Knowtator is a general-purpose text annotation tool that is integrated with the Protégé knowledge representation system. Knowtator facilitates the manual creation of training and evaluation corpora for a variety of biomedical language processing tasks. Building on the strengths of the widely used Protégé knowledge representation system, we have developed Knowtator as a Protégé plugin that leverages Protégé's knowledge representation capabilities to specify annotation schemas. Knowtator's unique advantage over other annotation tools is the ease with which complex annotation schemas (e.g. schemas which have constrained relationships between entity types) can be defined and incorporated into use. Additionally, because annotation schemas are defined using a Protégé ontology, it is straightforward to incorporate domain knowledge into an annotation schema for semantic annotation.

We are interested in your feedback about this tool. Please direct all questions, comments, and suggestions to the Knowtator help/discussion ( forum.


Philip Ogren

Associated Institutions

Center for Computational Pharmacology (CCP)
University of Colorado Denver Health Sciences Center

Application Domains
  • Domain independent
Other Resource Type
Software Subtype
  • Annotation
Programming Languages
  • Java
Operating Systems
  • Linux
  • OS X
  • Unix
  • Windows
Included Components
  • Graphical User Interface
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

@inproceedings{1225791, author = {Ogren, Philip V.}, title = {Knowtator: a prot\'{e}g\'{e} plug-in for annotated corpus construction}, booktitle = {Proceedings of the 2006 Conference of the North American Chapter of the Association for Computational Linguistics on Human Language Technology}, year = {2006}, pages = {273--275}, location = {New York, New York}, doi = {}, publisher = {Association for Computational Linguistics}, address = {Morristown, NJ, USA}, }

Available Documentation
  • Web page/HTML documentation
Licensing Type
Open source
Licensing Notes
Knowtator is licensed under the Mozilla Public License Version 1.1. Please note that the 3rd party dependencies may have different licensing restrictions.