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wikipathways / wikipathways-development

Roadmap planning, developer documentation, contribution guidelines
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Update our schema-jsonld to use new bioschema terms #90

Open AlexanderPico opened 2 years ago

AlexanderPico commented 2 years ago

Currently, our new jekyll sites encode a list of keywords representing gene products, chemicals, diseases and pathway names found in a given pathway. Schemas now supports Gene, Protein, and other Biochem types, e.g., https://schema.org/Protein.

Egon, can you draft an example of how you think we should encoded one pathway? Then Alex and Tina can update the scripts that generate the Jekyll Frontmatter to update and maintain all the instances.

See the schema-jsonld section of this .md as an example: https://raw.githubusercontent.com/wikipathways/wikipathways.github.io/main/_pathways/WP0.md

egonw commented 2 years ago

I tried the idea of doing this with the header YAML, but that seems a no go. Keywords cannot be of type Gene. This is one of the options I tried:

image

So, this is currently a dead end. That does not mean we cannot make the metabolites/genes/etc Bioschemas, but just not this way.

AlexanderPico commented 2 years ago

Thanks for testing this out. I'll leave this open while we try other ways.