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

• Download binaries and dictionary
1. Bioentity extractor binary
2. Dependent libraries
3. Dictionary
• Unzip downloaded files.
• Import three jars to your project.
1. bioentityextractor.jar
2. lucene-analyzers-common-4.10.2.jar
3. lucene-core-4.10.2.jar

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());
			}
			System.out.println();
		}
	}
}
					

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: http://www.gnu.org/licenses/gpl.html

5. Contact - for bugs, comments and questions

Sunwon Lee: sunwonl@korea.ac.kr
Donghyeon Kim: donghyeon@korea.ac.kr
Jaewoo Kang: kangj@korea.ac.kr