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Emiliania metadata: qualify IAA effector language and revisit source-backed cultivation limits #1456

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@realmarcin

Emiliania_Phaeobacter_Dynamic_Interaction.yaml, PMID:27855786.

related_ingredients calls IAA the established effector driving promotion and killing, although coculture IAA was not detected and mutants were not IAA-null. Review taxonomy SYNTROPHIC_PARTNER and broader endogenous-tryptophan claims against those limitations. Cultivation notes omit working_volume because the source allegedly does not give the vessel; the cached Methods now explicitly describe 10 mL cocultures. Volume and vessel knowledge must be assessed separately. Preserve the established nonpermissive L1-Si and four-day assembly context and the prior #529/#583 guidance. Keep the original YAML anchor/alias shared between engineering_design and growth_media. These fields remain outside graph-only repairs.

Review scope: whole records and cached primary main bodies, tables and captions read. No figure images, separate supplements or raw data reviewed. Selected Emiliania published peer-review discussion was also read, not the entire exchange. Deduplication searched 772 all-state issue titles/bodies and ignored/hidden-inclusive local content; #583/#529 and #1091/#1094 bodies reviewed. No exact duplicate within that scope; not every issue comment or PR reviewed. This is source-based self-adversarial review, not independent approval.

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  1. realmarcin commented on Oct 6, 2026

    @realmarcin
    ContributorAuthor

    Graph-only repairs published in #1458. This separate follow-up remains OPEN; non-graph raw blocks preserved, not certified. No culture-protocol, cache, top-level wording or taxonomy-role repair is claimed.

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