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Converting the file: NetworkML_v1.7.1.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.
|
| targetNamespace | http://morphml.org/networkml/schema |
| elementFormDefault | qualified |
| attributeFormDefault | unqualified |
|
Imported Schemas
Other schemas used by this file, with different target namespaces
|
| Namespace: http://morphml.org/metadata/schema | Location: ../Level1/Metadata_v1.7.1.xsd |
| Namespace: http://morphml.org/biophysics/schema | Location: ../Level2/Biophysics_v1.7.1.xsd |
Elements
| Element: networkml |
| The root element.
Note: this element will only be present in a standalone NetworkML 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: | |
|
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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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... |
| |
| projections |
| In theory there can be no projections, if the file is intended only to specify positions |
| |
| 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). |
| |
| spacing |
| Separation of the cells in each dimension |
|
|
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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 | |
|
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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 |
| name | Type:
xs:string
, Use: optional |
| lengthUnits |
| Unit of all length measurements. |
| Type:
meta:LengthUnits
, Use: required |
| volumeUnits |
| Unit of all volume measurements. |
| Type:
meta:VolumeUnits
, Use: optional, default: cubic_millimetre |
|
|
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 | |
|
|
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 | |
| 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. Should this 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 | |
| Only one of the following SUB elements may appear.
|
| pulse_input | |
| random_stim | |
| Attributes |
| name | Type:
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.
|
|
|
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PulseInput used by:
Input (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 |
| frequency | Type:
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: 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 | |
| site_pattern | |
| Attributes |
| cell_group |
| The cell group to which to apply the stimulation |
| Type:
xs:string
, Use: required |
|
|
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 |
|
|
| percentage_cells |
| Apply input to a certain percentage of cells in a group |
|
|
|
|
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 |
| percentage | Type:
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 | |
|
|
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
|
|
|
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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! |
| |
| Only one of the following SUB elements may appear.
|
| instances | |
| pop_location | |
| 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 | |
| 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: will very likely become REQUIRED in v2.0 |
| Type:
xs:nonNegativeInteger
, Use: optional |
|
|
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! |
| |
| 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! |
| |
| synapse_props |
| Properties of a synapse associated with this connection. |
| |
| Only one of the following SUB elements may appear.
|
| connections | |
| connectivity_pattern | |
| 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 | |
| default_values | |
|
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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. |
| |
| default_values |
| For compatability to pre v1.7.1. Will be removed in v2.0. |
| |
| 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 |
|
|
| fixed_probability |
| For each pre - post pair, there is a fixed probability of connection |
|
|
| per_cell_connection |
| Connection built iteratively from each pre (or post) cell based on a number of parameters |
| |
|
|
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 |
| probability | Type:
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_source | Type:
meta:PositiveDouble
, Use: required |
| max_per_target | Type:
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 | |
|
|
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 | |
| 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 is a preliminary
attempt to allow exchange of neuronal networks partitioned for optimal running in
distributed computing environments. |
| 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 |
| |
| post |
| NOTE: Attributes post_cell_id etc. for WILL BE PREFERRED FORMAT IN v2.0 |
| |
| properties | |
| 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 | |
| grid_arrangement | |
| Attributes |
| reference | Type:
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 |
| |
| Only one of the following SUB elements may appear.
|
| spherical_location | |
| rectangular_location | |
|
|
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 |
| |
|
|
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 | |
|
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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 |
| |
| 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 |
| |
| synapse_direction |
| Whether this synapse location allows a presynaptic connection, a postsynaptic
connection or either |
| |
| group |
| List of groups of sections allowing the synapse |
| |
|
|
PotentialSynapticLocation used by:
BiophysicsNetworkElements (xs:group)
Instances of this element which are used by other elements in this document
|
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|
