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SPARQL Query Examples

• SPARQL Queries for CORD-19-on-FHIR dataset
• SPARQL Queries for Pubtator dataset
• SPARQL Queries for Metadata dataset
• SPARQL Queries for LitCovid dataset

COVID-19 PICO Ontology

• CPICO Documentation

Analysis of the CORD-19 dataset

CORD-19 dataset content

• Commercial use subset (includes PMC content) -- 9000 papers, 186Mb
  • sample
• Non-commercial use subset (includes PMC content) -- 1973 papers, 36Mb
  • sample
• PMC custom license subset -- 1426 papers, 19Mb
  • sample
• bioRxiv/medRxiv subset (pre-prints that are not peer reviewed) -- 803 papers, 13Mb
  • sample

Proposed approach:

1. Run documents through the NLP2FHIR pipeline, producing FHIR R4 resources descriptions.
2. Convert FHIR R4 resources to RDF using the FHIR to RDF converter
3. Load resulting RDF into into a SPARQL Endpoint (target host at the moment: https://graph.fhircat.org/graphdb)