Building Entities¶
ModelBuildingConfig¶
The ModelBuildingConfig serves as the master configuration for the entire model building workflow, encompassing all generator configurations required at each stage of the process.
CellCompositionConfig¶
The CellCompositionConfig is a configuration entity that stores the settings used to update the densities of an existing CellComposition.
Distribution Keys¶
Key |
Explanation |
|---|---|
variantDefinition |
CWL definition to be used. |
inputs |
Inputs to placement. A CellComposition entry. |
configuration |
Overrides for the CellComposition input. |
inputs is used to list the base CellComposition that will be used and configuration to specify the optional overrides of which densities to modify.
To specify an overrides the region/mtype/etype combination must be specified as follows:
"overrides": {
"http://api.brain-map.org/api/v2/data/Structure/23": {
"hasPart": {
"https://bbp.epfl.ch/ontologies/core/bmo/GenericExcitatoryNeuronMType": {
"hasPart": {
"https://bbp.epfl.ch/ontologies/core/bmo/GenericExcitatoryNeuronEType": {
"composition": {
"neuron": {
"density": 1200
}
}
}
}
}
}
}
}
There are two keys that can be used to update a density composition:
density
density_ratio
where density is used to update the voxels with the specific value and density-ratio adjusts the values relative to an existing density.
Distribution Schema¶
%YAML 1.1
---
"$schema": https://json-schema.org/draft/2020-12/schema
title: CellCompositionConfig distribution schema
'$defs':
uri:
type: string
format: uri
pattern: '^https?:\/\/[^?#]*$' # uri without query or fragment
revision:
type: integer
minimum: 1
variant_info:
type: object
required:
- algorithm
- version
algorithm:
type: string
version:
type: string
input_entry:
type: object
required:
- name
- type
- id
properties:
name:
type: string
type:
type: string
id:
type: string
additionalProperties: false
patternProperties:
'^http://api.brain-map.org/api/v2/data/Structure/997$':
type: object
required:
- variantDefinition
- inputs
- configuration
additionalProperties: false
properties:
variantDefinition:
'$ref': '#/$defs/variant_info'
inputs:
type: array
items:
'$ref': '#/$defs/input_entry'
configuration:
type: object
required:
- overrides
properties:
overrides:
additionalProperties: false
patternProperties:
'^https?:\/\/.*\/Structure\/\d*$': # brain regions finishing in /Structure/int
type: object
required:
- label
- hasPart
properties:
label:
type: string
hasPart:
type: object
additionalProperties: false
patternProperties:
'^https?:\/\/[^?#]*$': # etypes
type: object
properties:
label:
type: string
'_rev':
type: integer
composition:
type: object
required:
- neuron
properties:
neuron:
type: object
required:
- density
properties:
density:
type: number
Distribution Example¶
{
"http://api.brain-map.org/api/v2/data/Structure/997": {
"variantDefinition": {
"algorithm": "cell_composition_manipulation",
"version": "v3"
},
"inputs": [
{
"name": "base_cell_composition_id",
"type": "Dataset",
"id": "https://bbp.epfl.ch/neurosciencegraph/data/cellcompositions/54818e46-cf8c-4bd6-9b68-34dffbc8a68c?tag=v1.1.0"
}
],
"configuration": {
"version": 1,
"unitCode": {
"density": "mm^-3"
},
"overrides": {
"http://api.brain-map.org/api/v2/data/Structure/23": {
"label": "Anterior amygdalar area",
"about": "BrainRegion",
"hasPart": {
"https://bbp.epfl.ch/ontologies/core/bmo/GenericExcitatoryNeuronMType": {
"label": "GEN_mtype",
"about": "MType",
"hasPart": {
"https://bbp.epfl.ch/ontologies/core/bmo/GenericExcitatoryNeuronEType": {
"label": "GEN_etype",
"about": "EType",
"composition": {
"neuron": {
"density": 1200
}
}
}
}
}
}
}
}
}
}
}
CellPositionConfig¶
The CellPositionConfig is a configuration entity that stores the settings used for placing cells in space.
Distribution Keys¶
Key |
Explanation |
|---|---|
variantDefinition |
CWL definition to be used. |
inputs |
Inputs to placement. Currently Empty. |
configuration |
Placement algorithm configuration options. |
Distribution Schema¶
%YAML 1.1
---
"$schema": https://json-schema.org/draft/2020-12/schema
title: CellCompositionConfig distribution schema
'$defs':
variant_info:
type: object
required:
- algorithm
- version
algorithm:
type: string
version:
type: string
additionalProperties: false
patternProperties:
'^http://api.brain-map.org/api/v2/data/Structure/997$':
type: object
required:
- variantDefinition
- configuration
properties:
variantDefinition:
'$ref': '#/$defs/variant_info'
configuration:
type: object
required:
- place_cells
properties:
place_cells:
type: object
properties:
soma_placement:
type: string
density_factor:
type: number
seed:
type: integer
Distribution Example¶
{
"http://api.brain-map.org/api/v2/data/Structure/997": {
"variantDefinition": {
"algorithm": "neurons_cell_position",
"version": "v3"
},
"inputs": [],
"configuration": {
"place_cells": {
"soma_placement": "basic",
"density_factor": 1,
"sort_by": [
"region",
"mtype"
],
"seed": 0,
"mini_frequencies": false
}
}
}
}
MorphologyAssignmentConfig¶
The MorphologyAssignmentConfig is a configuration entity that stores the settings used for assigning morphologies to a node population.
Distribution Keys¶
Key |
Explanation |
|---|---|
variantDefinition |
CWL definitions to be used. |
defaults |
Default configurations for synthesis and placeholders. |
configuration |
Configuration for topological synthesis entries. |
There are two main ways of asignment:
placeholder_assignment: Use placeholder cells.
topological_synthesis: Synthesize morphologies using topological branching information.
defaults¶
The configurations for placeholders and synthesis are stored under defaults corresponding to the following entities:
which define a canonical model or placeholder morphologies for each (region, mtype) combination in the atlas.
"defaults": {
"topological_synthesis": {
"@id": "https://bbp.epfl.ch/data/bbp/mmb-point-neuron-framework-model/fae6eb46-3007-41c6-af69-941a82aada68",
"@type": "CanonicalMorphologyModelConfig"
},
"placeholder_assignment": {
"@id": "https://bbp.epfl.ch/data/bbp/mmb-point-neuron-framework-model/9503a07d-8337-48eb-8637-acc26b0f13bf",
"@type": "PlaceholderMorphologyConfig"
}
Note
Both default configurations should be computed on the same Atlas Release and be in sync with each other.
configuration¶
In the configuration section only the (region, mtype) combinations that will be synthesized are listed:
"configuration": {
"topological_synthesis": {
"http://api.brain-map.org/api/v2/data/Structure/632": {
"https://bbp.epfl.ch/ontologies/core/bmo/GenericExcitatoryNeuronMType": {}
}
}
}
The entries in configuration determine which entries will be selected from the default CanonicalMorphologyModelConfig. By convention the rest of the entries will be assigned placeholders from the default PlaceholderMorphologyConfig.
It is also possible to specify overrides for the topological synthesis configuration as follows:
"configuration": {
"topological_synthesis": {
"http://api.brain-map.org/api/v2/data/Structure/632": {
"https://bbp.epfl.ch/ontologies/core/bmo/GenericExcitatoryNeuronMType": {
"@id": "https://bbp.epfl.ch/data/bbp/mmb-point-neuron-framework-model/canonicalmorphologymodels/dfda5210-39b5-428d-ac0c-43852f99df02",
"overrides": {
"apical_dendrite": {
"randomness": 0.11,
"step_size": {
"norm": {
"mean": 7.6,
"std": 0.2
}
},
"targeting": 0.34
}
}
}
}
}
}
Distribution Schema¶
%YAML 1.1
---
"$schema": https://json-schema.org/draft/2020-12/schema
title: MorphologyAssignmentConfig distribution schema
'$defs':
uri:
type: string
format: uri
pattern: '^https?:\/\/[^?#]*$' # uri without query or fragment
revision:
type: integer
minimum: 1
variant_info:
type: object
required:
- algorithm
- version
algorithm:
type: string
version:
type: string
variant_entry:
type: object
required:
- '@id'
properties:
'@id':
'$ref': '#/$defs/uri'
'_rev':
'$ref': '#/$defs/revision'
type: object
required:
- variantDefinition
- defaults
- configuration
properties:
version:
type: integer
variantDefinition:
type: object
required:
- topological_synthesis
- placeholder_assignment
properties:
topological_synthesis:
"$ref": "#/$defs/variant_info"
placeholder_assignment:
"$ref": "#/$defs/variant_info"
defaults:
type: object
required:
- topological_synthesis
- placeholder_assignment
properties:
topological_synthesis:
"$ref": "#/$defs/variant_entry"
placeholder_assignment:
"$ref": "#/$defs/variant_entry"
configuration:
type: object
properties:
topological_synthesis:
type: object
patternProperties:
'^https?:\/\/.*\/Structure\/\d*$': # brain regions finishing in /Structure/int
type: object
patternProperties:
'^https?:\/\/[^?#]*$': # mtypes
type: object
properties:
'@id':
'$ref': '#/$defs/uri'
'_rev':
'$ref': '#/$defs/revision'
overrides:
type: object
properties:
apical_dendrite:
type: object
properties:
randomness:
type: number
step_size:
type: object
properties:
norm:
type: object
properties:
mean:
type: number
std:
type: number
additionalProperties: false
additionalProperties: false
targeting:
type: number
additionalProperties: false
additionalProperties: false
additionalProperties: false
Distribution Example¶
{
"variantDefinition": {
"topological_synthesis": {
"algorithm": "topological_synthesis",
"version": "v1"
},
"placeholder_assignment": {
"algorithm": "placeholder_assignment",
"version": "v1"
}
},
"defaults": {
"topological_synthesis": {
"@id": "https://bbp.epfl.ch/data/bbp/mmb-point-neuron-framework-model/5ec117b5-8ffa-4f3b-95ca-1dc8ad1b0c4d",
"@type": [
"CanonicalMorphologyModelConfig",
"Entity"
]
},
"placeholder_assignment": {
"@id": "https://bbp.epfl.ch/neurosciencegraph/data/06b340d4-ac99-4459-bab4-013ef7199c36",
"@type": [
"PlaceholderMorphologyConfig",
"Entity"
],
"_rev": 2
}
},
"configuration": {
"topological_synthesis": {
"http://api.brain-map.org/api/v2/data/Structure/632": {
"https://bbp.epfl.ch/ontologies/core/bmo/GenericExcitatoryNeuronMType": {
"@id": "https://bbp.epfl.ch/data/bbp/mmb-point-neuron-framework-model/canonicalmorphologymodels/dfda5210-39b5-428d-ac0c-43852f99df02",
"overrides": {
"apical_dendrite": {
"randomness": 0.11,
"step_size": {
"norm": {
"mean": 7.6,
"std": 0.2
}
},
"targeting": 0.34
}
}
}
}
}
}
}
MEModelConfig¶
The MEModelConfig is a configuration entity that stores the settings used for assigning emodels to node populations with morphologies.
Distribution Keys¶
Key |
Explanation |
|---|---|
variantDefinition |
CWL definitions to be used. |
defaults |
Placeholder configurations for emodels. |
overrides |
Overrides to placeholder emodel configuration. |
defaults¶
The defaults contain the following placeholder configurations:
neurons_me_model: PlaceholderEModelConfig
overrides¶
Distribution Schema¶
%YAML 1.1
---
"$schema": https://json-schema.org/draft/2020-12/schema
title: MorphologyAssignmentConfig distribution schema
'$defs':
uri:
type: string
format: uri
pattern: '^https?:\/\/[^?#]*$' # uri without query or fragment
revision:
type: integer
minimum: 1
variant_info:
type: object
required:
- algorithm
- version
algorithm:
type: string
version:
type: string
entity_entry:
type: object
required:
- '@id'
properties:
'@id':
'$ref': '#/$defs/uri'
'_rev':
'$ref': '#/$defs/revision'
type: object
required:
- variantDefinition
- defaults
properties:
version:
type: integer
minimim: 1
variantDefinition:
type: object
properties:
neurons_me_model:
"$ref": "#/$defs/variant_info"
defaults:
type: object
properties:
neurons_me_model:
"$ref": "#/$defs/entity_entry"
overrides:
type: object
properties:
neurons_me_model:
type: object
patternProperties:
'^https?:\/\/.*\/Structure\/\d*$': # brain regions finishing in /Structure/int
type: object
patternProperties:
'^https?:\/\/[^?#]*$': # mtypes
type: object
patternProperties:
'^https?:\/\/[^?#]*$': # etypes
type: object
properties:
assignmentAlgorithm:
const: "assignOne"
eModel:
"$ref": "#/$defs/entity_entry"
axonInitialSegmentAssignment:
type: object
properties:
fixedValue:
type: object
properties:
value:
type: number
additionalProperties: false
additionalProperties: false
additionalProperties: false
Distribution Example¶
{
"variantDefinition": {
"neurons_me_model": {
"algorithm": "neurons_me_model",
"version": "v1"
}
},
"defaults": {
"neurons_me_model": {
"@id": "https://bbp.epfl.ch/data/bbp/mmb-point-neuron-framework-model/2ec96e9f-7254-44b5-bbcb-fdea3e18f110",
"@type": ["PlaceholderEModelConfig", "Entity"]
}
},
"overrides": {
"neurons_me_model": {
"http://api.brain-map.org/api/v2/data/Structure/614454342": {
"http://uri.interlex.org/base/ilx_0381367": {
"http://bbp.epfl.ch/neurosciencegraph/ontologies/etypes/cADpyr": {
"assignmentAlgorithm": "assignOne",
"emodel": {
"@id": "https://bbp.epfl.ch/neurosciencegraph/data/f91eeb30-c6e7-40f8-8917-fd8007ec8917",
"_rev": 2
},
"axonInitialSegmentAssignment": {"fixedValue": {"value": 1}}
}
}
}
}
}
}
MacroConnectomeConfig¶
The MacroConnectomeConfig is a configuration entity that stores the settings used for macroscopic connectome configuration.
Distribution Keys¶
Key |
Explanation |
|---|---|
initial |
Initial connectome configurations. |
overrides |
Connectome overrides on the initial configuration. |
Distribution Schema¶
%YAML 1.1
---
"$schema": https://json-schema.org/draft/2020-12/schema
title: MacroConnectomeConfig distribution schema
'$defs':
uri:
type: string
format: uri
pattern: '^https?:\/\/[^?#]*$' # uri without query or fragment
revision:
type: integer
minimum: 1
required:
- initial
properties:
initial:
type: object
properties:
connection_strength:
type: object
additionalProperties: false
properties:
id:
'$ref': '#/$defs/uri'
type:
'oneOf':
- type: string
const: BrainConnectomeStrength
- type: array
contains:
type: string
const: BrainConnectomeStrength
rev:
'$ref': '#/$defs/revision'
overrides:
type: object
properties:
connection_strength:
type: object
additionalProperties: false
properties:
id:
'$ref': '#/$defs/uri'
type:
'oneOf':
- type: string
const: BrainConnectomeStrengthOverrides
- type: array
contains:
type: string
const: BrainConnectomeStrengthOverrides
rev:
'$ref': '#/$defs/revision'
Distribution Example¶
{
"initial": {
"connection_strength": {
"id": "https://bbp.epfl.ch/neurosciencegraph/data/connectomestrength/8e285d4b-4d09-4357-98ae-9e9fc61face6",
"type": [
"Entity",
"Dataset",
"BrainConnectomeStrength"
],
"rev": 10
}
},
"overrides": {
"connection_strength": {
"id": "https://bbp.epfl.ch/neurosciencegraph/data/wholebrainconnectomestrengths/9357f9b4-8e94-45cd-b701-8d18648a17a6",
"type": [
"Entity",
"Dataset",
"BrainConnectomeStrengthOverrides"
],
"rev": 1
}
},
"_ui_data": {
"editHistory": []
}
}
MicroConnectomeConfig¶
The MicroConnectomeConfig is a configuration entity that stores the settings used for microscopic connectome configuration.
Distribution Keys¶
Key |
Explanation |
|---|---|
variants |
Variant CWL definitions for connectome algorithms. |
initial |
Initial micro connectome configurations. |
overrides |
Connectome overrides on the initial configuration. |
Distribution Schema¶
%YAML 1.1
---
"$schema": https://json-schema.org/draft/2020-12/schema
title: MicroConnectomeConfig distribution schema
'$defs':
uri:
type: string
format: uri
pattern: '^https?:\/\/[^?#]*$' # uri without query or fragment
revision:
type: integer
minimum: 1
param:
type: object
additionalProperties: false
properties:
type:
type: string
unitCode:
type: string
default:
type: number
type: object
required:
- variants
- initial
- overrides
properties:
variants:
type: object
properties:
placeholder__erdos_renyi:
type: object
additionalProperties: false
properties:
algorithm:
type: string
version:
type: string
params:
type: object
properties:
weight:
'$ref': '#/$defs/param'
nsynconn_mean:
'$ref': '#/$defs/param'
nsynconn_std:
'$ref': '#/$defs/param'
delay_velocity:
'$ref': '#/$defs/param'
delay_offset:
'$ref': '#/$defs/param'
placeholder__distance_dependent:
type: object
additionalProperties: false
properties:
algorithm:
type: string
version:
type: string
params:
type: object
properties:
weight:
'$ref': '#/$defs/param'
exponent:
'$ref': '#/$defs/param'
nsynconn_mean:
'$ref': '#/$defs/param'
nsynconn_std:
'$ref': '#/$defs/param'
delay_velocity:
'$ref': '#/$defs/param'
delay_offset:
'$ref': '#/$defs/param'
initial:
type: object
additionalProperties: false
required:
- variants
- placeholder__erdos_renyi
- placeholder__distance_dependent
properties:
variants:
type: object
required:
- id
- type
properties:
id:
'$ref': '#/$defs/uri'
type:
'oneOf':
- type: string
const: MicroConnectomeVariantSelection
- type: array
items:
type: string
contains:
type: string
const: MicroConnectomeVariantSelection
rev:
'$ref': '#/$defs/revision'
placeholder__erdos_renyi:
type: object
required:
- id
- type
properties:
id:
'$ref': '#/$defs/uri'
type:
'oneOf':
- type: string
const: MicroConnectomeData
- type: array
items:
type: string
contains:
type: string
const: MicroConnectomeData
rev:
'$ref': '#/$defs/revision'
placeholder__distance_dependent:
type: object
required:
- id
- type
properties:
id:
'$ref': '#/$defs/uri'
type:
'oneOf':
- type: string
const: MicroConnectomeData
- type: array
items:
type: string
contains:
type: string
const: MicroConnectomeData
rev:
'$ref': '#/$defs/revision'
overrides:
type: object
additionalProperties: false
required:
- variants
- placeholder__erdos_renyi
- placeholder__distance_dependent
properties:
variants:
type: object
required:
- id
- type
properties:
id:
'$ref': '#/$defs/uri'
type:
'oneOf':
- type: string
const: MicroConnectomeVariantSelectionOverrides
- type: array
items:
type: string
contains:
type: string
const: MicroConnectomeVariantSelectionOverrides
rev:
'$ref': '#/$defs/revision'
placeholder__erdos_renyi:
type: object
required:
- id
- type
properties:
id:
'$ref': '#/$defs/uri'
type:
'oneOf':
- type: string
const: MicroConnectomeDataOverrides
- type: array
items:
type: string
contains:
type: string
const: MicroConnectomeDataOverrides
rev:
'$ref': '#/$defs/revision'
placeholder__distance_dependent:
type: object
required:
- id
- type
properties:
id:
'$ref': '#/$defs/uri'
type:
'oneOf':
- type: string
const: MicroConnectomeDataOverrides
- type: array
items:
type: string
contains:
type: string
const: MicroConnectomeDataOverrides
rev:
'$ref': '#/$defs/revision'
Distribution Example¶
{
"variants": {
"placeholder__erdos_renyi": {
"algorithm": "placeholder",
"version": "v3",
"params": {
"weight": {
"type": "float32",
"unitCode": "#synapses/connection",
"default": 0
},
"nsynconn_mean": {
"type": "float32",
"unitCode": "#synapses/connection",
"default": 3
},
"nsynconn_std": {
"type": "float32",
"unitCode": "#synapses/connection",
"default": 1.5
},
"delay_velocity": {
"type": "float32",
"unitCode": "um/ms",
"default": 250
},
"delay_offset": {
"type": "float32",
"unitCode": "ms",
"default": 0.8
}
}
},
"placeholder__distance_dependent": {
"algorithm": "placeholder",
"version": "v3",
"params": {
"weight": {
"type": "float32",
"unitCode": "#synapses/connection",
"default": 0
},
"exponent": {
"type": "float32",
"unitCode": "1/um",
"default": 0.008
},
"nsynconn_mean": {
"type": "float32",
"unitCode": "#synapses/connection",
"default": 3
},
"nsynconn_std": {
"type": "float32",
"unitCode": "#synapses/connection",
"default": 1.5
},
"delay_velocity": {
"type": "float32",
"unitCode": "um/ms",
"default": 250
},
"delay_offset": {
"type": "float32",
"unitCode": "ms",
"default": 0.8
}
}
}
},
"initial": {
"variants": {
"id": "https://bbp.epfl.ch/neurosciencegraph/data/a46a442c-5baa-4a5c-9907-bfb359dd9e5d",
"rev": 9,
"type": [
"Entity",
"Dataset",
"MicroConnectomeVariantSelection"
]
},
"placeholder__erdos_renyi": {
"id": "https://bbp.epfl.ch/neurosciencegraph/data/microconnectomedata/009413eb-e51b-40bc-9199-8b98bfc53f87",
"rev": 7,
"type": [
"Entity",
"Dataset",
"MicroConnectomeData"
]
},
"placeholder__distance_dependent": {
"id": "https://bbp.epfl.ch/neurosciencegraph/data/microconnectomedata/c7e1d215-2dad-4216-8565-6b1e4c161f46",
"rev": 7,
"type": [
"Entity",
"Dataset",
"MicroConnectomeData"
]
}
},
"overrides": {
"variants": {
"id": "https://bbp.epfl.ch/data/bbp/mmb-point-neuron-framework-model/deee5e86-1d7b-45f6-8fad-259a71c35c6a",
"type": [
"Entity",
"Dataset",
"MicroConnectomeVariantSelectionOverrides"
],
"rev": 1
},
"placeholder__erdos_renyi": {
"id": "https://bbp.epfl.ch/data/bbp/mmb-point-neuron-framework-model/36426136-201d-4dfd-93d9-b541e113a6bf",
"type": [
"Entity",
"Dataset",
"MicroConnectomeDataOverrides"
],
"rev": 1
},
"placeholder__distance_dependent": {
"id": "https://bbp.epfl.ch/data/bbp/mmb-point-neuron-framework-model/4bb03c2b-b99d-4a5d-8a8b-12e1a30619aa",
"type": [
"Entity",
"Dataset",
"MicroConnectomeDataOverrides"
],
"rev": 1
}
},
"_ui_data": {
"editHistory": []
}
}
SynapseConfig¶
The SynapseConfig is a configuration entity that stores the settings for assigning synaptic parameters to circuits.
Distribution Keys¶
Key |
Explanation |
|---|---|
variantDefinition |
Variant CWL definition information. |
defaults |
Initial synaptic parameter configurations. |
configuration |
Final synaptic parameter configuration. |
Distribution Schema¶
%YAML 1.1
---
"$schema": https://json-schema.org/draft/2020-12/schema
title: SynapseConfig distribution schema
'$defs':
uri:
type: string
format: uri
pattern: '^https?:\/\/[^?#]*$' # uri without query or fragment
revision:
type: integer
minimum: 1
variant_info:
type: object
required:
- algorithm
- version
algorithm:
type: string
version:
type: string
synaptic_parameter_assignment:
type: object
required:
- id
- type
properties:
id:
'$ref': '#/$defs/uri'
type:
'oneOf':
- type: string
const: SynapticParameterAssignment
- type: array
maxItems: 2
items:
type: string
enum:
- Dataset
- SynapticParameterAssignment
rev:
'$ref': '#/$defs/revision'
synaptic_parameter:
type: object
required:
- id
- type
properties:
id:
'$ref': '#/$defs/uri'
type:
'oneOf':
- type: string
const: SynapticParameter
- type: array
maxItems: 2
items:
type: string
enum:
- Dataset
- SynapticParameter
rev:
'$ref': '#/$defs/revision'
type: object
required:
- variantDefinition
- defaults
- configuration
properties:
variantDefinition:
'$ref': '#/$defs/variant_info'
defaults:
type: object
required:
- synapse_properties
- synapses_classification
properties:
synapse_properties:
'$ref': '#/$defs/synaptic_parameter_assignment'
synapses_classification:
'$ref': '#/$defs/synaptic_parameter'
additionalProperties: false
configuration:
type: object
required:
- synapse_properties
- synapses_classification
properties:
synapse_properties:
'$ref': '#/$defs/synaptic_parameter_assignment'
synapses_classification:
'$ref': '#/$defs/synaptic_parameter'
additionalProperties: false
Distribution Example¶
{
"variantDefinition": {
"algorithm": "synapses",
"version": "v2"
},
"defaults": {
"synapse_properties": {
"id": "https://bbp.epfl.ch/neurosciencegraph/data/synapticassignment/d57536aa-d576-4b3b-a89b-b7888f24eb21",
"type": [
"Dataset",
"SynapticParameterAssignment"
],
"rev": 9
},
"synapses_classification": {
"id": "https://bbp.epfl.ch/neurosciencegraph/data/synapticparameters/cf25c2bf-e6e4-4367-acd8-94004bfcfe49",
"type": [
"Dataset",
"SynapticParameter"
],
"rev": 6
}
},
"configuration": {
"synapse_properties": {
"id": "https://bbp.epfl.ch/data/bbp/mmb-point-neuron-framework-model/839a8b83-1620-4fe7-8f58-658ded0ea1e8",
"type": [
"Dataset",
"SynapticParameterAssignment"
],
"rev": 1
},
"synapses_classification": {
"id": "https://bbp.epfl.ch/data/bbp/mmb-point-neuron-framework-model/d133e408-bd00-41ca-9334-e5fab779ad99",
"type": [
"Dataset",
"SynapticParameter"
],
"rev": 3
}
}
}
CanonicalMorphologyModelConfig¶
The CanonicalMorphologyModelConfig is a configuration entity that stores the canonical models for each (region, mtype) combination, used for topological synthesis.
Distribution Schema¶
%YAML 1.1
---
"$schema": https://json-schema.org/draft/2020-12/schema
title: CanonicalMorphologyModelConfig distribution schema
type: object
required:
- hasPart
properties:
version:
type: integer
const: 2
hasPart:
additionalProperties: false
patternProperties:
'^https?:\/\/.*\/Structure\/\d*$': # brain regions finishing in /Structure/int
type: object
required:
- notation
- hasPart
properties:
notation:
type: string
hasPart:
type: object
additionalProperties: false
patternProperties:
'^https?:\/\/[^?#]*$': # mtypes
type: object
required:
- label
- hasPart
properties:
label:
type: string
hasPart:
type: object
additionalProperties: false
patternProperties:
'^https?:\/\/[^?#]*$': # canonical model ids
type: object
properties:
"_rev":
type: integer
Distribution Example¶
{
"hasPart": {
"http://api.brain-map.org/api/v2/data/Structure/23": {
"label": "Anterior amygdalar area",
"notation": "AAA",
"about": "BrainRegion",
"hasPart": {
"https://bbp.epfl.ch/ontologies/core/bmo/GenericExcitatoryNeuronMType": {
"label": "GEN_mtype",
"about": "NeuronMorphology",
"hasPart": {
"https://bbp.epfl.ch/data/bbp/mmb-point-neuron-framework-model/canonicalmorphologymodels/dfda5210-39b5-428d-ac0c-43852f99df02": {
"about": "CanonicalMorphologyModel",
"_rev": 3
}
}
},
"https://bbp.epfl.ch/ontologies/core/bmo/GenericInhibitoryNeuronMType": {
"label": "GIN_mtype",
"about": "NeuronMorphology",
"hasPart": {
"https://bbp.epfl.ch/data/bbp/mmb-point-neuron-framework-model/canonicalmorphologymodels/c58fceb9-a61e-49c8-a6fa-603a99450914": {
"about": "CanonicalMorphologyModel",
"_rev": 3
}
}
}
}
},
"http://api.brain-map.org/api/v2/data/Structure/935": {
"label": "Anterior cingulate area, dorsal part, layer 1",
"notation": "ACAd1",
"about": "BrainRegion",
"hasPart": {
"http://uri.interlex.org/base/ilx_0383192": {
"label": "L1_DAC",
"about": "NeuronMorphology",
"hasPart": {
"https://bbp.epfl.ch/data/bbp/mmb-point-neuron-framework-model/canonicalmorphologymodels/3b5e4f0a-2631-4898-b323-907522b07f2c": {
"about": "CanonicalMorphologyModel",
"_rev": 3
}
}
}
}
}
}
}
PlaceholderMorphologyConfig¶
The PlaceholderMorphologyConfig is a configuration entity that stores placeholder morphologies for each (region, mtype) combination, used for morphology assignment.
Distribution Schema¶
%YAML 1.1
---
"$schema": https://json-schema.org/draft/2020-12/schema
title: PlaceholderMorphologyConfig distribution schema
type: object
required:
- hasPart
properties:
version:
type: integer
const: 2
hasPart:
additionalProperties: false
patternProperties:
'^https?:\/\/.*\/Structure\/\d*$': # brain regions finishing in /Structure/int
type: object
required:
- notation
- hasPart
properties:
notation:
type: string
hasPart:
type: object
additionalProperties: false
patternProperties:
'^https?:\/\/[^?#]*$': # mtypes
type: object
required:
- label
- hasPart
properties:
label:
type: string
hasPart:
type: object
additionalProperties: false
patternProperties:
'^https?:\/\/[^?#]*$': # morphology ids
type: object
required:
- '_rev'
Distribution Example¶
{
"hasPart": {
"http://api.brain-map.org/api/v2/data/Structure/23": {
"label": "Anterior amygdalar area",
"notation": "AAA",
"about": "BrainRegion",
"hasPart": {
"https://bbp.epfl.ch/ontologies/core/bmo/GenericExcitatoryNeuronMType": {
"label": "GEN_mtype",
"about": "NeuronMorphology",
"hasPart": {
"https://bbp.epfl.ch/data/bbp/mmb-point-neuron-framework-model/9829da8e-33e1-4a04-97ec-7943a4a969eb": {
"about": "NeuronMorphology",
"_rev": 3
}
}
},
"https://bbp.epfl.ch/ontologies/core/bmo/GenericInhibitoryNeuronMType": {
"label": "GIN_mtype",
"about": "NeuronMorphology",
"hasPart": {
"https://bbp.epfl.ch/data/bbp/mmb-point-neuron-framework-model/9829da8e-33e1-4a04-97ec-7943a4a969eb": {
"about": "NeuronMorphology",
"_rev": 3
}
}
}
}
},
"http://api.brain-map.org/api/v2/data/Structure/935": {
"label": "Anterior cingulate area, dorsal part, layer 1",
"notation": "ACAd1",
"about": "BrainRegion",
"hasPart": {
"http://uri.interlex.org/base/ilx_0383192": {
"label": "L1_DAC",
"about": "NeuronMorphology",
"hasPart": {
"https://bbp.epfl.ch/data/bbp/mmb-point-neuron-framework-model/9829da8e-33e1-4a04-97ec-7943a4a969eb": {
"about": "NeuronMorphology",
"_rev": 3
}
}
}
}
}
}
}
PlaceholderEModelConfig¶
The PlaceholderEModelsConfig is a configuration entity that stores the placeholder emodels for each (region, etype) combination, used for emodel assignment.
Distribution Schema¶
%YAML 1.1
---
"$schema": https://json-schema.org/draft/2020-12/schema
title: PlaceholderEModelConfig distribution schema
type: object
required:
- hasPart
properties:
version:
type: integer
const: 1
hasPart:
additionalProperties: false
patternProperties:
'^https?:\/\/.*\/Structure\/\d*$': # brain regions finishing in /Structure/int
type: object
required:
- notation
- hasPart
properties:
notation:
type: string
hasPart:
type: object
additionalProperties: false
patternProperties:
'^https?:\/\/[^?#]*$': # mtypes
type: object
required:
- label
- hasPart
properties:
label:
type: string
hasPart:
type: object
patternProperties:
'^https?:\/\/[^?#]*$': # etypes
type: object
properties:
label:
type: string
hasPart:
type: object
patternProperties:
'^https?:\/\/[^?#]*$': # EModel ids
type: object
required:
- '_rev'
additionalProperties: false
additionalProperties: false
Distribution Example¶
{
"hasPart": {
"http://api.brain-map.org/api/v2/data/Structure/23": {
"label": "Anterior amygdalar area",
"notation": "AAA",
"about": "BrainRegion",
"hasPart": {
"https://bbp.epfl.ch/ontologies/core/bmo/GenericExcitatoryNeuronMType": {
"label": "GEN_mtype",
"about": "MType",
"hasPart": {
"https://bbp.epfl.ch/ontologies/core/bmo/GenericExcitatoryNeuronEType": {
"label": "GEN_etype",
"about": "EType",
"hasPart": {
"https://bbp.epfl.ch/data/bbp/mmb-point-neuron-framework-model/65d6a42a-ec6f-4a17-b1d2-b6ff1c7225b8": {
"about": "EModel",
"_rev": 2
}
}
}
}
},
"https://bbp.epfl.ch/ontologies/core/bmo/GenericInhibitoryNeuronMType": {
"label": "GIN_mtype",
"about": "MType",
"hasPart": {
"https://bbp.epfl.ch/ontologies/core/bmo/GenericInhibitoryNeuronEType": {
"label": "GIN_etype",
"about": "EType",
"hasPart": {
"https://bbp.epfl.ch/data/bbp/mmb-point-neuron-framework-model/ff571ada-fc08-4e6b-9b5c-1c21ee22ccb2": {
"about": "EModel",
"_rev": 1
}
}
}
}
}
}
},
"http://api.brain-map.org/api/v2/data/Structure/935": {
"label": "Anterior cingulate area, dorsal part, layer 1",
"notation": "ACAd1",
"about": "BrainRegion",
"hasPart": {
"http://uri.interlex.org/base/ilx_0383192": {
"label": "L1_DAC",
"about": "MType",
"hasPart": {
"http://uri.interlex.org/base/ilx_0738203": {
"label": "bNAC",
"about": "EType",
"hasPart": {
"https://bbp.epfl.ch/data/bbp/mmb-point-neuron-framework-model/af16d001-7e73-4b10-88ef-868567d77242": {
"about": "EModel",
"_rev": 1
}
}
},
"http://uri.interlex.org/base/ilx_0738201": {
"label": "cNAC",
"about": "EType",
"hasPart": {
"https://bbp.epfl.ch/data/bbp/mmb-point-neuron-framework-model/292427f3-fbdc-4e26-9731-d89b114441b3": {
"about": "EModel",
"_rev": 1
}
}
}
}
}
}
}
}
}