Transforming XML file: NeuroMLFiles/Schemata/v1.8.1/Level3/NetworkML_v1.8.1.xsd using XSL file: NeuroMLFiles/Schemata/XSD_Readable.xsl

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Converting the file: NetworkML_v1.8.1.xsd

Note: this representation of the contents of the XSD file is intended as a quick reference only.
** The original *.xsd file should be consulted if there is any doubt regarding data types **

There is also the option to view this file in Relax NG format.
Note this representation is for reference only (for those who prefer that format). The XSD should be used for final validation.

Conversion of an XSD file into human readable form

Description
Description of the Schema taken from the XSD file
The specification of populations and projections which allows network connections to be encoded in NeuroML


Schema info

Information on the namespaces, etc.

targetNamespacehttp://morphml.org/networkml/schema
elementFormDefaultqualified
attributeFormDefaultunqualified


Imported Schemas

Other schemas used by this file, with different target namespaces

Namespace: http://morphml.org/metadata/schemaLocation: ../Level1/Metadata_v1.8.1.xsd
Namespace: http://morphml.org/biophysics/schemaLocation: ../Level2/Biophysics_v1.8.1.xsd


Elements networkml  
Simple Types CellIdInNetwork   SynapseDirection  
Groups BiophysicsNetworkElements   CoreNetworkElements   SpatialLayout  
Complex Types CellInstance   Connection   Connections   ConnectivityPattern   GlobalSynapticProperties   GridArrangement   Input   Inputs   InputSite   InputSitePattern   InputSites   InputTarget   Instances   Level3Connectivity   LocalSynapticProperties   NetworkML   PerCellConnection   Population   PopulationLocation   Populations   PotentialSynapticLocation   PotentialSynLoc   Projection   Projections   PulseInput   RandomArrangement   RandomStim   RandomStimInstance   SynapseInternalProperties   SynapseProperties   SynapticLocation  

Elements

Element: networkml
The root element. Note: this element will only be present in a standalone NetworkML file (i.e. no cells or channels defined in the file). For files covering many levels, neuroml will be the root element
Type: NetworkML


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Simple Types

Simple Type: SynapseDirection

Indicated whether a potential synapse location allows a presynaptic connection of the specified type, a postsynaptic connection or either.

Restriction: Base: xs:string
Allowed values:
pre
post
preAndOrPost

SynapseDirection used by: PotentialSynLoc (xs:complexType) PotentialSynapticLocation (xs:complexType)

Instances of this element which are used by other elements in this document



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Simple Type: CellIdInNetwork

Id of individual cell in a network

Restriction: Base: xs:nonNegativeInteger

CellIdInNetwork used by: InputSite (xs:complexType)

Instances of this element which are used by other elements in this document



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Groups

Group: CoreNetworkElements

The elements needed to specify a network connection

The following elements must appear in the sequence outlined here.
populations
The least that's needed in a network is a population of cells...
Type : Populations
projections
In theory there can be no projections, if the file is intended only to specify positions
Type : Projections
Occurances: 0 ... 1
inputs
No inputs need be specified
Type : Inputs
Occurances: 0 ... 1


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Group: SpatialLayout

Layout of the cells according to x,y,z spatial coordinates

The following elements must appear in the sequence outlined here.
rectangular_location
3D box in which the cells are regularly packed. Note if one or two of dimensions of the box is zero it can be a 2D or 1D grid (respectively).
Type : meta:RectangularBox
spacing
Separation of the cells in each dimension
Type : spacing


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Group: BiophysicsNetworkElements

The elements in biophysics needed to specify a network connection. Note: from v1.7.1 the preferred way to specify a potential synaptic location is with a potential_syn_loc element under connectivity under cell, as opposed to the potentialSynapticLocation under biophysics under cell. The former will be the only option from v2.0

The following elements must appear in the sequence outlined here.
potentialSynapticLocation
Type : PotentialSynapticLocation
Occurances: 0 ... unbounded


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Complex Types

Complex Type: NetworkML

The main elements which make up a NetworkML compliant document.

The following elements must appear in the sequence outlined here.
Group
A group of elements to include with this element
Ref: meta:metadata
Group
A group of elements to include with this element
Ref: CoreNetworkElements
Attributes
nameType: xs:string , Use: optional
lengthUnits
Unit of all length measurements. Usually has the value micrometer. Note: length_units will be the preferred form in v2.0
Type: meta:LengthUnits , Use: optional
length_units
Unit of all length measurements. Usually has the value micrometer. Note: length_units will be the preferred form in v2.0
Type: meta:LengthUnits , Use: optional
volumeUnits
Unit of all volume measurements.
Type: meta:VolumeUnits , Use: optional, default: cubic_millimeter

NetworkML used by: networkml (xs:element)

Instances of this element which are used by other elements in this document



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Complex Type: Populations

The list of cell populations

The following elements must appear in the sequence outlined here.
Group
A group of elements to include with this element
Ref: meta:metadata
population
Type : Population

Populations used by: CoreNetworkElements (xs:group)

Instances of this element which are used by other elements in this document



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Complex Type: Projections

The list of projections from one cell population to another

The following elements must appear in the sequence outlined here.
Group
A group of elements to include with this element
Ref: meta:metadata
projection
Type : Projection
Occurances: 1 ... unbounded
Attributes
units
Unit system of all quantities in the projection descriptions, e.g. synaptic time constants
Type: meta:Units , Use: required

Projections used by: CoreNetworkElements (xs:group)

Instances of this element which are used by other elements in this document



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Complex Type: Inputs

The list of electrical inputs into the cells. This should be extended to allow voltage clamp inputs...

The following elements must appear in the sequence outlined here.
Group
A group of elements to include with this element
Ref: meta:metadata
input
Type : Input
Occurances: 1 ... unbounded
Attributes
units
Unit system of all quantities in the input description, e.g. input current amplitudes
Type: meta:Units , Use: required

Inputs used by: CoreNetworkElements (xs:group)

Instances of this element which are used by other elements in this document



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Complex Type: Input

Description of a single electrical input to a number of cells

The following elements must appear in the sequence outlined here.
Group
A group of elements to include with this element
Ref: meta:metadata
target
Type : InputTarget
Only one of the following SUB elements may appear.
pulse_input
Type : PulseInput
random_stim
Type : RandomStim
Attributes
nameType: xs:string , Use: required

Input used by: Inputs (xs:complexType)

Instances of this element which are used by other elements in this document



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Complex Type: PulseInput

A single input pulse. Note: this should be changed to allow easier specifications of pulse trains, input protocols, etc.

Attributes
delayType: bio:TimeValue , Use: required
durationType: bio:TimeValue , Use: required
amplitudeType: bio:CurrentValue , Use: required

PulseInput used by: Input (xs:complexType) InputSite (xs:complexType)

Instances of this element which are used by other elements in this document



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Complex Type: RandomStim

A random stimulation at a specific frequency. Note: can be interpreted differently by different simulators!!

Attributes
frequencyType: bio:FrequencyValue , Use: required
synaptic_mechanism
The name of a synaptic mechanism which will provides the conductance change. This will be fired once every 'spike' at the given frequency
Type: xs:string , Use: required

RandomStim used by: Input (xs:complexType)

Instances of this element which are used by other elements in this document



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Complex Type: RandomStimInstance

Instance/site specific random stimulation at a specific frequency. Note: can be interpreted differently by different simulators!!

Attributes
frequencyType: bio:FrequencyValue , Use: required

RandomStimInstance used by: InputSite (xs:complexType)

Instances of this element which are used by other elements in this document



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Complex Type: InputTarget

Specifies the cell group and which cells/segments to apply the stimulation

The following elements must appear in the sequence outlined here.
Group
A group of elements to include with this element
Ref: meta:metadata
Only one of the following SUB elements may appear.
sites
Type : InputSites
site_pattern
Type : InputSitePattern
Attributes
cell_group
The cell group to which to apply the stimulation. Note for v2.0 population is the preferred name of this attribute (not cell_group).
Type: xs:string , Use: optional
population
The cell group to which to apply the stimulation. Note for v2.0 population is the preferred name of this attribute (not cell_group).
Type: xs:string , Use: optional

InputTarget used by: Input (xs:complexType)

Instances of this element which are used by other elements in this document



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Complex Type: InputSitePattern

Information on the number of cells on which to apply inputs. Currently only two, but could be expanded to include other scenarios, e.g. all cells in 3d region.

Only one of the following elements may appear.
all_cells
Apply input on all cells in group
Type : all_cells
percentage_cells
Apply input to a certain percentage of cells in a group
Type : percentage_cells

InputSitePattern used by: InputTarget (xs:complexType)

Instances of this element which are used by other elements in this document



Element: all_cells
Apply input on all cells in group
 

all_cells is used by: InputSitePattern (xs:complexType)

Instances of this element which are used by other elements in this document



Element: percentage_cells
Apply input to a certain percentage of cells in a group
 
Attributes
percentageType: meta:Percentage , Use: optional

percentage_cells is used by: InputSitePattern (xs:complexType)

Instances of this element which are used by other elements in this document



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Complex Type: InputSites

The list of input sites

The following elements must appear in the sequence outlined here.
Group
A group of elements to include with this element
Ref: meta:metadata
site
Type : InputSite
Attributes
size
The number of instances of inputs. This is redundant information, but can be useful when the file is being parsed to allocate memory for an array of cells. NOTE: likely to be required from v2.0
Type: xs:nonNegativeInteger , Use: optional

InputSites used by: InputTarget (xs:complexType)

Instances of this element which are used by other elements in this document



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Complex Type: InputSite

Specifies a location on a cell where input is received

Only one of the following elements may appear.
pulse_input_instance
Type : PulseInput
Occurances: 0 ... 1
random_stim_instance
Type : RandomStimInstance
Occurances: 0 ... 1
Attributes
cell_idType: CellIdInNetwork, Use: required
segment_idType: meta:SegmentIdInCell , Use: optional, default: 0
fraction_alongType: meta:ZeroToOne , Use: optional, default: 0.5

InputSite used by: InputSites (xs:complexType)

Instances of this element which are used by other elements in this document



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Complex Type: Population

Description of a cell population of the same type

The following elements must appear in the sequence outlined here.
Group
A group of elements to include with this element
Ref: meta:metadata
cell_type
The cell type for this population. NOTE: an attribute value for cell_type WILL BE PREFERRED FORMAT IN v2.0. The option for this element will be removed!
Type : xs:string
Occurances: 0 ... 1
Only one of the following SUB elements may appear.
instances
Type : Instances
pop_location
Type : PopulationLocation
Attributes
name
The name of the population
Type: xs:string , Use: required
cell_type
The cell type for this population. Optional now, but WILL BE PREFERRED FORMAT IN v2.0
Type: xs:string , Use: optional

Population used by: Populations (xs:complexType)

Instances of this element which are used by other elements in this document



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Complex Type: Instances

Cell Instance position information

The following elements must appear in the sequence outlined here.
Group
A group of elements to include with this element
Ref: meta:metadata
instance
Type : CellInstance
Attributes
size
The number of instances of cells for this population. This is redundant information, but can be useful when the file is being parsed to allocate memory for an array of cells. NOTE: required from v1.7.3
Type: xs:nonNegativeInteger , Use: required

Instances used by: Population (xs:complexType)

Instances of this element which are used by other elements in this document



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Complex Type: Projection

Description of how one cell population makes synaptic connections with another

The following elements must appear in the sequence outlined here.
Group
A group of elements to include with this element
Ref: meta:metadata
source
Cell population where synaptic connection begins. NOTE: attribute values for source and target WILL BE THE PREFERRED FORMAT IN v2.0. The option for this element will be removed!
Type : xs:string
Occurances: 0 ... 1
target
Cell population where synaptic connection terminates. NOTE: attribute values for source and target WILL BE THE PREFERRED FORMAT IN v2.0. The option for this element will be removed!
Type : xs:string
Occurances: 0 ... 1
synapse_props
Properties of a synapse associated with this connection.
Type : GlobalSynapticProperties
Only one of the following SUB elements may appear.
connections
Type : Connections
connectivity_pattern
Type : ConnectivityPattern
Attributes
name
String reference for the projection
Type: xs:string , Use: required
source
Cell population where synaptic connection begins. Optional now, but WILL BE PREFERRED FORMAT IN v2.0
Type: xs:string , Use: optional
target
Cell population where synaptic connection terminates. Optional now, but WILL BE PREFERRED FORMAT IN v2.0
Type: xs:string , Use: optional

Projection used by: Projections (xs:complexType)

Instances of this element which are used by other elements in this document



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Complex Type: SynapseProperties

Pre v1.7.1 format for global synapse properties. Preferred format is GlobalSynapticProperties. This option will be disabled in v2.0

The following elements must appear in the sequence outlined here.
Group
A group of elements to include with this element
Ref: meta:metadata
synapse_type
Type : xs:string
default_values
Type : SynapseInternalProperties


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Complex Type: GlobalSynapticProperties

Information on synapse type and default values for weight, delay, threshold, etc.

Extension:
The child elements and attributes of the base element will be required in this element too.
Base: SynapseInternalProperties
The following elements must appear in the sequence outlined here.
synapse_type
For compatability to pre v1.7.1. Will be removed in v2.0.
Type : xs:string
Occurances: 0 ... 1
default_values
For compatability to pre v1.7.1. Will be removed in v2.0.
Type : SynapseInternalProperties
Occurances: 0 ... 1
Attributes
synapse_type
Including synapse_type as attribute in synapse_props will be required in v2.0
Type: xs:string , Use: optional

GlobalSynapticProperties used by: Projection (xs:complexType)

Instances of this element which are used by other elements in this document



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Complex Type: LocalSynapticProperties

Variables specifying a single synapse

Extension:
The child elements and attributes of the base element will be required in this element too.
Base: SynapseInternalProperties
Attributes
synapse_type
Optional for a single synaptic connection. Only needed in the case where multiple synapses are present at one connection and there are non default values for each synapse's weights, etc. This field gives the name of the synapse type referred to.
Type: xs:string , Use: optional

LocalSynapticProperties used by: Connection (xs:complexType)

Instances of this element which are used by other elements in this document



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Complex Type: SynapseInternalProperties

Variables specifying a single synapse or default values for a set of connections

The following elements must appear in the sequence outlined here.
Group
A group of elements to include with this element
Ref: meta:metadata
Attributes
internal_delay
Delay due to diffusion across the synaptic cleft. If only one delay value is known, this can be used
Type: bio:SynapticDelayValue , Use: optional, default: 0
pre_delay
Delay due to presynaptic mechanism
Type: bio:SynapticDelayValue , Use: optional, default: 0
post_delay
Delay due to postsynaptic mechanism
Type: bio:SynapticDelayValue , Use: optional, default: 0
prop_delay
Delay due to simulated AP propagation along an axon
Type: bio:SynapticDelayValue , Use: optional, default: 0
weight
Multiplicative weighting factor for the synapse
Type: meta:NonNegativeDouble , Use: optional, default: 1
threshold
Presynaptic membrane potential level above which the synapse fires
Type: bio:VoltageValue , Use: optional, default: 0

SynapseInternalProperties used by: SynapseProperties (xs:complexType) GlobalSynapticProperties (xs:complexType)

Instances of this element which are used by other elements in this document



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Complex Type: ConnectivityPattern

Information on the number of target cells connected to source cells, etc.

Only one of the following elements may appear.
all_to_all
Connect every pre cell to every post cell
Type : all_to_all
fixed_probability
For each pre - post pair, there is a fixed probability of connection
Type : fixed_probability
per_cell_connection
Connection built iteratively from each pre (or post) cell based on a number of parameters
Type : PerCellConnection

ConnectivityPattern used by: Projection (xs:complexType)

Instances of this element which are used by other elements in this document



Element: all_to_all
Connect every pre cell to every post cell
 

all_to_all is used by: ConnectivityPattern (xs:complexType)

Instances of this element which are used by other elements in this document



Element: fixed_probability
For each pre - post pair, there is a fixed probability of connection
 
Attributes
probabilityType: meta:ZeroToOne , Use: optional

fixed_probability is used by: ConnectivityPattern (xs:complexType)

Instances of this element which are used by other elements in this document



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Complex Type: PerCellConnection

Connection built iteratively from each pre (or post) cell based on a number of parameters

Attributes
direction
Whether the settings below (e.g. number per source cell) refer to PreToPost or PostToPre connections. Note more info could be known about numbers of connections on post synaptic cells, so this possibility should be allowed.
Type: , Use: optional, default: PreToPost
num_per_sourceType: meta:PositiveDouble , Use: required
max_per_targetType: xs:positiveInteger , Use: optional

PerCellConnection used by: ConnectivityPattern (xs:complexType)

Instances of this element which are used by other elements in this document



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Complex Type: Connections

The list of cell connections

The following elements must appear in the sequence outlined here.
Group
A group of elements to include with this element
Ref: meta:metadata
connection
Type : Connection
Attributes
size
The number of instances of connections. This is redundant information, but can be useful when the file is being parsed to allocate memory for an array of cells. NOTE: likely to be required from v2.0
Type: xs:nonNegativeInteger , Use: optional

Connections used by: Projection (xs:complexType)

Instances of this element which are used by other elements in this document



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Complex Type: CellInstance

An instance of a cell at a the specified location

The following elements must appear in the sequence outlined here.
Group
A group of elements to include with this element
Ref: meta:metadata
location
Type : meta:Point3D
Attributes
id
A unique non negative integer id for the cell instance
Type: xs:nonNegativeInteger , Use: required
node_id
An optional specification of the node id on which this cell should run. This can be used to allow exchange of neuronal networks partitioned for execution in distributed computing environments. A parsing appliction can ignore this inforation and create its own partition.
Type: xs:nonNegativeInteger , Use: optional

CellInstance used by: Instances (xs:complexType)

Instances of this element which are used by other elements in this document



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Complex Type: Connection

A single synaptic connection

The following elements must appear in the sequence outlined here.
Group
A group of elements to include with this element
Ref: meta:metadata
pre
NOTE: Attributes pre_cell_id etc. for WILL BE PREFERRED FORMAT IN v2.0
Type : SynapticLocation
Occurances: 0 ... 1
post
NOTE: Attributes post_cell_id etc. for WILL BE PREFERRED FORMAT IN v2.0
Type : SynapticLocation
Occurances: 0 ... 1
properties
Type : LocalSynapticProperties
Occurances: 0 ... unbounded
Attributes
id
The unique ID of the single synaptic connection.
Type: xs:integer , Use: required
pre_cell_id
The ID of the presynaptic cell. Must be listed in populations, so that too must list instances. Optional now, but attributes pre_cell_id, etc. WILL BE PREFERRED FORMAT IN v2.0
Type: xs:integer , Use: optional
pre_segment_id
The segment on the presynaptic cell where the synapse is located. Attributes pre_cell_id, etc. WILL BE PREFERRED FORMAT IN v2.0
Type: xs:integer , Use: optional, default: 0
pre_fraction_along
The fraction along the length of the specified segment on the presynaptic cell where the synapse is located. Attributes pre_cell_id, etc. WILL BE PREFERRED FORMAT IN v2.0
Type: meta:ZeroToOne , Use: optional, default: 0.5
post_cell_id
The ID of the postsynaptic cell. Must be listed in populations, so that too must list instances. Optional now, but attributes pre_cell_id, etc. WILL BE PREFERRED FORMAT IN v2.0
Type: xs:integer , Use: optional
post_segment_id
The segment on the postsynaptic cell where the synapse is located. Attributes pre_cell_id, etc. WILL BE PREFERRED FORMAT IN v2.0
Type: xs:integer , Use: optional, default: 0
post_fraction_along
The fraction along the length of the specified segment on the postsynaptic cell where the synapse is located. Attributes pre_cell_id, etc. WILL BE PREFERRED FORMAT IN v2.0
Type: meta:ZeroToOne , Use: optional, default: 0.5

Connection used by: Connections (xs:complexType)

Instances of this element which are used by other elements in this document



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Complex Type: SynapticLocation
Attributes
cell_id
The ID of the cell. Must be listed in populations, so that too must list instances
Type: xs:integer , Use: required
segment_id
The segment where the synapse is located.
Type: xs:integer , Use: optional, default: 0
fraction_along
The fraction along the length of the specified segment where the synapse is located.
Type: meta:ZeroToOne , Use: optional, default: 0.5

SynapticLocation used by: Connection (xs:complexType) Connection (xs:complexType)

Instances of this element which are used by other elements in this document



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Complex Type: PopulationLocation

Description of the 3D positioning of cells in the population, in place of giving explicit locations for each cell

The following elements must appear in the sequence outlined here.
Group
A group of elements to include with this element
Ref: meta:metadata
Only one of the following SUB elements may appear.
random_arrangement
Type : RandomArrangement
grid_arrangement
Type : GridArrangement
Attributes
referenceType: xs:string , Use: optional

PopulationLocation used by: Population (xs:complexType)

Instances of this element which are used by other elements in this document



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Complex Type: RandomArrangement

A random arrangement of cells in a 3D location. Note other 3D regions besides spheres and rectangles can be added if required.

The following elements must appear in the sequence outlined here.
Group
A group of elements to include with this element
Ref: meta:metadata
population_size
Number of cells to place randomly in the specified 3D location
Type : xs:nonNegativeInteger
Only one of the following SUB elements may appear.
spherical_location
Type : meta:Sphere
rectangular_location
Type : meta:RectangularBox

RandomArrangement used by: PopulationLocation (xs:complexType)

Instances of this element which are used by other elements in this document



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Complex Type: GridArrangement

A regular placement of the cells in a number of dimensions

The following elements must appear in the sequence outlined here.
Group
A group of elements to include with this element
Ref: meta:metadata
Only one of the following SUB elements may appear.
Group
A group of elements to include with this element
Ref: SpatialLayout
non_spatial_grid
Specifying this means the precise spatial location of the cells is irrelvant
Type : meta:NonSpatialGrid

GridArrangement used by: PopulationLocation (xs:complexType)

Instances of this element which are used by other elements in this document



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Complex Type: Level3Connectivity

Biophysics of Level3 cell, including specification for allowable synaptic locations. Note: from v1.7.1 the preferred way to specify a potential synaptic location is with a potential_syn_loc element under connectivity under cell, as opposed to the potentialSynapticLocation under biophysics under cell. The former will be the only option from v2.0

The following elements must appear in the sequence outlined here.
potential_syn_loc
Type : PotentialSynLoc
Occurances: 0 ... unbounded


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Complex Type: PotentialSynLoc

Subset of sections on cell where synaptic connection of a particular type is allowed. Note: from v1.7.1 the preferred way to specify a potential synaptic location is with a potential_syn_loc element under connectivity under cell, as opposed to the potentialSynapticLocation under biophysics under cell. The former will be the only option from v2.0

The following elements must appear in the sequence outlined here.
Group
A group of elements to include with this element
Ref: meta:metadata
The following SUB elements must appear in the sequence outlined here. Minimum occurances allowed: Maximum occurances allowed:
group
List of groups of sections allowing the synapse
Type : xs:string
Occurances: 1 ... unbounded
Attributes
synapse_type
Which of the synaptic mechanisms can be present
Type: xs:string , Use: required
synapse_direction
Whether this synapse location allows a presynaptic connection, a postsynaptic connection or either
Type: SynapseDirection, Use: optional, default: preAndOrPost

PotentialSynLoc used by: Level3Connectivity (xs:complexType)

Instances of this element which are used by other elements in this document



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Complex Type: PotentialSynapticLocation

Subset of sections on cell where synaptic connection of a particular type is allowed. Note: from v1.7.1 the preferred way to specify a potential synaptic location is with a potential_syn_loc element under connectivity under cell, as opposed to the potentialSynapticLocation under biophysics under cell. The former will be the only option from v2.0

The following elements must appear in the sequence outlined here.
Group
A group of elements to include with this element
Ref: meta:metadata
The following SUB elements must appear in the sequence outlined here. Minimum occurances allowed: Maximum occurances allowed:
synapse_type
Which of the synaptic mechanisms can be present
Type : xs:string
synapse_direction
Whether this synapse location allows a presynaptic connection, a postsynaptic connection or either
Type : SynapseDirection
Occurances: 0 ... 1
group
List of groups of sections allowing the synapse
Type : xs:string

PotentialSynapticLocation used by: BiophysicsNetworkElements (xs:group)

Instances of this element which are used by other elements in this document



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