IAMsystem

A general dictionary-based approach for semantic annotation.
It stores a terminology in a tree data structure for fast lookup.
It handles abbreviations and typos (with Levenshtein distance) at the token level. Brat output is available.

Getting started

Add the dependency to your pom.xml to download it from the Maven Repository:

<dependency>
 	<groupId>fr.erias</groupId>
	<artifactId>IAMsystem</artifactId>
	<version>1.0.1</version>
</dependency>

To build it, you will need Java 1.8 (or higher) JDK a recent version of Maven (https://maven.apache.org/download.cgi) and put the mvn command on your path. Now you can run mvn clean install in the IAMsystem folder to compile the project.

Quick start

// Initiate TermDetector
TermDetector termDetector = new TermDetector();
// add terms manually or by loading a CSV file
termDetector.addTerm("high blood pressure", "I10");
termDetector.addTerm("fever", "R50.9");
// add abbreviations
termDetector.addAbbreviations("blood pressure", "bp");
String inputString = "The patient denied any fever and has high BP.";
DetectOutput detectOutput = termDetector.detect(inputString);
System.out.println(detectOutput.toString());
// fever and high BP detected

See how it works by loading the Maven project in the example folder using your favorite IDE.
If you notice some problems, please open an issue.

Reference

• Cossin S, Jouhet V, Mougin F, Diallo G, Thiessard F. IAM at CLEF eHealth 2018: Concept Annotation and Coding in French Death Certificates. https://arxiv.org/abs/1807.03674
• Cossin S and Jouhet V. IAM at CLEF eHealth 2020: Concept Annotation in Spanish Electronic Health Records. http://www.dei.unipd.it/~ferro/CLEF-WN-Drafts/CLEF2020/paper_198.pdf

Demo

• Detect French UMLS concepts: https://www.erias.fr/detectUMLS/
• Detect Spanish ICD-10 diagnosis and procedure: https://www.erias.fr/codiesp/

Call it from R

See https://github.com/scossin/RIAMsystem

Handles context (negation...) with FastContext

See https://github.com/scossin/IAMsystemFastContext

Acknowledgement

This annotation tool is part of the Drugs Systematized Assessment in real-liFe Environment (DRUGS-SAFE) research platform that is funded by the French Medicines Agency (Agence Nationale de Sécurité du Médicament et des Produits de Santé, ANSM). This platform aims at providing an integrated system allowing the concomitant monitoring of drug use and safety in France.