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create json schema for electrophysiology metadata #18

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145 changes: 145 additions & 0 deletions Data-Standards/Patch-Seq/electrophysiology-metadata-schema.json
Original file line number Diff line number Diff line change
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{
"$schema": "http://json-schema.org/draft-07/schema#",
"$id": "electrophysiology-metadata-schema.json",
"title": "Intracellular electrophysiology metadata",
"description": "Formal description of the IC Ephys Metadata List",
"author": "Ben Dichter",
"contact": "[email protected]",
"version": "0.1.0",
"type": "object",
"required": [
"species",
"subject_id",
"subject_age",
"subject_sex",
"subject_date_of_birth",
"citation_policy",
"institution",
"genotype",
"cre_line",
"external_solution_recipe",
"recording_temperature",
"electrode_resistance",
"electrode_internal_solution_recipe",
"specimen_id",
"electrode_id",
"stimulus_electrode_id",
"stimulus_id",
"stimulus_type_name"
],
"properties": {
"species": {"type": "string"},
"subject_id": {"type": "string"},
"subject_age": {
"type": "object",
"properties": {
"value": {
"type": "string",
"description": "Using ISO 8601 duration"
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How does this handle ages reported as P14?

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Does P14 mean 14 days after birth? Then age in ISO 8106 would be P14D.

},
"type": {
"type": "string",
"description": "Fetal age or birth age.",
"default": "birth"
}
}
},
"subject_sex": {"type": "string"},
"subject_date_of_birth": {"type": "string", "format": "datetime"},
"specimen_id": {"type": "string"},
"citation_policy": {"type": "string"},
"institution": {"type": "string"},
"genotype": {"type": "string"},
"cre_line": {"type": "string"},
"external_solution_recipe": {"type": "string"},
"recording_temperature": {"type": "number", "description": "temperature of bath in Celsius"},
"electrode_id": {"type": "string"},
"electrode_resistance": {"type": "number", "description": "Electrode resistance in MOhms"},
"electrode_internal_solution_recipe": {"type": "string"},
"current_clamp_amp_settings":
{
"allOf": [
{ "$ref": "#/definitions/amp_settings" },
{
"required": [
"bridge_balance_enabled",
"fast_capacitance_compensation_enabled",
"leak_current_enabled",
"leak_current_value"
],
"properties": {
"bridge_balance_enabled": {"type": "boolean"},
"bridge_balance_value": {"type": "number", "description": "in MOhs"},
"fast_capacitance_compensation_enabled": {"type": "boolean"},
"fast_capacitance_compensation_value": {"type": "number", "description": "in MOhms"},
"leak_current_enabled": {"type": "boolean"},
"leak_current_value": {"type": "number"},
"pipette_capacitance_neutralization": {"type": "number", "description": "in pF"},
"pipette_offset": {"type": "number", "description": "in nA"}
}
}
]
},
"voltage_clamp amp_settings":
{
"allOf": [
{ "$ref": "#/definitions/amp_settings" },
{
"required": [
"whole_cell_capacitance_compensation_enabled",
"electrode_capacitance_compensation_enabled",
"series_resistance_correction_enabled"
],
"properties":
{
"whole_cell_capacitance_compensation_enabled": {"type": "boolean"},
"whole_cell_capacitance_compensation_value": {"type": "number", "description": "in pF"},
"whole_cell_capacitance_compensation_resistance": {"type": "number", "description": "in MOhms"},
"electrode_capacitance_compensation_enabled": {"type": "boolean"},
"electrode_capacitance_compensation_value_fast": {"type": "number", "description": "in pF"},
"electrode_capacitance_compensation_value_slow": {"type": "number", "description": "in pF"},
"electrode_capacitance_compensation_fast_time_constant": {"type": "number", "description": "in µs"},
"electrode capacitance compensation_slow_time_constant": {"type": "number", "description": "in µs"},
"series_resistance_correction_enabled": {"type": "boolean"},
"series_resistance_correction_value": {"type": "number", "description": "ratio"},
"series_resistance_correction_prediction": {"type": "number", "description": "ratio"},
"series_resistance_bandwidth": {"type": "number", "description": "in kHz"},
"pipette_offset": {"type": "number", "description": "in mV"},
"leak_subtraction": {"type": "number", "description": "in MOhms"}
}
}
]
},
"stimulus_type_name": {"type": "string"},
"stimulus_id": {"type": "string"},
"stimulus_electrode_id": {"type": "string"},
"cell_location": {"type": "string"},
"electrode_zeroed_bias_current": {"type": "string", "description": " in pA"},
"initial_access_resistance": {"type": "number", "description": "in MOhms"},
"tight_seal_resistance": {"type": "number", "description": "in MOhms"},
"input_resistance": {"type": "number", "description": "in MOhms"}
},
"definitions":
{
"amp_settings": {
"type": "object",
"required": [
"gain",
"output_high_pass_cutoff_frequency",
"output_high_pass_filter_type",
"output_low_pass_cutoff_frequency",
"output_low_pass_filter_type",
"holding"
],
"properties": {
"gain": {"type": "number"},
"output_low_pass_filter_type": {"type": "string"},
"output_low_pass_cutoff_frequency": {"type": "number"},
"output_high_pass_filter_type": {"type": "string"},
"output_high_pass_cutoff_frequency": {"type": "number"},
"holding": {"type": "number", "description": "in mV"},
"output_zero/zero_offset": {"type": "number", "description": "in mV"}
}
}
}
}