Text Mining Tools
brat: annotation visualization and editing
Intuitive visualization and editing of text annotations is important for communicating the "meaning" of annotations and for reducing the effort of creating new annotations.
brat supports a rich set of fully configurable annotation primitives:
- Typed text spans (e.g. entity mention)
- Binary relations (e.g. coreference)
- n-ary associations (e.g. events)
- Attributes/meta-knowledge (e.g. Negation, Speculation, etc.)
- Free-form text "notes"
These allow the tool to be applied to a wide range of text annotation tasks, including, for example, entity mention annotation, chunking, binary relation annotation, dependency syntax, and structured n-ary event annotation.
8/11/2012: Version 1.3 released
New features in v1.3 include:
- entity normalisation / linking / grounding support
- supporting embedded visualisations for web pages and web-based applications
- discontinuous text annotations
- in-built annotation tutorials and additional example corpora
- new annotation comparison functionality
- a fast, easy-to-use standalone server (experimental)
For details, please see: http://brat.nlplab.org/new-in-v1.3.html
The brat visualization functionality is based on the stav, a visualization tool created by the Tsujii laboratory of the University of Tokyo for the BioNLP Shared Task 2011. The initial focus of the tool was on the visualization of annotations for event extraction, and the visualization is thus originally designed to work also for complex structured annotations.
The functionality of brat has been extended to support visualization for many other annotation tasks, and brat provides also support features such as text and annotation search and concordancing in addition to visualization.
Click here to see visualizations of annotated biomedical domain corpora.
brat includes annotation capabilities using intuitive mouse-based editing "gestures" familiar from text editors, presentation software, and many other tools.
An annotation for a text span can be created simply by selecting that span with the mouse:
Annotations can be connected by "dragging" from one annotation to the other:
brat has been developed in close collaboration with experienced annotators working on mid-to-large-scale annotation efforts (tens of thousands of annotations), and the tool implements a full set of features for annotation support such as automatic validation of annotations against task-specific semantic constraints.
For more information, please see the brat homepage.
The primary stav and brat developers are
- Pontus Stenetorp (Aizawa laboratory, University of Tokyo) (server development)
- Goran Topić (Tsujii laboratory, University of Tokyo) (client development)
- Sampo Pyysalo (NaCTeM and University of Manchester) (project lead)
- Tomoko Ohta (Tsujii laboratory, University of Tokyo) (quality assurance)
stav and brat development has been supported in part by
- Aizawa laboratory, University of Tokyo (PI: Akiko Aizawa)
- Tsujii laboratory, University of Tokyo (PI: Jun'ichi Tsujii)
- Grant-in-Aid for Specially Promoted Research (MEXT, Japan)
- NaCTeM and University of Manchester (PI: Sophia Ananiadou)
- UK Biotechnology and Biological Sciences Research Council (BBSRC) (reference number: BB/G013160/1)
NaCTeM is contributing to the development of brat as a collaborative open-source project.
brat is freely available with full source code under the open-source MIT license.
(The older visualization tool, stav, has been superseded by brat but remains available from the stav repository.)
If you use brat in your work, please cite the following paper:
- Pontus Stenetorp, Sampo Pyysalo, Goran Topić, Tomoko Ohta, Sophia Ananiadou and Jun'ichi Tsujii (2012). brat: a Web-based Tool for NLP-Assisted Text Annotation. In Proceedings of the Demonstrations Session at EACL 2012. (to appear)
Other related studies:
- Pontus Stenetorp, Goran Topić, Sampo Pyysalo, Tomoko Ohta, Jin-Dong Kim and Jun'ichi Tsujii (2011). BioNLP Shared Task 2011: Supporting Resources. In Proceedings of BioNLP Shared Task 2011 Workshop. (manuscript introducing stav)
- NaCTeM to support the development of innovative pathology tests
- Release of BMC Bioinformatic special issue on BIoNLP Shared Task 2013:Part 1
- New article on improving drug named entity recognition by aggregating heterogeneous methods
- NaCTeM mentioned in The Lancet
- New article on extracting phenotypic information from text
- New article on detecting biomedical term translations
- NaCTeM mentioned in The Guardian
- Text Mining the History of Medicine Workshop at Wellcome Trust, London
- Keynote talk at SIMBig 2015
- Prof. Tsujii appointed director of new Artificial Intelligence Research Center at AIST, Japan
Other News & Events
- Invited Talk at Imperial College, London
- Invited Talk at Lancaster University
- Invited Seminar at Institute of Historical Research
- Invited Talk at BMJ Editors' seminar
- BioNLP 2015 - call for papers