PRA3006-SPARQL

PubChem RDF

Website	[https://pubchem.ncbi.nlm.nih.gov/](https://pubchem.ncbi.nlm.nih.gov/]
SPARQL endpoint (website)	https://qlever.dev/pubchem
SPARQL endpoint	https://qlever.dev/api/pubchem

PubChem is the world’s largest collection of freely accessible chemical information [1,2].

Entities

The main classes are:

• Metabolite: ligand, e.g. drug / drug-like compound
• Assay: measures some property of, for example, the protein-ligand binding

Data model

The data model is described in the 2015 paper [2].

References

1. Kim S, Chen J, Cheng T, Gindulyte A, He J, He S, et al. PubChem 2025 update. NAR. 2024 Nov 18;53(D1):D1516–25. doi:10.1093/NAR/GKAE1059 (Scholia)
2. Fu G, Batchelor C, Dumontier M, Hastings J, Willighagen E, Bolton E. PubChemRDF: towards the semantic annotation of PubChem compound and substance databases. J Cheminform [Internet]. 2015 Feb;7(1):34. Available from: http://europepmc.org/article/MED/26175801 doi:10.1186/S13321-015-0084-4 (Scholia)

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