Bell Eapen

Physician | HealthIT Developer | Digital Health Consultant

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
UMLS for NLP

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 CONTRIBUTING.md file on the repository for instructions. If you use it and find any issues, please report it on GitHub.

Natural language processing (NLP) tools for health analytics

Natural language processing (NLP) is the process of using computer algorithms to identify key elements in language and extract meaning from unstructured spoken or written text. NLP combines artificial intelligence, computational linguistics, and other machine learning disciplines.

natural language processing

In the healthcare industry, NLP has many applications such as interpreting clinical documents in an electronic health record. Natural language processing is important in clinical decision support systems by extracting meaningful information from free-text query interfaces. It may reduce transcription costs by allowing providers to dictate their notes, or generate tailored educational materials for patients ready for discharge. At a high-level NLP includes processes such as structure extraction, tokenization, tagging, part of speech identification and lemmatization.

“cTAKES is a natural language processing system for extraction of information from electronic medical record clinical free-text. Originally developed at the Mayo Clinic, it has expanded to being used by various institutions internationally.”

cTAKES is relatively difficult to install and use, especially if the service needs to be shared by several systems. I have integrated cTakes into an easy to use spring boot application that provides REST web services for clinical document annotation. The repository is here.

  • SSH URL
  • Clone URL

You need a UMLS username and password for deploying the application. RysannMD is an efficient and fast system for annotating clinical documents developed at Ryerson University. Some of my other experiments with NLP are available here.

Are you working on any NLP projects in medicine?