virulence, culture or disinfection optimization details.
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Phenanthrene: soil carbon stocks and modeled guild associations are not measured fixation flux or traced carbon transfer. Keep positive lettuce-pot endpoints with IN_VIVO evidence and partial statistical interpretation. Existing random-forest/PLS-PM methods are preserved without invented software versions. Prior847/848 changes remain; those open issues are not duplicated.
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Lignin: the source describes coculture systems plural, not demonstrated simultaneous products in one formulation. Preserve observed muconate conversion separately from gallate potential and reuse the existing local CHEBI16918 descriptor. Whole primary abstract confirms all six linkage classes; the three retained class snippets are representative examples, not exhaustive quotations. Remove the background-study quotation and ecological niche label; keep the existing cleavage-to-conversion direction only as HYPOTHESIZED/PARTIAL.
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Manure: preserve distinct broth-density and water-control plant comparators; keep observed transcript upregulation rather than direct activity, flux or pathway mediation. Narrow the transcript node to canonical identity-only Ensifer S2-8-1. No inferred transcript-to-broth or transcript-to-host edges. Earlier cross-feeder removals and IN_VIVO pot classification preserved.
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Seventeen graph and five discussion quotations match fresh primary text and unchanged caches. Space-habitat main-text coverage is bounded; three other sources are abstract-only. Wiley redirected to an abstract/access page; OUP and the phenanthrene DOI requests returned Internal Error, not a verified HTTP403. No global full-text absence claim, bypass, cache import, supplement/figure-pixel or raw-data certification.
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Four guarded writes and four append-only histories;456 other records/all923 caches and prior history/decision files byte-identical. Non-graph raw blocks unchanged. Ensifer-only transcript scope does not change the global community-level census because other whole-consortium observations remain. No census threshold, schema or runtime-rule changes.
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Eight focused tests and951 combined regressions pass. Four full-record schema/strict/term/reference/snippet checks and four histories validate. Network equals56 baseline warnings with zero structural defects. Deterministic rendering and exact HTML parser cover456pages/1373descriptions/550arrows, not screenshots. Plain just-lint passed; explicit-runtime no-incremental mypy additionally checked.
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Repairs1823-1826 addressed but remain open until protected-main merge; non-graph1827 remains open. Existing license949, loader1703, DOIcache1091, denied and unansweredEdison scopes are not resolved. Self-review is not independent approval; no artificial CI, protection bypass or premature cleanup.
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Corpus334reviewed/76pending/50needs_research is not completion. Postcommit docs-current and exact-head publication require separate receipts, not preasserted here.
951 passed in 379.05s (0:06:19); eight new focused tests. Four full-record schema, strict, ontology-term, reference and snippet checks passed; four append-only histories validated. 42 recorded gate outputs/digests. Plain just-lint passed; explicit-runtime no-incremental mypy additionally checked. Explicit-runtime non-incremental mypy passed. All22 reviewed graph/discussion quotations match fresh primary text and existing caches; literal matching is not entailment.
All nine nodes remain, with three renames; one qualified existing direction remains and one substrate-range restatement arrow is removed. All four targets changed; 456 other records, all923 caches, taxonomy and non-graph raw blocks preserved. Corpus334reviewed/76pending/50needs_research. Network56existingwarnings/zero structural defects. The manure transcript node gains Ensifer-only participant scope; the community-level census and its thresholds are unchanged.
Decisions, provenance, validation and self-adversarial review are committed under reports/causal_graph_review, with four append-only history records. Postcommit docs-current passed clean, SHA256 0a3ea00a167624b12bb938210219798eafa40251452b68d680b72de6c666ad71. Deterministic rendering and HTML parser checks are not screenshots. Four full-record CLI and local snippet checks executed on macOS,not Linux; DOI-cache casing issue1091 remains. Literal matches do not establish entailment; per-source read and access limits are recorded. CLI Total checks counts issues,not executed checks. Loader1703 not certified.
Phenanthrene/lignin/manure independent evidence is abstract-bounded. Space-habitat primary body coverage is bounded, not full methods/supplement/figure/raw-data certification. No new topology or Edison spend. Non-graph1827 stays open. This COMMENT is self-review, not independent approval. Protected-main merge remains required.
Network integrity findingsWarnings 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. The full report is attached to the workflow run as an artifact. |
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Exact-head self-adversarial restack review at 97f1617c4b3de4b09f9a48c0ff9fd39e68327f80.
COMMENT, not independent approval.
The batch-owned binary patch remains byte-identical:
SHA-256 468474a9a60edb449d84c6e242bc6a547d4278328dff1a61f49a3c07c52432fa.
Tree 960e80c9b61887db8027bc7738a738b19b6842f2 matches the independently computed clean merge.
Compared with historical tree eea2b5739e61f7587840dfa918f79ec5474bdb23, 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.
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Superseded by the protected cumulative merge #1975 at 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. |
1 participant
Scope
Closes #1823.
Closes #1824.
Closes #1825.
Closes #1826.
Non-graph #1827 remains open.
Adversarial Review
Verification And Output Records
951 passed in 379.05s (0:06:19); eight new focused tests. Four full-record schema, strict, ontology-term, reference and snippet checks passed; four append-only histories validated. 42 recorded gate outputs/digests. Plain just-lint passed; explicit-runtime no-incremental mypy additionally checked. Explicit-runtime non-incremental mypy passed. All22 reviewed graph/discussion quotations match fresh primary text and existing caches; literal matching is not entailment.
All nine nodes remain, with three renames; one qualified existing direction remains and one substrate-range restatement arrow is removed. All four targets changed; 456 other records, all923 caches, taxonomy and non-graph raw blocks preserved. Corpus334reviewed/76pending/50needs_research. Network56existingwarnings/zero structural defects. The manure transcript node gains Ensifer-only participant scope; the community-level census and its thresholds are unchanged.
Decisions, provenance, validation and self-adversarial review are committed under reports/causal_graph_review, with four append-only history records. Postcommit docs-current passed clean, SHA256 0a3ea00a167624b12bb938210219798eafa40251452b68d680b72de6c666ad71. Deterministic rendering and HTML parser checks are not screenshots. Four full-record CLI and local snippet checks executed on macOS,not Linux; DOI-cache casing issue1091 remains. Literal matches do not establish entailment; per-source read and access limits are recorded. CLI Total checks counts issues,not executed checks. Loader1703 not certified.
Phenanthrene/lignin/manure independent evidence is abstract-bounded. Space-habitat primary body coverage is bounded, not full methods/supplement/figure/raw-data certification. No new topology or Edison spend. Non-graph1827 stays open. This COMMENT is self-review, not independent approval. Protected-main merge remains required.
Source Limits
Dependency
Draft depends on #1822. Do not merge into the topic parent. Require exact-head checks and independent approval through protected main. Move dependents before deleting parent branches.