NeuroMLCoreCompTypes

Original ComponentType definitions: NeuroMLCoreCompTypes.xml. Schema against which NeuroML based on these should be valid: NeuroML_v2.2.xsd. Generated on 25/08/21 from this commit. Please file any issues or questions at the issue tracker here.


notes

Human readable notes/description for a Component.

<notes>A Simple Spiking cell for testing purposes</notes>
<notes>Multicompartmental cell</notes>
<notes>Leak conductance</notes>

annotation

A structured annotation containing metadata, specifically RDF or property elements.

rdf:RDF

rdf_RDF

property

property

Go to the libNeuroML documentation

from neuroml import Annotation

variable = Annotation(anytypeobjs_=None, **kwargs_)
<annotation>
            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
              <rdf:Description rdf:about="HippoCA1Cell">
                <bqbiol:is>
                  <rdf:Bag>
                    
                    <rdf:li rdf:resource="urn:miriam:neurondb:258"/>
                  </rdf:Bag>
                </bqbiol:is>
              </rdf:Description>
            </rdf:RDF>
        </annotation>

property

A property ( a tag and value pair ), which can be on any baseStandalone either as a direct child, or within an annotation. Generally something which helps the visual display or facilitates simulation of a Component, but is not a core physiological property. Common examples include: numberInternalDivisions, equivalent of nseg in NEURON; radius, for a radius to use in graphical displays for abstract cells ( i.e. without defined morphologies ); color, the color to use for a population or populationList of cells; recommended_dt_ms, the recommended timestep to use for simulating a network, recommended_duration_ms the recommended duration to use when running a network.

tag

Name of the property

value

Value of the property

Go to the libNeuroML documentation

from neuroml import Property

variable = Property(tag=None, value=None, **kwargs_)
<property tag="numberInternalDivisions" value="9"/>

baseStandalone

Base type of any Component which can have notes, annotation, or a property list.

notes

notes

annotation

annotation

property

property

rdf_RDF

Structured block in an annotation based on RDF. See https://github.com/OpenSourceBrain/OSB_API/blob/master/python/examples/grancelllayer.xml.

xmlns:rdf

rdf:Description

rdf_Description

rdf_Description

Structured block in an annotation based on RDF.

rdf:about

bqbiol:encodes

bqbiol_encodes

bqbiol:hasPart

bqbiol_hasPart

bqbiol:hasProperty

bqbiol_hasProperty

bqbiol:hasVersion

bqbiol_hasVersion

bqbiol:is

bqbiol_is

bqbiol:isDescribedBy

bqbiol_isDescribedBy

bqbiol:isEncodedBy

bqbiol_isEncodedBy

bqbiol:isHomologTo

bqbiol_isHomologTo

bqbiol:isPartOf

bqbiol_isPartOf

bqbiol:isPropertyOf

bqbiol_isPropertyOf

bqbiol:isVersionOf

bqbiol_isVersionOf

bqbiol:occursIn

bqbiol_occursIn

bqbiol:hasTaxon

bqbiol_hasTaxon

bqmodel:is

bqmodel_is

bqmodel:isDescribedBy

bqmodel_isDescribedBy

bqmodel:isDerivedFrom

bqmodel_isDerivedFrom

baseBqbiol

Structured block in an annotation based on RDF.

rdf:Bag

rdf_Bag

bqbiol_hasProperty

extends baseBqbiol

See http://co.mbine.org/standards/qualifiers.

bqbiol_isDescribedBy

extends baseBqbiol

See http://co.mbine.org/standards/qualifiers.

bqbiol_isEncodedBy

extends baseBqbiol

See http://co.mbine.org/standards/qualifiers.

bqbiol_isHomologTo

extends baseBqbiol

See http://co.mbine.org/standards/qualifiers.

bqbiol_isPropertyOf

extends baseBqbiol

See http://co.mbine.org/standards/qualifiers.

bqbiol_isVersionOf

extends baseBqbiol

See http://co.mbine.org/standards/qualifiers.

xmlns:bqbiol

bqmodel_isDescribedBy

extends baseBqbiol

See http://co.mbine.org/standards/qualifiers.

xmlns:bqmodel

bqmodel_isDerivedFrom

extends baseBqbiol

See http://co.mbine.org/standards/qualifiers.

rdf_Bag

Structured block in an annotation based on RDF.

rdf:li

schema:rdf:li

rdf_li

Structured block in an annotation based on RDF.

rdf:resource

point3DWithDiam

Base type for ComponentTypes which specify an ( x, y, z ) coordinate along with a diameter. Note: no dimension used in the attributes for these coordinates! These are assumed to have dimension micrometer ( 10^-6 m ). This is due to micrometers being the default option for the majority of neuronal morphology formats, and dimensions are omitted here to facilitate reading and writing of morphologies in NeuroML.

diameter

Diameter of the ppoint. Note: no dimension used, see description of point3DWithDiam for details.

Dimensionless

x

x coordinate of the point. Note: no dimension used, see description of point3DWithDiam for details.

Dimensionless

y

y coordinate of the ppoint. Note: no dimension used, see description of point3DWithDiam for details.

Dimensionless

z

z coordinate of the ppoint. Note: no dimension used, see description of point3DWithDiam for details.

Dimensionless

radius

A dimensional quantity given by half the _diameter.

length

xLength

A version of _x with dimension length.

length

yLength

A version of _y with dimension length.

length

zLength

A version of _z with dimension length.

length

MICRON = 1um

length

Go to the libNeuroML documentation

from neuroml import Point3DWithDiam

variable = Point3DWithDiam(x=None, y=None, z=None, diameter=None, **kwargs_)