Data Mining and Information Systems Laboratory
Laboratory of Prof. Jaewoo Kang

  Biomedical entity extractor

Biomedical Entity Extractor is a dictionary-based biomedical entity extraction tool. It recognizes biomedical entities from text automatically, and returns them. It is utilized at BEST: Biomedical Entity Search Tool to recognize the entities. Biomedical entity extractor is implemented in Java.

1. Program availability and requirements

  • Operating systems : Windows, Linux, Mac
  • Java version :  1.7 or later

2. Preparation to use

3. Usage

import java.util.*;
import org._dmis.object.*;

public class BioEntityExtractTest {
	public static void main(String[] args) {
		String dictPath = "DOWNLOADED_DICTIONARY_PATH.txt";
		BioEntityExtractor bee = new BioEntityExtractor(dictPath);
		String text = "Lapatinib inhibitid cell growth in cell lines.";
		HashSet<BioEntityInfo> entitySet = bee.extractEntities(text);
		for(BioEntityInfo entity : entitySet) {
			System.out.println(entity.getIdStr() + " : " + entity.getName());
			ArrayList<BioEntityType> types = entity.getTypes();
			for(BioEntityType bet : types) {
				System.out.print("\t" + bet.getName4EndUser());

4. License

Bioentity extractor is licensed under the GNU General Public License and is 100% freely available to both commercial and academic users. For the full text of the license:

5. Contact - for bugs, comments and questions

Sunwon Lee:
Donghyeon Kim:
Jaewoo Kang:

Last updated on June 11, 2018