Bell Eapen

Physician | HealthIT Developer | Digital Health Consultant

NLP for Clinical Notes – Tools and Techniques

Clinicians add clinical notes to the EMR on each visit. The clinical notes are unstructured in most cases and can benefit from NLP (natural language processing) tools and techniques. Some are created by dictation software or by medical scribes. Family physicians and family practice-centric EMRs like OSCAR EMR rely on unstructured clinical notes.

natural language processing
NLP for Clinical Notes

Clinical notes, because of the unstructured nature is difficult to analyze for statistical insights. Besides, the notes may require further processing for billing and for generating problem charts. The analysis is becoming increasingly important for quality assessments as well.

NLP can be useful in automated analysis of clinical notes. Here I have listed some of the open-source tools (some maintained by me) for such automated analysis of clinical notes.

Apache cTakes for NLP

Apache cTakes (clinical Text Analysis and Knowledge Extraction System) is one of the first open-source NLP systems that extract clinical information from electronic health record unstructured text. Though it is relatively slow, it is still widely used. I have packaged it as a Quarkus application, that is fast. Quarkus (Supersonic Subatomic Java) is designed primarily for docker containers and the quarkus based containers are easy to be deployed and scaled using platforms such as Kubernetes.

SpaCy and related tools for NLP

SpaCy is an open-source python library for NLP. It features NER, POS tagging, dependency parsing, word vectors and is widely used. But spacy is not designed for clinical workflows and may not be directly usable. Scispacy is SpaCy pipeline and models for scientific/biomedical documents trained on biomedical data. MedaCy is a healthcare-specific NLP framework built over spaCy to support the fast prototyping, training, and application of medical NLP models. One of the advantages of Medacy is that it is fast and lightweight.


Unified Medical Language System (UMLS), is a set of files and software that brings together biomedical vocabularies for health information systems. UMLS provides a set of RESTful APIs for licensed users. I have created a JavaScript wrapper for the UMLS APIs that are easy to be called from JavaScript programs. It is available from the npm package repository. See the update on UmlsBERT below.


Medical  Concept Annotation Tool (MedCAT) is a relatively new tool for extraction and linking of terms from vocabularies such as UMLS and SNOMED for free text in EMRs. The paper describing MedCAT is here. MedCAT models can be further refined by training on a domain-specific corpus of text. MedCAT is fast and very useful.

Word Embeddings for NLP

A word embedding is a weighted model for text where words that have the same meaning have a similar weight. It is one of the most popular methods of deep learning for NLP problems. Word2Vec is a method to construct embeddings and the word2vec model based on the entire Wikipedia corpus is available for use. This paper describes the creation of a clinical concept embedding based on a large corpus of clinical documents. I have created a gensim wrapper for this model that can be used for concept similarity search in python.

BERT and related

Bidirectional Encoder Representations from Transformers (BERT) is a technique for NLP pre-training developed by Google. Here is the highly cited official paper. BERT has replaced embeddings as the most successful NLP technique in most domains including healthcare. Some of the refined BERT models used in healthcare are BioBERT and ClinicalBERT.

It is vital to deploy these models in a scalable and maintainable manner to be available for use within EMR systems. We are working on such a framework called ‘Serverless on FHIR’. Give me a shout if you want to know more.

Update (Dec 2020):

Researchers from the University of Waterloo have introduced the novel concept of UmlsBERT. Current clinical embedding such as BioBERT described above are generic models, trained further on clinical corpora applying the concept of transfer learning. Most biomedical ontologies such as UMLS define the hierarchies of concepts defined in them. UmlsBERT makes use of these hierarchical group information at the pre-training stage for augmenting the clinical concept embeddings. Table 3 in the paper compares the results with other embeddings, and it is quite impressive. The GitHub repo is here
Way to go George Michalopoulos and team!

Kickstart NLP with UMLS

The UMLS, or Unified Medical Language System, is a set of files and software that brings together many health and biomedical vocabularies and standards to enable interoperability between computer systems.

Natural Language Processing (NLP) on the vast amount of data captured by electronic medical records (EMR) is gaining popularity. The recent advances in machine learning (ML) algorithms and the democratization of high-performance computing (HPC) have reduced the technical challenges in NLP. However, the real challenge is not the technology or the infrastructure, but the lack of interoperability — in this case, the inconsistent use of terminology systems.

natural language processing

NLP tasks start with recognizing medical terms in the corpus of text and converting it into a standard terminology space such as SNOMED and ICD. This requires a terminology mapping service that can do this mapping in an easy and consistent manner. The Unified Medical Language System (UMLS) terminology server is the most popular for integrating and distributing key terminology, classification and coding standards. The consistent use of  UMLS resources leads to effective and interoperable biomedical information systems and services, including EMRs.

To make things easier, UMLS provides both REST-based and SOAP-based services that can be integrated into software applications. A high-level library that encapsulated these services, making the REST calls easy to the user is required for the efficient use of these resources.  Umlsjs is one such high-level library for the UMLS REST web services for javascript. It is free, open-source and available on NPM, making it easy to integrate into any javascript (for browsers) or any nodejs applications.

The umlsjs package is available on GitHub and the NPM. It is still work in progress and any coding/documentation contributions are welcome. Please read the file on the repository for instructions. If you use it and find any issues, please report it on GitHub.

OSCAR in a BOX – Virtualized and fault-tolerant OSCAR EMR

TL;DR: OSCAR in a BOX is a fault-tolerant OSCAR instance that you can use out of the box and is virtually maintenance-free!

Image credit DarkoStojanovic @ Pixabay

OSCAR EMR is an open-source Electronic Medical Record (EMR) for the Canadian family physicians. The official OSCAR repository is available here:

OSCAR is a spring java application deployed in a tomcat container with MySQL database backend. OSCAR project being relatively old, with few users outside Canada, has struggled to keep pace with the developments in the electronic health records domain. However, OSCAR is still useful and popular among family physicians and some public health organizations as it is free and well supported.

Oscar is known for its support for the billing workflow, data collection forms (eForms) and comprehensive patient charts (eCharts). Some of the limitations of OSCAR include lack of scalability beyond a handful of users and limited support for data analytics. Oscar by design is hard to be virtualized as a docker container. Availability of a docker container is crucial for sustainable and fault-tolerant deployment on the cloud and distributed systems such as Kubernetes.

Docker is the world’s leading software container platform, used mostly for DevOps. Docker is also useful for developers to set up a development environment in a few easy steps. I was one of the first few who worked on virtualizing OSCAR. Thanks for all those who forked (and hopefully used) this repository.

I have continued my work on OSCAR docker container and has been successful in creating a (reasonably stable) container. It is now available on docker hub. I am now working on a fault-tolerant deployment of OSCAR in customized hardware. I (and some of my friends who know about and encouraged this project) call it OSCAR in a BOX! It has multiple instances of OSCAR with each instance capable of self-healing when a JAVA process hangs (fairly common for OSCAR). The database is replicated, and both the database and documents incrementally back up to an additional disk.

OSCAR in a BOX is ideal for family physicians who wish to adopt OSCAR but does not have the technical support for maintaining the system. OSCAR in a BOX is plug and play and is virtually maintenance-free. The virtualization workflow will also be useful for existing bigger user groups reeling under the sluggish pace of OSCAR. Please let me know if anybody is interested in collaborating.

BTW, did you check out Drishti?

DHIS2 and longitudinal health records: Connecting systems to get the best of both worlds!

DHIS2 is a health information system that revolutionized the way healthcare data is managed. It is open source and is a byproduct of a multinational action research project initiated from Oslo and first implemented in India. 1Currently, DHIS2 is the world’s largest health management information system (HMIS) platform, in use by 67 low and middle-income countries. 2.28 billion (30% of the world’s population) people live in countries where DHIS2 is used.

DHIS2 is a public health information system (PHIS) where the unit of management is a group or a geographical region and not individuals. It is unfortunate that this distinction between a typical EMR (a longitudinal health record) and a public health information system to manage population health is not clear to many policymakers.

The growing popularity of machine learning and artificial intelligence applications make the PH agencies rethink their data management strategies. A longitudinal health record is essential for most ML and AI applications for creating complex predictive models. PH agencies are gradually realizing the importance of data warehouses in managing the changing healthcare data management applications and workflows. Hence, the next generation of public health information systems should be able to efficiently handle longitudinal as well as group/cross-sectional data.

The easiest strategy to adopt may be to make existing PHIS systems talk to each other by leveraging the recent advances in health information exchange. HL7 may not be ideal for this purpose as it relies on a patient-centric model. FHIR may be more capable to deal with this, but the underlying REST interface may not support real-time data exchange.

RabbitMQ and Apache Kafka are industry standard open-source messaging frameworks that can be leveraged for real-time communication between disparate systems such as DHIS2 and OSCAR EMR / OpenMRS. DHIS2 supports both out of the box, and I have modified the DHIS2 docker container optimized for message exchange. A sample Java client is also available from my fork. The repo is here.

If you have ideas/want to work on creating DHIS2 connectors for EMRs like OSCAR EMR or OpenMRS, please comment below. OpenMRS has an existing module that can pull certain reports from DHIS2.


Braa, Monteiro, Sahay. Networks of Action: Sustainable Health Information Systems across Developing Countries. M. 2004;28(3):337. doi:10.2307/25148643

Dockerized OSCAR EMR for developers

I have created a simple docker-compose script to set up Oscar for developers. The script checks out the master branch from OSCAR repository, compile with maven, create Docker containers and deploy them.


CDS-Hooks specification describes a “hook”-based pattern for invoking decision support from within a clinician’s EHR workflow.