Deprecate "environmental exposure measurement" terms and replace with imported ECTO terms

[jamesamcl]

CC @eks-ebi

[jamesamcl]

Draft ECTO new-term request (to be filed on the ECTO tracker)

Recording here for tracking — this session was scoped to ebispot/efo only, so the request couldn't be filed directly on EnvironmentOntology/environmental-exposure-ontology.

Context: PR #2738 migrates this branch to ECTO. 18 of the 25 terms had ECTO equivalents (obsoleted with IAO_0100001 → ECTO); the 7 below have no ECTO equivalent and were kept/re-parented under measurement. This NTR requests the missing ECTO classes so they can be migrated in a follow-up.

Suggested title: NTR: exposure terms for EFO environmental-exposure migration (EBISPOT/efo#2737)

Body:

New term requests arising from the EFO → ECTO migration
(EBISPOT/efo#2737, PR EBISPOT/efo#2738).

EFO is deprecating its native "… exposure measurement" terms and pointing
them at ECTO "exposure to …" classes via IAO_0100001. The concepts below
have no current ECTO equivalent; requesting them would let the remaining
EFO terms migrate. All are used to annotate GWAS Catalog studies.

Pattern: *exposure to X* — "An exposure event involving the interaction of
an exposure receptor to X."

1. exposure to noise
   - Def: An exposure event involving the interaction of an exposure
     receptor to noise (unwanted or harmful sound).
   - Suggested superclass: exposure to environmental process (ECTO:8000000)
   - EFO source: noise exposure measurement (EFO:0600015); cf. non-ECTO
     LFID:0000230 "exposure to noise pollution".

2. exposure to sunlight
   - Def: An exposure event involving the interaction of an exposure
     receptor to sunlight.
   - Suggested superclass: exposure to environmental process (ECTO:8000000);
     sibling of exposure to ultraviolet radiation (ECTO:0000006).
   - EFO source: sun exposure measurement (EFO:0010729); cf. non-ECTO
     LFID:0000226. Broader than ECTO:0000006 (UV component only).

3. exposure to dietary supplement
   - Def: An exposure event involving the interaction of an exposure
     receptor to a dietary/nutritional supplement.
   - Suggested superclass: exposure to environmental process (ECTO:8000000).
     Would serve as genus for the supplement exposures below and for the
     existing ECTO:0070164 "exposure to fish oil supplement via ingestion".
   - EFO source: nutritional supplement exposure measurement (EFO:0600066).

4. exposure to vitamin supplement
   - Def: An exposure event involving the interaction of an exposure
     receptor to a vitamin supplement.
   - Suggested superclass: exposure to dietary supplement (requested above).
   - EFO source: vitamin supplement exposure measurement (EFO:0009116).

5. exposure to mastiha
   - Def: An exposure event involving the interaction of an exposure
     receptor to mastiha (Chios mastic gum).
   - Suggested superclass: exposure to dietary supplement (requested above).
   - EFO source: mastiha supplement exposure measurement (EFO:0600067).
     Note: niche/low priority.

Flagged for discussion (not requesting a class yet):
- in utero exposure (EFO:0009114) — ECTO appears to model this
  compositionally via the "… via maternal" route (ExO:0000159) rather than
  a standalone class. Preferred pattern welcome.
- time spent outdoors (EFO:0600081) — a behavioural duration, not
  "exposure to a stressor"; likely outside ECTO's exposure-event model.

Happy to adjust definitions/placements to ECTO conventions.

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Generated by Claude Code

[jamesamcl]

Update: ECTO terms created (supersedes the draft NTR above)

The missing ECTO classes have now been created directly in a PR rather than filed as a request: EBISPOT/environmental-exposure-ontology#1.

All fillers were verified via OLS (bidirectional label↔ID match); ENVO and FOODON are already imported by ECTO.

Created (3):

New ECTO class	Filler	EFO term it enables migrating
ECTO:8000061 exposure to insolation process	ENVO:01001734	sun exposure measurement (EFO:0010729)
ECTO:0070211 exposure to dietary supplement via ingestion	FOODON:03401298	nutritional supplement exposure measurement (EFO:0600066)
ECTO:0070212 exposure to dietary supplement, vitamin via ingestion	FOODON:03401302	vitamin supplement exposure measurement (EFO:0009116)

Not created:

• noise exposure measurement (EFO:0600015) — no new ECTO term needed: ECTO already has ECTO:8000044 exposure to sound radiation (ENVO:01001027). This EFO term can migrate to that existing class. (No distinct ENVO "noise" class exists.)
• mastiha supplement exposure measurement (EFO:0600067) — deferred: no usable FOODON class for mastic/mastiha exists (only a FoodEx2 flavour code with a misleading "arabic gum" synonym). Needs a FOODON term first.
• in utero exposure measurement (EFO:0009114) and time spent outdoors measurement (EFO:0600081) — out of scope for ECTO's exposure-event model (route-composed / behavioural duration respectively).

Follow-up sequencing: once ECTO PR #1 is merged and released, the 4 EFO terms above (EFO:0010729, EFO:0600066, EFO:0009116 → the 3 new ECTO classes; EFO:0600015 → existing ECTO:8000044) can be obsoleted with IAO_0100001 and migrated, leaving only mastiha / in utero / time-spent-outdoors as kept. This completes the migration begun in PR #2738.

Generated by Claude Code

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Generated by Claude Code