# CODIAC for Health

## About

- [Introduction](https://docs.bcbi.brown.edu/codiac-for-health/introduction.md)
- [Table of Contents](https://docs.bcbi.brown.edu/codiac-for-health/table-of-contents.md)
- [Contributors](https://docs.bcbi.brown.edu/codiac-for-health/contributors.md)
- [Releases](https://docs.bcbi.brown.edu/codiac-for-health/releases.md)

## Foundations

- [Introduction](https://docs.bcbi.brown.edu/codiac-for-health/foundations/introduction.md)
- [Biomedical Informatics](https://docs.bcbi.brown.edu/codiac-for-health/foundations/biomedical-informatics.md)
- [Implementation Science](https://docs.bcbi.brown.edu/codiac-for-health/foundations/implementation-science.md)
- [Learning Health Systems](https://docs.bcbi.brown.edu/codiac-for-health/foundations/learning-health-systems.md)
- [DIKW Model](https://docs.bcbi.brown.edu/codiac-for-health/foundations/dikw-model.md)
- [Health Data](https://docs.bcbi.brown.edu/codiac-for-health/foundations/health-data.md)
- [Electronic Health Record Data](https://docs.bcbi.brown.edu/codiac-for-health/foundations/health-data/electronic-health-record-data.md)
- [Health Data Standards](https://docs.bcbi.brown.edu/codiac-for-health/foundations/health-data-standards.md)
- [HL7 FHIR](https://docs.bcbi.brown.edu/codiac-for-health/foundations/health-data-standards/hl7-fhir.md)
- [Knowledge Discovery](https://docs.bcbi.brown.edu/codiac-for-health/foundations/knowledge-discovery.md)
- [Observational Health Research](https://docs.bcbi.brown.edu/codiac-for-health/foundations/observational-health-research.md)
- [Health Research Data Governance](https://docs.bcbi.brown.edu/codiac-for-health/foundations/health-research-data-governance.md)
- [Artificial Intelligence in Health ](https://docs.bcbi.brown.edu/codiac-for-health/foundations/artificial-intelligence-in-health.md)
- [5x5 Framework](https://docs.bcbi.brown.edu/codiac-for-health/foundations/artificial-intelligence-in-health/5x5-framework.md)
- [Statistics](https://docs.bcbi.brown.edu/codiac-for-health/foundations/artificial-intelligence-in-health/5x5-framework/statistics.md)
- [Machine Learning](https://docs.bcbi.brown.edu/codiac-for-health/foundations/artificial-intelligence-in-health/5x5-framework/machine-learning.md)
- [Deep Learning](https://docs.bcbi.brown.edu/codiac-for-health/foundations/artificial-intelligence-in-health/5x5-framework/deep-learning.md)
- [Natural Language Processing](https://docs.bcbi.brown.edu/codiac-for-health/foundations/artificial-intelligence-in-health/5x5-framework/natural-language-processing.md)
- [Large Language Models](https://docs.bcbi.brown.edu/codiac-for-health/foundations/artificial-intelligence-in-health/5x5-framework/large-language-models.md)

## Observational Research with EHR Data

- [Introduction](https://docs.bcbi.brown.edu/codiac-for-health/observational-research/introduction.md)
- [The Electronic Health Record (EHR)](https://docs.bcbi.brown.edu/codiac-for-health/observational-research/the-electronic-health-record-ehr.md)
- [Health Terminologies](https://docs.bcbi.brown.edu/codiac-for-health/observational-research/health-terminologies.md)
- [Finding Health Terminology Codes](https://docs.bcbi.brown.edu/codiac-for-health/observational-research/health-terminologies/finding-health-terminology-codes.md)
- [OHDSI Standards and Tools](https://docs.bcbi.brown.edu/codiac-for-health/observational-research/ohdsi-standards-and-tools.md)
- [OHDSI Infrastructure](https://docs.bcbi.brown.edu/codiac-for-health/observational-research/ohdsi-standards-and-tools/ohdsi-infrastructure.md)
- [Communities, Platforms, and Organizations](https://docs.bcbi.brown.edu/codiac-for-health/observational-research/communities-platforms-and-organizations.md)
- [Best Practices](https://docs.bcbi.brown.edu/codiac-for-health/observational-research/best-practices.md)
- [Protected Health Information (PHI)](https://docs.bcbi.brown.edu/codiac-for-health/observational-research/best-practices/protected-health-information-phi.md)
- [Research Pipeline](https://docs.bcbi.brown.edu/codiac-for-health/observational-research/research-pipeline.md)
- [Research Pipeline](https://docs.bcbi.brown.edu/codiac-for-health/observational-research/research-pipeline-1.md)
- [ExCITE Platform](https://docs.bcbi.brown.edu/codiac-for-health/observational-research/excite-platform.md)
- [WintEHR - An Open-Source Educational EHR](https://docs.bcbi.brown.edu/codiac-for-health/observational-research/excite-platform/wintehr-an-open-source-educational-ehr.md)

## Computing Skills

- [Introduction](https://docs.bcbi.brown.edu/codiac-for-health/computing/introduction.md)
- [File Directory Structures](https://docs.bcbi.brown.edu/codiac-for-health/computing/file-directory-structures.md)
- [Text Editors](https://docs.bcbi.brown.edu/codiac-for-health/computing/text-editors.md)
- [GitHub](https://docs.bcbi.brown.edu/codiac-for-health/computing/github.md)
- [Unix](https://docs.bcbi.brown.edu/codiac-for-health/computing/unix.md)
- [Structured Query Language (SQL)](https://docs.bcbi.brown.edu/codiac-for-health/computing/structured-query-language-sql.md)
- [Julia](https://docs.bcbi.brown.edu/codiac-for-health/computing/julia.md)
- [Installation](https://docs.bcbi.brown.edu/codiac-for-health/computing/julia/installation.md)
- [REPL](https://docs.bcbi.brown.edu/codiac-for-health/computing/julia/repl.md)
- [Basic Syntax](https://docs.bcbi.brown.edu/codiac-for-health/computing/julia/basic-syntax.md)
- [Numbers and Math](https://docs.bcbi.brown.edu/codiac-for-health/computing/julia/numbers-and-math.md)
- [Strings and Characters](https://docs.bcbi.brown.edu/codiac-for-health/computing/julia/strings-and-characters.md)
- [Regular Expressions](https://docs.bcbi.brown.edu/codiac-for-health/computing/julia/regular-expressions.md)
- [Control Flow](https://docs.bcbi.brown.edu/codiac-for-health/computing/julia/control-flow.md)
- [Collections and Data Structures](https://docs.bcbi.brown.edu/codiac-for-health/computing/julia/collections-and-data-structures.md)
- [File Input/Output](https://docs.bcbi.brown.edu/codiac-for-health/computing/julia/file-input-output.md)
- [Packages](https://docs.bcbi.brown.edu/codiac-for-health/computing/julia/packages.md)
- [DataFrames](https://docs.bcbi.brown.edu/codiac-for-health/computing/julia/dataframes.md)
- [JuliaPlots](https://docs.bcbi.brown.edu/codiac-for-health/computing/julia/juliaplots.md)
- [ScikitLearn.jl](https://docs.bcbi.brown.edu/codiac-for-health/computing/julia/scikitlearn.jl.md)
- [JuliaStats](https://docs.bcbi.brown.edu/codiac-for-health/computing/julia/juliastats.md)
- [Exercises](https://docs.bcbi.brown.edu/codiac-for-health/computing/julia/exercises.md): List of exercises found across the different Julia pages.
- [Python](https://docs.bcbi.brown.edu/codiac-for-health/computing/python.md)
- [Installation](https://docs.bcbi.brown.edu/codiac-for-health/computing/python/installation.md)
- [REPL](https://docs.bcbi.brown.edu/codiac-for-health/computing/python/repl.md)
- [Basic Syntax](https://docs.bcbi.brown.edu/codiac-for-health/computing/python/basic-syntax.md)
- [Numbers and Math](https://docs.bcbi.brown.edu/codiac-for-health/computing/python/numbers-and-math.md)
- [Strings and Characters](https://docs.bcbi.brown.edu/codiac-for-health/computing/python/strings-and-characters.md)
- [Regular Expressions](https://docs.bcbi.brown.edu/codiac-for-health/computing/python/regular-expressions.md)
- [Control Flow](https://docs.bcbi.brown.edu/codiac-for-health/computing/python/control-flow.md)
- [Collections and Data Structures](https://docs.bcbi.brown.edu/codiac-for-health/computing/python/collections-and-data-structures.md)
- [File Input/Output](https://docs.bcbi.brown.edu/codiac-for-health/computing/python/file-input-output.md)
- [Packages](https://docs.bcbi.brown.edu/codiac-for-health/computing/python/packages.md)
- [Data Frames and Data Manipulation](https://docs.bcbi.brown.edu/codiac-for-health/computing/python/data-frames-and-data-manipulation.md)
- [Machine Learning with Python](https://docs.bcbi.brown.edu/codiac-for-health/computing/python/machine-learning-with-python.md): More information to come!
- [Large Language Models (LLMs)](https://docs.bcbi.brown.edu/codiac-for-health/computing/python/large-language-models-llms.md): More information to come!
- [R](https://docs.bcbi.brown.edu/codiac-for-health/computing/r.md)
- [Installation](https://docs.bcbi.brown.edu/codiac-for-health/computing/r/installation.md)
- [REPL](https://docs.bcbi.brown.edu/codiac-for-health/computing/r/repl.md)
- [Basic Syntax](https://docs.bcbi.brown.edu/codiac-for-health/computing/r/basic-syntax.md)
- [Numbers and Math](https://docs.bcbi.brown.edu/codiac-for-health/computing/r/numbers-and-math.md)
- [Strings and Characters](https://docs.bcbi.brown.edu/codiac-for-health/computing/r/strings-and-characters.md)
- [Regular Expressions](https://docs.bcbi.brown.edu/codiac-for-health/computing/r/regular-expressions.md)
- [Control Flow](https://docs.bcbi.brown.edu/codiac-for-health/computing/r/control-flow.md)
- [Collections and Data Structures](https://docs.bcbi.brown.edu/codiac-for-health/computing/r/collections-and-data-structures.md)
- [File Input/Output](https://docs.bcbi.brown.edu/codiac-for-health/computing/r/file-input-output.md)
- [Packages](https://docs.bcbi.brown.edu/codiac-for-health/computing/r/packages.md)
- [DataFrames](https://docs.bcbi.brown.edu/codiac-for-health/computing/r/dataframes.md)
- [Data Analysis and Manipulation](https://docs.bcbi.brown.edu/codiac-for-health/computing/r/data-analysis-and-manipulation.md)
- [R Basics](https://docs.bcbi.brown.edu/codiac-for-health/computing/r-basics.md)
- [Comparing Julia, Python, and R](https://docs.bcbi.brown.edu/codiac-for-health/computing/comparing-julia-python-and-r.md)
- [Statistics and Machine Learning](https://docs.bcbi.brown.edu/codiac-for-health/computing/statistics-and-machine-learning.md)
- [Unified Modeling Language (UML)](https://docs.bcbi.brown.edu/codiac-for-health/computing/unified-modeling-language-uml.md)
- [HTML](https://docs.bcbi.brown.edu/codiac-for-health/computing/html.md)

## URSA Initiative in Rhode Island

- [Introduction](https://docs.bcbi.brown.edu/codiac-for-health/ursa-ri/introduction.md)
- [Computing Environments](https://docs.bcbi.brown.edu/codiac-for-health/ursa-ri/computing-environments.md)
- [Health Data Partners](https://docs.bcbi.brown.edu/codiac-for-health/ursa-ri/health-data-partners.md)
- [Data Requests](https://docs.bcbi.brown.edu/codiac-for-health/ursa-ri/health-data-partners/data-requests.md)
- [Datasets](https://docs.bcbi.brown.edu/codiac-for-health/ursa-ri/datasets.md): Table of Contents
- [10x Genomics Dataset Repository](https://docs.bcbi.brown.edu/codiac-for-health/ursa-ri/datasets/10x-genomics-dataset-repository.md)
- [All of Us](https://docs.bcbi.brown.edu/codiac-for-health/ursa-ri/datasets/all-of-us.md)
- [Behavioral Risk Factor Surveillance System (BRFSS)](https://docs.bcbi.brown.edu/codiac-for-health/ursa-ri/datasets/behavioral-risk-factor-surveillance-system-brfss.md)
- [Data Dictionary](https://docs.bcbi.brown.edu/codiac-for-health/ursa-ri/datasets/behavioral-risk-factor-surveillance-system-brfss/data-dictionary.md)
- [Data Counts](https://docs.bcbi.brown.edu/codiac-for-health/ursa-ri/datasets/behavioral-risk-factor-surveillance-system-brfss/data-counts.md): Table headers are shown in this format Variable (Code)
- [Data Statistics](https://docs.bcbi.brown.edu/codiac-for-health/ursa-ri/datasets/behavioral-risk-factor-surveillance-system-brfss/data-statistics.md)
- [cBioPortal for Cancer Genomics](https://docs.bcbi.brown.edu/codiac-for-health/ursa-ri/datasets/cbioportal-for-cancer-genomics.md): Unless otherwise noted, information in this overview is adapted from the official cBioPortal documentation at docs.cbioportal.org. See references.
- [Data Dictionary](https://docs.bcbi.brown.edu/codiac-for-health/ursa-ri/datasets/cbioportal-for-cancer-genomics/data-dictionary.md)
- [DailyMed SPL Dataset](https://docs.bcbi.brown.edu/codiac-for-health/ursa-ri/datasets/dailymed-spl-dataset.md)
- [Healthcare Cost and Utilization Project (HCUP)](https://docs.bcbi.brown.edu/codiac-for-health/ursa-ri/datasets/healthcare-cost-and-utilization-project-hcup.md)
- [MIMIC-IV](https://docs.bcbi.brown.edu/codiac-for-health/ursa-ri/datasets/mimic-iv.md)
- [Dataset Demographics](https://docs.bcbi.brown.edu/codiac-for-health/ursa-ri/datasets/mimic-iv/dataset-demographics.md)
- [Condition Prevalences](https://docs.bcbi.brown.edu/codiac-for-health/ursa-ri/datasets/mimic-iv/condition-prevalences.md): The table below lists the most frequently occurring ICD-10-CM diagnosis codes recorded in the diagnoses\_icd table of the MIMIC-IV Hosp module, ranked by number of unique patients.
- [National Plan and Provider Enumeration System (NPPES)](https://docs.bcbi.brown.edu/codiac-for-health/ursa-ri/datasets/national-plan-and-provider-enumeration-system-nppes.md)
- [Dataset Demographics](https://docs.bcbi.brown.edu/codiac-for-health/ursa-ri/datasets/national-plan-and-provider-enumeration-system-nppes/dataset-demographics.md): NPPES follows a fixed schema, so the full file supports aggregate statistics across the entire registry — summarized below for the most recent monthly release.
- [Code Values](https://docs.bcbi.brown.edu/codiac-for-health/ursa-ri/datasets/national-plan-and-provider-enumeration-system-nppes/code-values.md): Allowed values for coded fields. Source: CMS NPPES Code Values, February 1, 2025.
- [Data Dictionary](https://docs.bcbi.brown.edu/codiac-for-health/ursa-ri/datasets/national-plan-and-provider-enumeration-system-nppes/data-dictionary.md)
- [Pediatric Psychiatry Emergency Services (PediPES) at Hasbro Children’s](https://docs.bcbi.brown.edu/codiac-for-health/ursa-ri/datasets/pediatric-psychiatry-emergency-services-pedipes-at-hasbro-childrens.md)
- [Surveillance, Epidemiology, and End Results (SEER)](https://docs.bcbi.brown.edu/codiac-for-health/ursa-ri/datasets/surveillance-epidemiology-and-end-results-seer.md)
- [SyntheticMass](https://docs.bcbi.brown.edu/codiac-for-health/ursa-ri/datasets/syntheticmass.md)
- [SyntheticRI 2026: Synthetic Healthcare Records for Rhode Island](https://docs.bcbi.brown.edu/codiac-for-health/ursa-ri/datasets/syntheticri-2026-synthetic-healthcare-records-for-rhode-island.md)
- [Synthea Modules Used in the Generation of SyntheticRI 2026](https://docs.bcbi.brown.edu/codiac-for-health/ursa-ri/datasets/syntheticri-2026-synthetic-healthcare-records-for-rhode-island/synthea-modules-used-in-the-generation-of-syntheticri-2026.md)
- [Dataset Demographics](https://docs.bcbi.brown.edu/codiac-for-health/ursa-ri/datasets/syntheticri-2026-synthetic-healthcare-records-for-rhode-island/dataset-demographics.md)
- [Youth Risk Behavior Surveillance System (YRBSS)](https://docs.bcbi.brown.edu/codiac-for-health/ursa-ri/datasets/youth-risk-behavior-surveillance-system-yrbss.md)
- [Data Dictionary](https://docs.bcbi.brown.edu/codiac-for-health/ursa-ri/datasets/youth-risk-behavior-surveillance-system-yrbss/data-dictionary.md)
- [Data Counts](https://docs.bcbi.brown.edu/codiac-for-health/ursa-ri/datasets/youth-risk-behavior-surveillance-system-yrbss/data-counts.md)
- [Data Statistics](https://docs.bcbi.brown.edu/codiac-for-health/ursa-ri/datasets/youth-risk-behavior-surveillance-system-yrbss/data-statistics.md)


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