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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
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Schema info
Information on the namespaces, etc.
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| targetNamespace | http://morphml.org/morphml/schema |
| elementFormDefault | qualified |
| attributeFormDefault | unqualified |
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Imported Schemas
Other schemas used by this file, with different target namespaces
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| Namespace: http://morphml.org/metadata/schema | Location: ../Level1/Metadata_v1.8.1.xsd |
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
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Simple Type: Metric
Metric for use in InhomogeneousParam
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| Restriction: | Base:
xs:string
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| Allowed values: |
| Path Length from root |
| 3D radial position |
| 3D path length from line |
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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.
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| Restriction: | Base:
xs:string
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| Allowed values: | |
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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
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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
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| The following elements must appear in the sequence outlined here.
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| Group |
| A group of elements to include with this element |
| Ref:
meta:metadata
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| cells | |
| features |
| Collection of all extracellular histological features. |
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| propertyDetails |
| Collection of all PropertyDetails for this instance. |
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| groupDetails |
| Collection of all GroupDetails for this instance. |
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| 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 |
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Morphology used by:
morphml (xs:element)
Instances of this element which are used by other elements in this document
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| 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
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| feature |
| A single feature of note. |
| |
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features is used by: Morphology (xs:complexType)
Instances of this element which are used by other elements in this document
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| Element: propertyDetails |
| Collection of all PropertyDetails for this instance. |
| |
| The following elements must appear in the sequence outlined here.
Occurances: 1 |
| propertyDetail | |
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propertyDetails is used by: Morphology (xs:complexType)
Instances of this element which are used by other elements in this document
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| Element: groupDetails |
| Collection of all GroupDetails for this instance. |
| |
| The following elements must appear in the sequence outlined here.
Occurances: 1 |
| groupDetail | |
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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.
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| The following elements must appear in the sequence outlined here.
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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.
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| The following elements must appear in the sequence outlined here.
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| Group |
| A group of elements to include with this element |
| Ref:
meta:metadata
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| Group |
| A group of elements to include with this element |
| Ref:
meta:referencedata
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| 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. |
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| cables |
| The collection of cables. Each cable will be associated with a number of connected segments. |
| | Type : cables |
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Occurances: 0
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1 |
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| 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). |
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| spines |
| The collection of spines. |
| | Type : spines |
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Occurances: 0
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1 |
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| freePoints |
| The collection of varicosities or synaptic connections. |
| |
| Attributes |
| name | Type:
xs:string
, Use: optional |
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Cell used by:
Cells (xs:complexType)
Instances of this element which are used by other elements in this document
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| 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
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| segment | |
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segments is used by: Cell (xs:complexType)
Instances of this element which are used by other elements in this document
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| 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
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| cable | |
| cablegroup | |
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cables is used by: Cell (xs:complexType)
Instances of this element which are used by other elements in this document
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| 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
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| Only one of the following SUB elements may appear.
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| polygon | |
| polyhedron | |
| sphere | |
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cellBody is used by: Cell (xs:complexType)
Instances of this element which are used by other elements in this document
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| 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
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| spine | |
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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
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| The following elements must appear in the sequence outlined here.
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| 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. |
| |
| 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. |
| |
| properties |
| Some optional properties associated with the segment. |
| |
| 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 |
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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
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| The following elements must appear in the sequence outlined here.
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| Group |
| A group of elements to include with this element |
| Ref:
meta:metadata
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| 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 |
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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
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| The following elements must appear in the sequence outlined here.
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| cable |
| The id of a single cable in the group |
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| inhomogeneous_param | |
| Attributes |
| name |
| Name of the cable group |
| Type:
xs:string
, Use: required |
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CableGroup used by:
Cell (xs:complexType)
Instances of this element which are used by other elements in this document
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| Element: cable |
| The id of a single cable in the group |
| |
| Attributes |
| id | Type:
xs:nonNegativeInteger
, Use: required |
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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.
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| The following elements must appear in the sequence outlined here.
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| metric |
| The metric used to determine the variable |
| |
| 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 |
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| 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 |
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Occurances: 0
...
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| 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 |
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InhomogeneousParam used by:
CableGroup (xs:complexType)
Instances of this element which are used by other elements in this document
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| 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 |
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| Attributes |
| translationStart |
| The variable is translated to this value at the proximal point |
| Type:
xs:double
, Use: required |
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proximal is used by: InhomogeneousParam (xs:complexType)
Instances of this element which are used by other elements in this document
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| 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 |
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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.
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| The following elements must appear in the sequence outlined here.
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| proximal | |
| distal | |
| Attributes |
| parent |
| The segment with which this spine is associated. |
| Type:
meta:SegmentIdInCell
, Use: optional |
| length | Type:
xs:double
, Use: optional |
| volume | Type:
xs:double
, Use: optional |
| shape | Type: SpineShape, Use: optional |
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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.
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| Extension: |
| The child elements and attributes of the base element will be required in this element too. |
| Base:
meta:Points
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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.
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| Extension: |
| The child elements and attributes of the base element will be required in this element too. |
| Base:
meta:Points
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| Attributes |
| id | Type:
xs:nonNegativeInteger
, Use: required |
| parent |
| A path id. A way to connect this path to another. |
| Type:
xs:nonNegativeInteger
, Use: optional |
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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.
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| The following elements must appear in the sequence outlined here.
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| Group |
| A group of elements to include with this element |
| Ref:
meta:metadata
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| path | | Type : Path |
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Occurances: 0
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unbounded |
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| freePoints | |
| manifold | |
| polygon | |
| polyhedron | |
| sphere | |
| Attributes |
| name | Type:
xs:string
, Use: optional |
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Feature used by:
Morphology (xs:complexType)
Instances of this element which are used by other elements in this document
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