Wire BioModels reproducibility paper into Kefir community#66
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PMID:41343683 (Smith et al. 2025 PLoS Comp Biol, "Verification and reproducible curation of the BioModels repository") is an orphan cache that audited and SED-ML-corrected the 1055 curated mechanistic models in BioModels, including MODEL2204300001 (the kefir community model). Wire as PARTIAL evidence on the BioModels-entry external_resource of BioModels_MODEL2204300001_Kefir_Community_Model to anchor reproducibility/verification of the underlying record. PARTIAL because the paper addresses the BioModels collection as a whole rather than the kefir entry specifically; the 1055-curated-models scope inherits this entry but the audit is not kefir-specific. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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Pull request overview
Adds partial evidence from the BioModels reproducibility/curation paper to the Kefir community BioModels external resource, tying the repository-wide SED-ML reproducibility work to this BioModels record.
Changes:
- Adds
PMID:41343683asPARTIALcomputational evidence for the BioModels entry. - Includes a publication quote and explanation describing repository-wide SED-ML updates and reproducibility relevance.
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- Snippet/explanation alignment: extend the snippet with a `..` splitter to also include the abstract's verification clause: "we used a wrapper architecture for interpreting SED-ML, and report verification results across five different ODE-based biosimulation engines". Now the snippet substantiates both the SED-ML curation and the cross-engine verification claims that the explanation makes about the kefir BioModels record's reproducibility. - Journal abbreviation fix: "PLoS Comp Biol" -> "PLoS Comput Biol" to match the PubMed cache entry's journal field. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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realmarcin
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May 18, 2026
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>
realmarcin
added a commit
that referenced
this pull request
May 18, 2026
* 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
`PMID:41343683` (Smith et al. 2025 PLoS Comp Biol, "Verification and reproducible curation of the BioModels repository") is an orphan cache that audited and SED-ML-corrected the 1055 curated mechanistic models in BioModels — including MODEL2204300001 (the kefir community model).
Wire as PARTIAL evidence on the BioModels-entry external_resource of `BioModels_MODEL2204300001_Kefir_Community_Model` to anchor the reproducibility/verification of the underlying BioModels record.
PARTIAL because the paper addresses the BioModels collection as a whole, not the kefir entry specifically; the 1055-curated-models scope includes this entry but the audit is not kefir-specific.
Test plan
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