/
allen_ephys_dataset.hjson
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/
allen_ephys_dataset.hjson
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{
type: [
Dataset
Trace
]
id: forge.format("identifier", "traces", str(x.specimen__id))
brainLocation:
{
type: BrainLocation
brainRegion:
{
id: f"http://api.brain-map.org/api/v2/data/Structure/{x.structure__id}"
label: x.structure__acronym
}
coordinatesInBrainAtlas:
{
valueX: x.csl__x
valueY: x.csl__y
valueZ: x.csl__z
}
layer: x.structure__layer
hemisphere: x.specimen__hemisphere
}
contribution:
{
type: Contribution
agent:
{
type: Organization
id: https://www.grid.ac/institutes/grid.417881.3
name: Allen Institute for Brain Science
}
}
generation:
{
type: Generation
activity:
{
type: nsg:StimulusExperiment
hadProtocol:
{
type: Protocol
id: http://help.brain-map.org/display/celltypes/Documentation?preview=/8323525/10813530/CellTypes_Morph_Overview.pdf
name: Technical White Paper: Cell Morphology and Histology
description: Protocol used to generate Allen Cell Types Database.
}
}
}
distribution: forge.attach(f"./allen_cell_types_database/specimen_{x.specimen__id}/ephys.nwb", content_type="application/nwb")
identifier: x.specimen__id
name: x.specimen__name
subject:
{
type: Subject
name: x.donor__name
species: {
label: x.donor__species
}
identifier: x.donor__id
age:
{
period: Post-natal
unitCode: x.donor__age.split(" ")[-1]
value: x.donor__age.split(" ")[0]
}
strain: {
label: x.line_name
}
sex: {
label: x.donor__sex
}
}
license:
{
type: License
id: https://alleninstitute.org/legal/terms-use/
}
objectOfStudy:
{
type: ObjectOfStudy
id: http://bbp.epfl.ch/neurosciencegraph/taxonomies/objectsofstudy/singlecells
label: Single Cell
}
derivation:
{
type: Derivation
entity: {
name: x.specimen__name
identifier: x.specimen__id
}
}
cell_reporter_status: x.cell_reporter_status
csl__normalized_depth: x.csl__normalized_depth
donor__disease_state: x.donor__disease_state
donor__race: x.donor__race
donor__years_of_seizure_history: x.donor__years_of_seizure_history
}