Tag Archives: Annotation tools

[repost ]text mining Annotation tools.


Here is a list of projects that allow users to perform biocuration tasks.
This list is not exhaustive. Please contact us if you know other systems not listed here.

This table has been adapted from : “Tools for Annotating Biomedical Texts” prepared by Mariana Neves at Humboldt-Universitat in Berlin (Neves M and Leser U. Tools for Annotating Biomedical Texts, Poster in the Fifth International Biocuration Conference, 2012, Washington, USA)

System name Short description Biocuration tasks Link
Callisto annotation tool The Callisto annotation tool was developed to support linguistic annotation of textual sources for any Unicode-supported language. Entity tagging http://callisto.mitre.org
WordFreak WordFreak is a java-based linguistic annotation tool designed to support human, and automatic annotation of linguistic data as well as employ active-learning for human correction of automatically annotated data. Entity tagging, machine learning based http://wordfreak.sourceforge.net/index.html
Knowtator 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. Entity tagging http://knowtator.sourceforge.net/
GATE GATE is a complete architecture for language processing which contains, amongst other applications, tools to perform manual and automatic textual annotation. POS tagging, classification, relation extractions, … http://gate.ac.uk/
BRAT brat is a web-based tool for text annotation; that is, for adding notes to existing text documents. brat is designed in particular for structured annotation, where the notes are not freeform text but have a fixed form that can be automatically processed and “interpreted” by a computer. Entity tagging, entity relation extraction, entity linking http://brat.nlplab.org/
MMAX2 MMAX2 features separation of base data and annotations (i.e. markables) on the file level by means of stand-off annotation. MMAX2 supports arbitrarily many levels of annotation, each of which resides in a separate file. entity identification, relation between entities http://mmax.eml-research.de
DOMEO Domeo is an extensible web application enabling users to visually and efficiently create and share ontology-based stand-off annotation on HTML or XML document targets. The tool supports manual, fully automated, and semi-automated annotation with complete provenance records, as well as personal or community annotation with access authorization and control. Entity tagging, entity relation extraction, entity linking http://annotationframework.org/
Genia Tagger N/A N/A N/A
BioNotate BioNotate is a text annotation tool written in Javascript that allows collaborative annotation of relationships between biomedical entities in scientific texts. Entity tagging http://bionotate.sourceforge.net/
SWAN Tool to annotate text with ontologies Entity tagging and linking http://code.google.com/p/annotation-ontology/
OntoMat-Annotizer OntoMat-Annotizer is an interactive webpage annotation tool. It supports the user with the task of creating and maintaining ontology-based OWL-markups i.e. creating of OWL-instances, attributes and relationships N/A http://annotation.semanticweb.org/ontomat/
@Note @Note is Biomedical Text Mining platform that copes with major Information Retrieval and Information Extraction tasks and promotes multi-disciplinary research. Information Retrieval (IR) and Information Extraction(IE) http://sysbio.di.uminho.pt/anote.php
CLaRK CLaRK is an XML-based software system for corpora development implemented in JAVA. The main aim behind the design of the system is the minimization of human intervention during the creation of language resources. N/A http://www.bultreebank.org/clark/index.html
Djangology Djangology is a web application for distributed collaborative text annotation. Text annotation, Inter-annotator agreement statistics http://sourceforge.net/projects/djangology/
Ellogon Ellogon is a multi-lingual, cross-platform, general-purpose language engineering environment, developed in order to aid both researchers who are doing research in computational linguistics, as well as companies who produce and deliver language engineering systems. Text annotation http://www.ellogon.org/
LingPipe LingPipe is tool kit for processing text using computational linguistics. Text annotation, entity recognition, word variants http://alias-i.com/lingpipe/index.html
UAM CorpusTool The UAM CorpusTool is a state-of-the-art environment for annotation of text corpora. Text annotation http://www.wagsoft.com/CorpusTool/
UIMA CAS Editor The CAS Editor is an eclipse based annotation tool which supports manual and automatic annotation (via running UIMA annotators) of CASes stored in files. Text annotation http://uima.apache.org/d/uimaj-2.3.1/to