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DRAFT: CHEBI-route related_ingredients suggester (issue #30, pending MIM#119)#215

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DRAFT: CHEBI-route related_ingredients suggester (issue #30, pending MIM#119)#215
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@realmarcin realmarcin commented Jul 19, 2026

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⚠️ DRAFT — do not merge until MediaIngredientMech#119 confirms the CHEBI route (ask c).
Everything is implemented, tested, and green; this is parked ready to finalize.

Context

The ingredient analog of the media suggester (#211), built now so it lands the
moment MIM confirms. It links via the ingredient's CHEBI term
(RelatedIngredient.chebi_term) — the "CHEBI route" — which needs no
MediaIngredientMech:NNNNNN id (the schema pattern MIM doesn't use; see MIM#119).

What

  • cross_repo_environment.py: IngredientHit + mim_ingredients_by_environment()
    (byte-prefiltered; chebi_id set only when the MIM identifier is a CHEBI CURIE),
    plus get_chebi_adapter() and a shared _cached_oak_adapter() helper.
  • scripts/suggest_related_ingredients.py + just suggest-related-ingredients:
    for each community, matches environment_term against MIM environmental_context
    and emits related_ingredients blocks:
    • chebi_term with the canonical ChEBI label (resolved from the local ChEBI
      sqlite — not MIM's free-text name) so the id↔label gate stays green;
    • shared_environment_term (the ENVO join key);
    • skips already-linked CHEBI ids, generic environments, and records whose
      canonical label can't be resolved (reported, not silently dropped);
    • --subsumption supported; suggestion-only, prints a DRAFT banner.
  • Tests: test_suggest_related_ingredients.py + a mim_ingredients_by_environment
    case (fake OAK adapters, offline).

Verified

An emitted block LinkML-validates in a real record — Sulfur (CHEBI:26833, label
"sulfur atom") for a hot-spring phototrophic mat community, keyed on shared
ENVO:00000051.

Honest yield

~3 CHEBI-identified MIM env-context ingredients today, so immediate output is tiny.
The tool scales as MIM populates environmental_context (the field it committed to
in MIM#1). This PR is about having the capability ready, not bulk output.

Before finalizing

  • MIM#119 ask (c): confirm citing the ingredient's CHEBI: id is an acceptable
    cross-repo link. If yes → mark ready, merge. If MIM prefers MIM:<name> → add a
    mim_id field and emit that instead (small change).

Verification

  • just test — 229 passed (+6)
  • just lint — black + ruff + mypy clean

🤖 Generated with Claude Code

@realmarcin @claude
DRAFT: CHEBI-route related_ingredients suggester (issue #30, pending …
5eda920 
…MIM#119)

The ingredient analog of the media suggester, ready to finalize once MIM confirms
the CHEBI route (MediaIngredientMech#119 ask c). For each community, matches
environment_term against MIM environmental_context and emits RelatedIngredient
blocks via the ingredient's CHEBI term — no MediaIngredientMech:NNNNNN id needed.

- cross_repo_environment.py: IngredientHit + mim_ingredients_by_environment()
  (chebi_id set only when the MIM identifier is a CHEBI CURIE); get_chebi_adapter()
  and a shared _cached_oak_adapter() helper.
- scripts/suggest_related_ingredients.py + `just suggest-related-ingredients`:
  emits chebi_term + shared_environment_term (+ preferred_term); resolves the
  CANONICAL ChEBI label (not MIM's free-text name) so the id-label gate stays green;
  skips/reports records with an unresolvable label; supports --subsumption; skips
  already-linked CHEBI ids and generic environments. Suggestion-only. Prints a
  DRAFT banner.
- tests/test_suggest_related_ingredients.py + a mim_ingredients_by_environment case.

Verified an emitted block LinkML-validates in a real record (Sulfur CHEBI:26833 for
a hot-spring mat community, keyed on ENVO:00000051). Current yield is tiny (~3
CHEBI-identified MIM env ingredients today); scales as MIM populates
environmental_context.

Held as a DRAFT PR — do not merge until MIM#119 confirms the CHEBI route.

229 tests pass; lint clean.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
@realmarcin
realmarcin force-pushed the feat/draft-ingredient-suggester branch from 046a482 to 5eda920 Compare July 19, 2026 23:26
This was referenced Jul 20, 2026
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realmarcin added a commit that referenced this pull request Jul 20, 2026
@realmarcin @claude
Finalize CHEBI-route ingredient suggester per MediaIngredientMech#119
551d20e 
MIM#119 (now closed as answered) settled the two blockers: MediaIngredientMech:NNNNNN
is vestigial (drop it), and the equivalence-safe join is the ingredient's CHEBI term
from MIM's SSSOM skos:exactMatch rows — NOT the record identifier field, NOT
close/narrowMatch (which would generalise). Coverage is 10 environmental_context
records, not ~44.

Rebuilt the suggester (supersedes draft PR #215) on that basis:
- cross_repo_environment.py: mim_exactmatch_chebi() parses the SSSOM (skipping the #
  preamble; keeps only skos:exactMatch → CHEBI:); mim_ingredients_by_environment()
  joins each environmental_context record (MIM:<file-stem> subject) to it and scans
  data/ingredients/ (not the repo root — MIM keeps multi-MB aggregate dumps under
  data/curated/ that would blow up YAML parsing). + get_chebi_adapter/_cached_oak_adapter.
- scripts/suggest_related_ingredients.py + `just suggest-related-ingredients`: emits
  RelatedIngredient with chebi_term (CANONICAL ChEBI label, not MIM's free-text name,
  so the id-label gate stays green) + shared_environment_term; env keys are
  environment_term + modeled_environment; --subsumption supported; skips already-linked
  CHEBI ids, generic envs, and unresolved labels (reported). Not a draft.
- tests: SSSOM join (exactMatch/narrowMatch/non-CHEBI filtering) + suggester helpers.

Verified: real run emits Sulfur (CHEBI:26833, "sulfur atom") for the hot-spring mat
community (exact ENVO:00000051 match); block LinkML-validates. Yield is 1 today —
data-limited by MIM's 10 context records, correct and scales. 254 tests pass; lint clean.

Follow-up (NEXT_TASKS): drop the vestigial ^MediaIngredientMech:\d{6}$ pattern from
RelatedIngredient.mediaingredientmech_id.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
@realmarcin

realmarcin commented Jul 20, 2026

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Superseded by #220, which rebuilds the ingredient suggester on MIM#119's resolution (CHEBI route via SSSOM skos:exactMatch, not the record identifier field). Closing this draft.

@realmarcin realmarcin closed this Jul 20, 2026
realmarcin added a commit that referenced this pull request Jul 20, 2026
@realmarcin @claude
Finalize CHEBI-route ingredient suggester per MediaIngredientMech#119 (…
7db8ebf 
…#220)

MIM#119 (now closed as answered) settled the two blockers: MediaIngredientMech:NNNNNN
is vestigial (drop it), and the equivalence-safe join is the ingredient's CHEBI term
from MIM's SSSOM skos:exactMatch rows — NOT the record identifier field, NOT
close/narrowMatch (which would generalise). Coverage is 10 environmental_context
records, not ~44.

Rebuilt the suggester (supersedes draft PR #215) on that basis:
- cross_repo_environment.py: mim_exactmatch_chebi() parses the SSSOM (skipping the #
  preamble; keeps only skos:exactMatch → CHEBI:); mim_ingredients_by_environment()
  joins each environmental_context record (MIM:<file-stem> subject) to it and scans
  data/ingredients/ (not the repo root — MIM keeps multi-MB aggregate dumps under
  data/curated/ that would blow up YAML parsing). + get_chebi_adapter/_cached_oak_adapter.
- scripts/suggest_related_ingredients.py + `just suggest-related-ingredients`: emits
  RelatedIngredient with chebi_term (CANONICAL ChEBI label, not MIM's free-text name,
  so the id-label gate stays green) + shared_environment_term; env keys are
  environment_term + modeled_environment; --subsumption supported; skips already-linked
  CHEBI ids, generic envs, and unresolved labels (reported). Not a draft.
- tests: SSSOM join (exactMatch/narrowMatch/non-CHEBI filtering) + suggester helpers.

Verified: real run emits Sulfur (CHEBI:26833, "sulfur atom") for the hot-spring mat
community (exact ENVO:00000051 match); block LinkML-validates. Yield is 1 today —
data-limited by MIM's 10 context records, correct and scales. 254 tests pass; lint clean.

Follow-up (NEXT_TASKS): drop the vestigial ^MediaIngredientMech:\d{6}$ pattern from
RelatedIngredient.mediaingredientmech_id.

Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
@realmarcin
realmarcin deleted the feat/draft-ingredient-suggester branch July 20, 2026 18:19
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