Node-grounding pass: ground 39 causal-graph nodes via kg-microbe ontology index

[realmarcin]

What

Continues the grounding pipeline on the node side. Matches residual causal-node labels against the kg-microbe merged-kg node index (CHEBI/GO/ENVO/PATO) by exact case-insensitive name/synonym — constrained to the prefix/category appropriate for each node_type so types can't cross-map — then runs the write-safeguarded ground_causal_nodes.py --apply.

Node grounding: 946 → 985 / 1643 (58% → 59%).

31 new mappings (mappings/node_grounding.tsv)

node_type	targets
CHEMICAL → CHEBI	organic molecule, staphyloxanthin, bacteriochlorophyll, homogentisic acid, crystal violet, prodigiosin, dipicolinic acid, hydroxylamine, autoinducer, nitrogen oxides, adp, nadph, lipopolysaccharide, elemental sulfur, acetyl phosphate, coenzyme f430
BIOLOGICAL_PROCESS / PATHWAY → GO	cellular growth, melanin biosynthesis, tyrosine catabolism, cytokinesis, pigment biosynthesis, nutrient sensing, sulfur oxidation, formaldehyde assimilation, ribulose monophosphate cycle
CELLULAR_LOCALIZATION → GO-CC	flagellar filament, flagellar hook, forespore
ENVIRONMENTAL_FACTOR → PATO/ENVO	high temperature, high osmolarity, cold environment

Each row carries the skos predicate_id strength (exactMatch / closeMatch).

Rejected during review (not grounded)

• nutrient uptake → GO:0009935 (obsolete GO term)
• spore coat → GO:0031160 "spore wall" (distinct bacterial structures — coat ≠ wall)
• plant tissue colonization, intracellular membrane (semantic mismatch / too loose)
• charge/role-ambiguous chemicals: electron acceptor, pyocyanin

Residual (deferred)

658 node instances / 561 (label, type) keys remain — a long tail of idiosyncratic descriptive phrases (precursor metabolites, lateral cell-wall elongation, compatible-solute transport) plus GENE_OR_PROTEIN labels needing UniProt lookups. Exact matching keeps precision high; raising recall would require label normalization or fuzzy matching (higher risk).

Verification

• just validate-strict: 477 files, 0 errors.
• Idempotent (re-run grounds 0).
• Matching done against the real ontology index, not from memory.

🤖 Generated with Claude Code