# Neuroscience domain profile
# Filename (without .yaml) is the domain key: "neuroscience"
# Sources: eNeuro reporting standards, MINSCOPE wiki, RRID:Antibody Registry

name: "Neuroscience"

journals:
  - Neuron
  - Nature
  - "Nature Neuroscience"
  - "Nature Methods"
  - Cell
  - eNeuro
  - "Journal of Neuroscience"

# Neuroscience papers span many species — species is intentionally absent.

# Nomenclature
nomenclature:
  - rule: "Brain region abbreviations: CA1, CA3, V1, S1, M1, DG (dentate gyrus), PFC (prefrontal cortex)"
  - rule: "Neuron types: pyramidal, interneuron (parvalbumin+, somatostatin+, VIP+)"
  - rule: "Receptor names: AMPA, NMDA, GABA-A, GABA-B (no italics)"
  - rule: "Channel names: Nav1.1, Kv3.1 (gene/protein convention per species)"
  - rule: "Recording types: patch-clamp (whole-cell, cell-attached), extracellular (single-unit, multi-unit), two-photon, calcium imaging (GCaMP)"
  - rule: "Always report animal species, strain, age, sex for in vivo experiments"
  - rule: "Brain coordinates: use Allen Brain Atlas reference atlas"

# Standard assays
standard_assays:
  - "patch-clamp recording"
  - "extracellular recording"
  - "two-photon imaging"
  - "calcium imaging (GCaMP)"
  - "optogenetics"
  - "chemogenetics (DREADD)"
  - "fiber photometry"
  - "miniscope imaging"
  - "behavioral assay (open field, fear conditioning, Morris water maze)"
  - "immunohistochemistry"
  - "in situ hybridization"

# Auto-detect keywords
detect_keywords: [neuron, synapse, cortex, hippocampus, amygdala, "brain region", "patch-clamp", "two-photon", GCaMP, "action potential", "membrane potential", optogenetics, DREADD, "fiber photometry", pyramidal, interneuron, "Allen Brain"]

# Term mappings
term_mappings:
  - source: "brain activity"
    target: "neural activity"
  - source: "neuronal firing"
    target: "action potential firing"

# Reporting standards
reporting:
  rrid_required: true
  rrid_types: [antibody, "mouse line", "plasmid", virus]
  key_resources_table: true
  arrive2: false  # only if using animals — paper should specify
  rigorous_statistics: "Statistics for neuroscience research: use estimation statistics (effect sizes with CIs), not just NHST"

# Voice rules
voice:
  introduction: "HIGH assertiveness. State the gap; state the question."
  methods: "HIGHEST assertiveness. Detail species, strain, recording method, sample size."
  results: "HIGH assertiveness. State findings with n (cells, animals), p, effect size, 95% CI."
  discussion: "Moderate hedging. Speculation only in final paragraph."

# Sex
sex:
  - female
  - male