feat(core-types): add annotation component types #225
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This is what an example annotation looks like: <rdf:RDF
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"
xmlns:dc="http://purl.org/dc/elements/1.1/"
xmlns:dcterms="http://purl.org/dc/terms/"
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
xmlns:scoro="http://purl.org/spar/scoro"
xmlns:bqmodel="http://biomodels.net/model-qualifiers/"
xmlns:collex="http://www.collex.org/schema"
xmlns:prism="http://prismstandard.org/namespaces/basic/2.0/"
>
<rdf:Description rdf:about="http://omex-library.org/ArchiveName.omex/model.nml">
<dc:title>None</dc:title>
<dcterms:abstract>lol, something nice</dcterms:abstract>
<dc:description>A tests model</dc:description>
<prism:keyword>something</prism:keyword>
<prism:keyword>and something</prism:keyword>
<collex:thumbnail rdf:resource="http://omex-library.org/ArchiveName.omex/lol.png"/>
<bqbiol:hasTaxon>
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/taxonomy/4896"/>
</rdf:Bag>
</bqbiol:hasTaxon>
<bqbiol:encodes>
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/GO:0009653"/>
</rdf:Bag>
</bqbiol:encodes>
<bqbiol:encodes>
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/kegg:ko04111"/>
</rdf:Bag>
</bqbiol:encodes>
<dc:source>
<rdf:Bag>
<rdf:li rdf:resource="https://github.com/lala"/>
</rdf:Bag>
</dc:source>
<bqmodel:isDerivedFrom>
<rdf:Bag>
<rdf:li rdf:resource="http://omex-library.org/BioSim0001.omex/model.xml"/>
</rdf:Bag>
</bqmodel:isDerivedFrom>
<rdfs:seeAlso>
<rdf:Bag>
<rdf:li rdf:resource="http://link.com"/>
</rdf:Bag>
</rdfs:seeAlso>
<dcterms:references>
<rdf:Bag>
<rdf:li rdf:resource="http://reference.com"/>
</rdf:Bag>
</dcterms:references>
<dc:creator>
<rdf:Bag>
<rdf:li>John Doe</rdf:li>
<rdf:li>https://someurl.com</rdf:li>
<rdf:li>https://anotherurl</rdf:li>
</rdf:Bag>
</dc:creator>
<dc:creator>
<rdf:Bag>
<rdf:li>Jane Smith</rdf:li>
</rdf:Bag>
</dc:creator>
<dc:contributor>
<rdf:Bag>
<rdf:li>Jane Smith</rdf:li>
</rdf:Bag>
</dc:contributor>
<dc:contributor>
<rdf:Bag>
<rdf:li>Jane Doe</rdf:li>
</rdf:Bag>
</dc:contributor>
<dc:contributor>
<rdf:Bag>
<rdf:li>John Smith</rdf:li>
</rdf:Bag>
</dc:contributor>
<dcterms:license>
<rdf:Bag>
<rdf:li rdf:resource="CC0"/>
</rdf:Bag>
</dcterms:license>
<scoro:funder>
<rdf:Bag>
<rdf:li rdf:resource="http://afundingbody.org"/>
</rdf:Bag>
</scoro:funder>
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2024-04-18</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
<dcterms:modified>
<rdf:Description>
<dcterms:W3CDTF>2024-04-18</dcterms:W3CDTF>
<dcterms:W3CDTF>2024-04-19</dcterms:W3CDTF>
</rdf:Description>
</dcterms:modified>
</rdf:Description>
</rdf:RDF>Here's the pyneuroml code that will create it: https://github.com/NeuroML/pyNeuroML/blob/development/pyneuroml/annotations.py#L90 Not entirely sure if these bits should also be in bags: <dc:title>None</dc:title>
<dcterms:abstract>lol, something nice</dcterms:abstract>
<dc:description>A tests model</dc:description>
<prism:keyword>something</prism:keyword>
<prism:keyword>and something</prism:keyword>
<collex:thumbnail rdf:resource="http://omex-library.org/ArchiveName.omex/lol.png"/> |
sanjayankur31
added
T: enhancement
|
Update: any entry that can have multiple values goes into a "bag" in the MIRIAM way of doing things. So that's what we'll follow. RDF seems to be quite flexible when it comes to how information is represented, so this is the convention we'll use for reading/writing NeuroML. This is required for NeuroML/pyNeuroML#354 |
sanjayankur31
commented
May 7, 2024
Not sure why this is given that Child is meant to mean "one and only one" and Children mean "one or more". But, using Children causes tests to fail in org.neuroml.export etc. when building jNeuroML. This needs looking into. See also #54
sanjayankur31
added a commit
to sanjayankur31/243446
that referenced
this pull request
May 7, 2024
Requires jNeuroML with these changes so that new annotations are known to LEMS: NeuroML/NeuroML2#225
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Fixes #224