# Curated bridge: IMPReSS behavioural assay TYPE -> the GO behaviour process(es) # a positive result can legitimately inform. THIS FILE IS HAND-CURATED (unlike # the auto-ingested procedures.tsv / behavioural_assays.yaml). # # `assay_type` matches the canonical type emitted by ingest_impress.py, so this # map joins to behavioural_assays.yaml on that key (see check_behaviour_assays.py). # # Rationale: no public ontology maps a behavioural assay to the GO process it # licenses (NBO/MP describe the process/phenotype, IMPReSS/OBI the assay, CogPO # the human task). This file fills that gap for the IMPReSS battery, and encodes # the over-annotation caution from the ASSAY_TO_FUNCTION framework: a behavioural # assay is the extreme phenotypic + high-convergence readout, so a hit licenses # at most a NON-CORE biological-process term and never an MF or a core call. All # `supports_go` ids verified against QuickGO. proximity: phenotypic # every behavioural assay measures a whole-animal output convergence: high # ... that integrates the entire nervous system + more default_curation: KEEP_AS_NON_CORE # the most a behavioural-assay hit should license assays: - assay_type: Open Field measures: spontaneous locomotion, exploration and (thigmotaxis-based) anxiety in a novel arena supports_go: - {id: GO:0007626, label: locomotory behavior} - {id: GO:0008344, label: adult locomotory behavior} - {id: GO:0035641, label: locomotory exploration behavior} - {id: GO:0035640, label: exploration behavior} note: >- Anxiety/thigmotaxis has no clean GO term; do not invent one. Locomotor change here is distal — skeletal, muscular or metabolic defects move it too. - assay_type: Light-Dark Test measures: light/dark compartment preference as an anxiety/exploration index supports_go: - {id: GO:0035640, label: exploration behavior} note: An anxiety proxy with no direct GO anxiety term; weak, non-core evidence only. - assay_type: Y-maze measures: spontaneous alternation (spatial working memory) / arm exploration supports_go: - {id: GO:0007613, label: memory} - {id: GO:0007612, label: learning} note: Reduced alternation is a distal cognitive readout downstream of hippocampal/circuit function. - assay_type: Morris Water Maze not_in_impress: true # classic assay, widely used in the literature, not in the IMPC battery measures: latency/path to a hidden platform in a water pool (spatial learning and memory) supports_go: - {id: GO:0007613, label: memory} - {id: GO:0007612, label: learning} - {id: GO:0008306, label: associative learning} note: >- A SPATIAL-MEMORY test that happens to use swimming. The swimming is the assay modality, NOT the readout: a gene measured in the MWM (e.g. caspase-3 as an apoptosis marker) must not be annotated to `swimming behavior` (GO:0036269) — see the Casp3 case in the BEHAVIOR project. - assay_type: Fear Conditioning measures: conditioned freezing to context/cue (associative fear learning and memory) supports_go: - {id: GO:0008306, label: associative learning} - {id: GO:0001662, label: behavioral fear response} - {id: GO:0007613, label: memory} note: Among the more specific behavioural assays, but still phenotypic; non-core. - assay_type: Acoustic Startle and Pre-pulse Inhibition (PPI) measures: whole-body startle reflex amplitude and its sensorimotor-gating inhibition by a prepulse supports_go: - {id: GO:0001964, label: startle response} - {id: GO:0060134, label: prepulse inhibition} note: PPI deficits are a sensorimotor-gating endophenotype; informative but convergent. - assay_type: Rotarod measures: latency to fall from an accelerating rotating rod (motor coordination and balance) supports_go: - {id: GO:0061744, label: motor behavior} - {id: GO:0007626, label: locomotory behavior} note: >- A motor-coordination readout; cerebellar, neuromuscular, skeletal or even body-weight differences all move it, so it is highly convergent — non-core. - assay_type: Hole-board Exploration measures: head-dipping into floor holes as an exploration / novelty-seeking index supports_go: - {id: GO:0035640, label: exploration behavior} note: Distal exploratory readout; non-core. - assay_type: Hot Plate (nociception) measures: latency to a nociceptive response (paw lick/jump) on a heated surface (thermal pain) supports_go: - {id: GO:0048266, label: behavioral response to pain} - {id: GO:0019233, label: sensory perception of pain} note: A thermal-nociception readout; supports a pain-response BP term, non-core. - assay_type: Von Frey Test (nociception) measures: paw-withdrawal threshold to calibrated filaments (mechanical pain sensitivity) supports_go: - {id: GO:0048266, label: behavioral response to pain} - {id: GO:0050966, label: detection of mechanical stimulus involved in sensory perception of pain} note: A mechanical-nociception readout; supports a pain-response BP term, non-core. - assay_type: Sleep-Wake measures: sleep/wake architecture and amount (e.g. PiezoSleep / activity-based) supports_go: - {id: GO:0030431, label: sleep} - {id: GO:0048512, label: circadian behavior} - {id: GO:0045187, label: "regulation of circadian sleep/wake cycle, sleep"} - {id: GO:0042321, label: "negative regulation of circadian sleep/wake cycle, sleep"} note: >- Sleep amount/architecture is a distal whole-animal output; non-core — except for bona fide circadian-clock components (e.g. CRY), for which a sleep/wake term can be near-core (the documented behaviour-rubric exception). - assay_type: SHIRPA / Dysmorphology battery measures: broad observational battery of reflexes, posture, gait, tremor, grooming and provoked behaviours supports_go: - {id: GO:0007610, label: behavior} note: >- A screen, not a specific assay — low specificity. Use the most specific sub-observation, not the umbrella `behavior` term, and keep non-core. - assay_type: Indirect Calorimetry measures: primarily metabolic rate; also logs home-cage locomotor activity supports_go: - {id: GO:0007626, label: locomotory behavior} note: >- Primarily a metabolic assay; the activity channel is a side parameter, so a behavioural call from it is especially weak. Metabolic is the core readout. # ---- Fenced: assays that should NOT license a GO behaviour term ---- - assay_type: Auditory Brain Stem Response measures: electrophysiological hearing thresholds (an evoked potential, not a behaviour) supports_go: - {id: GO:0007605, label: sensory perception of sound} note: >- ABR is electrophysiology, NOT a behavioural assay. It supports a hearing (sensory) term at most; do NOT use it to assign `auditory behavior` (GO:0031223), which requires a behavioural readout. - assay_type: Grip Strength measures: peak forelimb/all-limb force (neuromuscular function) supports_go: [] note: >- A neuromuscular-strength readout, not a behaviour. It should NOT license any behaviour GO term; flagged so grip-strength phenotypes are not mis-annotated to the behaviour branch. - assay_type: Tail Suspension measures: immobility time during tail suspension (a depression-like / behavioural-despair index) supports_go: [] note: >- No precise GO term exists for "behavioural despair"/depression-like immobility; do NOT invent or stretch one. Treat as a non-specific affective endophenotype, not a basis for a behaviour-branch annotation.