Backfill related_ingredients in 4 more biocontrol/agri SynCom files (round 2) by realmarcin · Pull Request #119 · CultureBotAI/CommunityMech

realmarcin · 2026-06-09T20:32:07Z

Summary

Continues #118 — six more OAK-verified metabolites across four files, all sourced verbatim from already-cited references.

File	New related_ingredients	Source
Aerobic_Denitrification_Disturbance_SynCom	N-butyryl-L-homoserine lactone (CHEBI:29643), N-(3-oxododecanoyl)-L-homoserine lactone (CHEBI:44534), phenazine-1-carboxylic acid (CHEBI:62412)	PMID:40020349
GLBRC_Populus_Variovorax_SynCom28	L-fucose (CHEBI:18287)	PMID:41543249
Peanut_Seed_Bacterial_CS_SynCom	salicylic acid (CHEBI:16914)	PMID:38520150
Sorghum_SRC1_Subset	lignin (CHEBI:6457)	doi:10.1093/ismejo/wrae126

Adoption: 101 → 105 of 265 (+4 files; +6 metabolites).

Test plan

`just validate` clean for all four files.
CHEBI ids OAK-verified canonical.

🤖 Generated with Claude Code

…round 2) Continues the deferred ~38 thin biocontrol/agri SynCom backfill. Six more metabolites added across four files, all OAK-verified and sourced verbatim from the already-cited references — no new references added. - Aerobic_Denitrification_Disturbance_SynCom → N-butyryl-L-homoserine lactone (CHEBI:29643), N-(3-oxododecanoyl)-L-homoserine lactone (CHEBI:44534), phenazine-1-carboxylic acid (CHEBI:62412). Source: PMID:40020349 (Wang 2025) names C4-HSL + 3OC12-HSL quorum-sensing AHLs and the DBP-stimulated phenazine-1-carboxylic acid as the electron-transfer mediator. - GLBRC_Populus_Variovorax_SynCom28 → L-fucose (CHEBI:18287). Source: PMID:41543249 (Beals 2026) — experimentally-verified L-fucose utilization pathway enabling Populus endosphere colonization. - Peanut_Seed_Bacterial_CS_SynCom → salicylic acid (CHEBI:16914). Source: PMID:38520150 (Yu 2024) — SA-mediated systemic induced resistance is the host defense axis activated by the CS SynCom against root rot. - Sorghum_SRC1_Subset → lignin (CHEBI:6457). Source: doi:10.1093/ismejo/wrae126 — host lignin biosynthesis transcriptional dampening correlates with SRC1-driven growth promotion. All snippets verbatim from cached abstracts; every CHEBI id `runoak info`- verified pre-commit. Adoption: 101 → 105 of 265 (+4 files; +6 metabolites). Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

realmarcin

Reviewed the round-2 backfill of related_ingredients. All six CHEBI ids/labels are OAK-verified canonical (CHEBI:29643, 44534, 62412, 18287, 16914, 6457 all match their asserted labels exactly), all six snippet strings are verbatim-exact against the cached abstracts, and the cited PMIDs (40020349, 41543249, 38520150) and DOI (10.1093/ismejo/wrae126) all match the cached references. Schema shape matches the round-1 pattern already in these files. One citation-attribution bug and two minor nits below.

RISK

kb/communities/Peanut_Seed_Bacterial_CS_SynCom.yaml:66 — relevance prose attributes the finding to "Yu et al. 2024", but cited PMID:38520150 is authored by Luo DL, Huang SY, Ma CY, Zhang XY, Sun K, Zhang W, Dai CC (no "Yu" author). Fix: change to "(Luo et al. 2024)".

NIT

kb/communities/GLBRC_Populus_Variovorax_SynCom28.yaml:842 — new entry maps "L-fucose" to CHEBI:18287 (correct canonical label), but the same file's existing metabolites block (line 774) maps the same compound to CHEBI:2181 "L-fucopyranose". Same compound, two CHEBI ids within one file. The new CHEBI:18287 is the better label match; consider reconciling the older CHEBI:2181 reference.
kb/communities/Sorghum_SRC1_Subset.yaml:343 — relevance states the lignin-biosynthesis dampening correlates with growth promotion without the abstract's qualifier; the abstract scopes this correlation to "in laboratory conditions" (growth promotion itself was shown in both lab and field). Minor scope overreach in the prose; the snippet itself is verbatim and fine.

Findings not anchorable to diff lines

(Context, not a defect) The L-fucose snippet on line 851 reuses the same verbatim snippet already present in the existing metabolites evidence block (line 786). Legitimate reuse across blocks, no action needed.

realmarcin · 2026-06-10T07:45:58Z

+    label: salicylic acid
+  relevance: Plant defense hormone underlying the systemic induced resistance that the combined
+    seed-bacterial SynCom (CS) activates in peanut seedlings to resist Fusarium oxysporum root rot
+    (Yu et al. 2024).


RISK: Wrong author attribution. Cited PMID:38520150 ("Seed-borne bacterial synthetic community resists seed pathogenic fungi...") is authored by Luo DL, Huang SY, Ma CY, Zhang XY, Sun K, Zhang W, Dai CC — there is no "Yu" author. Fix: change "(Yu et al. 2024)" to "(Luo et al. 2024)". The CHEBI id/label and verbatim snippet are correct.

realmarcin · 2026-06-10T07:45:58Z

+related_ingredients:
+- preferred_term: L-fucose
+  chebi_term:
+    id: CHEBI:18287


NIT: This new entry maps "L-fucose" to CHEBI:18287 (canonical label "L-fucose", OAK-verified). But the existing metabolites block in this same file (line 774) maps the same compound to CHEBI:2181 "L-fucopyranose". Same compound, two different CHEBI ids in one file. CHEBI:18287 is the more accurate label match here; consider reconciling the older CHEBI:2181 reference to avoid divergence.

realmarcin · 2026-06-10T07:45:58Z

+  chebi_term:
+    id: CHEBI:6457
+    label: lignin
+  relevance: Cell-wall phenolic polymer whose host biosynthesis is transcriptionally dampened when


NIT: The relevance prose presents the lignin-biosynthesis dampening as correlating with SynCom-driven growth promotion without the abstract's qualifier. The abstract scopes the lignin correlation specifically to "in laboratory conditions" (whereas growth promotion was demonstrated in both lab and field). Consider adding the lab-conditions qualifier. The verbatim snippet and CHEBI:6457 mapping are correct.

- relevance prose for PMID:38520150 cited 'Yu et al. 2024'; real first author is Luo (Luo DL). Changed to 'Luo et al. 2024' (confirmed against cached abstract) Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

…h (issue #30) Actions the two ingredient-linking blockers from NEXT_TASKS §2c. Blocker 1 (schema, ours) — RESOLVED: add shared_environment_term (Term, id-binding REQUIRED) to RelatedIngredient, mirroring RelatedMedia, so environment->ingredient links are expressible. Datamodel regenerated; a related_ingredient with shared_environment_term + chebi_term LinkML-validates; regression test added. Blocker 2 (MIM id scheme) — RAISED with MIM (MediaIngredientMech#119). Investigation found MIM's canonical ingredient CURIE is MIM:<name> (2200 SSSOM subjects; MIM: expands to data/ingredients/mapped/), NOT MediaIngredientMech:NNNNNN (which exists only in two MIM analysis reports). So RelatedIngredient.mediaingredientmech_id's pattern references a scheme MIM never adopted; its description now says so and points at #119. The CHEBI route (RelatedIngredient.chebi_term, already present) is the likely fast path and needs no id decision. 213 tests pass; lint clean. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

…h (issue #30) (#212) Actions the two ingredient-linking blockers from NEXT_TASKS §2c. Blocker 1 (schema, ours) — RESOLVED: add shared_environment_term (Term, id-binding REQUIRED) to RelatedIngredient, mirroring RelatedMedia, so environment->ingredient links are expressible. Datamodel regenerated; a related_ingredient with shared_environment_term + chebi_term LinkML-validates; regression test added. Blocker 2 (MIM id scheme) — RAISED with MIM (MediaIngredientMech#119). Investigation found MIM's canonical ingredient CURIE is MIM:<name> (2200 SSSOM subjects; MIM: expands to data/ingredients/mapped/), NOT MediaIngredientMech:NNNNNN (which exists only in two MIM analysis reports). So RelatedIngredient.mediaingredientmech_id's pattern references a scheme MIM never adopted; its description now says so and points at #119. The CHEBI route (RelatedIngredient.chebi_term, already present) is the likely fast path and needs no id decision. 213 tests pass; lint clean. Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

realmarcin mentioned this pull request Jun 9, 2026

Backfill related_ingredients in 3 more biocontrol/agri SynCom files (round 3) #120

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realmarcin commented Jun 10, 2026

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realmarcin mentioned this pull request Jun 10, 2026

Fix wrong first-author in related_ingredients backfill citations #128

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realmarcin merged commit c6da761 into main Jun 10, 2026
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realmarcin deleted the backfill-biocontrol-batch-2 branch June 10, 2026 20:02

realmarcin mentioned this pull request Jul 20, 2026

Finalize CHEBI-route ingredient suggester (MediaIngredientMech#119) #220

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Backfill related_ingredients in 4 more biocontrol/agri SynCom files (round 2) - #119

Backfill related_ingredients in 4 more biocontrol/agri SynCom files (round 2)#119
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realmarcin commented Jun 9, 2026

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RISK

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