Growth conditions for 10 records + dark-mode contrast fix + page regen#203
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…pages Deep-research growth-conditions sweep over the 45 records lacking any growth_media/cultivation_setup (via the add-growth-conditions skill + the new sweep runner). One agent per record extracted only source-backed conditions with verbatim evidence snippets; 35 records were correctly left unchanged (uncultured/metagenomic/computational/paywalled — no fabrication). Enriched (10): - ANME_SRB_Marine_Methane_Seep_Consortium (OA full text: anaerobic seawater microcosm, CH4 ± HPG, 4/24/50 C) - Chromium_Sulfur_Reduction_Enrichment (aerobic, pH 8, 30-37 C; dominant strain) - Phylogenetically_Diverse_Denitrifying_SynCom (marine broth 2216 + 20 mM NaNO3, anaerobic, 25 C; OA companion study, attributed) - BioModels_MODEL2209060002_DPigrum_SAureus (in silico SNM3 medium, COMPUTATIONAL) - Aerobic_Denitrification_Disturbance_SynCom, Aerobic_Denitrification_QQ_SynCom, Shewanella_Pseudomonas_Fe0_*, BSFL_Gut_SynCom, SynCom_BsBv_Cigar_*, Thermophilic_Lignocellulose_Composting_* (abstract-level conditions) Dark-mode contrast fix (community.html): preparation_notes, .interaction-flow, .evidence-item, and inline code hardcoded light backgrounds with no text color, rendering invisible (light-on-light) in dark mode — switched to theme variables. Regenerated all 295 community pages (+ browser/index): bakes in the dark-mode fix and syncs page content with already-merged #185 (GTDB), #187 (GO-term cleanup) and #189 (growth media) data that predated the last render. reports/growth_conditions_sweep/INDEX.md: sweep prep/progress report (24 OA full text, 21 abstract-only). Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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Growth-conditions deep-research sweep
Ran the
add-growth-conditionsskill (with the newgrowth_conditions_sweep.pyrunner from #202) over the 45 records lacking anygrowth_media/cultivation_setup. One subagent per record extracted only source-backed conditions with verbatim evidence snippets; 35 records were correctly left unchanged — uncultured/metagenomic field communities, in-silico metabolic models, or paywalled-with-no-Methods — with zero fabrication.10 records enriched:
All 10 pass
linkml-validate+ the id↔label term gate. Agents avoided CHEBI grounding on composition entries to stay clear of the id↔label gate. Records left unchanged retain an author-request draft in the prep bundle for a later institutional-access pass.Dark-mode contrast fix (
community.html)preparation_notes,.interaction-flow,.evidence-item, and the inline idcodehardcoded light backgrounds with no text color → invisible (light-on-light) in dark mode (reported on the Kombucha KMC-IMBG1 growth-media section). Switched to theme variables so they flip correctly.Page regeneration
Regenerated all 295 community pages (+ browser/index). This bakes in the dark-mode fix and syncs page content with already-merged #185 (GTDB), #187 (GO-term cleanup), and #189 (growth media) data that predated the last render — hence the broad docs diff.
Sweep prep/progress report:
reports/growth_conditions_sweep/INDEX.md(24 OA full text, 21 abstract-only).🤖 Generated with Claude Code