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realmarcinclaude
realmarcin
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Regenerate community HTML and UMAP (#71)
* Regenerate community HTML and UMAP Refresh docs/ to reflect community additions and evidence updates since the last regen (PR #54). UMAP grows from 252 -> 261 embedded communities; 7 existing community pages are refreshed with the evidence additions from PRs #55, #58, #60, #61, #62, #63, #66, #67; 9 new community pages are added (2 from this session: Alaska Tundra Permafrost Iron-Redox and Saccharomyces-Acinetobacter Lignocellulose Detox; 7 from other curation work merged in between). - gen-html: 264 community pages rendered without error - gen-umap: 261 communities embedded (3 host-only skipped because none of their taxa have NCBITaxon embeddings) Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * Address Copilot review on PR #71: render evidence everywhere it lives Three template/data fixes triggered by the Copilot review on the HTML/UMAP regen: - src/communitymech/templates/community.html: - Extend the interaction-network color map and legend with PREDATION, NICHE_PARTITIONING, STRAIN_COMPETITION, and COLONIZATION_FACILITATION. Previously these enum values fell back to generic gray on the force-directed graph and were omitted from the legend, making 5+ community pages (Cellulomonas-Rhodobacter, Sphingobium-Rhodococcus, Clostridium-Carboxidivorans-Kluyveri, Rhodopseudomonas- Geobacter-Magnetite, plus any others) hard to read. - Render evidence on taxonomy entries via an "evidence-row" span. The previous template only rendered evidence inside ecological_interactions and growth_media, so evidence wired onto taxon blocks in PRs like #61 and #62 was on-disk in the YAML but invisible in the rendered HTML. - Render evidence on environmental_factors with the same expanding-row pattern. This is where PR #62 wired the Ter Horst 2021 peat-virome evidence on the SPRUCE community; it now appears in the HTML. - Add an "External Resources" section (analogous to Associated Datasets) that renders external_resources entries including their per-resource evidence. This is where PR #66 wired the Smith 2025 BioModels reproducibility paper on the Kefir BioModels community; it now appears in the HTML. - kb/communities/Alaska_Tundra_Permafrost_Iron_Redox_Community.yaml: add `metals_present: [IRON]`, `metal_relevance: SIGNIFICANT`, and metal_notes describing the Fe(III) reduction / Fe(II) oxidation cycle this community is built around. The community was previously absent from the iron/metal index filter despite being entirely iron-centric. - docs/: regenerate all 264 community pages with the new template + the Alaska_Tundra metals metadata. Many pages pick up the new evidence-row block; the four pages with NICHE_PARTITIONING interactions now render those nodes with the dedicated color and include the new legend entries. Verified after regen: - SPRUCE community page now shows PMID:38515239 and PMID:34836550 (zero matches before, two each after). - Kefir BioModels community page now shows PMID:41343683 (zero matches before, two after). Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> --------- Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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‎docs/communities/AMD_Acidophile_Heterotroph_Network.html‎

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‎docs/communities/AMD_Nitrososphaerota_Archaeal.html‎

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‎docs/communities/ANME_SRB_Marine_Methane_Seep_Consortium.html‎

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@@ -432,6 +432,37 @@ <h2>Taxonomy</h2>
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<td>N/A</td>
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</tr>
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<tr class="evidence-row-container">
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<td colspan="4">
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<ul class="evidence-list">
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<li class="evidence-item">
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<a href="https://pubmed.ncbi.nlm.nih.gov/37747940/"
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class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:37747940</a>
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- SUPPORT (COMPUTATIONAL)
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<div class="snippet">"anaerobic methanotrophic archaea (ANME) in obligate syntrophic partnership"</div>
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</li>
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<li class="evidence-item">
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<a href="https://pubmed.ncbi.nlm.nih.gov/34986141/"
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class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:34986141</a>
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- SUPPORT (COMPUTATIONAL)
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<div class="snippet">"none of which have been isolated in pure culture"</div>
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</li>
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</ul>
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</td>
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</tr>
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<tr>
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<td>
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<strong>sulfate-reducing bacterial partners</strong>
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<td>N/A</td>
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</tr>
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<tr class="evidence-row-container">
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<td colspan="4">
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<ul class="evidence-list">
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<li class="evidence-item">
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<a href="https://pubmed.ncbi.nlm.nih.gov/19383036/"
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class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:19383036</a>
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- SUPPORT (IN_VITRO)
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<div class="snippet">"sulfate-reducing bacteria (DSS), frequently found as organized consortia"</div>
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</li>
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<li class="evidence-item">
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<a href="https://pubmed.ncbi.nlm.nih.gov/11034209/"
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class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:11034209</a>
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- SUPPORT (IN_VITRO)
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<div class="snippet">"a bacterium related to sulphate-reducing bacteria"</div>
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</li>
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</ul>
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</td>
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</tr>
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</tbody>
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</section>
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<div class="legend-item">
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<span class="legend-swatch" style="background: #f97316;"></span> Commensalism
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</div>
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<div class="legend-item">
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<span class="legend-swatch" style="background: #14b8a6;"></span> Niche partitioning
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</div>
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<div class="legend-item">
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<span class="legend-swatch" style="background: #eab308;"></span> Colonization facilitation
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</div>
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<div class="legend-item">
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<span class="legend-swatch" style="background: #fb7185;"></span> Strain competition
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</div>
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<div class="legend-item">
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<span class="legend-swatch" style="background: #dc2626;"></span> Predation
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</div>
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</div>
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</div>
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<!-- Environmental Factors -->
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<section>
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<h2>Environmental Factors</h2>
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<table>
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<td>N/A</td>
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<tr class="evidence-row-container">
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<td colspan="3">
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<ul class="evidence-list">
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<li class="evidence-item">
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<a href="https://pubmed.ncbi.nlm.nih.gov/11034209/"
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class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:11034209</a>
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- SUPPORT (IN_VITRO)
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<div class="snippet">"abundant in gas-hydrate-rich sediments"</div>
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</li>
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<td><strong>Sulfate availability</strong></td>
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<td>Sulfate as terminal electron acceptor</td>
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<td>N/A</td>
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<tr class="evidence-row-container">
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<ul class="evidence-list">
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<a href="https://pubmed.ncbi.nlm.nih.gov/34986141/"
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class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:34986141</a>
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- SUPPORT (COMPUTATIONAL)
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<div class="snippet">"anaerobic oxidation of methane coupled to sulfate reduction"</div>
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MUTUALISM: "#3b82f6",
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SYNTROPHY: "#a855f7",
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COMPETITION: "#ef4444",
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COMMENSALISM: "#f97316"
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COMMENSALISM: "#f97316",
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PREDATION: "#dc2626",
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NICHE_PARTITIONING: "#14b8a6",
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STRAIN_COMPETITION: "#fb7185",
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COLONIZATION_FACILITATION: "#eab308"
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};
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// Build taxon lookup keyed by preferred_term

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