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Merged
merged 7 commits into from
Jun 11, 2024
Merged

feat(core-types): add annotation component types #225

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8c5b644
feat(core-types): add annotation component types
sanjayankur31 Apr 29, 2024
23fabbe
feat(annotations): update keywords
sanjayankur31 May 3, 2024
09f066d
feat(annotations): update combine specifications URL
sanjayankur31 May 3, 2024
ff2587f
feat(annotations): add remaining FOAF bits
sanjayankur31 May 3, 2024
1d248b3
Merge branch 'development' into feat/annotations
sanjayankur31 May 7, 2024
0895147
feat(annotations): use Child instead of Children
sanjayankur31 May 7, 2024
c989b81
Merge branch 'development' into feat/annotations
pgleeson May 29, 2024
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169 changes: 143 additions & 26 deletions NeuroML2CoreTypes/NeuroMLCoreCompTypes.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -36,12 +36,37 @@
<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.">
Expand Down