Transforming XML file: NeuroMLFiles/Schemata/v1.8.1/Level1/MorphML_v1.8.1.xsd using XSL file: NeuroMLFiles/Schemata/XSD_Readable.xsl

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Converting the file: MorphML_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

Schema info

Information on the namespaces, etc.

targetNamespacehttp://morphml.org/morphml/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


Elements morphml  
Simple Types Metric   SpineShape  
Complex Types Cable   CableGroup   Cell   Cells   Feature   FreePoints   InhomogeneousParam   Morphology   Path   Segment   Spine  

Elements

Element: morphml
The root element, and so will start any MorphML (NeuroML Level 1) compliant document.
Type: Morphology


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Simple Types

Simple Type: Metric

Metric for use in InhomogeneousParam

Restriction: Base: xs:string
Allowed values:
Path Length from root
3D radial position
3D path length from line

Metric used by: InhomogeneousParam (xs:complexType)

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



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Simple Type: SpineShape

Enumeration of allowed spine shapes.

Restriction: Base: xs:string
Allowed values:
mushroom
stubby
thin

SpineShape used by: Spine (xs:complexType)

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



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Complex Types

Complex Type: Morphology

The main element which details the neuronal morphology. Cells, various histological features, and properties associated with the data can be contained in this element

The following elements must appear in the sequence outlined here.
Group
A group of elements to include with this element
Ref: meta:metadata
cells
Type : Cells
features
Collection of all extracellular histological features.
Type : features
Occurances: 0 ... 1
propertyDetails
Collection of all PropertyDetails for this instance.
Type : propertyDetails
Occurances: 0 ... 1
groupDetails
Collection of all GroupDetails for this instance.
Type : groupDetails
Occurances: 0 ... 1
Attributes
name
An optional name which can be given to the morphology
Type: 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

Morphology used by: morphml (xs:element)

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



Element: features
Collection of all extracellular histological features.
 
The following elements must appear in the sequence outlined here. Occurances: 1
Group
A group of elements to include with this element
Ref: meta:metadata
feature
A single feature of note.
Type : Feature

features is used by: Morphology (xs:complexType)

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



Element: propertyDetails
Collection of all PropertyDetails for this instance.
 
The following elements must appear in the sequence outlined here. Occurances: 1
propertyDetail
Type : meta:PropertyDetail

propertyDetails is used by: Morphology (xs:complexType)

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



Element: groupDetails
Collection of all GroupDetails for this instance.
 
The following elements must appear in the sequence outlined here. Occurances: 1
groupDetail
Type : meta:GroupDetail

groupDetails is used by: Morphology (xs:complexType)

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



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Complex Type: Cells

Collection of all cells.

The following elements must appear in the sequence outlined here.
cell
A single cell.
Type : Cell

Cells used by: Morphology (xs:complexType)

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



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Complex Type: Cell

Definition of a cell.

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: meta:referencedata
status
Status of the cell model: stable, in progress, etc. Further test comments explaining the current status should be added.
Type : meta:Status
Occurances: 0 ... 1
segments
A segment defines the smallest unit within a possibly branching structure, such as a dendrite or axon. The first segment should represent the soma, if needed for downstream applications.
Type : segments
Occurances: 1 ... 1
cables
The collection of cables. Each cable will be associated with a number of connected segments.
Type : cables
Occurances: 0 ... 1
cellBody
Used for anatomical representation of the soma. Use a Segment with equivalent properties to retain connectivity of branches to the soma for downstream applications (e.g. neuronal simulators).
Type : cellBody
Occurances: 0 ... 1
spines
The collection of spines.
Type : spines
Occurances: 0 ... 1
freePoints
The collection of varicosities or synaptic connections.
Type : FreePoints
Occurances: 0 ... 1
Attributes
nameType: xs:string , Use: optional

Cell used by: Cells (xs:complexType)

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



Element: segments
A segment defines the smallest unit within a possibly branching structure, such as a dendrite or axon. The first segment should represent the soma, if needed for downstream applications.
 
The following elements must appear in the sequence outlined here. Occurances: 1
Group
A group of elements to include with this element
Ref: meta:metadata
segment
Type : Segment

segments is used by: Cell (xs:complexType)

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



Element: cables
The collection of cables. Each cable will be associated with a number of connected segments.
 
The following elements must appear in the sequence outlined here. Occurances: 1
Group
A group of elements to include with this element
Ref: meta:metadata
cable
Type : Cable
cablegroup
Type : CableGroup
Occurances: 0 ... unbounded

cables is used by: Cell (xs:complexType)

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



Element: cellBody
Used for anatomical representation of the soma. Use a Segment with equivalent properties to retain connectivity of branches to the soma for downstream applications (e.g. neuronal simulators).
 
The following elements must appear in the sequence outlined here. Occurances: 1
Group
A group of elements to include with this element
Ref: meta:metadata
Only one of the following SUB elements may appear.
polygon
Type : meta:Polygon
polyhedron
Type : meta:Polyhedron
sphere
Type : meta:Sphere

cellBody is used by: Cell (xs:complexType)

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



Element: spines
The collection of spines.
 
The following elements must appear in the sequence outlined here. Occurances: 1
Group
A group of elements to include with this element
Ref: meta:metadata
spine
Type : Spine

spines is used by: Cell (xs:complexType)

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



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Complex Type: Segment

Defines the smallest unit within a possibly branching structure, such as a segment of a dendrite or axon. The parent attribute is used to define connectivity. A segment would be mapped to a compartment in a compartmental modelling application such as GENESIS

The following elements must appear in the sequence outlined here.
proximal
The start point (and diameter) of the segment. If absent, it is assumed that the distal point of the parent is the start point of this segment.
Type : meta:Point
Occurances: 0 ... 1
distal
The end point (and diameter) of the segment. Note if the 3D location of the distal point is the same as the proximal point, the segment is assumed to be spherical.
Type : meta:Point
properties
Some optional properties associated with the segment.
Type : meta:Properties
Occurances: 0 ... 1
Attributes
id
The ID of the segment, which should be unique within the cell.
Type: meta:SegmentIdInCell , Use: required
name
As many simulators use a string to identify the compartments, etc. a unique name can be given to the segment.
Type: xs:string , Use: optional
parent
Used to indicate logical connectivity between segments. Note that there is no requirement that the end point of this parent segment is equal to the start point of this segment.
Type: meta:SegmentIdInCell , Use: optional
cable
The cable ID of which this segment is part. Numerous segments will make up one cable, and it is assumed these are connected electrically.
Type: xs:nonNegativeInteger , Use: optional

Segment used by: Cell (xs:complexType)

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



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Complex Type: Cable

Definition of a cable. A cable is a non-branching group of connected segments. A cable would be mapped to a section in a cable modelling based simulator such as NEURON

The following elements must appear in the sequence outlined here.
Group
A group of elements to include with this element
Ref: meta:metadata
Attributes
id
ID of the cable, unique within this cell
Type: xs:nonNegativeInteger , Use: required
name
As many simulators use a string to identify the sections, etc. a unique name can be given to the segment.
Type: xs:string , Use: optional
parent
A cable ID. A way to connect cables logically.
Type: xs:nonNegativeInteger , Use: optional
fractAlongParent
Approximate location of this section's proximal point along the parent cable. NOTE: this attribute will be removed in v2.0!! Use fract_along_parent instead. Changed for consistency with ChannelML and NetworkML naming conventions.
Type: meta:ZeroToOne , Use: optional
fract_along_parent
Connection location of this section's proximal point along the parent cable. Normally this could be determined by the 3D points, but this option is needed as many reconstructed neurons have dendrites "floating in space", possibly due to drift of the slice. In this case the fract_along_parent determines electrical connectivity, and it is up to the loading application/its user to decide to ignore the discrepancy, move the dendrite or fill in an extra section. NOTE: this attribute will be required in v2.0!! Don't use fractAlongParent anymore. Changed for consistency with ChannelML and NetworkML naming conventions.
Type: meta:ZeroToOne , Use: optional

Cable used by: Cell (xs:complexType)

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



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Complex Type: CableGroup

Definition of a cable group. Cable groups can also be specified by adding an element group to the cable element

The following elements must appear in the sequence outlined here.
cable
The id of a single cable in the group
Type : cable
inhomogeneous_param
Type : InhomogeneousParam
Occurances: 0 ... unbounded
Attributes
name
Name of the cable group
Type: xs:string , Use: required

CableGroup used by: Cell (xs:complexType)

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



Element: cable
The id of a single cable in the group
 
Attributes
idType: xs:nonNegativeInteger , Use: required

cable is used by: CableGroup (xs:complexType)

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



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Complex Type: InhomogeneousParam

Definition of a parameter which varies along a cable group.

The following elements must appear in the sequence outlined here.
metric
The metric used to determine the variable
Type : Metric
proximal
Information on the value of the variable at the proximal point. If this element is absent, the value of the variable is determined simply from the metric, e.g. absolute path length
Type : proximal
Occurances: 0 ... 1
distal
Information on the value of the variable at the distal point. If this element is absent, the value of the variable is determined simply from the metric, e.g. path length
Type : distal
Occurances: 0 ... 1
Attributes
name
Name of the inhomogeneous parameter specification
Type: xs:string , Use: required
variable
Name of the variable which will change over the length
Type: xs:string , Use: required

InhomogeneousParam used by: CableGroup (xs:complexType)

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



Element: proximal
Information on the value of the variable at the proximal point. If this element is absent, the value of the variable is determined simply from the metric, e.g. absolute path length
 
Attributes
translationStart
The variable is translated to this value at the proximal point
Type: xs:double , Use: required

proximal is used by: InhomogeneousParam (xs:complexType)

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



Element: distal
Information on the value of the variable at the distal point. If this element is absent, the value of the variable is determined simply from the metric, e.g. path length
 
Attributes
normalizationEnd
The variable is normalised so that it has this value at the distal point
Type: xs:double , Use: required

distal is used by: InhomogeneousParam (xs:complexType)

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



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Complex Type: Spine

A spine with location, shape, and direction.

The following elements must appear in the sequence outlined here.
proximal
Type : meta:Point
distal
Type : meta:Point
Occurances: 0 ... 1
Attributes
parent
The segment with which this spine is associated.
Type: meta:SegmentIdInCell , Use: optional
lengthType: xs:double , Use: optional
volumeType: xs:double , Use: optional
shapeType: SpineShape, Use: optional

Spine used by: Cell (xs:complexType)

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



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Complex Type: FreePoints

A set of varicosities or synaptic connections.

Extension:
The child elements and attributes of the base element will be required in this element too.
Base: meta:Points

FreePoints used by: Cell (xs:complexType) Feature (xs:complexType)

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



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Complex Type: Path

Possibly branching histological structures.

Extension:
The child elements and attributes of the base element will be required in this element too.
Base: meta:Points
Attributes
idType: xs:nonNegativeInteger , Use: required
parent
A path id. A way to connect this path to another.
Type: xs:nonNegativeInteger , Use: optional

Path used by: Feature (xs:complexType)

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



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Complex Type: Feature

The group of things allowed in features.

The following elements must appear in the sequence outlined here.
Group
A group of elements to include with this element
Ref: meta:metadata
path
Type : Path
Occurances: 0 ... unbounded
freePoints
Type : FreePoints
Occurances: 0 ... unbounded
manifold
Type : meta:Manifold
Occurances: 0 ... unbounded
polygon
Type : meta:Polygon
Occurances: 0 ... unbounded
polyhedron
Type : meta:Polyhedron
Occurances: 0 ... unbounded
sphere
Type : meta:Sphere
Occurances: 0 ... unbounded
Attributes
nameType: xs:string , Use: optional

Feature used by: Morphology (xs:complexType)

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



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