BioEnEx (Bio-entity Extractor)

BioEnEx is a tool designed to annotate multiple biomedical entity types (i.e. genes/proteins, diseases, species, chemicals, etc) with high performance. It uses a first order CRF classifier. Separate feature sets are used for diseases and genes/proteins. For other types of entities (e.g. species) a generic feature set is used. More information available in the tool's website.


Md. Faisal Mahbub Chowdhury

Associated Institutions

University of Trento

Application Domains
  • Domain independent
Other Resource Type
Software Subtype
  • Named entity recognition
  • NLP / information extraction
Programming Languages
  • Java
Operating Systems
  • Linux
  • OS X
  • Unix
  • Windows
Included Components
  • Library of modular components
  • Plug-in to other software
Dataset Subtype
Data Model Subtype
Online Resource Subtype
Knowledge Base Subtype
Intended User Types
  • Clinician
  • Clinical researcher
  • Informatics researcher
  • NLP researcher or developer
  • Software developer

Md. Faisal Mahbub Chowdhury, Alberto Lavelli, “Disease Mention Recognition with Specific Features”, In Proceedings of the 2010 Workshop on Biomedical Natural Language Processing (BioNLP), ACL 2010, pages 91-98, Uppsala, Sweden, July, 2010

Md. Faisal Mahbub Chowdhury and Alberto Lavelli, "Assessing the practical usability of an automatically annotated corpus", In Proceedings of the 5th Linguistics Annotation Workshop (LAW V), ACL-HLT 2011, pages 101–109, Portland, Oregon, USA, June 23-24, 2011

Md. Faisal Mahbub Chowdhury, Alberto Lavelli, “Robust Biomedical Entity Recognition Using Optimal Feature Set”, In Proceedings of the 1st CALBC Workshop, pages 29-30, EMBL-EBI, Hinxton, Cambridge, U.K., 17-18 June, 2010

Available Documentation
Licensing Type
Open source
Development Milestones

Currently, the tools is optimized for disease and gene/protein identification. A generic feature set is included which allows to identify chemical and specie with a reasonably high accuracy.

Date of Latest Version