Recheck interaction semantics and preserve review history (batch91)

docs/communities/GLBRC_UFMP_Fermentation_Community.html

@@ -920,12 +920,17 @@ <h2>Ecological Interactions</h2>
                 <div class="network-tooltip" id="network-tooltip" role="status" aria-live="polite"></div>
                 <svg id="network-svg" role="img" aria-labelledby="network-svg-title network-svg-desc">
                     <title id="network-svg-title">Ecological interaction network for GLBRC Ultra-Filtered Milk Permeate Fermentation Community</title>
-                    <desc id="network-svg-desc">Bipartite graph where circle nodes represent taxa and each ecological interaction is drawn as a distinct non-circular symbol, with colour repeating the same distinction.</desc>
+                    <desc id="network-svg-desc">Bipartite graph where circle nodes represent taxa and each ecological interaction is drawn as a distinct non-circular symbol, with colour repeating the same distinction (cross-feeding).</desc>
                 </svg>
                 <div class="network-legend">
                     <div class="legend-item">
                         <span class="legend-swatch legend-circle" style="background: #7a7a7a;"></span> Taxon
                     </div>
+                    <div class="legend-item">
+                        <svg class="legend-symbol" width="14" height="14" viewBox="-9 -9 18 18"
+                             aria-hidden="true" data-symbol="symbolDiamond"
+                             data-color="#57c7ab"></svg> Cross-feeding
+                    </div>
                     <div class="legend-item">
                         <svg class="legend-symbol" width="14" height="14" viewBox="-9 -9 18 18"
                              aria-hidden="true" data-symbol="symbolTriangle2"
@@ -1086,8 +1091,9 @@ <h4>Evidence</h4>
             <div class="interaction-card">
                 <div class="interaction-header">
                     <h3>Proposed Actinobacteriota-to-CLOS1 Lactate Cross-Feeding</h3>
+                    <span class="interaction-type">CROSS_FEEDING</span>
                 </div>
-                <p class="prewrap interaction-description">HYPOTHESIZED: The conceptual model proposes that lactate made by some lactose-fermenting Actinobacteriota can supply CLOS1 chain elongation. ATO3 and Bifidobacterium MAGs represent proposed donor candidates, not a measured set of donor-recipient transfers. CLOS1 contains the inferred LacT, electron-confurcating LDH and associated EtfAB machinery; the other two abundant Firmicutes have different proposed substrates. The study did not directly trace ATO3-to-CLOS1 carbon flow, establish obligatory syntrophy, determine lactate stereochemistry or show complete conversion of lactose into medium-chain fatty acids. The canonical labels retain their existing genus-level or ambiguous groundings rather than assert newly identified species.</p>
+                <p class="prewrap interaction-description">HYPOTHESIZED: The conceptual model proposes that lactate made by some lactose-fermenting Actinobacteriota can supply CLOS1 chain elongation. ATO3 and Bifidobacterium MAGs represent proposed donor candidates, not a measured set of donor-recipient transfers. CLOS1 contains the inferred LacT, electron-confurcating LDH and associated EtfAB machinery; the other two abundant Firmicutes have different proposed substrates. The study did not directly trace ATO3-to-CLOS1 carbon flow, establish product-removal feedback on upstream fermentation, determine lactate stereochemistry or show complete conversion of lactose into medium-chain fatty acids. The canonical labels retain their existing genus-level or ambiguous groundings rather than assert newly identified species. CROSS_FEEDING denotes the hypothesized transfer model. SYNTROPHY does not require obligacy in the local schema, but adds product-removal feedback that this study does not resolve.</p>
 
 
 
@@ -1141,6 +1147,19 @@ <h4>Evidence</h4>
 
                     </li>
 
+                    <li class="evidence-item">
+                        <div>
+
+                            <a href="https://pubmed.ncbi.nlm.nih.gov/37324413/"
+                               class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:37324413</a>
+
+                            - PARTIAL (COMPUTATIONAL)
+                        </div>
+
+                        <div class="snippet">"The inferred connection between some Actinobacteriota fermenting lactose to lactic acid and some Firmicutes utilizing lactic acid for chain elongation"</div>
+
+                    </li>
+
                 </ul>
 
             </div>
@@ -1195,7 +1214,7 @@ <h3>
                     <span class="role-badge">OPEN</span>
                     Which MAGs exchange carbon and determine terminal chain length?
                 </h3>
-                <p class="prewrap">The reactor measurements support fermentation, whereas member roles and both retained model arrows are hypotheses. Metatranscriptomics, isotope tracing and selective member/substrate perturbations would test donor identity, CLOS1 uptake, ACID1 substrate and chain-length allocation. SPH2 has a separate proposed ethanol role outside these existing Actinobacteriota/lactate and Firmicute nodes; no new node is invented to hide its disconnected warning. Unsupported stereospecific CHEBI:422 entries are removed from graph nodes without guessing a replacement. Non-graph ingredient/taxonomy role text and all #486/#624 grounding history remain unchanged and are not certified by this graph-only review.</p>
+                <p class="prewrap">The reactor measurements support fermentation, whereas member roles and both retained model arrows are hypotheses. Metatranscriptomics, isotope tracing and selective member/substrate perturbations would test donor identity, CLOS1 uptake, ACID1 substrate and chain-length allocation. SPH2 has a separate proposed ethanol role outside these existing Actinobacteriota/lactate and Firmicute nodes; no new node is invented to hide its disconnected warning. Unsupported stereospecific CHEBI:422 entries are removed from graph nodes without guessing a replacement. Non-graph ingredient/taxonomy role text and all #486/#624 grounding history remain unchanged and are not certified by this graph-only review. The local SYNTROPHY definition does not assert obligacy. The existing lactate-transfer model is typed CROSS_FEEDING with PARTIAL evidence because the study proposes a producer-consumer connection without resolving product-removal feedback on upstream metabolism.</p>
 
                 <p class="muted small">Attaches to: <code>ecological_interactions#Proposed Actinobacteriota Lactose Fermentation Roles</code>, <code>ecological_interactions#Proposed Firmicutes Chain Elongation Roles</code>, <code>ecological_interactions#Proposed Actinobacteriota-to-CLOS1 Lactate Cross-Feeding</code></p>
 
@@ -1590,12 +1609,12 @@ <h4 style="color: var(--text);">Evidence</h4>
 
         (function() {
             var intId = "interaction:2";
-            var intType = "UNKNOWN";
+            var intType = "CROSS_FEEDING";
             var metabolites = [];
 
             var processes = [];
 
-            var evidenceCount = 1;
+            var evidenceCount = 2;
 
             nodes.push({
                 id: intId,

docs/communities/Multi_stage_Anaerobic_Digestion_SynCom_YSJ_and_SynCom_J.html

@@ -712,7 +712,7 @@ <h4>Evidence</h4>
                 <div class="interaction-header">
                     <h3>Putative interspecies electron transfer supporting methanogenesis</h3>
                 </div>
-                <p class="prewrap interaction-description">PARTIAL - Metagenomic analysis associates YSJ bioaugmentation with hydrolysis, acidogenesis, interspecies electron transfer, energy metabolism and methanogenesis functions. The abstract calls this gene upregulation; this metagenomic statement alone does not establish transcription, protein activity, measured electron flux, direct electrical transfer or obligate syntrophy. Methane gains are retained independently of the unresolved transfer mechanism.</p>
+                <p class="prewrap interaction-description">PARTIAL - Metagenomic analysis associates YSJ bioaugmentation with hydrolysis, acidogenesis, interspecies electron transfer, energy metabolism and methanogenesis functions. The abstract calls this gene upregulation; this metagenomic statement alone does not establish transcription, protein activity, measured electron flux, direct electrical transfer or product-removal feedback making upstream metabolism favourable. Methane gains are retained independently of the unresolved transfer mechanism. SYNTROPHY does not require obligacy in the local schema; the unresolved feedback mechanism, not unproven obligacy, is the reason this node remains untyped.</p>
 
 
 
@@ -843,7 +843,7 @@ <h3>
                     <span class="role-badge">OPEN</span>
                     Which selective mechanisms explain the measured community responses?
                 </h3>
-                <p class="prewrap">Primary abstract supports positive bioaugmentation outcomes, not individually isolated links in the staged hand-off/electron-transfer/environment-selection chain. Obtain authorized full Methods to distinguish metagenomic abundance from expression, native from inoculated contributions, and direct from carrier-mediated electron exchange. Preserve the observed function/stability trade-off and the existing membership follow-up #183. Abstract-only access does not show that controls were absent.</p>
+                <p class="prewrap">Primary abstract supports positive bioaugmentation outcomes, not individually isolated links in the staged hand-off/electron-transfer/environment-selection chain. Obtain authorized full Methods to distinguish metagenomic abundance from expression, native from inoculated contributions, and direct from carrier-mediated electron exchange. Preserve the observed function/stability trade-off and the existing membership follow-up #183. Abstract-only access does not show that controls were absent. The local SYNTROPHY definition concerns product-removal feedback and does not assert obligacy. Metagenomic functional association alone does not resolve that feedback; retain the putative transfer interpretation without a categorical SYNTROPHY label.</p>
 
                 <p class="muted small">Attaches to: <code>ecological_interactions#Staged metabolic hand-off across hydrolytic, acidogenic and methanogenic members</code>, <code>ecological_interactions#Putative interspecies electron transfer supporting methanogenesis</code>, <code>ecological_interactions#Deterministic selection of the resident community by SynCom colonization</code></p>
 

docs/communities/Pleuromutilin_Degrading_Artificial_Consortium_5_Strain.html

@@ -703,7 +703,7 @@ <h2>Ecological Interactions</h2>
                 <div class="interaction-header">
                     <h3>Ninety-Two-Percent Pleuromutilin Degradation</h3>
                 </div>
-                <p class="prewrap interaction-description">The defined five-strain artificial consortium achieved reported pleuromutilin degradation of 91.97%. Preserve this positive community-level endpoint without asserting obligatory syntrophy, partner-specific flux, complete mineralization or a superiority comparison not stated in the accessible abstract.</p>
+                <p class="prewrap interaction-description">The defined five-strain artificial consortium achieved reported pleuromutilin degradation of 91.97%. Preserve this positive community-level endpoint without asserting product-removal cooperation, partner-specific flux, complete mineralization or a superiority comparison not stated in the accessible abstract. SYNTROPHY does not require obligacy, but a measured community degradation endpoint is not itself the product-removal mechanism.</p>
 
 
 
@@ -832,7 +832,7 @@ <h3>
                     <span class="role-badge">OPEN</span>
                     Which compatibility and degradation mechanisms belong to the defined five-strain community?
                 </h3>
-                <p class="prewrap">Natural En4 enrichment showed reduced diversity and enriched pollutant-associated genera; preserve those positives as parent-community context, not interactions among the five selected strains. Assembly/isolation workflow remains in engineering_design. Public Table S1 lists bacterial and fungal isolates and identifies W12, rather than same-species W10, as the selected Pseudomonas songnenensis in Table S2. Table S2 reports no inhibition zones, not cross-feeding or long-term stability. Table S3 supports differential metabolomics, not compound provenance or partner flux. Main text remains inaccessible; source DOCX tables were read by OOXML, not rendered pages. Missing compatibility/pathway topology remains #1715 pending a reviewed, explicitly authorized Edison report; no new structure is added. Non-graph isolate and strain identity remains #1716.</p>
+                <p class="prewrap">Natural En4 enrichment showed reduced diversity and enriched pollutant-associated genera; preserve those positives as parent-community context, not interactions among the five selected strains. Assembly/isolation workflow remains in the record description. Public Table S1 lists bacterial and fungal isolates and identifies W12, rather than same-species W10, as the selected Pseudomonas songnenensis in Table S2. Table S2 reports no inhibition zones, not cross-feeding or long-term stability. Table S3 supports differential metabolomics, not compound provenance or partner flux. Main text remains inaccessible; source DOCX tables were read by OOXML, not rendered pages. Missing compatibility/pathway topology remains #1715 pending a reviewed, explicitly authorized Edison report; no new structure is added. Non-graph isolate and strain identity remains #1716. The local SYNTROPHY definition does not assert obligacy. The retained outcome and proposed-products nodes remain untyped because they do not themselves establish product-removal feedback, not because obligatory dependence is unproven.</p>
 
                 <p class="muted small">Attaches to: <code>ecological_interactions#Ninety-Two-Percent Pleuromutilin Degradation</code>, <code>ecological_interactions#Proposed Artificial-Consortium Degradation Products and Pathways</code></p>
 
@@ -871,7 +871,7 @@ <h3>
                         </div>
                         <p class="snippet small prewrap">The metabolic profile of the artificial microbial consortia during the degradation of pleuromutilin were studied, and potential degradation products and metabolic pathways were proposed
 </p>
-                        <p class="muted small prewrap">Supports proposed products/pathways, not experimentally resolved interspecies exchange or obligate syntrophy.</p>
+                        <p class="muted small prewrap">Supports proposed products/pathways, not experimentally resolved interspecies exchange or product-removal feedback on upstream metabolism.</p>
                     </div>
 
                 </details>

history/records/GLBRC_UFMP_Fermentation_Community/2026-10-07T134453Z-codex-9cf7ab.yaml

@@ -0,0 +1,28 @@
+history_version: 1
+target:
+  kind: record
+  path: kb/communities/GLBRC_UFMP_Fermentation_Community.yaml
+  slug: GLBRC_UFMP_Fermentation_Community
+session:
+  id: 2026-10-07T134453Z-codex-9cf7ab
+  timestamp: '2026-10-07T13:44:53Z'
+  actors:
+  - type: ai_agent
+    name: codex
+    model: unspecified
+    agent_tool: codex
+links:
+  issues:
+  - https://github.com/CultureBotAI/CommunityMech/issues/1744
+events:
+- type: EDIT
+  outcome: changed
+  sections:
+  - interactions
+  - discussions
+  summary: Preserve heterogeneous genome-inferred producer roles without new member assignments.;
+    Preserve substrate-distinct proposed chain elongation and terminal-product limits.; Type
+    the existing hypothesized lactate-transfer model CROSS_FEEDING with primary Discussion
+    evidence; distinguish product-removal feedback from obligacy.
+  details: Schema-semantics re-review; original ledgers and history artifacts remain unchanged.
+    No node, arrow, participant, cache, experimental protocol or provider-spend change.

history/records/Multi_stage_Anaerobic_Digestion_SynCom_YSJ_and_SynCom_J/2026-10-07T134453Z-codex-8dae13.yaml

@@ -0,0 +1,28 @@
+history_version: 1
+target:
+  kind: record
+  path: kb/communities/Multi_stage_Anaerobic_Digestion_SynCom_YSJ_and_SynCom_J.yaml
+  slug: Multi_stage_Anaerobic_Digestion_SynCom_YSJ_and_SynCom_J
+session:
+  id: 2026-10-07T134453Z-codex-8dae13
+  timestamp: '2026-10-07T13:44:53Z'
+  actors:
+  - type: ai_agent
+    name: codex
+    model: unspecified
+    agent_tool: codex
+links:
+  issues:
+  - https://github.com/CultureBotAI/CommunityMech/issues/1744
+events:
+- type: EDIT
+  outcome: changed
+  sections:
+  - interactions
+  - discussions
+  summary: Preserve measured methane/comparator outcomes and the qualified staged-transfer
+    model.; Keep the metagenomically inferred transfer node untyped for unresolved product-removal
+    feedback, not unproven obligacy.; Preserve environmental selection interpretation and
+    function/stability distinction.
+  details: Schema-semantics re-review; original ledgers and history artifacts remain unchanged.
+    No node, arrow, participant, cache, experimental protocol or provider-spend change.

history/records/Pleuromutilin_Degrading_Artificial_Consortium_5_Strain/2026-10-07T134453Z-codex-f66458.yaml

@@ -0,0 +1,27 @@
+history_version: 1
+target:
+  kind: record
+  path: kb/communities/Pleuromutilin_Degrading_Artificial_Consortium_5_Strain.yaml
+  slug: Pleuromutilin_Degrading_Artificial_Consortium_5_Strain
+session:
+  id: 2026-10-07T134453Z-codex-f66458
+  timestamp: '2026-10-07T13:44:53Z'
+  actors:
+  - type: ai_agent
+    name: codex
+    model: unspecified
+    agent_tool: codex
+links:
+  issues:
+  - https://github.com/CultureBotAI/CommunityMech/issues/1744
+events:
+- type: EDIT
+  outcome: changed
+  sections:
+  - interactions
+  - discussions
+  summary: 'Keep the positive degradation endpoint distinct from a product-removal mechanism;
+    obligacy is not required by SYNTROPHY.; Preserve proposed products/pathways without treating
+    metabolomic differences as partner feedback; unresolved topology remains #1715.'
+  details: Schema-semantics re-review; original ledgers and history artifacts remain unchanged.
+    No node, arrow, participant, cache, experimental protocol or provider-spend change.