NeuroMLCoreCompTypes

NeuroMLCoreCompTypes#

Original ComponentType definitions: NeuroMLCoreCompTypes.xml. Schema against which NeuroML based on these should be valid: NeuroML_v2.3.xsd. Generated on 14/08/24 from this commit. Please file any issues or questions at the issue tracker here.

notes#

Human readable notes/description for a Component.

Schema

<xs:simpleType name="Notes">
  <xs:annotation>
    <xs:documentation>Textual human readable notes related to the element in question. It's useful to put these into
         the NeuroML files instead of XML comments, as the notes can be extracted and repeated in the files to which the NeuroML is mapped.
            </xs:documentation>
  </xs:annotation>
  <xs:restriction base="xs:string"/>
</xs:simpleType>

Usage: XML

<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.

Child list

rdf:RDF

rdf_RDF

Children list

property

property

Schema

<xs:complexType name="Annotation">
  <xs:complexContent>
    <xs:extension base="BaseWithoutId">
      <xs:sequence>
        <xs:any processContents="skip" minOccurs="0" maxOccurs="unbounded"/>
      </xs:sequence>
    </xs:extension>
  </xs:complexContent>
</xs:complexType>

Usage: Python

Go to the libNeuroML documentation

from neuroml import Annotation
from neuroml.utils import component_factory

variable = component_factory(
    Annotation,
    anytypeobjs_=None,
)

Usage: XML

<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.

Text fields

tag	Name of the property
value	Value of the property

Schema

<xs:complexType name="Property">
  <xs:complexContent>
    <xs:extension base="BaseWithoutId">
      <xs:attribute name="tag" type="xs:string" use="required"/>
      <xs:attribute name="value" type="xs:string" use="required"/>
    </xs:extension>
  </xs:complexContent>
</xs:complexType>

Usage: Python

Go to the libNeuroML documentation

from neuroml import Property
from neuroml.utils import component_factory

variable = component_factory(
    Property,
    tag: 'a string (required)' = None,
    value: 'a string (required)' = None,
)

Usage: XML

<property tag="numberInternalDivisions" value="9"/>

baseStandalone#

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

Child list

notes		notes
annotation		annotation

Children list

property

property

Schema

<xs:complexType name="Standalone">
  <xs:complexContent>
    <xs:extension base="Base">
      <xs:sequence>
        <xs:element name="notes" type="Notes" minOccurs="0"/>
        <xs:element name="property" type="Property" minOccurs="0" maxOccurs="unbounded"/>
        <xs:element name="annotation" type="Annotation" minOccurs="0"/>
      </xs:sequence>
      <xs:attribute name="metaid" type="MetaId" use="optional"/>
    </xs:extension>
  </xs:complexContent>
</xs:complexType>

rdf_RDF#

Structured block in an annotation based on RDF. See OpenSourceBrain/OSB_API.

Text fields

xmlns:rdf

Child list

rdf:Description

rdf_Description

rdf_Description#

Structured block in an annotation based on RDF.

Text fields

rdf:about

Child list

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.

Child list

rdf:Bag

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

NeuroMLCoreCompTypes

Contents

NeuroMLCoreCompTypes#

notes#

annotation#

property#

baseStandalone#

rdf_RDF#

rdf_Description#

baseBqbiol#

bqbiol_encodes#

bqbiol_hasPart#

bqbiol_hasProperty#

bqbiol_hasVersion#

bqbiol_is#

bqbiol_isDescribedBy#

bqbiol_isEncodedBy#

bqbiol_isHomologTo#

bqbiol_isPartOf#

bqbiol_isPropertyOf#

bqbiol_isVersionOf#

bqbiol_occursIn#

bqbiol_hasTaxon#

bqmodel_is#

bqmodel_isDescribedBy#

bqmodel_isDerivedFrom#

rdf_Bag#

rdf_li#

point3DWithDiam#