FHIR and Generative AI Tools and Resources
FHIR and Generative AI Resources
| Resource Name | URL | Focus of Resource | Resource Description | Author Name | Author Description |
|---|---|---|---|---|---|
| Cumulus | smarthealthit.org/cumulus | SMART on FHIR, FHIR Bulk Access, Information Extraction, Data sharing, Data analysis, Federated networks | Turnkey functions to annotate FHIR data for analytics, de-identify data, and query for cohorts. Uses FHIR APIs and NLP/LLMs to process population data for care, research, and public health. | SMART on FHIR (Boston Children’s Hospital) | The SMART Health IT project develops open technologies for digital health. |
| FHIR-GPT | ai.nejm.org/doi/10.1056/AIcs2300301 | FHIR, Few-Shot Learning | Converts clinical narratives into FHIR resources using large language models. Developed FHIR-GPT for transforming clinical texts into FHIR medication statements. | Northwestern University, Siemens Healthineers | Peer-reviewed research from Northwestern and Siemens Healthineers. |
| Vertex AI Agent Builder | cloud.google.com/generative-ai-app-builder | Development tool | Build AI agents and applications using natural language or a code-first approach. | Alphabet | Services for production tools using Google Cloud Platform. |
| LLM-FHIR-Eval | github.com/flexpa/llm-fhir-eval | FHIR, LLMs, Benchmarking, Evaluation | Framework to benchmark LLMs on FHIR-specific tasks like generation, validation, and extraction. | Flexpa | Developer of APIs for claims and health data. |
| RAG on FHIR | github.com/samschifman/RAG_on_FHIR | FHIR, Retrieval Augmented Generation | Uses Retrieval-Augmented Generation (RAG) to combine FHIR with Generative AI. | Independently developed | Independent project. |
| LLM on FHIR | github.com/StanfordBDHG/LLMonFHIR | FHIR, Digital Health, Mobile Apps, LLMs | Interprets, summarizes, and explains health record data using OpenAI GPT and FHIR. | Stanford Biodesign Digital Health Group | Develops digital health solutions and modular, interoperable tools. |
| HealthGPT | github.com/StanfordBDHG/HealthGPT | FHIR, Digital Health, Mobile Apps, LLMs | iOS app that lets users interact with Apple Health data using natural language. | Stanford Biodesign Digital Health Group | Develops digital health solutions and modular, interoperable tools. |
| HealthChain | github.com/dotimplement/HealthChain | EHR Integration, NLP, Testing and Evaluation, Pipeline | Open-source framework for scalable AI and NLP apps in healthcare. | dotimplement | Builds dev tools and consults on healthcare AI. |
| Doctor Dok | github.com/CatchTheTornado/doctor-dok | Storage, Digitization, LLM Query and Summarization | Secure open-source framework for storing and managing medical records via LLMs. | Catch the Tornado | Open-source framework for record management. |
| pyomop | github.com/dermatologist/pyomop | FHIR, OMOP, Query and Analysis | Python library to query OMOP CDM databases and convert results to DataFrames. Uses Llama Index. | Independently developed | Independent project. |
| MEDPrompt | github.com/329162516/medprompt | Text Conversion | Prompt tools including FHIR2Text, which converts FHIR to plain text. | Independently developed | Independent project. |
| IRIS FHIRfy | github.com/jrpereirajr/iris-fhirfy | FHIR Resource Generator | Converts raw data into FHIR resources using InterSystems IRIS platform and LLMs. | Independently developed from Intersystems template | Independent project. |
NIH-Supported FHIR Tools
| Resource Name | URL | Focus of Resource | Resource Description | Author Name | Author Description | Funding |
|---|---|---|---|---|---|---|
| LHC FHIR tools | lhcforms.nlm.nih.gov | FHIR tools, widgets, services | Web tools including the LHC-Forms Widget for rendering FHIR Questionnaires and producing QuestionnaireResponses and Observations. | NLM | Developed by and hosted at the National Library of Medicine. | NIH |
| DbGaP FHIR API | github.com/ncbi/DbGaP-FHIR-API-Docs | FHIR API | API returning Bundles of ResearchStudy FHIR resources from dbGaP. | NCBI dbGaP project | dbGaP is the Database of Genotypes and Phenotypes. | NCBI |
| NIH Cloud Lab | cloud.nih.gov/resources/cloudlab | Cloud system support | Cloud services open to the NIH biomedical research community. | NIH STRIDES Initiative | NIH STRIDES partners with commercial cloud providers. | NIH |
| FAIR4Health | github.com/fair4health | CDM model, data curation and privacy tools, FHIR IG | GitHub repositories applying FAIR principles in health research using FHIR. | European Union Horizon 2020 | EU research and innovation program (2014–2020). | HL7 Europe |
| Sync for Science (S4S) | syncfor.science | FHIR API | FHIR API enabling research participants to share clinical data like labs, meds, vitals, and documents. | NIH, ONC, Harvard Med School | Collaboration among agencies, providers, and EHR vendors. | All of Us |
| FhirExtinguisher | github.com/JohannesOehm/FhirExtinguisher | Converter | Tool that flattens FHIR Bundles for statistical analysis. | Univ. of Münster, Germany | Independent academic project. | BMBF (HiGHmed/Münster) |
| NLP2FHIR | github.com/BD2KOnFHIR/NLP2FHIR | Converter | FHIR-based clinical data normalization pipeline. | Mayo Clinic | BD2K initiative project. | — |
| FHIR PIT | researchsoftwareinstitute.github.io/data-translator/apps/fhir-pit | Converter | Combines clinical + environmental data and removes PHI to create integrated datasets. | UNC Health Care System | Data Translator program participant. | — |
| REDMATCH (FHIRCAT) | github.com/aehrc/redmatch | Converter | REDCap module for exporting data as FHIR resources. | Australian Genomics | REDCap integration tool. | NHMRC (GNT1113531) |
| FHIR Ontology External Module | github.com/aehrc/redcap_fhir_ontology_provider | REDCap module | REDCap external module for referencing FHIR ontology servers. | Australian e-Health Research Centre | CSIRO + Queensland Government initiative. | — |
| EBMonFHIR | hl7.org: EBMonFHIR | FHIR IG | IG for exchanging computable scientific knowledge and creating derivative guides. | HEvKA | The Health Evidence Knowledge Accelerator, formerly COKA. | — |
| FHIR to CDISC Mapping IG | hl7.org/fhir/uv/cdisc-mapping | FHIR IG | Maps FHIR R4 to CDISC standards (SDTMIG, CDASH, LAB). | HL7 and CDISC | Promotes clinical research data interoperability. | — |
| Vulcan | build.fhir.org/ig/HL7/vulcan-rwd | FHIR IG | Defines a minimal set of research-ready FHIR resources for EHR systems. | HL7 Accelerator | HL7 project to advance FHIR in clinical research. | — |
| MedMorph | fhir-medmorph IG | FHIR IG | Standardizes data partner onboarding and data sharing with research networks. | MedMorph (CDC/HHS) | Enables access to clinical data using HL7 FHIR and CQL. | HHS, CDC |
| ClinicalTrials.gov FHIR API | clinicaltrials.gov/data-api/fhir | FHIR API | Enables trial search, patient matching, and results extraction via FHIR. | ClinicalTrials.gov | Global clinical trial database and service. | NLM |
| FEvIR Platform | fevir.net | FHIR tool collection | Suite of tools to create, convert, and visualize FHIR representations of evidence and knowledge. | HEvKA | Open virtual group for evidence interoperability standards. | Computable Publishing |
Common Data Model (CDM) and FHIR Harmonization
| Resource Name | URL | Focus of Resource | Resource Description | Related CDMs | Author Name | Author Description |
|---|---|---|---|---|---|---|
| CDM - FHIR Gap Analysis | CDM-FHIR Mappings | Documentation for Mappings | List of mappings between FHIR and CDMs: ACT(i2b2) to FHIR, OMOP to FHIR, and PCORnet(v4.1) to FHIR. | i2b2, OMOP, PCORnet | Data Harmonization Project (CD2H) | Identifies tools and frameworks to harmonize clinical data using FAIR principles. |
| Federated Data Query Workshop | Baltimore Workshop | Educational | Presentations, videos, and slides from a 2-day workshop on federated queries and data harmonization. | i2b2, OMOP, PCORnet | Data Harmonization Project | Hosted by CD2H as part of the Next Gen Data Repository Core initiative. |
| Data Model Harmonization Subgroup | Confluence Link | Educational | HL7–OHDSI working group minutes and documents focused on mapping, ETL specs, adoption, and expanding use cases. | OMOP | FHIR-OMOP Collaborative | HL7 & OHDSI partnership to integrate OMOP and FHIR into a unified CDM. |
| FHIR-OMOP Collaborative | Confluence Home | Educational | Central hub for meeting minutes, documentation, and announcements. | OMOP | FHIR-OMOP Collaborative | Ongoing collaboration between HL7 and OHDSI. |
| ASPE Code Map Services | Code Map Services | Mapping Service | Automated code mapping tools for OMOP, Sentinel, PCORNet, i2b2/ACT, TriNetX, and CDISC SDTM. | OMOP, Sentinel, PCORnet, i2b2/ACT, TriNetX, CDISC SDTM | — | U.S. HHS ASPE initiative. |
| LinuxForHealth FHIR IG | Implementation Guide | FHIR IG | Common Data Model IG supporting data interoperability across healthcare systems. | LinuxForHealth CDM | — | Developed by the LinuxForHealth team. |
| PGHD CDM to FHIR | GitHub Repo | FHIR IG | Converter from SNUBH CDM to FHIR, including an API and visualization tool. | SNUBH CDM | — | Seoul National University Bundang Hospital (SNUBH). |
| FHIR-to-OMOP Cookbook | GitHub Repo | Cookbook | Guide for mapping FHIR resources to OMOP CDM with examples, use cases, and comparison of design principles. | OMOP | — | Developed under the CodeX HL7 FHIR Accelerator. |
| REDHotOMOP | GitHub Repo | Plug-in Module in REDCap | Converter plugin to map between OMOP and FHIR for clinical trial data inside REDCap. | OMOP | — | Independent project. |