Building Healthcare Research Data Platform using Microsoft Fabric
Co-Authors: Manoj Kumar, Mustafa Al-Durra PhD, Kemal Kepenek, Matt Dearing, Praneeth Sanapathi, Naveen Valluri Overview Research data platforms in healthcare providers, academic medical centers (AMCs), and research institutes support research, clinical decision making, and innovation. They consolidate data from various sources, making it accessible for comprehensive analysis and fostering collaboration among research teams. These platforms automate data collection, processing, and delivery, reducing time and effort needed for data management. This allows researchers to focus on their core activities while ensuring data security and regulatory compliance. The ability to work with multimodal data encourages interdisciplinary and interorganizational collaboration, uniting experts to address complex healthcare challenges. Current challenges Researchers face many common challenges as they work with multimodal healthcare data: Data integration and curation: The process of integrating various data types, such as clinical notes, imaging data, genomic information, and sensor data, presents significant challenges due to differences in formats, standards, and sources. Each AMC employs unique methods for data curation, with some utilizing on-premises solutions and others adopting hybrid cloud systems. No standardized approach currently exists for data curation, necessitating considerable organizational efforts to ensure data consistency and quality. Furthermore, data deidentification is often required to safeguard patient privacy. Data discovery and building cohorts: The lack of a unified multimodal data platform leads to the segregation of data across different modalities. Cohort discovery for each modality is performed separately and often lacks a self-service option, necessitating additional human resources to assist researchers in the data discovery process. This issue is particularly significant because researchers who require Institutional Review Board (IRB) approval cannot access the data beforehand but still need an effective method to identify and explore cohorts. Data delivery: Sensitive patient data, after institutional review board approval, must comply with privacy regulations like the Health Insurance Portability and Accountability Act (HIPAA) and the General Data Protection Regulation (GDPR), requiring secure transfer to prevent breaches. The data, sourced from various systems, needs processing for research readiness. Delivering unified data from modalities like imaging, genomics, and health records is challenging. Typically, research IT teams curate cohort data and deliver it to an SQL database or a file share, accessed by researchers via secure virtual machines. This method often leads to data duplication, creating significant overhead due to numerous ongoing research projects. Cost management: Research projects are funded by government grants and private organizations. Managing these costs is challenging. Research IT departments often implement chargebacks for transparency and accountability in resource use. However, there is a disconnect between funding models and operations. Research teams favor capital expenditure (CapEx) with upfront funding for long-term resources, while cloud platforms operate on operational expenditure (OpEx), incurring ongoing costs based on usage. This shift can lead to concerns about unpredictable costs and budgeting difficulties. Bridging this gap requires careful planning, communication, and hybrid financial strategies to align research needs with cloud-based systems. Compliance with regulations: Healthcare research uses sensitive patient data, requiring strict adherence to HIPAA and GDPR. Transparency in data handling is essential but complex. Researchers must document disclosures thoroughly, detailing who accessed the data and for what purpose. However, tracking and auditing are often fragmented due to inconsistent systems. Variability in disclosure requirements from different agencies adds to compliance challenges. Balancing an auditable trail with privacy and manageable administrative tasks is crucial. Research data platform requirements Ability to curate multi modal data into the research data platform Ability for researchers to identify cohorts (without seeing data) to submit data requests to IRB Automated data delivery after IRB workflow approves the request to access relevant data Tools for researchers as part of the same platform Secure and regulatory-compliant environment for research. An approach to building a research data platform using Microsoft Fabric This article serves as a guide to healthcare organizations, offering a point of view and a prescriptive guidance on building a research data platform using Microsoft Fabric. The solution uses several features from healthcare data solutions in Microsoft Fabric, including its discover and build cohorts capability, and features from the Fabric platform. Microsoft Fabric: is a unified, AI-powered data platform designed to simplify data management and analytics. It integrates various tools and services to handle every stage of the data lifecycle, including ingestion, preparation, storage, analysis, and visualization. Fabric is built on a Software as a Service (SaaS) foundation, offering seamless experience for organizations to make data-driven decisions. For additional details, refer to the following link: What is Microsoft Fabric - Microsoft Fabric | Microsoft Learn Healthcare data solutions in Fabric: Healthcare data solutions in Fabric help you accelerate time to value by addressing the critical need to efficiently transform healthcare data into a suitable format for analysis. With these solutions, you can conduct exploratory analysis, run large-scale analytics, and power generative AI with your healthcare data. By using intuitive tools such as data pipelines and transformations, you can easily navigate and process complex datasets, overcoming the inherent challenges associated with unstructured data formats. For additional details, refer to the following links: Healthcare data solutions in Microsoft Fabric - Microsoft Cloud for Healthcare | Microsoft Learn Discover and build cohorts: Discover and build cohorts (preview) capability in healthcare data solutions enables healthcare organizations to efficiently analyze and query healthcare data from multiple sources and formats. It simplifies the preparation of data for health trend studies, clinical trials, quality assessments, historical research, and AI development. It supports natural language queries for multimodal data exploration and cohort building, making it ideal for research and AI-driven projects. For additional details, refer to the following link: Overview of discover and build cohorts (preview) - Microsoft Cloud for Healthcare | Microsoft Learn The proposal for research data platform architecture builds upon the following foundational premises: Recognition of Fabric as the all-in-one data storage, processing, management and analytics platform with enterprise-level features around security, availability and self-service. Adoption of Fabric Workspace(s) as the security boundary (a secure logical container) for maintaining data platform items (data storage and processing assets). Fabric workspaces may be provisioned for and used by different research data platform stakeholders (groups of users) with different requirements around use cases, data privacy, data sensitivity and access security. Use of healthcare data solutions in Fabric, as the core capability to maintain healthcare data assets in a standard (interoperable) manner. Healthcare data solutions enables the storage and processing of several healthcare data modalities and formats that follow industry standards (for example, clinical modality in FHIR® NDJSON format and Clinical-Imaging modality’s DICOM® format). Industry standards make it easier for research data platform stakeholders to share (exchange) data and insights within their own organization as well as (when needed) with other organizations that they collaborate with. Use of Fabric native capabilities to address requirements that may not (yet) have been implemented for healthcare specific needs. This provides the research data platform stakeholders with the flexibility to develop various data storage and processing workloads easily in a low (or no) code manner. Fig – Conceptual architecture of research data platform in Microsoft Fabric Note: This diagram is an architectural pattern and does not constitute one to one mapping of existing Microsoft products. Organizing source data in data workspace (One Data Hub in the above diagram) Organize your enterprise data into a data workspace that could be leveraged for research purposes. This acts as a ‘One Data Hub’ for the research data platform. Multiple Lakehouse can be present in this workspace. There should be at least one Lakehouse that organizes data using ‘unified folder structure’ best practice. Convert data from non-supported format to healthcare data solutions supported format to leverage out of the box transformation for multimodal data: For healthcare data solutions supported modalities: Implement custom transformations to convert data to supported modalities/format. For unsupported modalities: Implement extensions to bronze Lakehouse to accommodate additional data modalities. Epic data availability: Epic supports FHIR data export using Bulk FHIR APIs. If your dataset meets the use cases of Epic Bulk Data, you can store the resulting FHIR resources into One Data Hub for further transformation. Avoid data content duplication: Data duplication cannot be totally avoided. However, the same file and same content are never duplicated. There will be situations when data needs to be transformed to suit the needs of existing transformation pipelines for accelerating research data platform development. Additionally, OneLake in Fabric storage, where Lakehouse is maintained, uses file compression. Healthcare data solutions in Fabric has functionality to compress raw files to zip and always writes structured data to delta parquet which is a higher compressed format. More information can be found here - Data architecture and management in healthcare data solutions - Microsoft Cloud for Healthcare | Microsoft Learn Curating data for research (One Analytics workspace in the above diagram) Implement and extend Silver Lakehouse: A flattened FHIR® data model is provided by healthcare data solutions out of the box within the Silver Lakehouse. Extending the existing data model is possible through adding new columns to existing tables or through adding new tables in the Silver Lakehouse. If there is a need to introduce a different data model altogether, it is best to implement it using a different Lakehouse. Implement and extend Gold Lakehouse: Deploy and extend Observational Medical Outcomes Partnership Common Data Model (OMOP CDM): Deploy OMOP CDM 5.4 out of the box with healthcare data solutions deployment. Extend OMOP CDM to accommodate additional modalities. For example, implement Gene sequencing, Variant occurrence and Variant annotation tables to add genomics modality into OMOP CDM or implement medical imaging data on OMOP CDM as described here - Development of Medical Imaging Data Standardization for Imaging-Based Observational Research: OMOP Common Data Model Extension - PubMed Implement custom Gold Lakehouse(s): Implement other custom Gold Lakehouse using Fabric tools that run your transformation logic from Silver to Gold. These Lakehouse cannot be connected to discover and build cohorts capability within healthcare data solutions. Customers that need access to custom data can connect their custom cohort browsers to the SQL Analytics Endpoint(s) of their custom Gold Lakehouse(s). Enable data de-identification: Microsoft provides several solutions that can be used to implement a comprehensive de-identification solution that customers expect. Refer to the articles below for details. Dynamic data masking in Fabric Data Warehouse - Microsoft Fabric | Microsoft Learn Row-level security in Fabric data warehousing - Microsoft Fabric | Microsoft Learn Column-level security in Fabric data warehousing - Microsoft Fabric | Microsoft Learn Announcing a de-identification service for Health and Life Sciences | Microsoft Community Hub Cohort discovery using cohort builder tool Microsoft’s cohort browser: Today Discovery and Build Cohort supports eyes-on cohort discovery. This is an out of the box solution that is part of healthcare data solutions in Fabric. When eyes off discovery is supported, researchers as well as research IT can benefit from both eyes off and eyes on discovery and cohort building. 3rd-party cohort browser (e.g., OHDSI Atlas): Most 3rd party cohort browsers (E.g. OHDSI Atlas) and home-grown cohort browsers typically support connection to a SQL endpoint. Microsoft Fabric platform provides the capability of exposing SQL endpoint from a Lakehouse that can be connected to a 3rd party cohort browser to perform cohort discovery. Automated data delivery Creating research workspaces with cohort needed for research: Create separate workspaces for different research projects to keep Fabric items distinct and project specific using Fabric APIs. Assign workspaces to a Fabric capacity: Note: When needed, and if the organization has more than one Fabric capacity provisioned, workspace assignment can be spread across different capacities to help manage cost and performance. Next, set up a Lakehouse and provide access for team members (as per IRB approval list). This ensures both access and security at the workspace level. Export data to research workspace (format desired by researchers): Currently, DBC exports data as CSV/JSON files stored in a Lakehouse within the same workspace. Shortcut the destination Lakehouse into research workspace to keep the sanity of cohort data. Tools for researchers: Fabric provides several data engineering and data science tools out of the box that researchers can leverage to perform research. The following are some of the documents that customers can use to enable researchers with the tools of choice. Data science in Microsoft Fabric - Microsoft Fabric | Microsoft Learn Create, configure, and use an environment in Fabric - Microsoft Fabric | Microsoft Learn Migrate libraries and properties to a default environment - Microsoft Fabric | Microsoft Learn Charge back: Fabric compute pricing depends on the chosen Fabric capacity SKU. Assigning different Fabric capacities to different projects or groups within the same cost center can facilitate chargeback. See the step mentioned above on assigning a workspace to a Fabric capacity during workspace creation. Manage historic data migration to the research data platform on Fabric In most instances, customers already possess a research data platform. They seek to transition to this proposed solution without disrupting their current research data flow and obligations. Follow this approach to migrate or use data from the existing platform to the new one: Use your current research data platform as a Lakehouse or a Data Warehouse in Fabric (take advantage of Shortcut and Mirroring features available in Fabric). Fabric offers cross-database query, i.e. allowing to query and join multiple Lakehouse and data warehouses in a single query. Customers can choose how and where to implement such queries to augment the healthcare data solutions datasets with their existing datasets, all natively in Fabric. A bridge/mapping layer can be built to link the old and the new in a cross-relational way. Conceptually, such an approach has also ties to Bring Your Own Database (BYO-DB) requirement, which is the ability to bring custom defined format and still be able to easily convert to healthcare data solutions specific format. Other workflow integration Integrate research data platform with IRB workflow: IRB workflows are dependent on the tools utilized. For instance, eIRB solution from Huron. While there is currently no direct integration between IRB workflows and the research data platform on Fabric, it is possible to develop a connector using Power Platform integration with Fabric. Specific details are not available at this time as this remains an exploratory initiative. Another approach will be to use Fabric REST APIs (as a pro-code method) that can enable richer integration between Fabric and the 3 rd -party system, and a better consuming user experience at the end. Capture logs necessary for “accounting of disclosures”: Logs in Fabric can be captured at event level. It’s up to the customer to decide the level and type of logs that need to be captured for accounting of disclosure. This will need some custom implementation. One such capability of Fabric that can be used is: Track user activities in Microsoft Fabric - Microsoft Fabric | Microsoft Learn FHIR® is a registered trademark of Health Level Seven International, registered in the U.S. Trademark Office and is used with their permission. DICOM® is the registered trademark of the National Electrical Manufacturers Association (NEMA) for its Standards publications relating to digital communications of medical information. If you are a Microsoft customer needing further information, support, or guidance related to the content in this blog, we recommend you reach out to your Microsoft account team in order to set up a discussion with the authors.
