ORNL Clostridium-Desulfovibrio-Geobacter trophic model: curate causal graph#249
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… graph Add directed `downstream` causal edges to CommunityMech:000176 from the Edison causal-graph run (PaperQA3; doi:10.1186/1471-2180-10-149, Miller et al. 2010). The run was deliberately conservative — the primary full text was not retrievable, so only two abstract-level/directly-implied edges are justified (no perturbation evidence): - Cellobiose Fermentation Supports Partner Growth -> Sulfate-Linked Dependence of D. vulgaris (C. cellulolyticum products are the electron donor D. vulgaris consumes while reducing supplied sulfate). - Cellobiose Fermentation Supports Partner Growth -> Fumarate-Linked Dependence of G. sulfurreducens (same products; G. sulfurreducens reduces supplied fumarate). The modeled "Electron Donor and Acceptor Limitation" node is left isolated per the conservative disposition. Add a KNOWLEDGE_GAP discussion recording that the exact exchanged products and any perturbation evidence remain unresolved pending the primary full text, and that products from a related two-species fuel-cell system must not be imported without exact-system verification. InteractionDownstream carries target + causal description only; evidence stays on the parent nodes / the discussion reuses an in-record snippet. Schema validates; no new terms. Record HTML page regenerated. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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Pull request overview
This PR curates two conservative, abstract-implied causal downstream edges for CommunityMech:000176 (ORNL Clostridium–Desulfovibrio–Geobacter trophic model) and records an explicit KNOWLEDGE_GAP discussion about the unknown exchanged fermentation products and the lack of perturbation-level evidence, then regenerates the rendered community HTML page to reflect these additions.
Changes:
- Add two directed
downstreamcausal edges from Cellobiose Fermentation Supports Partner Growth to the sulfate- and fumarate-linked partner-growth interactions. - Add an
OPENKNOWLEDGE_GAPdiscussion attached to the two partner interactions, capturing the metabolite/perturbation uncertainty with supporting evidence. - Regenerate the corresponding
docs/communities/...htmlpage so the downstream wiring and discussion render.
Reviewed changes
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| File | Description |
|---|---|
| kb/communities/ORNL_Clostridium_Desulfovibrio_Geobacter_Trophic_Model.yaml | Adds two downstream causal links and a KNOWLEDGE_GAP discussion attached to the relevant interactions. |
| docs/communities/ORNL_Clostridium_Desulfovibrio_Geobacter_Trophic_Model.html | Regenerated HTML to display the new downstream effects and discussion section. |
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…#250) Add CommunityMech:000176 to the causal "done" list and note the conservative pattern for records whose primary full text can't be retrieved (abstract- supported edges only + a KNOWLEDGE_GAP discussion; 000176 is the worked example). Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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Adds directed
downstreamcausal edges to CommunityMech:000176 from an Edison causal-graph run (PaperQA3; doi:10.1186/1471-2180-10-149, Miller et al. 2010).Conservative by design
The primary full text could not be retrieved, so the run justified only two abstract-level / directly-implied edges (no perturbation evidence). Honored that:
Each edge description carries the "(directly implied, not perturbation-demonstrated)" caveat. The modeled Electron Donor and Acceptor Limitation node is left isolated per the disposition.
Knowledge gap recorded
Added a
KNOWLEDGE_GAPdiscussion: the exact exchanged fermentation products and any sulfate/fumarate-removal or inhibitor evidence remain unresolved pending the primary full text; products from a related two-species fuel-cell system (acetate/ethanol/H2) must not be imported without exact-system verification.InteractionDownstreamcarries target + description only; the discussion reuses an in-record verbatim snippet. Schema validates; no new terms. Page regenerated (2 edges render).Continues the causal thread (#226/#229/#230/#243/#246).
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