Resource Description Framework (RDF) Modeling of Named Entity Co-occurrences in Biomedical Literature and Its Integration with PubChemRDF

This Zenodo record contains the co-occurrence RDF data generated in the work described in the paper “A resource description framework (RDF) model of named entity co-occurrences in biomedical literature and its integration with PubChemRDF” by Li et al., published in the Journal of Cheminformatics (https://doi.org/10.1186/s13321-025-01017-0). It also contains the SPARQL query examples, the RDF schema in SHACL and ShEx, and the validation scripts. All content in this Zenodo record is for archival purposes. The latest version of the co-occurrence RDF data and other PubChemRDF data can be accessed via the PubChem FTP site (https://ftp.ncbi.nlm.nih.gov/pubchem/RDF/). The up-to-date RDF schema in various formats is available on the PubChemRDF Schema page (https://pubchem.ncbi.nlm.nih.gov/docs/rdf-schema). A set of SPARQL query examples can be found on the PubChemRDF use case pages (https://pubchem.ncbi.nlm.nih.gov/docs/rdf-use-cases).