# 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) - [Health Data Standards](https://docs.bcbi.brown.edu/codiac-for-health/foundations/health-data-standards.md) - [Artificial Intelligence in Health ](https://docs.bcbi.brown.edu/codiac-for-health/foundations/artificial-intelligence-in-health.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) ## Observational Research with EHR Data - [Introduction](https://docs.bcbi.brown.edu/codiac-for-health/observational-research/introduction.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) - [Communities, Platforms, and Organizations](https://docs.bcbi.brown.edu/codiac-for-health/observational-research/communities-platforms-and-organizations.md) - [The Electronic Health Record (EHR)](https://docs.bcbi.brown.edu/codiac-for-health/observational-research/the-electronic-health-record-ehr.md) - [OHDSI Standards and Tools](https://docs.bcbi.brown.edu/codiac-for-health/observational-research/ohdsi-standards-and-tools.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) ## 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) - [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) - [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) - [Structured Query Language (SQL)](https://docs.bcbi.brown.edu/codiac-for-health/computing/structured-query-language-sql.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) - [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) - [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. - [Data Dictionary](https://docs.bcbi.brown.edu/codiac-for-health/ursa-ri/datasets/cbioportal-for-cancer-genomics/data-dictionary.md) - [10x Genomics Dataset Repository](https://docs.bcbi.brown.edu/codiac-for-health/ursa-ri/datasets/10x-genomics-dataset-repository.md) - [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) - [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. - [All of Us](https://docs.bcbi.brown.edu/codiac-for-health/ursa-ri/datasets/all-of-us.md) - [DailyMed SPL Dataset](https://docs.bcbi.brown.edu/codiac-for-health/ursa-ri/datasets/dailymed-spl-dataset.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) - [Youth Risk Behavior Surveillance System (YRBSS)](https://docs.bcbi.brown.edu/codiac-for-health/ursa-ri/datasets/youth-risk-behavior-surveillance-system-yrbss.md) --- # Agent Instructions This documentation is published with GitBook. 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