Where the critical path lives. This repo is focused on building the underlying architecture necessary to fulfill clinical use cases. The code for specific use cases can be found in the Credentialed Access repo.
This repository contains general notebooks/scripts, for which credentialed access is not required.
The repo has the following structure:
📦Public
┣ 📂Data_import
┃ ┣ 📂images
┃ ┃ ┣ 📜Causal_expansion1.png
┃ ┃ ┣ 📜Causal_expansion2.png
┃ ┃ ┣ 📜Concept_nodes_example.png
┃ ┃ ┣ 📜MED_RT_content_model.png
┃ ┃ ┣ 📜MED_RT_relationships.png
┃ ┃ ┣ 📜MeSH_broader_narrower_in_UMLSbrowser.png
┃ ┃ ┣ 📜MeSH_relationships.png
┃ ┃ ┣ 📜RxNorm_CUIs_related_to_coumadin.png
┃ ┃ ┣ 📜RxNorm_class_relationships.png
┃ ┃ ┣ 📜RxNorm_clinical_properties_relationships.png
┃ ┃ ┣ 📜RxNorm_drug_interactions_warfarin.png
┃ ┃ ┣ 📜RxNorm_relationships_among_RXCUIs.png
┃ ┃ ┣ 📜Schema_SemMedDB_4.2.png
┃ ┃ ┣ 📜UMLS_CUI_map.jpg
┃ ┃ ┣ 📜UMLS_Structure.png
┃ ┃ ┣ 📜UMLS_find_all_data_for_cui.gif
┃ ┃ ┣ 📜relations_in_UMLS_semantic_network.png
┃ ┃ ┣ 📜sentence_parsing.svg
┃ ┃ ┗ 📜tech_challenge_intro.png
┃ ┣ 📜MIMIC-III v1.4_import.ipynb
┃ ┣ 📜MIMIC-IV_import.ipynb
┃ ┣ 📜Mimic4 Schema.ods
┃ ┣ 📜Multi-source_import.ipynb
┃ ┣ 📜Scrape_causality_from_pubmed_NLP_CHALLENGE.ipynb
┃ ┣ 📜SemMedDB_Import.ipynb
┃ ┣ 📜SemMedDB_Validation.ipynb
┃ ┣ 📜SemRep_test_input.txt
┃ ┣ 📜UMLS_2020AB.ipynb
┃ ┣ 📜Untitled.ipynb
┃ ┣ 📜mimic3_relational_schema.csv
┃ ┣ 📜mimic_iii_demo_import.ipynb
┃ ┗ 📜untitled.txt
┣ 📂Other
┃ ┣ 📂images
┃ ┃ ┣ 📜TimeTree_demo.png
┃ ┃ ┗ 📜graph-b161d64e-45fd-4401-ab32-748828e2d308.html
┃ ┣ 📜Dev_Neo4j using Python.ipynb
┃ ┣ 📜MIMIC-III_timestamp_fields.csv
┃ ┣ 📜Python_Neo4j_Playground.ipynb
┃ ┣ 📜Time tree for MIMIC-III v1.4.ipynb
┃ ┗ 📜Time_demo_data.ipynb
┣ 📂docs
┃ ┗ 📜index.md
┣ 📂gitignore_files
┃ ┣ 📜large_files.gitignore
┃ ┗ 📜other.gitignore
┣ 📂img
┃ ┗ 📜thumbnail_group_name.png
┣ 📜.gitignore
┣ 📜LICENSE
┣ 📜add_large_files_to_gitignore.sh
┣ 📜readme.md
┗ 📜requirements.txt
This directory __
The images ___. They include:
The notebooks in this directory are primarily concerned with