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Lung model metadata: update abstract-era strain and model-limit annotations from full text #1463

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@realmarcin

CommunityMech:000432, FourSpecies_Aerobic_Lung_Microbiome_Model.yaml; PMID:42545019.

Taxonomy notes currently justify species-only curation using abstract-only access. The public primary full text now names DSMZ16610, DSMZ14556, DSMZ4630 and DSMZ5635 for the four canonical species. Review these strain annotations without guessing GTDB mappings or altering species IDs. The nutrient-rich BHI model and pH 9-10 endpoint are not physiological healthy-airway conditions; ten-day persistence is not universal stability or pharmacological efficacy. CFU, DNA-qPCR, vPCR and protein fractions are not interchangeable abundance or viability measures. Supplementary files and images were not inspected.

Acceptance: separately refresh strain/source-access notes and qualify the model's scope and endpoints. Preserve #1080 DOI evidence; challenge-community additions do not expand the original four-member roster. These non-graph fields remain unchanged by graph review.

Deduplication: 778 all-state issue titles/bodies plus ignored/hidden-inclusive local reports, research, history and tests searched. All seven matched issue bodies read (#1358/#1356/#1173/#1171/#1170/#1169/#1080); relevant prior curation histories inspected. No exact duplicate within that scope; comments and PR reviews were not exhaustively searched. Source-based self-adversarial review, not independent approval.

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  1. realmarcin commented on Oct 6, 2026

    @realmarcin
    ContributorAuthor

    Graph-only review published in #1464. This non-graph followup remains OPEN; original raw metadata blocks were preserved, not certified. No strain, medium, taxonomy-role or top-level wording repair is claimed.

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