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.

Authors

Md. Faisal Mahbub Chowdhury

Associated Institutions

FBK-irst
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
Citations

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