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Write out file with semantic similarity of all pairs of ontology terms in a given ontology

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Write out file with semantic similarity of all pairs of HP terms

Workflow:

  • download HPOA file in order to calculate frequencies for each term
  • download HPO
  • turn HPO into DAG
    • drop singletons
    • drop non-HP terms
    • confirm DAG-ness
  • load graph into Ensmallen
  • make Resnik model, calculate all by all Resnik similarity
  • make Jaccard model, calculate all by all Jaccard similarity
  • pandas join tables
  • write out to file
  • upload file to S3 (KG-Hub?) # decide on this later

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Write out file with semantic similarity of all pairs of ontology terms in a given ontology

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