Cite Marinobacter HP15 genome paper for diatom-aggregation evidence#55
Merged
Conversation
The HP15 type-strain genome paper (doi:10.4056/sigs.922139, Gärdes et al. 2010, Stand Genomic Sci) directly describes HP15's specific attachment to diatom cells and in vitro aggregation of algal cells into marine snow particles. This is a perfect fit for the Bacteria-Dependent Diatom Aggregation interaction in the existing Thalassiosira-Marinobacter coculture community: it complements the two PMID:20827289 evidence items with an orthogonal source that characterizes HP15 itself rather than the aggregation assay. The cached abstract for this paper was previously an orphan references_cache file (committed alongside the literature-fetcher PMC fallback infrastructure but not referenced by any community). This wires it up to actual curated evidence. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
There was a problem hiding this comment.
Pull request overview
This PR adds the Marinobacter adhaerens HP15 type-strain genome paper as supporting evidence for the bacteria-dependent diatom aggregation interaction in the Thalassiosira–Marinobacter coculture knowledge base.
Changes:
- Adds DOI evidence for HP15 attachment to diatom cells.
- Adds a verbatim evidence snippet describing exopolymer formation and algal aggregation into marine snow particles.
- Explains how the genome paper supports the curated aggregation phenotype.
💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.
2 tasks
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>
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Summary
Wire the orphan `references_cache/DOI_10.4056_sigs.922139.md` cache into the curated knowledge base by citing the HP15 type-strain genome paper (Gärdes et al. 2010, Stand Genomic Sci) on the Bacteria-Dependent Diatom Aggregation interaction in the Thalassiosira-Marinobacter coculture community.
The HP15 genome paper directly describes:
These are the same phenotypes anchoring the COLONIZATION_FACILITATION interaction in the community, so adding this reference gives the assertion an orthogonal source (the strain's characterization itself) on top of the two PMID:20827289 assay-based items already present.
Test plan
🤖 Generated with Claude Code