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Unified Biomedical Knowledge Graph (UBKG)

Source and Generation Framework Scripts

Scripts in this repo compose the following components of the UBKG:

Source Framework

The source framework

  • extracts from a data warehouse assertion data from the UMLS
  • formats output as CSVs for import into a neo4j knowledge graph

UMLS data is obtained from releases of the UMLS in Rich Release Format. The University of Pittsburgh's Department of Biomedical Informatics maintains the data warehouse that the source framework uses.

Generation framework

The generation framework is a suite of Extract-Transform-Load (ETL) scripts that

  • extract assertion data from sources, including OWL files
  • appends assertions to the set of UMLS CSVs

Additional information

For more information on the UBKG, consult the GitHub Docs site.