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Merge pull request #228 from NeuroML/experimental
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To v1.10.1; adds annotations support; schema requires at least one specificCapacitance & init_memb_pot
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@pgleeson
pgleeson authored Jun 11, 2024
2 parents ab06e87 + 59bce36 commit fef11a1
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75 changes: 0 additions & 75 deletions .travis.yml
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169 changes: 143 additions & 26 deletions NeuroML2CoreTypes/NeuroMLCoreCompTypes.xml
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<ComponentType name="rdf_RDF" description="Structured block in an _annotation_ based on RDF. See https://github.com/OpenSourceBrain/OSB_API/blob/master/python/examples/grancelllayer.xml">
<Child name="rdf:Description" type="rdf_Description"/>
<Text name="xmlns:rdf"/>
<Text name="xmlns:rdfs"/>
<Text name="xmlns:dcterms"/>
<Text name="xmlns:dc"/>
<Text name="xmlns:prism"/>
<Text name="xmlns:bqbiol"/>
<Text name="xmlns:bqmodel"/>
<Text name="xmlns:scoro"/>
<Text name="xmlns:collex"/>
<Dynamics/>
</ComponentType>


<ComponentType name="rdf_Description" description="Structured block in an _annotation_ based on RDF.">

<Child name="dc:title" type="dc_title"/>
<Child name="dc:description" type="dc_description"/>
<Child name="dcterms:abstract" type="dcterms_abstract"/>
<Child name="dcterms:license" type="dcterms_license"/>
<Child name="dcterms:created" type="dcterms_created"/>

<!-- for people info from FOAF: not complete -->
<Child name="foaf:name" type="foaf_name"/>
<Child name="foaf:homepage" type="foaf_homepage"/>
<Child name="foaf:account" type="foaf_account"/>
<Child name="foaf:fundedBy" type="foaf_fundedBy"/>
<Child name="foaf:mbox" type="foaf_mbox"/>
<Child name="foaf:weblog" type="foaf_weblog"/>
<Child name="foaf:thumbnail" type="foaf_thumbnail"/>
<Child name="foaf:publications" type="foaf_publications"/>
<Child name="orcid:id" type="orcid_id"/>

<Child name="bqbiol:encodes" type="bqbiol_encodes"/>
<Child name="bqbiol:hasPart" type="bqbiol_hasPart"/>
<Child name="bqbiol:hasProperty" type="bqbiol_hasProperty"/>
Expand All @@ -58,65 +83,157 @@
<Child name="bqmodel:is" type="bqmodel_is"/>
<Child name="bqmodel:isDescribedBy" type="bqmodel_isDescribedBy"/>
<Child name="bqmodel:isDerivedFrom" type="bqmodel_isDerivedFrom"/>
<Child name="bqmodel:isIntanceOf" type="bqmodel_isInstanceOf"/>
<Child name="bqmodel:hasInstance" type="bqmodel_hasInstance"/>
<Child name="prism:keyword" type="prism_keyword"/>
<Child name="collex:thumbnail" type="collex_thumbnail"/>
<Child name="scoro:successor" type="scoro_successor"/>
<Child name="rdfs:seeAlso" type="rdfs_seeAlso"/>
<Child name="dcterms:references" type="dcterms_references"/>
<Child name="dc:creator" type="dc_creator"/>
<Child name="dc:contributor" type="dc_contributor"/>
<Child name="dc:source" type="dc_source"/>
<Child name="scoro:funder" type="scoro_funder"/>
<Child name="dcterms:modified" type="dcterms_modified"/>
<Text name="rdf:about"/>
<Dynamics/>
</ComponentType>


<ComponentType name="baseBqbiol" description="Structured block in an _annotation_ based on RDF.">
<!-- base RDF types -->
<ComponentType name="baseAnnotation_without_ns" description="Structured block in an _annotation_ based on RDF.">
<Child name="rdf:Bag" type="rdf_Bag"/>
<Dynamics/>
</ComponentType>

<ComponentType name="baseBqbiol" description="Structured block in an _annotation_ based on RDF." extends="baseAnnotation_without_ns">
<Text name="xmlns:bqbiol"/>
<Dynamics/>
</ComponentType>

<ComponentType name="baseBqmodel" description="Structured block in an _annotation_ based on RDF." extends="baseAnnotation_without_ns">
<Text name="xmlns:bqmodel"/>
<Dynamics/>
</ComponentType>

<ComponentType name="rdf_Bag" description="Structured block in an _annotation_ based on RDF.">
<Child name="rdf:li" type="rdf_li"/>
<Dynamics/>
</ComponentType>

<ComponentType name="rdf_li" description="Structured block in an _annotation_ based on RDF.">
<Text name="rdf:resource"/>
<Dynamics/>
</ComponentType>

<ComponentType name="bqbiol_encodes" description="See http://co.mbine.org/standards/qualifiers" extends="baseBqbiol"/>

<ComponentType name="bqbiol_hasPart" description="See http://co.mbine.org/standards/qualifiers" extends="baseBqbiol"/>
<ComponentType name="bqbiol_encodes" description="See https://github.com/combine-org/combine-specifications" extends="baseBqbiol"/>

<ComponentType name="bqbiol_hasProperty" description="See http://co.mbine.org/standards/qualifiers" extends="baseBqbiol"/>
<ComponentType name="bqbiol_hasPart" description="See https://github.com/combine-org/combine-specifications" extends="baseBqbiol"/>

<ComponentType name="bqbiol_hasVersion" description="See http://co.mbine.org/standards/qualifiers" extends="baseBqbiol"/>
<ComponentType name="bqbiol_hasProperty" description="See https://github.com/combine-org/combine-specifications" extends="baseBqbiol"/>

<ComponentType name="bqbiol_is" description="See http://co.mbine.org/standards/qualifiers" extends="baseBqbiol"/>
<ComponentType name="bqbiol_hasVersion" description="See https://github.com/combine-org/combine-specifications" extends="baseBqbiol"/>

<ComponentType name="bqbiol_isDescribedBy" description="See http://co.mbine.org/standards/qualifiers" extends="baseBqbiol"/>
<ComponentType name="bqbiol_is" description="See https://github.com/combine-org/combine-specifications" extends="baseBqbiol"/>

<ComponentType name="bqbiol_isEncodedBy" description="See http://co.mbine.org/standards/qualifiers" extends="baseBqbiol"/>
<ComponentType name="bqbiol_isDescribedBy" description="See https://github.com/combine-org/combine-specifications" extends="baseBqbiol"/>

<ComponentType name="bqbiol_isHomologTo" description="See http://co.mbine.org/standards/qualifiers" extends="baseBqbiol"/>
<ComponentType name="bqbiol_isEncodedBy" description="See https://github.com/combine-org/combine-specifications" extends="baseBqbiol"/>

<ComponentType name="bqbiol_isPartOf" description="See http://co.mbine.org/standards/qualifiers" extends="baseBqbiol"/>
<ComponentType name="bqbiol_isHomologTo" description="See https://github.com/combine-org/combine-specifications" extends="baseBqbiol"/>

<ComponentType name="bqbiol_isPropertyOf" description="See http://co.mbine.org/standards/qualifiers" extends="baseBqbiol"/>
<ComponentType name="bqbiol_isPartOf" description="See https://github.com/combine-org/combine-specifications" extends="baseBqbiol"/>

<ComponentType name="bqbiol_isVersionOf" description="See http://co.mbine.org/standards/qualifiers" extends="baseBqbiol">
<Text name="xmlns:bqbiol"/>
</ComponentType>
<ComponentType name="bqbiol_isPropertyOf" description="See https://github.com/combine-org/combine-specifications" extends="baseBqbiol"/>

<ComponentType name="bqbiol_occursIn" description="See http://co.mbine.org/standards/qualifiers" extends="baseBqbiol"/>
<ComponentType name="bqbiol_isVersionOf" description="See https://github.com/combine-org/combine-specifications" extends="baseBqbiol" />

<ComponentType name="bqbiol_hasTaxon" description="See http://co.mbine.org/standards/qualifiers" extends="baseBqbiol"/>
<ComponentType name="bqbiol_occursIn" description="See https://github.com/combine-org/combine-specifications" extends="baseBqbiol"/>

<ComponentType name="bqmodel_is" description="See http://co.mbine.org/standards/qualifiers" extends="baseBqbiol"/>
<ComponentType name="bqbiol_hasTaxon" description="See https://github.com/combine-org/combine-specifications" extends="baseBqbiol"/>

<ComponentType name="bqmodel_isDescribedBy" description="See http://co.mbine.org/standards/qualifiers" extends="baseBqbiol">
<Text name="xmlns:bqmodel"/>
<ComponentType name="bqmodel_is" description="See https://github.com/combine-org/combine-specifications" extends="baseBqmodel"/>

<ComponentType name="bqmodel_isDescribedBy" description="See https://github.com/combine-org/combine-specifications" extends="baseBqmodel" />

<ComponentType name="bqmodel_isDerivedFrom" description="See https://github.com/combine-org/combine-specifications" extends="baseBqmodel"/>

<ComponentType name="bqmodel_isInstanceOf" description="See https://github.com/combine-org/combine-specifications" extends="baseBqmodel"/>

<ComponentType name="bqmodel_hasInstance" description="See https://github.com/combine-org/combine-specifications" extends="baseBqmodel"/>

<ComponentType name="dc_title" description="https://docs.biosimulations.org/concepts/conventions/simulation-project-metadata/" />

<ComponentType name="dc_description" description="https://docs.biosimulations.org/concepts/conventions/simulation-project-metadata/"/>

<ComponentType name="dcterms_abstract" description="https://docs.biosimulations.org/concepts/conventions/simulation-project-metadata/"/>

<ComponentType name="dcterms_license" description="https://docs.biosimulations.org/concepts/conventions/simulation-project-metadata/"/>

<ComponentType name="dcterms_created" description="https://docs.biosimulations.org/concepts/conventions/simulation-project-metadata/">
<Child name="rdf:Description" type="dcterms_created_description"/>
</ComponentType>

<ComponentType name="bqmodel_isDerivedFrom" description="See http://co.mbine.org/standards/qualifiers" extends="baseBqbiol"/>
<ComponentType name="dcterms_created_description" description="https://docs.biosimulations.org/concepts/conventions/simulation-project-metadata/">
<Child name="dcterms:W3CDTF" type="dcterms_date" />
</ComponentType>

<ComponentType name="dcterms_date" description="https://docs.biosimulations.org/concepts/conventions/simulation-project-metadata/" />

<ComponentType name="rdf_Bag" description="Structured block in an _annotation_ based on RDF.">
<Children name="rdf:li" type="rdf:li"/>
<Dynamics/>
<ComponentType name="dcterms_modified" description="https://docs.biosimulations.org/concepts/conventions/simulation-project-metadata/">
<Child name="rdf:Description" type="dcterms_modified_description"/>
</ComponentType>

<ComponentType name="dcterms_modified_description" description="https://docs.biosimulations.org/concepts/conventions/simulation-project-metadata/">
<Child name="dcterms:W3CDTF" type="dcterms_date_list" />
</ComponentType>

<ComponentType name="dcterms_date_list" description="https://docs.biosimulations.org/concepts/conventions/simulation-project-metadata/" extends="baseAnnotation_without_ns"/>
<ComponentType name="dc_source" description="https://docs.biosimulations.org/concepts/conventions/simulation-project-metadata/" extends="baseAnnotation_without_ns"/>

<ComponentType name="prism_keyword" description="https://docs.biosimulations.org/concepts/conventions/simulation-project-metadata/" extends="baseAnnotation_without_ns"/>

<ComponentType name="collex_thumbnail" description="https://docs.biosimulations.org/concepts/conventions/simulation-project-metadata/" extends="baseAnnotation_without_ns"/>

<ComponentType name="scoro_successor" description="https://docs.biosimulations.org/concepts/conventions/simulation-project-metadata/" extends="baseAnnotation_without_ns"/>

<ComponentType name="rdf:li" description="Structured block in an _annotation_ based on RDF.">
<ComponentType name="rdfs_seeAlso" description="https://docs.biosimulations.org/concepts/conventions/simulation-project-metadata/" extends="baseAnnotation_without_ns"/>

<ComponentType name="dcterms_references" description="https://docs.biosimulations.org/concepts/conventions/simulation-project-metadata/" extends="baseAnnotation_without_ns"/>
<ComponentType name="dc_creator" description="https://docs.biosimulations.org/concepts/conventions/simulation-project-metadata/" extends="baseAnnotation_without_ns"/>

<ComponentType name="dc_contributor" description="https://docs.biosimulations.org/concepts/conventions/simulation-project-metadata/" extends="baseAnnotation_without_ns"/>

<ComponentType name="scoro_funder" description="https://docs.biosimulations.org/concepts/conventions/simulation-project-metadata/" extends="baseAnnotation_without_ns"/>

<ComponentType name="foaf_name" description="https://docs.biosimulations.org/concepts/conventions/simulation-project-metadata/" >
<Text name="rdf:resource"/>
</ComponentType>
<ComponentType name="foaf_homepage" description="https://docs.biosimulations.org/concepts/conventions/simulation-project-metadata/" >
<Text name="rdf:resource"/>
</ComponentType>
<ComponentType name="foaf_account" description="https://docs.biosimulations.org/concepts/conventions/simulation-project-metadata/" >
<Text name="rdf:resource"/>
</ComponentType>
<ComponentType name="foaf_fundedBy" description="https://docs.biosimulations.org/concepts/conventions/simulation-project-metadata/" >
<Text name="rdf:resource"/>
</ComponentType>
<ComponentType name="foaf_mbox" description="https://docs.biosimulations.org/concepts/conventions/simulation-project-metadata/" >
<Text name="rdf:resource"/>
</ComponentType>
<ComponentType name="foaf_weblog" description="https://docs.biosimulations.org/concepts/conventions/simulation-project-metadata/" >
<Text name="rdf:resource"/>
</ComponentType>
<ComponentType name="foaf_thumbnail" description="https://docs.biosimulations.org/concepts/conventions/simulation-project-metadata/" >
<Text name="rdf:resource"/>
</ComponentType>
<ComponentType name="foaf_publications" description="https://docs.biosimulations.org/concepts/conventions/simulation-project-metadata/" >
<Text name="rdf:resource"/>
</ComponentType>
<ComponentType name="orcid_id" description="https://docs.biosimulations.org/concepts/conventions/simulation-project-metadata/" >
<Text name="rdf:resource"/>
<Dynamics/>
</ComponentType>


<ComponentType name="point3DWithDiam"
description="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.">
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4 changes: 2 additions & 2 deletions Schemas/NeuroML2/NeuroML_v2.3.1.xsd
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Expand Up @@ -2118,8 +2118,8 @@
<xs:element name="channelDensityNonUniformNernst" type="ChannelDensityNonUniformNernst" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="channelDensityNonUniformGHK" type="ChannelDensityNonUniformGHK" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="spikeThresh" type="SpikeThresh" minOccurs="1" maxOccurs="unbounded"/>
<xs:element name="specificCapacitance" type="SpecificCapacitance" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="initMembPotential" type="InitMembPotential" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="specificCapacitance" type="SpecificCapacitance" minOccurs="1" maxOccurs="unbounded"/>
<xs:element name="initMembPotential" type="InitMembPotential" minOccurs="1" maxOccurs="unbounded"/>
<!-- Taking this out until confirmation it's needed
<xs:element name="reversalPotential" type="ReversalPotential" minOccurs="0" maxOccurs="unbounded"/>-->
</xs:sequence>
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4 changes: 3 additions & 1 deletion examples/NML2_FullCell.nml
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Expand Up @@ -88,12 +88,14 @@

<channelDensity id="naChansSoma" ionChannel="NaConductance" segmentGroup="soma_group" condDensity="120.0 mS_per_cm2" erev="50mV" ion="na"/>

<spikeThresh value="-10mV" />
<spikeThresh value="0mV"/>

<specificCapacitance segmentGroup="soma_group" value="1.0 uF_per_cm2"/>

<specificCapacitance segmentGroup="dendrite_group" value="2.0 uF_per_cm2"/>

<initMembPotential value="-65mV"/>

</membraneProperties>

<intracellularProperties>
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18 changes: 8 additions & 10 deletions examples/NML2_FullNeuroML.nml
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Expand Up @@ -9,9 +9,8 @@
<!-- Example containing a range of different elements from NeuroML 2 -->



<!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
<!-- Strucure of cell neurites -->
<!-- Structure of cell neurites -->

<morphology id="NeuroMorpho_PyrCell123"> <!-- see FullCell.xml for more details -->

Expand All @@ -21,6 +20,10 @@
<distal x="10" y="0" z="0" diameter="10"/>
</segment>

<segmentGroup id="soma_group">
<member segment="0"/>
</segmentGroup>

<!-- more needed -->

</morphology>
Expand Down Expand Up @@ -63,21 +66,16 @@
ion="na"
erev="50mV"/> <!-- Temporarily specifying erev in the channelDensity element-->

<!-- Ions present inside the cell. Note: a fixed reversal potential is specified here
<reversalPotential species="na" value="50mV"/>
<reversalPotential species="k" value="-77mV"/>-->
<spikeThresh value="0mV"/>
<specificCapacitance segmentGroup="soma_group" value="1.0 uF_per_cm2"/>
<initMembPotential value="-65mV"/>

<!-- more needed -->
<spikeThresh value="-10mV" />
</membraneProperties>

<intracellularProperties> <!-- used for bioelectrical properties inside a cell -->

<resistivity value="0.1 kohm_cm"/> <!-- Used for specific axial resistance -->

<!-- REMOVED UNTIL WE CHECK HOW THE USAGE OF LEMS IMPACTS THIS...
<biochemistry reactionScheme="InternalCaDynamics"/> Ref to earlier pathway -->

</intracellularProperties>

</biophysicalProperties>
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