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.Data Science & Engineering Copilot - Leverage Advanced AI Machine Learning Models
Are you looking to harness the power of AI to streamline your data science and engineering workflows in healthcare? In our upcoming webinar episode, " Data Science & Engineering Copilot - Leverage Advanced AI Machine Learning Models for Healthcare," we’ll showcase how Data Science and Data Engineering Copilot from Microsoft Fabric are transforming the way healthcare organizations manage, analyze, and derive insights from data. These AI-powered copilots enable healthcare teams to streamline complex data engineering pipelines and accelerate the development of advanced data science models.
Driving Better Patient Outcomes with Care Management Analytics in Healthcare data solutions
In today's rapidly evolving healthcare landscape, effective data driven decision is more crucial than ever. The ability to analyse, manage, and optimize patient care processes relies on the seamless integration of diverse data sources like clinical, claims, social determinants of health etc. Leveraging the innovative medallion Lakehouse architecture, care management analytical template capabilities provide a robust platform for organizations to derive actionable insights and drive better patient outcomes. The Medallion Lakehouse for Care Management analytics Built on the foundation of the healthcare data solutions in Microsoft Fabric which utilizes the medallion Lakehouse architecture. This architecture consists of three foundational layers, each playing a critical role in transforming raw data into actionable insights: Bronze: The Raw Zone The Bronze layer serves as the raw data zone, storing all data in its original format. This data includes various sources such as patient encounters, conditions, treatment adherence records, and other relevant care management information. By maintaining this data in its raw form, organizations ensure the integrity and completeness of the dataset, providing a solid foundation for subsequent processing and analysis. Silver: The Enriched Zone In the Silver layer, data from the Bronze Lakehouse is enriched and transformed into a standardized format for analysis. This layer stores metadata and file references based on healthcare interoperability standards such as FHIR (Fast Healthcare Interoperability Resources). The enriched data provides a holistic view of the patient record, integrating different modalities in healthcare data solutions which are critical for comprehensive care analysis. Gold: The Curated Zone The Gold layer represents the curated zone, where data is refined and structured for advanced analytics and reporting. By building a comprehensive data model, the data is optimized for, predictive analytics, and reporting dashboards that can provide deep insights into care quality, patient outcomes, and operational efficiency. Conceptual Architecture Care management analytics involves integrating and analysing diverse datasets, including clinical, claims and social determinants of health data. The medallion Lakehouse architecture in Microsoft Fabric offers the flexibility to ingest and process these data types at scale. The data flows from raw data ingestion to transformation into the Gold Lakehouse format. End to End execution steps Step 1: Create a workspace and add health solutions capability. Step 2: Set up healthcare data solutions on your Fabric workspace. Follow the guidance from the deployment wizard and add sample data if needed. Step 3: Select the Care Management analytics capability and click on Deploy. Step 4: Copy the sample data downloaded into the bronze lakehouse under Process\Clinical\FHIR-HDS folder Step 5: Run the care management analytical data pipeline to transform the data from the bronze lakehouse to gold lakehouse. Step 6: Access the Power BI dashboards once the above steps are completed to view detailed visualization on Clinical and Claims data. Transforming Care Management analytics with healthcare data solutions Healthcare data solutions care management analytics capability provides a comprehensive template solution for customers and partners to unify and analyze diverse data. By leveraging the medallion Lakehouse architecture, healthcare organizations can unlock the potential of their data, enhance care coordination, and drive better patient outcomes. The seamless integration of raw, enriched, and curated data layers ensures that insights are not only actionable but also scalable and sustainable. For more information on how Healthcare data solutions can revolutionize your care management analytics, please review our detailed documentation and get started with transforming your healthcare data landscape today. https://go.microsoft.com/fwlink/?linkid=2284603 FHIR® is a registered trademark of Health Level Seven International, registered in the U.S. Trademark Office, and is used with their permission. Medical device disclaimer: Microsoft products and services (1) are not designed, intended or made available as a medical device, and (2) are not designed or intended to be a substitute for professional medical advice, diagnosis, treatment, or judgment and should not be used to replace or as a substitute for professional medical advice, diagnosis, treatment, or judgment. Customers/partners are responsible for ensuring solutions comply with applicable laws and regulations.
Seamlessly use social determinants of health data in healthcare data solutions in Microsoft Fabric
Social determinants of health are the social conditions that contribute to an individual’s or a population group’s health outcomes, like place of birth, median household income, and access to transportation. Research and real-world evidence have established that SDOH information can complement medical information. This helps healthcare organizations understand their patients’ health profile more comprehensively and facilitate tailored care interventions. However, a fundamental challenge in leveraging SDOH data arises due to the lack of a standard data collection and exchange mechanism. To simplify this process, we are thrilled to announce the public preview of SDOH datasets- transformations (SDOH) in healthcare data solutions in Microsoft Fabric. It fuels large-scale analytics by enabling the unification of social determinants of health data with core healthcare domains like clinical & claims. Key features SDOH information can be seen in two forms- Public datasets that contain social determinant details aggregated at a geographic level, and patient-level SDOH data that depict those characteristics of an individual that might pose health risks. This release focuses on the public SDOH datasets, which comes with, A simple and intuitive data preparation mechanism to ready the datasets for ingestion into healthcare data solutions. The supported data formats are .csv and .xlsx. A set of powerful pipelines and notebooks that allow effortless transformation of the datasets into tabular shapes. Eight sample datasets across various SDOH domains that you can readily leverage for your use cases. As the data progresses through the medallion Lakehouse, it gets persisted within a robust data model, custom-built for the SDOH modality. This eases the process of combining SDOH data with other modalities, unlocking use cases such as Care management analytics, Risk stratification, and Population health. How it works The SDOH capability follows three simple steps to transform the disparate datasets into a unified data model, Data preparation and ingestion- As there are no established standards to collect and exchange the information captured in these datasets, it is necessary to unify them into a common shape before they can be ingested. This step requires you to add three sheets in your original dataset to capture key details like publisher information, description of the data columns, and location information. The shipped sample datasets are pre-populated with all the necessary information. Landing zone to bronze- Once the datasets are prepared, they can be uploaded into the landing zone. The bronze notebook will then populate all the key details in the bronze lake in delta table format. Bronze to silver- This notebook normalizes the data from the bronze lake into the custom SDOH data model in the silver lake by creating dedicated tables and establishing relationships between them. It preserves the context of the source tables to help you easily identify or query the data. You can trigger the SDOH pipeline to run all the steps after data preparation at one go and thereafter utilize the normalized silver lake data to build your analytical scenarios. Get started today The SDOH public preview is available in healthcare data solutions for teams to start using today. For a more detailed overview of the capability and the necessary configurations needed to deploy it, please check out the official documentation. Medical device disclaimer: Microsoft products and services (1) are not designed, intended or made available as a medical device, and (2) are not designed or intended to be a substitute for professional medical advice, diagnosis, treatment, or judgment and should not be used to replace or as a substitute for professional medical advice, diagnosis, treatment, or judgment. Customers/partners are responsible for ensuring solutions comply with applicable laws and regulations.Unlocking the Potential of Claims Data Insights in Healthcare data solutions in Microsoft Fabric
As part of the continuous innovation within healthcare data solutions in Microsoft Fabric, we are excited to introduce our CMS Claims data transformations capability. This feature specifically tailored to handle CMS CCLF formats. By ingesting, CMS Claims data into healthcare data solutions enables customers to assess the effectiveness of their care management programs, monitor population-level trends and utilization, also and measure their performance against benchmarks to reduce overall claim expenses and improve patient care. Leveraging the Medallion Lakehouse architecture, this feature allows healthcare organizations to seamlessly integrate claims data into the unified data platform provided in Microsoft Fabric. This solution supports scalable data ingestion and transformation workflows that convert claims data into tabular shapes, promoting efficient healthcare delivery and decision-making. The Medallion Lakehouse for Claims Data The Medallion Lakehouse architecture for claims data is built on the foundational layers of Microsoft Fabric’s healthcare data solutions. This architecture is designed to support the ingestion, transformation, and analysis of healthcare claims data. It comprises three fundamental layers: Bronze (Raw Zone): The first layer stores raw claims data in its original CCLF format. This raw zone acts as a staging area where files are ingested directly into the Lakehouse, maintaining the data’s original integrity. It supports native and compressed file types of the claims format, ensuring compatibility and flexibility in data processing. Silver (Enriched Zone): This intermediate layer focuses on processing and enriching the raw claims data by transforming it into structured formats based on the FHIR specifications. It leverages data transformation tools to parse and map the claims data into FHIR financial resources, storing the transformed data in a format optimized for querying and analysis. Gold (Curated Zone): The final layer aggregates the enriched data to create a highly curated dataset, optimized for reporting and analytics. In this zone, the data is further transformed into OMOP CDM (Observational Medical Outcomes Partnership Common Data Model) or a custom data model. The mapping ensures compatibility with various analytical and machine-learning models that healthcare organizations might deploy for deeper insights. Conceptual architecture The volume and complexity of claims data often require robust solutions to manage and extract valuable insights efficiently. Microsoft Fabric’s Medallion Lakehouse provides a comprehensive approach to handling these needs, offering three distinct ingestion patterns based on organizational requirements and existing data infrastructure: End to End execution steps Step 1: Create a workspace and add health solutions capability. Step 2: Setup healthcare data solutions on your Fabric workspace. Follow the guidance from the deployment wizard and add sample data if needed. Step 3: Select the CMS claims data transformations capability and click on Deploy. Step 4: Upload the CCLF files in following folder structure Ingest\Claims\CCLF\<namespace> Ingest folder structure to upload the CCLF files Step 5: Run the claims data pipeline to transform the data from the Bronze Lakehouse to Silver Lakehouse. Step 6: To validate the ingested and transformed data, check the ExplanationOfBenefits table to view the data The CMS claims data transformations capability within Microsoft Fabric’s Medallion Lakehouse architecture offers a powerful and scalable solution for healthcare organizations to integrate, manage, and analyse claims data effectively. By transforming raw claims data into FHIR, healthcare data solutions in Microsoft Fabric enables seamless interoperability and supports advanced analytics, providing a robust foundation for enhanced healthcare delivery and operational efficiency. For further details and documentation, Overview of CMS claims data transformations(preview) FHIR® is a registered trademark of Health Level Seven International, registered in the U.S. Trademark Office, and is used with their permission. Medical device disclaimer: Microsoft products and services (1) are not designed, intended or made available as a medical device, and (2) are not designed or intended to be a substitute for professional medical advice, diagnosis, treatment, or judgment and should not be used to replace or as a substitute for professional medical advice, diagnosis, treatment, or judgment. Customers/partners are responsible for ensuring solutions comply with applicable laws and regulations.
