Curate causal graphs for 4 syntrophy/DIET cocultures (000183/188/189/297)

[realmarcin]

Edison causal-graph runs (PaperQA3 causal-edge mode) for four syntrophy/DIET cocultures that lacked downstream edges. Curated conservatively, honoring each run's disposition. InteractionDownstream carries target + causal description only; evidence stays on parent nodes — no new snippets or terms. Pages regenerated.

Record	Source	Result
000183 Dehalococcoides–Syntrophomonas TCE dechlorination	PMID:25576615	2 edges → dechlorination: H₂ from syntrophic butyrate oxidation (demonstrated — nM H₂ + strain-195 threshold) + aggregation-shortened distance (lower-confidence)
000188 Trichococcus–Syntrophomonas–Methanospirillum butyrate	PMID:35699440	2 HYPOTHESIZED mediator edges → ES5-stimulation node (aggregation + proteome are correlates, not proven mediators) + KNOWLEDGE_GAP on ES5 bridging/DIET
000189 Syntrophomonas–Methanococcus butyrate	PMID:34603271	1 edge — syntrophic coupling → population-ratio convergence + KNOWLEDGE_GAP (aggregation→enhancement untested; DIET not established for CNT effect)
000297 DIETsimp lignocellulose→methane	PMID:42229598	No edge justified — two parallel proposed/unverified DIET pathways, no causal dependency; recorded as KNOWLEDGE_GAP

5 downstream edges + 3 knowledge-gap discussions across 4 records; ~65/304 records now carry causal edges. Excluded/unverified elements (DIET-for-CNT, aggregation→enhancement, neutral-red import) left out per each run's caution.

Continues the causal thread (#226/#229/#230/#243/#246/#249). Provenance bundles under research/communities/…-causal.* (gitignored). The six already-wired matches (000031–033 DIET, 000068–070 syntrophies) were left as-is.

🤖 Generated with Claude Code

[Copilot]

Pull request overview

Curates Edison causal-graph outputs into four existing CommunityMech community records by adding directed downstream causal edges where justified and filing unresolved/unsupported mechanisms as KNOWLEDGE_GAP discussions. This strengthens the causal-graph layer of the curated YAML knowledge base while keeping evidence anchored to the appropriate parent objects and regenerating the corresponding rendered HTML pages.

Changes:

• Added downstream causal edges to specific ecological_interactions in three coculture records (000183/188/189) where the source supports a directed dependency.
• Added KNOWLEDGE_GAP discussions entries to capture unresolved mediation/DIET questions (and explicitly documented “no causal edge justified” for DIETsimp).
• Regenerated the affected docs/communities/*.html pages to render downstream effects and discussions.

Reviewed changes

Copilot reviewed 8 out of 8 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
kb/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml	Adds two hypothesized downstream edges to the ES5-stimulation interaction and a knowledge-gap discussion capturing unresolved mediation mechanism.
kb/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml	Adds a downstream edge linking syntrophic coupling to population-ratio convergence and a knowledge-gap discussion for aggregation/DIET uncertainty.
kb/communities/DIETsimp_Lignocellulose_to_Methane_DIET_Consortia.yaml	Adds a knowledge-gap discussion documenting why no directed causal edge was justified from the available evidence.
kb/communities/Dehalococcoides_Syntrophomonas_TCE_Dechlorination_Coculture.yaml	Adds two downstream edges linking syntrophic butyrate oxidation/aggregation to reductive dechlorination.
docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html	Regenerated HTML to render downstream effects and the new discussions section.
docs/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.html	Regenerated HTML to render the new downstream effects and discussions section.
docs/communities/DIETsimp_Lignocellulose_to_Methane_DIET_Consortia.html	Regenerated HTML to render the new discussions section.
docs/communities/Dehalococcoides_Syntrophomonas_TCE_Dechlorination_Coculture.html	Regenerated HTML to render downstream effects on the relevant interactions.

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