Welcome to Semantic Similarity’s documentation!
# Semantic Similarity
This repository contains code meant to be run on the N3C Enclave for measuring semantic similarity between patients using their phenotype data as represented by HPO terms.
It also contains tools for applying statistical tests (chi squared and Fisher exact test) to determine overrepresentation of HPO terms in clustered data.
See here for more documentation of code:
https://national-covid-cohort-collaborative.github.io/semanticsimilarity/index.html
- Semantic Similarity
- semanticsimilarity package
- Submodules
- semanticsimilarity.annotation_counter module
- semanticsimilarity.hpo_cluster_analyzer module
- semanticsimilarity.hpo_ensmallen module
- semanticsimilarity.hpo_ensmallen_parser module
- semanticsimilarity.phenomizer module
PhenomizerPhenomizer.average_max_similarity()Phenomizer.center_to_cluster_generalizability()Phenomizer.check_term_pair_in_mica_d()Phenomizer.make_patient_disease_similarity_long_spark_df()Phenomizer.make_patient_similarity_long_spark_df()Phenomizer.make_similarity_matrix()Phenomizer.max_similarity_cluster()Phenomizer.patient_to_cluster_similarity()Phenomizer.patient_to_cluster_similarity_pd()Phenomizer.similarity_score()Phenomizer.update_mica_d()
TestPt
- semanticsimilarity.resnik module
- semanticsimilarity.term_pair module
- Module contents
- semanticsimilarity package