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Converting the file: ChannelML_v1.1.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 |
| Definition of the elements needed for specifying electrophysiological
cellular mechanisms. Voltage/concentration dependent channels can be
specified, but also activity dependent ion concentrations (e.g. decaying calcium pools)
and (eventually) synaptic mechanisms.
The mechanisms which can be specified by this schema can be mapped on into the scripting
languages of a number of common simulation platforms, e.g. NEURON, GENESIS. This mapping
can be done a number of XML based ways, but XSL mappings are included with the
NeuroMLValidator code.
The elements outlined below are linked together with with those in MorphML.xsd
and Biophysics.xsd in the NeuroML.xsd file to make Level 2 compliant NeuroML files |
|
Schema info
Information on the namespaces, etc.
|
| targetNamespace | http://morphml.org/channelml/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_v1.1.xsd |
Elements
| Element: channelml |
| The root element of any ChannelML file. |
| Type: ChannelML |
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Simple Types
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Simple Type: IonRole
Role ion plays in cellular mechanism, e.g. ion passes through the channel (Na, K), or the
concentration of the ion is a factor in the rate equations of gating, or the mechanism alters
the concentration of this ion. This greatly simplifies the number of roles an ion can play
in the channel, but these three options cover the majority of cases currently being modelled
|
| Restriction: | Base:
xs:string
|
| Allowed values: |
| Transmitted |
(Ion passes through the channel)
|
| RateDependence |
(Rate equations of channel depend on concentration of ion)
|
| ConcVaries |
(Signifies that the ion is involved in a process which alters its concentration)
|
|
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IonRole used by:
Ion (xs:complexType)
Instances of this element which are used by other elements in this document
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Simple Type: Units
Enumeration of unit scheme used. Only SI or Physiological units allowed
|
| Restriction: | Base:
xs:string
|
| Allowed values: |
| Physiological Units |
| SI Units |
|
|
Units used by:
ChannelML (xs:complexType)
Instances of this element which are used by other elements in this document
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Simple Type: CoreEquationType
Enumeration of core equation types, linoidal, sigmoidal, exponential
|
| Restriction: | Base:
xs:string
|
| Allowed values: |
| exponential |
| sigmoid |
| linoid |
|
|
CoreEquationType used by:
AkdEquation (xs:complexType)
Instances of this element which are used by other elements in this document
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Groups
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Group: AlphaBetaForm
alpha, beta form of rate equations. These will always be together if present
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| The following elements must appear in the sequence outlined here.
|
| alpha | |
| beta | |
|
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Group: AlphaBetaFormVoltConcDep
alpha, beta form of rate equations of voltage and conc dependent channels. These will always be together if present
|
| The following elements must appear in the sequence outlined here.
|
| alpha | |
| beta | |
|
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Complex Types
|
Complex Type: ChannelML
Root element containing the ions used in the channel mechanism, the unit system of the
file (as attribute), and information on channels and/or ion concentration dynamics
|
| The following elements must appear in the sequence outlined here.
|
| Group |
| A group of elements to include with this element |
| Ref:
meta:metadata
|
| ion | | Type : Ion |
|
Occurances: 0
...
unbounded |
|
| channel_type | |
| synapse_type | |
| ion_concentration | |
| Attributes |
| units |
| Unit system of all quantities. Only SI or Physiological units are allowed! |
| Type: Units, Use: required |
|
|
ChannelML used by:
channelml (xs:element)
Instances of this element which are used by other elements in this document
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Complex Type: ChannelType
Definition of a voltage/concentration dependent cell membrane conductance
|
| The following elements must appear in the sequence outlined here.
|
| Group |
| Some metadata (notes, etc.) to describe the conductance. |
| Ref:
meta:metadata
|
| Group |
| A group of elements to include with this element |
| Ref:
meta:referencedata
|
| current_voltage_relation | |
| Attributes |
| name | Type:
xs:string
, Use: required |
| density | Type:
meta:YesNo
, Use: optional |
|
|
ChannelType used by:
ChannelML (xs:complexType)
Instances of this element which are used by other elements in this document
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|
Complex Type: SynapseType
Definition of a synaptic process
|
| The following elements must appear in the sequence outlined here.
|
| Group |
| Some metadata (notes, etc.) to describe the synapse. |
| Ref:
meta:metadata
|
| Group |
| A group of elements to include with this element |
| Ref:
meta:referencedata
|
| Only one of the following SUB elements may appear.
|
| doub_exp_syn | |
| Attributes |
| name | Type:
xs:string
, Use: required |
| density | Type:
meta:YesNo
, Use: optional |
|
|
SynapseType used by:
ChannelML (xs:complexType)
Instances of this element which are used by other elements in this document
|
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|
Complex Type: DoubleExponentialSynapse
...
|
| The following elements must appear in the sequence outlined here.
|
| Group |
| A group of elements to include with this element |
| Ref:
meta:metadata
|
| Attributes |
| max_conductance | Type:
xs:double
, Use: required |
| rise_time | Type:
xs:double
, Use: required |
| decay_time | Type:
xs:double
, Use: required |
| reversal_potential | Type:
xs:double
, Use: required |
|
|
DoubleExponentialSynapse used by:
SynapseType (xs:complexType)
Instances of this element which are used by other elements in this document
|
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|
Complex Type: CurrentVoltageRelation
How the current through the channel depends on the conductance of the channel.
Only ohmic supported at the moment
|
| The following elements must appear in the sequence outlined here.
|
| ohmic | | Type : Ohmic |
|
Occurances: 0
...
1 |
|
| Attributes |
| name | Type:
xs:string
, Use: optional |
|
|
CurrentVoltageRelation used by:
ChannelType (xs:complexType)
Instances of this element which are used by other elements in this document
|
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|
Complex Type: Ohmic
Signifies an ohmic relation; the current is proportional to the potential difference across the channel
|
| The following elements must appear in the sequence outlined here.
|
| conductance |
|
| Attributes |
| NonSpecific | Type:
xs:string
, Use: optional |
| ion | Type:
xs:string
, Use: optional |
|
|
Ohmic used by:
CurrentVoltageRelation (xs:complexType)
Instances of this element which are used by other elements in this document
|
| Element: conductance | |
| The following elements must appear in the sequence outlined here.
Occurances: 1 |
| rate_adjustments | |
| gate | | Type : Gate |
|
Occurances: 0
...
unbounded |
|
| Attributes |
| default_gmax | Type:
xs:double
, Use: optional |
|
conductance is used by: Ohmic (xs:complexType)
Instances of this element which are used by other elements in this document
|
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|
Complex Type: RateAdjustments
Adjustments necessary to all the rate equations, e.g
temperature dependencies, voltage offsets introduced when moving
between species, etc. See the XSL mappings for more information on the
meaning of these adjustments
|
| The following elements must appear in the sequence outlined here.
|
| q10_settings |
|
| offset | | Type : offset |
|
Occurances: 0
...
1 |
|
|
|
RateAdjustments used by:
Ohmic (xs:complexType)
Instances of this element which are used by other elements in this document
|
| Element: q10_settings | |
| Attributes |
| q10_factor |
| Q10 factor if the cell is to be run at a different temp than that at which
the alpha and beta were determined |
| Type:
xs:double
, Use: optional |
| experimental_temp |
| The experimental temperature at which alpha and beta rate
equations were determined were measured |
| Type:
xs:double
, Use: optional |
|
q10_settings is used by: RateAdjustments (xs:complexType)
Instances of this element which are used by other elements in this document
|
| Element: offset | |
| Attributes |
| value |
| Offset introduced to alter voltage dependence of
rate equations, see NEURON/GENESIS mappings for details |
| Type:
xs:double
, Use: optional |
|
offset is used by: RateAdjustments (xs:complexType)
Instances of this element which are used by other elements in this document
|
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|
Complex Type: Ion
Definition of an ion which is involved in this channel mechanism
|
| Attributes |
| name |
| Simple name for the ion. Due to the conventions used in NEURON, it is usually best to use
the lower case form of the chemical symbol, e.g. na, ca, k |
| Type:
xs:string
, Use: required |
| default_erev |
| Most implementations of these channel mechanisms (e.g. a mod file) will need a value for the
reversal potential for the ion which flows through the channel. However, this is a property of the cell, as opposed to the channel.
For convenience though, a typical value can be used here, so a pretty self contained script can be produced, but when used in a real cell the
actual value for erev must be calculated |
| Type:
xs:double
, Use: optional |
| charge |
| Electrical charge of the ion in question
|
| Type:
xs:integer
, Use: required |
| role |
| What role the ion plays in the dynamics of the channel/cell mechanism |
| Type: IonRole, Use: optional, default: Transmitted |
|
|
Ion used by:
ChannelML (xs:complexType)
Instances of this element which are used by other elements in this document
|
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|
Complex Type: Gate
Definition of a single voltage/concentration dependent gate
|
| The following elements must appear in the sequence outlined here.
|
| state |
|
| Attributes |
| power | Type:
xs:integer
, Use: required |
|
|
Gate used by:
Ohmic (xs:complexType)
Instances of this element which are used by other elements in this document
|
| Element: state | |
| The following elements must appear in the sequence outlined here.
Occurances: 1 |
| transition | |
| Attributes |
| name | Type:
xs:string
, Use: optional |
| fraction | Type:
xs:double
, Use: optional |
|
state is used by: Gate (xs:complexType)
Instances of this element which are used by other elements in this document
|
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|
Complex Type: Transition
What causes the gate to open and close. A dependence on potential difference,
or a voltage and (ion) concentration dependence
|
| Only one of the following elements may appear.
|
| voltage_gate | |
| voltage_conc_gate | |
|
|
Transition used by:
Gate (xs:complexType)
Instances of this element which are used by other elements in this document
|
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|
Complex Type: VoltageGate
Definition of a voltage gate. Normally this will be specified as rate equations for alpha and beta,
or for tau and inf
|
| The following elements must appear in the sequence outlined here.
|
| Group |
| A group of elements to include with this element |
| Ref: AlphaBetaForm
Occurances: 0
...
1 |
| tau | |
| inf | |
|
|
VoltageGate used by:
Transition (xs:complexType)
Instances of this element which are used by other elements in this document
|
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|
Complex Type: VoltageConcGate
Definition of a mechanics of a gate which depends on voltage and concentration (e.g. Calcium conc dependent K channel).
Normally this will be specified as rate equations for alpha and beta (in terms of v and conc), or for tau and inf
|
| The following elements must appear in the sequence outlined here.
|
| Group |
| A group of elements to include with this element |
| Ref: AlphaBetaFormVoltConcDep
Occurances: 0
...
1 |
| conc_dependence | |
| tau | |
| inf | |
|
|
VoltageConcGate used by:
Transition (xs:complexType)
Instances of this element which are used by other elements in this document
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Complex Type: ConcDependence
Specification of what a gate is dependent on the concentration of
|
| Attributes |
| name |
| Name of substance, just for reference |
| Type:
xs:string
, Use: required |
| ion |
| If the substance is an ion, here is a reference the entry in the ion list at the start of the file |
| Type:
xs:string
, Use: optional |
| variable_name |
| How the value of conductance will be expressed in the rate equations |
| Type:
xs:string
, Use: required |
| min_conc |
| Minimum expected concentration. Quite likely to be needed by simulators (e.g. for generating tables) |
| Type:
xs:double
, Use: required |
| max_conc |
| Maximum expected concentration. Quite likely to be needed by simulators (e.g. for generating tables) |
| Type:
xs:double
, Use: required |
|
|
ConcDependence used by:
VoltageConcGate (xs:complexType)
Instances of this element which are used by other elements in this document
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Complex Type: RateConstantEqnChoice
Choice of the various rate constant expressions allowed
|
| Only one of the following elements may appear.
|
| parameterised_hh | |
| generic_equation_hh | |
|
|
RateConstantEqnChoice used by:
VoltageGate (xs:complexType)
VoltageGate (xs:complexType)
AlphaBetaForm (xs:group)
AlphaBetaForm (xs:group)
Instances of this element which are used by other elements in this document
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Complex Type: RateConstVoltConcDep
Rate constant expressions allowed for voltage and conc dependent channels. Note, at this stage no
Akd like expression for a generic voltage/conc dep experssion. Time will tell if there's an expression common enough
accross different models to be expressed in such a way
|
| Only one of the following elements may appear.
|
| generic_equation_hh | |
|
|
RateConstVoltConcDep used by:
VoltageConcGate (xs:complexType)
VoltageConcGate (xs:complexType)
AlphaBetaFormVoltConcDep (xs:group)
AlphaBetaFormVoltConcDep (xs:group)
Instances of this element which are used by other elements in this document
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Complex Type: RateConstantEqn
Definition of a rate constant equation. This is currently onlu used when mapped to either
AkdEquation or GenericEquation
|
| The following elements must appear in the sequence outlined here.
|
| parameter |
| A parameter which is used in the equation |
| |
| Attributes |
| type | Type:
xs:string
, Use: required |
| expr | Type:
xs:string
, Use: optional |
|
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Complex Type: AkdEquation
Definition of a type of rate constant equation which takes parameters A, k, d
and maps to either exponential, sigmoidal or linoidal.
|
|
|
|
AkdEquation used by:
RateConstantEqnChoice (xs:complexType)
Instances of this element which are used by other elements in this document
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Complex Type: GenericEquation
Definition of a type of rate constant equation
|
| The following elements must appear in the sequence outlined here.
|
| parameter | |
| Attributes |
| expr |
| Note: only variable allowed in expression is v (or for an expression for tau or inf,
alpha and beta can be used too). Also, liberal use of brackets, e.g. 5.0*(exp (-50*(v +46))) instead
of 5.0* exp (-50*(v +46)) is advised, due to GENESIS's handling of exp, abs, etc. |
| Type:
xs:string
, Use: required |
|
|
GenericEquation used by:
RateConstantEqnChoice (xs:complexType)
RateConstVoltConcDep (xs:complexType)
Instances of this element which are used by other elements in this document
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Complex Type: IonConcentration
Concentration of a particular ion species, the concentration
of which affects some channels
|
| 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
|
| ion_species | |
| Only one of the following SUB elements may appear.
|
| decaying_pool_model | |
| Attributes |
| name | Type:
xs:string
, Use: required |
|
|
IonConcentration used by:
ChannelML (xs:complexType)
Instances of this element which are used by other elements in this document
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Complex Type: DecayingPoolModel
Element for parameters in a decaying pool model of ion concentration (e.g. calcium pool)
|
| The following elements must appear in the sequence outlined here.
|
| resting_conc |
| Resting concentration of ion |
| |
| decay_constant |
| Exponential decay time of pool |
| |
| The following SUB elements must appear in the sequence outlined here.
Minimum occurances allowed: Maximum occurances allowed: |
| pool_volume_info | |
|
|
DecayingPoolModel used by:
IonConcentration (xs:complexType)
Instances of this element which are used by other elements in this document
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Complex Type: PoolVolumeInfo
Information on the volume of the ion pool
|
| The following elements must appear in the sequence outlined here.
|
| shell_thickness | |
|
|
PoolVolumeInfo used by:
DecayingPoolModel (xs:complexType)
Instances of this element which are used by other elements in this document
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Complex Type: Parameter
Generic parameter used in rate equations
|
| The following elements must appear in the sequence outlined here.
|
| Group |
| A group of elements to include with this element |
| Ref:
meta:metadata
|
| Attributes |
| name | Type:
xs:string
, Use: required |
| value | Type:
xs:double
, Use: required |
|
|
Parameter used by:
RateConstantEqn (xs:complexType)
AkdEquation (xs:complexType)
GenericEquation (xs:complexType)
Instances of this element which are used by other elements in this document
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