7 clinical challenges surrounding health data standardisation (and how to overcome them)

4 minute read
Hadley Sheppard, PhD

Hadley Sheppard, PhD

5 September 2023


Introduction to health data standardisation


The amount of health data required to address critical questions continuously grows in research and healthcare. New technologies have made it possible to create large health datasets, collected from all over the world and across numerous organisations. These technologies include digitising medical tools, accumulating electronic health records (EHRs), and lower-cost genome sequencing.

These vast datasets can provide important insights that may ultimately enhance lives. Recent groundbreaking studies that illustrate the power of big data in health research include:


However, to be able to use all this valuable data in analysis, it must first be standardised and made interoperable in order to accurately combine data from multiple sources.

This article specifically focuses on the clinical challenges associated with health data transformation, and the solutions to connect high quality datasets, to inform clinical decision making and progress life sciences research.


What are the challenges surrounding clinical data standardisation?


Health data transformation is crucial for ensuring consistency, interoperability, and quality of data across different systems and institutions. However, there are several challenges that include:


Diverse data sources

Clinical data originates from various sources, including different collection sites, EHR systems, medical devices, and more. These sources may use different data models, schemas, and formats for clinical data collection. This makes it challenging to integrate and standardise the data.

Data volume and complexity

Healthcare organisations often have vast amounts of data to process (terabytes in volume), which can include structured data (eg lab results) and unstructured data (eg clinical notes).

Data heterogeneity

Health data is documented in different formats, languages, and units. Standardising units of measurement, terminologies, and health codes is a challenge, especially when dealing with data from different organisations and geographic regions.


Designing interoperable application programming interfaces (APIs) that allow different health systems to communicate and seamlessly exchange standardised data is technically challenging. Ensuring these APIs are well-documented and adhere to industry standards is crucial.

Quality and consistency

When clinical data is standardised, ensuring data quality and consistency is essential. Inaccurate or incomplete data can lead to erroneous clinical or research decisions.

Evolving standards

Healthcare data standards and terminologies are continually evolving to accommodate new knowledge, technology advancements, and changes in healthcare practices. It is crucial to keep up with these changes, although time consuming.

Security and privacy

When standardising clinical data, organisations must maintain patient privacy and adhere to data security regulations (eg HIPAA). Further, moving the data to provide third party access ultimately increases the security risks.


Identifying solutions to connect high-quality datasets


Common Data Models (CDMs) are being increasingly utilised in the healthcare sector to overcome the lack of consistency in health data. Collaborative health research on data across nations, sources, and systems is made possible by the standard approach. Examples include the Observational Medical Outcomes Partnership (OMOP) CDM and Clinical Data Interchange Standards Consortium (CDISC) medical standards.


What is OMOP?

OMOP is an open community data standard created to standardise observational data formats and content and to facilitate quick analyses. The OHDSI standardised vocabulary is a key part of the OMOP CDM. The OHDSI vocabularies enable standard analytics and allow the organisation and standardisation of medical terms to be used across the various clinical domains of the OMOP CDM.


What is CDISC?

CDISC creates data standards for the gathering, analysing, and sharing of clinical trial data in conjunction with a wide spectrum of international professionals. Researchers, pharmaceutical and biotech firms, governmental organisations (such as the Food and Drug Administration (FDA), Pharmaceuticals and Medical Devices Agency (PMDA), and the National Medical Products Administration (NMPA)), and technology suppliers all utilise CDISC standards. The standards help to make data more easily accessible, interoperable, and reusable so that clinical research and global health can be improved.





Type of data

Clinical trial data

Observational data

Mode of collection

Collected via an experiment

Collected through real-world settings

Size of data

Small size (megabytes)

Gigantic (terabytes)

Use of data

Collected for the purpose of running a clinical trial

Collected for multiple research use cases




To leverage a breadth of health data types, both clinical trial and non-clinical trial health data, researchers must transform these datasets to CDMs. However, this is time consuming and costly, with data scientists estimated to devote 80% of their work to organising and cleaning data.


Researchers should be able to spend time on what matters most - analysis that will derive meaningful insights to benefit the lives of patients.


To empower researchers to effectively collaborate over their data, industry providers are now offering support services for the standardisation of data to CDMs. This saves researchers’ time and effort, with providers offering fully-dedicated, expert teams that have developed proprietary ETL pipelines to streamline the standardisation process while maintaining data quality standards. Working with providers who are experts in both the standardisation of clinical trial and observational data types can help connect these datasets for a variety of use cases, powering clinical and research breakthroughs.


Working with experts in multiple Common Data Models supports research for a variety of use cases.

*Image adapted from CDISC 2019 Europe Interchange

Finally, throughout the process of data standardisation, data security and patient privacy should always remain a primary concern.

When data is moved, for example to provide to an industry partner to standardise the data, it can become vulnerable to interception (and furthermore the movement of large datasets is often very costly). Trusted research environments and data federation allow virtual access to the data through Application Program Interfaces (APIs), avoiding moving or copying the data.

By using this approach, data can be standardised and made interoperable for collaborative research without compromising security.




Health data comes from various sources and exists in multiple formats. Combining this data to gain novel insights can only be achieved if the data is made interoperable. Standardising health datasets requires overcoming clinical challenges related to resources, technological capabilities and data governance to safely empower data consumers to maximise research insights and discoveries.

Look out for the next blog in our series, where we will describe further, specific benefits that standardisation of health data can bring to researchers and clinicians.

Once data is standardised, users can bring standardised analytical tools to where the data resides in its secure environment. However, access to and analysis of the data must also be harmonised to maximise insights that can be gained.

Author: Hadley E. Sheppard, PhD

Contributors: Hannah Gaimster, PhD and Amanda White



About Lifebit


Lifebit provides health data standardisation services for clients, including Genomics England, Boehringer Ingelheim, Flatiron Health and more, to help researchers transform data into discoveries.

Lifebit’s services are making health data usable quickly.  

Find out more about the value of data standardisation at our upcoming webinar, Data Harmony, on 14 September 2023. Secure your place today

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