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Update schema to ensure correct RDF serialisation #10

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matentzn opened this issue Apr 27, 2022 · 5 comments
Open

Update schema to ensure correct RDF serialisation #10

matentzn opened this issue Apr 27, 2022 · 5 comments
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@matentzn
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matentzn commented Apr 27, 2022

Right now, the RDF serialisation is wrong:

[ babelon:predicate_id "rdfs:label" ;
            babelon:source_language "en" ;
            babelon:source_value "Abnormal emotion/affect behavior" ;
            babelon:subject_id "HP:0100851" ;
            babelon:translation_language "nl" ;
            babelon:translation_value "Abnormaal emotioneel/affectief gedrag" ],

This should be:

<http://purl.obolibrary.org/obo/HP_0100851> rdfs:label "Abnormaal emotioneel/affectief gedrag"@nl
[] a owl:Axiom ;
           owl:annotatedSource <http://purl.obolibrary.org/obo/HP_0100851> ;
           owl:annotatedProperty rdfs:label ;
           owl:annotatedTarget Abnormaal emotioneel/affectief gedrag"@nl ;
           babelon:source_value "Abnormal emotion/affect behavior@en" ;
           babelon:translation_value "Abnormaal emotioneel/affectief gedrag".

@victoriasoesanto try to adjust the linkml model by looking at sssom, e.g. here:
https://github.com/mapping-commons/sssom/blob/master/src/sssom_schema/schema/sssom_schema.yaml#L108

Note:

  1. @nl is maybe not yet supported by linkml RDF translation. This would be a LinkML ticket, perhaps. I don't know.
  2. Everything you need for the above you can fine in sssom.yaml, linked above. Check, in particular, the Mapping class.

This is not an easy ticket but I think this is the next big step. Thank you :)

@matentzn
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matentzn commented Jun 6, 2022

See also linkml/linkml#827

@matentzn
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matentzn commented Jun 6, 2022

@victoriasoesanto just focus on the correct representation of the entities (rdfs:label, HP:123) and the rdf reification for now, we may have to solve the language tag issue with sparql construct depending on the linkml issue above.

@matentzn
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@victoriasoesanto I forgot, did we fix this yet? Can you share a link the correct rdf serialisation?

@matentzn
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@victoriasoesanto
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Fixed in #13

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