This reference guide provides a curated collection of essential resources for clinical informatics professionals, researchers, and developers. Navigate to the section most relevant to your work.
OHDSI Resources
Resources for Observational Health Data Sciences and Informatics (OHDSI) tools, OMOP CDM, and observational research.
Official Documentation
- OHDSI Website - Official OHDSI community portal
- The Book of OHDSI - Comprehensive open-source textbook
- OHDSI GitHub - Open-source repositories
- OMOP CDM Documentation - Common Data Model specification
Vocabulary Resources
- ATHENA - OHDSI vocabulary repository
- PHOEBE - Vocabulary exploration tool
- USAGI - Source code mapping tool
Data Characterization Tools
- ACHILLES - Automated database profiling
- Data Quality Dashboard - CDM data quality checks
- ARES - Analysis results viewer
Analysis Tools
- ATLAS - Web-based analysis platform
- WebAPI - RESTful services for ATLAS
- HADES - Health Analytics Data-to-Evidence Suite
Patient-Level Prediction
- PatientLevelPrediction - ML prediction models
- CohortMethod - Comparative effectiveness studies
- SelfControlledCaseSeries - SCCS analysis
ETL Tools
- WhiteRabbit - Source data profiling
- Rabbit-in-a-Hat - ETL design tool
- ETL-Synthea - Synthea to OMOP ETL
Database Connectors
- DatabaseConnector - R database connectivity
- SqlRender - SQL dialect translation
- Eunomia - Test CDM database
Learning & Community
- OHDSI Tutorials - Video tutorials from symposiums
- OHDSI Forums - Community discussion
- OHDSI Workgroups - Specialized working groups
- EHDEN Academy - Free online courses
FHIR & HL7 Resources
Resources for healthcare interoperability standards including FHIR, HL7, and clinical terminologies.
FHIR Specifications
- FHIR Official Site - HL7 FHIR specification
- FHIR R4 (Current) - R4 specification
- FHIR R5 (Latest) - R5 specification
- FHIR Shorthand - FSH for authoring IGs
HL7 Standards
- HL7 International - HL7 organization
- HL7 v2 Reference - HL7 v2 messages
- CDA (C-CDA) - Clinical Document Architecture
Clinical Terminologies
- LOINC - Laboratory observations codes
- SNOMED CT - Clinical terminology
- RxNorm - Drug terminology
- ICD-10-CM - Diagnosis codes
- CPT - Procedure codes
- UMLS - Unified Medical Language System
Implementation Guides
- US Core IG - US Core profiles
- USCDI - US Core Data for Interoperability
- Da Vinci Project - Payer-provider exchange
- Bulk Data Access - Backend services
- SMART on FHIR - App authorization
- CDS Hooks - Clinical decision support
Developer Tools
- FHIR Validator - Resource validation
- Inferno - US Core testing
- Touchstone - FHIR testing platform
FHIR Servers
- HAPI FHIR - Open-source Java server
- Microsoft FHIR Server - Azure FHIR
- Google Cloud Healthcare API - GCP FHIR
Development Libraries
- HAPI FHIR (Java) - Java library
- fhir.resources (Python) - Python models
- fhirclient (Python) - SMART client
Learning Resources
- FHIR DevDays - Annual conference
- HL7 FHIR Fundamentals - Official training
- FHIR Chat (Zulip) - Community chat
Clinical Data Resources
Resources for clinical data management, ETL processes, data quality, and common data models.
Common Data Models
- OMOP CDM Specification - Official documentation
- OMOP CDM Wiki - GitHub wiki
- PCORnet CDM - PCORnet Common Data Model
- i2b2 Data Model - Informatics for Integrating Biology and the Bedside
- Sentinel CDM - FDA Sentinel System
- CDISC Standards - Clinical trial data standards
ETL Platforms
- Apache Airflow - Workflow orchestration
- Prefect - Modern data orchestration
- dbt (data build tool) - Data transformation
- Great Expectations - Data validation
Data Quality Frameworks
- Data Quality Dashboard - OHDSI DQD
- Kahn Framework - DQ dimensions
- DAMA DMBOK - Data management body of knowledge
Synthetic Data
Privacy & De-identification
- ARX - Data anonymization
- HIPAA Safe Harbor - De-identification standard
Databases & Tools
- PostgreSQL - Popular OHDSI backend
- DBeaver - Universal database tool
- pgAdmin - PostgreSQL admin
Healthcare NLP & AI Resources
Resources for clinical natural language processing, machine learning, and healthcare AI.
Pre-trained Clinical Models
- BioBERT - Biomedical BERT
- ClinicalBERT - Clinical notes BERT
- PubMedBERT - PubMed pre-trained
- SciBERT - Scientific text BERT
- GatorTron - Large clinical LLM
Clinical NLP Tools
- MedSpaCy - Clinical NLP with spaCy
- scispaCy - Scientific/biomedical spaCy
- cTAKES - Apache clinical NLP
- MedCAT - Medical concept annotation
- QuickUMLS - Fast UMLS matching
- MetaMap - NLM concept extraction
General NLP Libraries
- Hugging Face Transformers - Transformer models
- spaCy - Industrial NLP
- NLTK - NLP toolkit
Clinical Datasets
- MIMIC-III/IV - ICU clinical notes
- i2b2 NLP Challenges - Annotated clinical text
- n2c2 (formerly i2b2) - NLP challenges
- PubMed - Biomedical literature
ML Frameworks & Tools
- scikit-learn - General ML
- PyTorch - Deep learning
- MLflow - ML lifecycle
- Weights & Biases - Experiment tracking
Model Interpretability
- SHAP - Feature importance
- LIME - Local explanations
- InterpretML - Microsoft interpretability
Research Venues
- JAMIA - Journal of AMIA
- npj Digital Medicine - Nature
- Papers With Code - Medical - Medical ML papers
Learning Resources
- Hugging Face Course - Transformers course
- Fast.ai - Practical Deep Learning
- MedSpaCy Tutorials - Clinical NLP
Related Posts on This Blog
OHDSI
- OHDSI Introduction: From Real-World Data to Reliable Evidence
- From EHR Chaos to Research-Ready Data: A Complete OHDSI Learning Journey
- Mastering ATLAS Cohort Definitions
- Predicting GI Hemorrhage with OHDSI PLP
FHIR & Interoperability
- From HL7 Pipes to FHIR APIs: Clinical Laboratory Interoperability
- Healthcare Interoperability: FHIR, HL7, LOINC, SNOMED-CT
This resource page is regularly updated. Last updated: December 30, 2025.