Curate DOI-backed nutrient physiology causal graphs - #1
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Addressed Copilot's file-count blocker by narrowing the generated HTML diff to the five curated physiology trait pages only. Re-requested Copilot review via GraphQL bot reviewer request. No inline review threads were created, so there are no conversations to resolve. |
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| - timestamp: '2026-05-09T00:00:00-07:00' | ||
| curator: Codex | ||
| action: CURATED_CAUSAL_GRAPH | ||
| changes: Added DOI-backed mixotrophy graph for dual organic/inorganic carbon use |
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| - timestamp: '2026-05-09T00:00:00-07:00' | ||
| curator: Codex | ||
| action: CURATED_CAUSAL_GRAPH | ||
| changes: Added DOI-backed copiotrophy graph for nutrient-rich environments, |
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| - timestamp: '2026-05-09T00:00:00-07:00' | ||
| curator: Codex | ||
| action: CURATED_CAUSAL_GRAPH | ||
| changes: Added DOI-backed oligotrophy graph for low nutrients, genome/cell |
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| - timestamp: '2026-05-09T00:00:00-07:00' | ||
| curator: Codex | ||
| action: CURATED_CAUSAL_GRAPH | ||
| changes: Added DOI-backed organotrophy graph for organic substrate oxidation, |
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| - timestamp: '2026-05-09T00:00:00-07:00' | ||
| curator: Codex | ||
| action: CURATED_CAUSAL_GRAPH | ||
| changes: Added DOI-backed chemoautolithotrophy graph for inorganic electron |
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| evidence: | ||
| - reference: DOI:10.3389/fmicb.2011.00165 | ||
| snippet: use light as the energy source | ||
| notes: Review supports light-driven ATP and reductant generation by phototrophic bacteria. | ||
| - reference: DOI:10.1093/femsre/fuv032 | ||
| snippet: bacteriochlorophyll-containing reaction centers | ||
| notes: Review supports bacteriochlorophyll reaction centers in aerobic anoxygenic phototrophs. | ||
| causal_graphs: | ||
| - graph_id: phototrophic_light_energy_capture | ||
| title: Phototrophic light-energy capture mechanism | ||
| description: DOI-backed graph for bacterial light capture, photosynthetic electron | ||
| transport, ATP generation, and reductant formation. |
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| mapping_status: DEPRECATED | ||
| curation_history: | ||
| - timestamp: '2026-05-05T01:35:46.980776+00:00' | ||
| curator: seed_from_metpo | ||
| action: SEEDED_FROM_METPO | ||
| changes: imported from data/raw/metpo.owl (DATATYPE_PROPERTY) | ||
| llm_assisted: false | ||
| - timestamp: '2026-05-08T00:00:00-07:00' | ||
| curator: codex | ||
| action: DEPRECATED_PROPERTY_RECORD | ||
| changes: Deprecated upper datatype-property carrier for observation data; later | ||
| replacement should use more specific trait records that combine the data | ||
| relation with chemicals, measurements, observations, or other entities. |
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| - node_id: atp | ||
| label: ATP | ||
| node_type: CHEMICAL | ||
| grounding: CHEBI:15422 | ||
| description: Energy-rich nucleotide product. |
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| - node_id: atp | ||
| label: ATP | ||
| node_type: CHEMICAL | ||
| grounding: CHEBI:15422 | ||
| description: Cellular energy currency generated by fermentation. |
This was referenced Aug 4, 2026
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--param max_tokens=...reach deep-research-client.Validation
just validate-allpassedjust testpassed (11 tests)just lintpassedNotes
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