Add behavioural stress (TGEMO_00210)

[ppavlidis]

Summary

Adds TGEMO_00210 — behavioural stress — as a subclass of EFO:0000470 (environmental stress).

Motivation: Paul 2026-06-12 review of GSE193284 (chronic mild stress / CMS) surfaced that the curation agent had no canonical URI for the behavioural-stress concept. The existing curation pattern was to bind EFO:0000470 directly with the typed phrase as a label, but EFO:0000470's canonical label is "environmental stress" — a different concept (environmental factors like thermal, chemical, etc.). Behavioural / psychological stress is a distinct kind of stressor that deserves its own term.

What the new term enables

With this term in place, a CMS-shape FV (the canonical example) can be emitted as compositional decomposition rather than as a compound subject:

typed FV label	emitted statements
Chronic mild stress	behavioural stress (TGEMO_00210) + has modifier + mild (HP:0012825) behavioural stress + has modifier + chronic (HP:0011010) behavioural stress + delivered for duration + "3 weeks" (free text)
Chronic mild stress + Phloretin	above three, plus Phloretin (CHEBI:17276) + delivered at dose + "20 mg/kg"

This pattern reuses existing HPO severity / chronicity terms for the modifier slots and keeps the experimental-duration as a separate delivered for duration statement. Conceptual chronicity ("this is a chronic stress paradigm") is queryable separately from the specific experimental window ("the protocol ran 3 weeks") — they answer different downstream questions.

Synonyms — stress is RELATED not EXACT

stress alone is ambiguous (environmental thermal, oxidative, mechanical, cellular, behavioural all exist) and is tagged as hasRelatedSynonym, not hasExactSynonym. Only behavioral stress (US spelling) and psychological stress are tagged exact — they refer to the same concept directly. stressor and stressful experience are also related.

Provisional parent

EFO:0000470 (environmental stress) is provisional per Paul. Strictly speaking behavioural stress is a stressor / protocol type, not a treatment effect, and a more appropriate parent may be chosen in a future revision. The provisional note is preserved in the definition.

Field summary

field	value
URI	http://gemma.msl.ubc.ca/ont/TGEMO_00210
label	behavioural stress
parent	EFO:0000470 (environmental stress) — provisional
definition	A behavioural or psychological stressor applied to an experimental subject. Combines with severity modifiers (mild / moderate / severe), temporal-pattern modifiers (acute / chronic), and delivered for duration for the experimental time course.
exact synonyms	behavioral stress · psychological stress
related synonyms	stress · stressor · stressful experience

Coordinated changes

Pairs with these PavlidisLab/gemma-curation-agents commits:

• 0917f5d — adds compositional-decomposition rule to curator_wisdom.md + D17 orchestrator-checklist invariant
• e1e5e98 — rewrites column_annotator.py Example A to teach the decomposition pattern (was teaching the wrong Chronic mild stress → EFO:0000470 direct binding)
• 8cae6ff — refines the wisdom-doc decomposition example to use behavioural stress specifically (not bare stress) per Paul's clarification that stress is too broad; also adds the general rule "existing curation is a signal, not authority"

Once this PR lands and Gemma reloads the ontology, those agent-side rules ground their canonical URIs.