FhirExtinguisher: A FHIR Resource Flattening Tool Using FHIRPath

A scalable and transparent data pipeline for AI-enabled health data ecosystems

Introduction

Transparency and traceability are essential for establishing trustworthy artificial intelligence (AI). The lack of transparency in the data preparation process is a significant obstacle in developing reliable AI systems which can lead to issues related to reproducibility, debugging AI models, bias and fairness, and compliance and regulation. We introduce a formal data preparation pipeline specification to improve upon the manual and error-prone data extraction processes used in AI and data analytics applications, with a focus on traceability.

Methods

We propose a declarative language to define the extraction of AI-ready datasets from health data adhering to a common data model, particularly those conforming to HL7 Fast Healthcare Interoperability Resources (FHIR). We utilize the FHIR profiling to develop a common data model tailored to an AI use case to enable the explicit declaration of the needed information such as phenotype and AI feature definitions. In our pipeline model, we convert complex, high-dimensional electronic health records data represented with irregular time series sampling to a flat structure by defining a target population, feature groups and final datasets. Our design considers the requirements of various AI use cases from different projects which lead to implementation of many feature types exhibiting intricate temporal relations.

Results

We implement a scalable and high-performant feature repository to execute the data preparation pipeline definitions. This software not only ensures reliable, fault-tolerant distributed processing to produce AI-ready datasets and their metadata including many statistics alongside, but also serve as a pluggable component of a decision support application based on a trained AI model during online prediction to automatically prepare feature values of individual entities. We deployed and tested the proposed methodology and the implementation in three different research projects. We present the developed FHIR profiles as a common data model, feature group definitions and feature definitions within a data preparation pipeline while training an AI model for "predicting complications after cardiac surgeries".

Discussion

Through the implementation across various pilot use cases, it has been demonstrated that our framework possesses the necessary breadth and flexibility to define a diverse array of features, each tailored to specific temporal and contextual criteria.

A Standardized Clinical Data Harmonization Pipeline for Scalable AI Application Deployment (FHIR-DHP): Validation and Usability Study

BACKGROUND

Increasing digitalization in the medical domain gives rise to large amounts of health care data, which has the potential to expand clinical knowledge and transform patient care if leveraged through artificial intelligence (AI). Yet, big data and AI oftentimes cannot unlock their full potential at scale, owing to nonstandardized data formats, lack of technical and semantic data interoperability, and limited cooperation between stakeholders in the health care system. Despite the existence of standardized data formats for the medical domain, such as Fast Healthcare Interoperability Resources (FHIR), their prevalence and usability for AI remain limited.

OBJECTIVE

In this paper, we developed a data harmonization pipeline (DHP) for clinical data sets relying on the common FHIR data standard.

METHODS

We validated the performance and usability of our FHIR-DHP with data from the Medical Information Mart for Intensive Care IV database.

RESULTS

We present the FHIR-DHP workflow in respect of the transformation of "raw" hospital records into a harmonized, AI-friendly data representation. The pipeline consists of the following 5 key preprocessing steps: querying of data from hospital database, FHIR mapping, syntactic validation, transfer of harmonized data into the patient-model database, and export of data in an AI-friendly format for further medical applications. A detailed example of FHIR-DHP execution was presented for clinical diagnoses records.

CONCLUSIONS

Our approach enables the scalable and needs-driven data modeling of large and heterogenous clinical data sets. The FHIR-DHP is a pivotal step toward increasing cooperation, interoperability, and quality of patient care in the clinical routine and for medical research.

HL7 FHIR-based tools and initiatives to support clinical research: a scoping review

OBJECTIVES

The HL7® fast healthcare interoperability resources (FHIR®) specification has emerged as the leading interoperability standard for the exchange of healthcare data. We conducted a scoping review to identify trends and gaps in the use of FHIR for clinical research.

MATERIALS AND METHODS

We reviewed published literature, federally funded project databases, application websites, and other sources to discover FHIR-based papers, projects, and tools (collectively, "FHIR projects") available to support clinical research activities.

RESULTS

Our search identified 203 different FHIR projects applicable to clinical research. Most were associated with preparations to conduct research, such as data mapping to and from FHIR formats (n = 66, 32.5%) and managing ontologies with FHIR (n = 30, 14.8%), or post-study data activities, such as sharing data using repositories or registries (n = 24, 11.8%), general research data sharing (n = 23, 11.3%), and management of genomic data (n = 21, 10.3%). With the exception of phenotyping (n = 19, 9.4%), fewer FHIR-based projects focused on needs within the clinical research process itself.

DISCUSSION

Funding and usage of FHIR-enabled solutions for research are expanding, but most projects appear focused on establishing data pipelines and linking clinical systems such as electronic health records, patient-facing data systems, and registries, possibly due to the relative newness of FHIR and the incentives for FHIR integration in health information systems. Fewer FHIR projects were associated with research-only activities.

CONCLUSION

The FHIR standard is becoming an essential component of the clinical research enterprise. To develop FHIR's full potential for clinical research, funding and operational stakeholders should address gaps in FHIR-based research tools and methods.