Wire HP15-diatom SEM cache into community + delete wrong-DOI cache#60
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Orphan curation pass: - references_cache/DOI_10.3354_meps09894.md: refresh via the new publisher-meta scraper (Inter-Research exposes the SEM figure caption in their description meta tag even though Crossref has no abstract). Wire as a PARTIAL evidence item on the Transparent-Exopolymer-Particle-Enhancement interaction in Thalassiosira_Marinobacter_Marine_Snow_Coculture: gives the interaction a direct visual citation of HP15 attaching to T. weissflogii inside a chitin-containing fibre network, on top of the two PMID-based assay citations already there. - Delete references_cache/DOI_10.1016_j.cej.2020.125159.md and its two CrossRef sidecars. The DOI was a typo - it points to an unrelated OLED chemistry paper. The real reference for the Chromium_Sulfur Cr(VI)/sulfur work is 10.1016/j.cej.2020.124801, which is already cached and cited. Keeping the wrong-paper cache around invites future mistakes. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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Pull request overview
Small reference-cache curation pass: refreshes the meps09894 cache with publisher-meta SEM caption content and wires it as a PARTIAL evidence item on the Transparent-Exopolymer-Particle-Enhancement interaction; deletes the cej.2020.125159 cache files (wrong-DOI typo pointing to an unrelated OLED paper).
Changes:
- Update
DOI_10.3354_meps09894.mdcontent_type toabstract_onlyand add SEM figure-caption excerpt; add matchingopenalex_*.txtsidecar. - Add a new PARTIAL evidence entry on the TEP interaction in
Thalassiosira_Marinobacter_Marine_Snow_Coculture.yamlciting meps09894. - Remove the wrong-paper cache files for DOI
10.1016/j.cej.2020.125159.
Reviewed changes
Copilot reviewed 6 out of 6 changed files in this pull request and generated no comments.
Show a summary per file
| File | Description |
|---|---|
| references_cache/DOI_10.3354_meps09894.md | Promote to abstract_only and add SEM figure-caption content. |
| references_cache/openalex_10.3354_meps09894.txt | New sidecar with the meta-scrape excerpt used as the verbatim snippet. |
| kb/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml | Add PARTIAL meps09894 evidence to TEP-Enhancement interaction. |
| references_cache/DOI_10.1016_j.cej.2020.125159.md | Delete wrong-paper cache (OLED paper, typoed DOI). |
| references_cache/doi_10.1016_j.cej.2020.125159.json | Delete wrong-paper CrossRef sidecar. |
| references_cache/doi_DOI:10.1016_j.cej.2020.125159.json | Delete duplicate wrong-paper CrossRef sidecar. |
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* 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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Summary
Small orphan-curation pass:
Test plan
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