Obsolete environmental exposure measurement terms (issue #2737)

[jamesamcl]

Summary

Completes the EFO→ECTO migration begun in #2380. The EFO-native "environmental exposure measurement" branch (EFO_0008360, 25 terms) is deprecated in favour of ECTO (Environmental Conditions, Treatments and Exposures Ontology) exposure classes. 18 terms had a verified ECTO equivalent and are obsoleted with obo:IAO_0100001 (term replaced by) → the ECTO class; 7 terms have no ECTO equivalent and are kept (re-parented under measurement). Closes #2737.

Obsoleted + replaced (18)

Each term gets: obsolete_ label · owl:deprecated=true · efo:obsoleted_in_version 3.92 · efo:reason_for_obsolescence (refs #2737) · obo:IAO_0100001 → ECTO class · all logical axioms removed.

EFO ID	EFO label	→ ECTO ID	ECTO label
EFO_0008360	environmental exposure measurement (branch root)	ECTO_8000000	exposure to environmental process
EFO_0004806	asbestos exposure measurement	ECTO_9000033	exposure to asbestos
EFO_0006924	household air pollution measurement	ECTO_8000036	exposure to air pollution
EFO_0007840	pesticide exposure measurement	ECTO_0000530	exposure to pesticide
EFO_0007908	traffic air pollution measurement	ECTO_8000036	exposure to air pollution
EFO_0007944	allergen exposure measurement	ECTO_0000726	exposure to allergen
EFO_0008255	particulate matter air pollution measurement	ECTO_7000068	exposure to particulate matter
EFO_0008361	environmental tobacco smoke exposure measurement	ECTO_6000029	exposure to tobacco smoking
EFO_0008362	farm exposure measurement	ECTO_1000034	exposure to farm
EFO_0009113	alcohol exposure measurement	ECTO_9000026	exposure to alcohol
EFO_0009115	tobacco smoke exposure measurement	ECTO_6000029	exposure to tobacco smoking
EFO_0009370	radon exposure measurement	ECTO_9000097	exposure to radon
EFO_0010233	genotoxic compound exposure measurement	ECTO_0000724	exposure to genotoxin
EFO_0020980	radiation exposure measurement	ECTO_0000001	exposure to radiation
EFO_0022039	ultraviolet radiation exposure measurement	ECTO_0000006	exposure to ultraviolet radiation
EFO_0600007	fish oil supplement exposure measurement	ECTO_0070164	exposure to fish oil supplement via ingestion
EFO_0801078	triclosan measurement	ECTO_9000078	exposure to triclosan
EFO_0801079	bisphenol A measurement	ECTO_9000057	exposure to bisphenol A

Mappings to double-check (best available in ECTO, flagged for reviewer):

• EFO_0008361 environmental tobacco smoke (passive / second-hand) → ECTO_6000029 exposure to tobacco smoking (active-smoking sense) — only ECTO option, semantically broader.
• EFO_0006924 household + EFO_0007908 traffic air pollution → both collapse to the generic ECTO_8000036 exposure to air pollution (no household- or traffic-specific ECTO class exists).
• EFO_0008360 root → ECTO_8000000 exposure to environmental process (ECTO's top-level environmental-exposure grouping).

Kept — no ECTO equivalent (7)

Not obsoleted. The 4 former direct children of the (obsoleted) root are re-parented to measurement (EFO_0001444); the other 3 stay under their kept intermediate parents.

EFO ID	EFO label	disposition
EFO_0009114	in utero exposure measurement	re-parented → measurement
EFO_0600015	noise exposure measurement	re-parented → measurement
EFO_0600066	nutritional supplement exposure measurement	re-parented → measurement
EFO_0600081	time spent outdoors measurement	re-parented → measurement
EFO_0009116	vitamin supplement exposure measurement	unchanged (under EFO_0600066)
EFO_0600067	mastiha supplement exposure measurement	unchanged (under EFO_0600066)
EFO_0010729	sun exposure measurement	unchanged (under EFO_0600081)

Terms that need creating in ECTO

These 7 have no ECTO class today. To eventually migrate them too, ECTO would need new exposure to … classes (new-term requests). Suggested labels + fit notes:

EFO term	suggested new ECTO class	note
noise exposure measurement (EFO_0600015)	exposure to noise	straightforward; cf. non-ECTO LFID:0000230 "exposure to noise pollution"
sun exposure measurement (EFO_0010729)	exposure to sunlight	cf. non-ECTO LFID:0000226; broader than the existing ECTO "exposure to ultraviolet radiation"
nutritional supplement exposure measurement (EFO_0600066)	exposure to dietary supplement	genus for the two below (ECTO already has "exposure to fish oil supplement via ingestion")
vitamin supplement exposure measurement (EFO_0009116)	exposure to vitamin supplement	child of the above
mastiha supplement exposure measurement (EFO_0600067)	exposure to mastiha	obscure; low priority
in utero exposure measurement (EFO_0009114)	(route-based, may not need a class)	ECTO models this compositionally as "exposure to X via maternal" (ExO route maternal), not as a standalone class
time spent outdoors measurement (EFO_0600081)	(poor fit)	a behavioural duration, not "exposure to a stressor" — likely outside ECTO's exposure-event model

Imports

Added ECTO_8000000 and ECTO_7000068 to src/ontology/iri_dependencies/ecto_terms.txt and regenerated src/ontology/imports/ecto_import.owl (via efo-importer). No hand-editing of generated import files — ECTO's own class / definition / hierarchy axioms come straight from the ECTO release.

Verification

• All 18 ECTO replacement targets verified non-obsolete via OLS (bidirectional label match).
• Branch is self-contained: no EFO term outside these 25 references any of them (only external GWAS annotation data does), so obsoletion creates no dangling references.
• make normalize_src clean; robot reason (ELK) → no unsatisfiable classes. (Run locally with a temporary empty stub for the gitignored, not-yet-generated imports/mondo_import.owl; CI runs the full import pipeline.)

Open question

The 7 "no ECTO equivalent" terms are kept (re-parented) rather than obsoleted-without-replacement, to avoid orphaning their existing GWAS annotations. If the branch should instead be fully retired, they can be obsoleted too (with no replacement).

Closes #2737

🤖 Generated with Claude Code

https://claude.ai/code/session_01Jki5T73Qgyb2VGMuWsWtZy