Japan’s EHR Databases Face Standardization Hurdles for Regulatory Use

A comprehensive review of electronic health record (EHR) databases in Japan reveals that while these systems offer broad coverage of patient demographics and clinical data, they currently lack the standardization and linkage capabilities required for robust regulatory decision-making. Published in the journal Drugs – Real World Outcomes, the report examines the characteristics of eight major EHR databases actively utilized in the country as of October 2024. The study, conducted by a working group from the PhRMA Japan Medical Affairs Committee, aims to organize the technical attributes of these databases and identify the specific challenges that hinder their use in drug approval and post-marketing surveillance. The findings suggest that although Japanese EHR databases are valuable for observational studies, significant structural gaps remain before they can fully support regulatory applications.

The global landscape for real-world data (RWD) is shifting as regulatory agencies increasingly rely on information from everyday medical care rather than solely on controlled clinical trials. In the United States, the Food and Drug Administration issued industry guidance in 2024 to support the use of RWD, while the European Medicines Agency released framework reports in 2023. Japan’s Pharmaceuticals and Medical Devices Agency (PMDA) has similarly promoted the use of RWD, with eight new drug applications to date utilizing such data. However, the report notes that most RWD in Japan is not yet collected with regulatory use in mind, except for specific registries. This review focuses specifically on EHR databases, which store patient information from hospitals and offer a distinct advantage over other data sources by providing easier access to detailed clinical laboratory values.

To identify the relevant databases, the researchers conducted an internet-based search using keywords such as ‘electronic medical record database’ combined with ‘Japan’ or ‘real-world data’. This process initially identified 347 websites, from which 13 EHR databases currently utilized in Japan were selected. After applying exclusion criteria, including the requirement for disclosed hospital counts and the ability to conduct qualitative interviews, eight databases were chosen for detailed analysis. The study team conducted online interviews with representatives from these eight vendors, asking standardized questions about database characteristics, regulatory intent, and future plans. The information was descriptively summarized and verified by the respective database vendors to ensure factual accuracy.

The eight databases profiled include CyberOncology, Millennial Medical Record, Flatiron Health, Real World Data, Japan Medical Data Survey (JAMDAS), TXP-Data Warehouse, MID-NET, and J-MIMO. Each system has unique operational characteristics. For instance, CyberOncology, operated by PRiME-R, is strong in the oncology field and is adapting its output data to the Observational Medical Outcomes Partnership (OMOP) Common Data Model. In contrast, Millennial Medical Record, operated by Life Data Initiative and NTT Data, is certified under the Next-Generation Medical Infrastructure Act and focuses on structuring text information using artificial intelligence. Flatiron Health Japan provides a global oncology RWD platform, with a network of five participating medical institutions in Japan as of January 2025, planning to expand to approximately 10 sites by the end of 2026.

Despite their individual strengths, the report highlights a fundamental limitation across all Japanese EHR databases: the inability to track patients who transfer between hospitals. This is due to a lack of data linkage between facilities, which prevents the tracing of patient data during ongoing treatment. Additionally, electronic medical records contain a significant amount of unstructured data, such as free-text clinical notes, which makes it difficult to extract uniform data. This often leads to a loss of information during the data abstraction process. The absence of a common standard across databases further complicates the merging of data from multiple facilities, a challenge that is critical for enhancing the generalizability of research findings.

Data collection methods in these databases are mostly retrospective, meaning data is collected after the care has been provided. However, some systems, like JAMDAS, offer real-time data extraction from clinics, providing excellent timeliness. J-MIMO and Millennial Medical Record are notable for their certifications under the Next Generation Medical Infrastructure Act, which allows them to link to public databases such as the National Database of Health Insurance Claims and Specific Health Checkups of Japan. This linkage is a unique feature of these certified databases, enabling a more comprehensive view of patient health by integrating electronic medical record data with nursing care and health checkup data.

The report identifies outcome validation as a critical area for improvement. Outcome validation verifies whether patient outcomes, defined by specific criteria, accurately reflect clinical reality. In Japan, such validation is rare, with the MID-NET database being a notable exception that has validated 14 outcome definitions so far. The revisions to the Next Generation Medical Infrastructure Act now permit verification using pseudonymized medical information, which could enable regulatory-grade data accuracy. However, the report notes that validation frameworks are not yet in place for most databases, and outcome data are not being systematically collected. Pharmaceutical companies typically conduct validation on a project basis, but medical institutions see limited benefit, making routine validation difficult without clear incentives.

Another major challenge is the standardization of data formats. The report confirms that multiple standards are used among EHR databases in Japan, with no overall standardization. This inconsistency poses a significant hurdle for linking databases for RWD utilization. Internationally, frameworks like the OMOP CDM are used to harmonize data sources, as seen in the DARWIN EU initiative led by the European Medicines Agency. In Japan, the data standards of various domestic vendors are not aligned with these international standards, which could become a challenge when attempting to conduct large-scale regulatory analyses. The report suggests that a distributed and federated approach, which links multiple data sources while preserving privacy, is crucial for building a large-scale database that can support regulatory decision-making.

The use of artificial intelligence to convert unstructured data into structured data is a growing trend, but regulatory authorities in Japan have not yet issued clear rules regarding the use of such advanced technologies. The report recommends that the government issue guidance on this matter to ensure that AI-driven data abstraction meets regulatory standards. International frameworks, such as the European Health Data Space, are actively defining regulatory expectations for the secondary use of unstructured data and advanced analytics. In contrast, corresponding guidance and standardized practices in Japan are still evolving, creating a gap between international best practices and domestic capabilities.

The report concludes that addressing the operational, technical, and methodological challenges in using EHR databases for regulatory approval applications requires coordinated efforts from multiple stakeholders, including industry, academia, and government. The Japanese government is advancing initiatives like a national medical information platform and EHR standardization under the Medical DX Reiwa Vision 2030. These efforts aim to establish an EHR information-sharing service using the international interoperability standard HL7 FHIR. By aligning national initiatives with international practices, Japan can strengthen outcome validation frameworks, promote interoperability through data standardization, and clarify regulatory pathways for the secondary use of EHR-based real-world data. This alignment is expected to contribute to faster development cycles and reduce drug lag, ultimately benefiting patients with safer and more effective medicines.

Subject of Research: Characteristics and limitations of electronic health record databases in Japan for regulatory use

Article Title: Characteristics and Future Perspectives of Available Electronic Health Record Databases in Japan

Article References: Piao, Y., Kimijima, Y., PhRMA Japan Medical Affairs Committee Working Group, Nakamura, M., & Matsui, N. (2026). Characteristics and Future Perspectives of Available Electronic Health Record Databases in Japan. Drugs – Real World Outcomes, 13(3), 317-327. https://doi.org/10.1007/s40801-026-00562-w

Image Credits: AI Generated

DOI: 10.1007/s40801-026-00562-w

Keywords: electronic health records, real-world data, Japan, regulatory affairs, data standardization, pharmacoepidemiology, health informatics, post-marketing surveillance, Characteristics, Future, Perspectives, Available