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biolink / biolink-model

Schema and generated objects for biolink data model and upper ontology
https://biolink.github.io/biolink-model/
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Add node properties for chemicals, e.g. inchikey #64

Closed cmungall closed 6 years ago

cmungall commented 6 years ago

From @stuppie in gdoc "What about string or numerical properties (such as the molecular weight or INCHIKEY for a compound)?"

is there a standard rdf pred for this?

stuppie commented 6 years ago

I don't know if there is a "standard"..

Looking at the docs from Pubchem RDF, they are listed as descriptors: http://pubchemdocs.ncbi.nlm.nih.gov/rdf$_4-3 Example: https://pubchem.ncbi.nlm.nih.gov/rest/rdf/compound/CID60823.html, which sio:has-attribute: https://pubchem.ncbi.nlm.nih.gov/rest/rdf/descriptor/CID60823_Molecular_Weight.html

and that descriptor has a sio:has-value, rdf:type, and sio:has-unit.

Case 3 has an example sparql query: http://pubchemdocs.ncbi.nlm.nih.gov/rdf$_8-3

It looks like CHEMBL also structures this the same way: https://www.ebi.ac.uk/rdf/static/chembl/chembl_18_rdf_full_schema.png

cmungall commented 6 years ago

I think creating a new object representing the property is nice and rigorous and works well in an RDF database, but I was thinking that here we would have simple shortcut literal-triples/node properties, as it's done in wikidata, e.g. https://www.wikidata.org/wiki/Property:P235