Deployment of a Free-Text Analytics Platform at a UK National Health Service Research Hospital: CogStack at University College London Hospitals

Kawsar Noor, Lukasz Roguski, Xi Bai, Alex Handy, Roman Klapaukh, Amos Folarin, Luis Romao, Joshua Matteson, Nathan Lea, Leilei Zhu, Folkert W Asselbergs, Wai Keong Wong, Anoop Shah, Richard JB Dobson

Research output: Contribution to journalArticlepeer-review

12 Citations (Scopus)
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BACKGROUND: As more health care organizations transition to using electronic health record (EHR) systems, it is important for these organizations to maximize the secondary use of their data to support service improvement and clinical research. These organizations will find it challenging to have systems capable of harnessing the unstructured data fields in the record (clinical notes, letters, etc) and more practically have such systems interact with all of the hospital data systems (legacy and current).

OBJECTIVE: We describe the deployment of the EHR interfacing information extraction and retrieval platform CogStack at University College London Hospitals (UCLH).

METHODS: At UCLH, we have deployed the CogStack platform, an information retrieval platform with natural language processing capabilities. The platform addresses the problem of data ingestion and harmonization from multiple data sources using the Apache NiFi module for managing complex data flows. The platform also facilitates the extraction of structured data from free-text records through use of the MedCAT natural language processing library. Finally, data science tools are made available to support data scientists and the development of downstream applications dependent upon data ingested and analyzed by CogStack.

RESULTS: The platform has been deployed at the hospital, and in particular, it has facilitated a number of research and service evaluation projects. To date, we have processed over 30 million records, and the insights produced from CogStack have informed a number of clinical research use cases at the hospital.

CONCLUSIONS: The CogStack platform can be configured to handle the data ingestion and harmonization challenges faced by a hospital. More importantly, the platform enables the hospital to unlock important clinical information from the unstructured portion of the record using natural language processing technology.

Original languageEnglish
Article numbere38122
Pages (from-to)e38122
JournalJMIR Medical Informatics
Issue number8
Publication statusPublished - 24 Aug 2022


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