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  • @Note2 2.1.4 is now available (November, 23rd - 2016)!
  • RELEASE NOTE: Some Bugs Fix

SOURCEFORGE NOW AVAILABLE: - All the code is now available at sourceforge.

@Note is now published. Please cite using:

  • Anália Lourenço , Rafael Carreira, Sónia Carneiro, Paulo Maia, Daniel Glez-Peña , Florentino Fdez-Riverola , Eugénio C Ferreira , Isabel Rocha and Miguel Rocha.

@Note: A workbench for Biomedical Text Mining. Journal of Biomedical Informatics 2009, 42 710-720


@Note is a Biomedical Text Mining platform that copes with major Information Retrieval and Information Extraction tasks and promotes multi-disciplinary research. In fact, it aims to provide support to three different usage roles: biologists, text miners and application developers.

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The major guidelines of its development were interoperability, extensibility and user-friendly interface. The workbench is meant for both BioTM research and curation. On one hand, it supports regular curation activities, providing an intuitive Graphical User Interface (GUI) interface that does not require any knowledge about workbench or technique implementation. On the other hand, it is also meant for people with programming skills that might wish to extend the workbench capabilities.

@Note is implemented over AIBench , a JAVA framework meant to ease the development of Artificial Intelligence and Data Analysis applications. The main strengths of AIBench are its clear design and available services. Its design is problem-independent, minimum framework-related code is required in order to produce new functionalities. Moreover, it generates GUI code and enforces well-designed MVC code, supporting three main artifacts: operations, data types and views. Operations and data types are used in problem modelling while views display data in a "friendly" way.

Regarding operations, @Note sustains the general workflow of BioTM , fully covering all activities performed in manual curation. The workbench supports the retrieval, processing and annotation of documents as well as their analysis at different levels.


University of Minho

University of Minho



Centre of Biological Engineering

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SilicoLife Lda.

SilicoLife Lda.- Computational Biology Solutions for the Life Science

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Copyright 2016
CEB - Centre of Biological Engineering
University of Minho
SilicoLife Lda.

This is free software: you can redistribute it and/or modify
it under the terms of the GNU Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.

This code is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
GNU Public License for more details.

You should have received a copy of the GNU Public License
along with this code. If not, see

Created inside the BISBII Research Group (
Supported by SilicoLife Lda. (