Getting molecular formula from metabolites (SPARQL)

[skye joby]

Bericht vertalen in het Nederlands  

Dear all,

Good day! I am building a metabolomics analysis tool that uses various databases to do identification, grouping based on pathway and such.

These databases for now contain the following columns:

Compound name | Description | Molecular Formula | Identifier | Formal charge

and have these built for ChEBI, HMDB, KEGG, PubChem. I would love to include Wikipathways as it is also more updated than KEGG.

I was playing with the SPARQL queries and can get info on names, description, identifier, but could not find a straightforward way to get for example all compounds with available InchiKeys (from which I could get structure and charge information). This is a bit challenging because the one (experimental) query I could find goes through Wikidata - but in various pathways on WP also see compounds with no Wikidata link, that do have an InchiKey listed when clicked on. 

Any tips? :-) Thank you for your time.

Kind regards,

Joanna Wolthuis (PhD student UMCU)