Pelotomaculum-Methanocella propionate syntrophy: curate causal graph#243
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Add directed `downstream` causal edges to the four existing ecological_interactions of CommunityMech:000190, from the Edison causal-graph run (PaperQA3; PMID:30038609 / DOI:10.3389/fmicb.2018.01551). Wiring (all grounded in the cited abstract; InteractionDownstream carries target + causal description, evidence stays on the parent nodes): - Propionate Oxidation Coupled to Methanogenesis → Catabolism and Methanogenesis Upregulation (syntrophic coculture drives the concerted catabolic/methanogenesis transcriptional shift). - Catabolism and Methanogenesis Upregulation → Formate and Electron Bifurcation Strategy, and → Signal Transduction and Amino Acid Exchange (the upregulation activates FDH/electron-bifurcation transfer and the flagellar-signaling / amino-acid-exchange mechanisms). - Formate and Electron Bifurcation Strategy → Propionate Oxidation Coupled to Methanogenesis, twice: a positive edge (formate/H2 transfer sustains methanogenesis, thermodynamically pulling propionate oxidation; 2-BES abolishes both) and a NEGATIVE product-inhibition edge (excess formate halts syntrophic activity). Forms the syntrophic feedback loop 1->2->3->1 with a negative regulatory edge. Regenerate the record's HTML page (single file). Schema validates; no new evidence snippets or terms introduced. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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Pull request overview
This PR curates Edison causal-graph output into CommunityMech:000190 by adding directed downstream causal edges to existing ecological_interactions in the Pelotomaculum–Methanocella propionate syntrophy record, and regenerates the corresponding HTML page so the downstream wiring is reflected in rendered docs.
Changes:
- Add
downstreamentries (target + causal description) to 3 existingecological_interactionsinCommunityMech:000190. - Regenerate the community’s HTML page to display downstream effects.
Reviewed changes
Copilot reviewed 2 out of 2 changed files in this pull request and generated 1 comment.
| File | Description |
|---|---|
| kb/communities/Pelotomaculum_Methanocella_Propionate_RNASeq_Coculture.yaml | Adds curated causal downstream edges (with descriptions) to existing interaction nodes. |
| docs/communities/Pelotomaculum_Methanocella_Propionate_RNASeq_Coculture.html | Regenerated output to show “Downstream Effects” sections for the updated interactions. |
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| <div class="interaction-flow"> | ||
| <strong>Downstream Effects:</strong> | ||
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| <span class="flow-arrow">→</span> Propionate Oxidation Coupled to Methanogenesis | ||
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| <span class="flow-arrow">→</span> Propionate Oxidation Coupled to Methanogenesis | ||
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| </div> |
realmarcin
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Jul 22, 2026
… resolved (#244) Add CommunityMech:000190 to the causal-graph "done" list (~59/304), and replace the Edison-auth blocker note with the resolution: the .env key was refreshed and authenticates, but the shell profile's stale EDISON_PLATFORM_API_KEY still shadows/403s it, so run causal jobs with `env -u EDISON_PLATFORM_API_KEY` until that export is fixed. Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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What
Adds directed
downstreamcausal edges to the four existingecological_interactionsof CommunityMech:000190 (Pelotomaculum_Methanocella_Propionate_RNASeq_Coculture), from an Edison causal-graph run (PaperQA3 causal-edge mode; single source PMID:30038609 / DOI:10.3389/fmicb.2018.01551).InteractionDownstreamcarriestarget+ a causaldescriptiononly (no evidence field) — the supporting evidence stays on the parent interaction nodes, whose existing snippets already validate against the cached abstract. No new evidence snippets or terms were introduced.Causal wiring (syntrophic feedback loop 1→2→3→1 + negative edge)
All taxa use the record's canonical NCBITaxon ids (110500 / 1175444).
Verification
just validate→ No issues found.Continues the causal-graph curation thread (after #226/#229/#230). Provenance bundle under
research/communities/…-causal.*(gitignored).🤖 Generated with Claude Code