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range:uriorcurie issue when generating jsonld-context #83

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puja-trivedi opened this issue Nov 6, 2024 · 1 comment
Open

range:uriorcurie issue when generating jsonld-context #83

puja-trivedi opened this issue Nov 6, 2024 · 1 comment
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@puja-trivedi
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puja-trivedi commented Nov 6, 2024

The new version of linkml 1.8.2+ fixed an issue with how range:uri is expressed in jsonld-context. After talking with LinkML community it seems like range:curie is not expressed in json format and all curie must be expanded into uri. Certain attributes from biolink i.e. category are range:uriorcurie and are now causing issues when we import the data into the graph, since the data value is forced into being interpreted as a uri. We need to resolve this issue but either changing the type of category to range:curie in our bican_biolink model or providing a uri data value to category.

Note: Since range:curie is not expressed in json, the type gets defaulted to range:string; which is how range:uri and range:uriorcurie were also expressed before the updates were made to linkml. Changing the range to curie will allow us to keep track of the ideal/correct type for this attribute in other formats i.e yaml and pydantic.

@djarecka
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djarecka commented Dec 5, 2024

I belive this should be fixed, but we should double check.

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