Difference between revisions of "Main Page"

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*'''@Note2 2.1.4 ''' is now available (November, 23rd  - 2016)!<br>
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*'''@Note2 2.5.0 ''' is now available (June, 23rd  - 2017)!<br>
*'''RELEASE NOTE:''' Some Bugs Fix
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*'''[[Release_Notes#2.5.0|Release Notes]]'''
 
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'''SOURCEFORGE NOW AVAILABLE:''' - All the code is now available at sourceforge.
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'''All the code is available at Sourceforge and GitHub'''
  
* Go to the [http://sourceforge.net/p/anote2/ @Note2 Sourceforge Project].
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* Go to the [http://sourceforge.net/p/anote2/ @Note2 Sourceforge Project] for @Note code and [https://github.com/orgs/biotextmining/dashboard GitHub] for the biomedical text mining libraries.
* You can also subscribe the [https://sourceforge.net/p/anote2/code/feed RSS Feed] to keep track of all the changes, releases and news !
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* You can also subscribe our mailing list on [http://anote-project.org/ @Note Project] to keep track of all the changes, releases and news !
 
* For Bug or Enhancement Report please visit [https://sourceforge.net/p/anote2/tickets/ @Note2 tickets]
 
* For Bug or Enhancement Report please visit [https://sourceforge.net/p/anote2/tickets/ @Note2 tickets]
  
'''@Note is now published'''. Please cite using:
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'''@Note is 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.
 
*Anália Lourenço , Rafael Carreira, Sónia Carneiro, Paulo Maia, Daniel Glez-Peña , Florentino Fdez-Riverola , Eugénio C Ferreira , Isabel Rocha and Miguel Rocha.
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== Introduction ==
 
== Introduction ==
  
'''@Note is a Biomedical Text Mining platform that copes with major <font color="#FF7800"> Information Retrieval and Information Extraction </font> 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 @Note project has been providing, over the last decade, open-source software libraries and tools addressing the most relevant tasks in the field of biomedical text mining (BTM). These tools have been developed as a collaboration between the Center of Biological Engineering from the University of Minho and the company SilicoLife, with the first version published in 2009.
  
 +
The current version 2 provides a set of core libraries with a well-defined programming interface (API) addressing the main BTM tasks in both Information Retrieval (IR) and Information Extraction (IE). IR
 +
libraries include functions to query specific databases (e.g. Pubmed, patent databases), manage and update query results, download relevant documents, convert PDF to text, assign relevance and corpora management.
 +
Regarding IE, the main tasks are Named Entity Recognition (NER), Relationship Extraction (RE) and document clustering, being available several methods for all cases, with both in-house and third-party
 +
algorithms, including a machine learning (ML) workbench (BioTML) able to train and apply ML models to user created or existing datasets.
  
[[Image:system_view_small.png|center]]
+
The main project libraries include: core - nuclear data structures and methods; processes - main processes for IR and IE; and machine learning - the framework for ML methods (training and prediction functions).
 +
These libraries make use of third-party software libraries in Java, including GATE, Mallet and Carrot. An API is provided allowing the use of the main methods by programmers in their applications, with appropriate examples being provided in the repository.
  
 +
The project also provides @Note2, an end-user application, which provides user-friendly interfaces for the above listed functionalities, also including the creation of lexical resources (e.g. dictionaries) and a powerful
 +
curation environment for NER and RE annotations. The development of the @Note application follows the Model-View-Controller (MVC) paradigm, taking advantage on the plug-in based AI Bench framework (http://www.aibench.org)), which provides a clear separation of core libraries and GUI tools, facilitating the development of new features in the form of plug-ins.
  
'''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.'''
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== Institutions ==
  
'''@Note is implemented over [http://www.aibench.org/ <font color="#FF7800"> AIBench </font>], 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 &quot;friendly&quot; way.
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=== SilicoLife Lda. ===
  
'''Regarding operations, <font color="#FF7800">@Note sustains the general workflow of BioTM </font>, 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.'''
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'''[http://www.silicolife.com/ SilicoLife Lda.- Computational Biology Solutions for the Life Science]'''
 +
 +
[[Image:Logo_silico.png]]
  
== Institutions ==
 
  
 
=== University of Minho ===
 
=== University of Minho ===
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  [[Image:Logo_ceb.png||300px]]
 
  [[Image:Logo_ceb.png||300px]]
  
 +
== Powered By ==
 +
 +
[[Image:Aibenchlogo.png|150px]] [http://www.aibench.org  www.aibench.org]
 +
 +
 +
[[Image:mysql.png|150px]] [http://www.mysql.com/ www.mysql.com/]
 +
 +
 +
[[Image:H2-logo-2.png|150px]] [http://www.h2database.com/html/main.html www.h2database.com/]
  
=== SilicoLife Lda. ===
 
  
'''[http://www.silicolife.com/ SilicoLife Lda.- Computational Biology Solutions for the Life Science]'''
+
[[Image:Gate.png|150px]] [http://gate.ac.uk/ www.gate.ac.uk]
 
[[Image:Logo_silico.png]]
 
  
== Powered By ==
 
  
[[Image:Aibenchlogo.png]] [http://www.aibench.org www.aibench.org]
+
[[Image:CArrot.gif|150px]] [http://project.carrot2.org/ http://project.carrot2.org/]
  
[[Image:mysql.png]] [http://www.mysql.com/ www.mysql.com/]
 
  
[[Image:Gate.png]] [http://gate.ac.uk/ www.gate.ac.uk]
+
[[Image:Download_(1).png|150px‎]] [http://hibernate.org/ http://hibernate.org/]
  
[[Image:CArrot.gif]] [http://project.carrot2.org/ http://project.carrot2.org/]
 
  
[[Image:Download_(1).png‎]] [http://hibernate.org/ http://hibernate.org/]
+
[[Image:Download.png‎|150px]] [https://spring.io/ https://spring.io/]
  
[[Image:Download.png‎]] [https://spring.io/ https://spring.io/]
 
  
 
== License ==
 
== License ==
  
<br><font color="#FF7800"><b>Copyright 2016<br>
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<br><font color="#FF7800"><b>Copyright 2017<br>
 
[http://www.ceb.uminho.pt/ CEB - Centre of Biological Engineering]<br>
 
[http://www.ceb.uminho.pt/ CEB - Centre of Biological Engineering]<br>
 
[http://www.uminho.pt/ University of Minho]<br>
 
[http://www.uminho.pt/ University of Minho]<br>

Latest revision as of 15:49, 3 July 2017


Anote2spash.png
1258649492 label new red.png

All the code is available at Sourceforge and GitHub

@Note is 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

Introduction

The @Note project has been providing, over the last decade, open-source software libraries and tools addressing the most relevant tasks in the field of biomedical text mining (BTM). These tools have been developed as a collaboration between the Center of Biological Engineering from the University of Minho and the company SilicoLife, with the first version published in 2009.

The current version 2 provides a set of core libraries with a well-defined programming interface (API) addressing the main BTM tasks in both Information Retrieval (IR) and Information Extraction (IE). IR libraries include functions to query specific databases (e.g. Pubmed, patent databases), manage and update query results, download relevant documents, convert PDF to text, assign relevance and corpora management. Regarding IE, the main tasks are Named Entity Recognition (NER), Relationship Extraction (RE) and document clustering, being available several methods for all cases, with both in-house and third-party algorithms, including a machine learning (ML) workbench (BioTML) able to train and apply ML models to user created or existing datasets.

The main project libraries include: core - nuclear data structures and methods; processes - main processes for IR and IE; and machine learning - the framework for ML methods (training and prediction functions). These libraries make use of third-party software libraries in Java, including GATE, Mallet and Carrot. An API is provided allowing the use of the main methods by programmers in their applications, with appropriate examples being provided in the repository.

The project also provides @Note2, an end-user application, which provides user-friendly interfaces for the above listed functionalities, also including the creation of lexical resources (e.g. dictionaries) and a powerful curation environment for NER and RE annotations. The development of the @Note application follows the Model-View-Controller (MVC) paradigm, taking advantage on the plug-in based AI Bench framework (http://www.aibench.org)), which provides a clear separation of core libraries and GUI tools, facilitating the development of new features in the form of plug-ins.

Institutions

SilicoLife Lda.

SilicoLife Lda.- Computational Biology Solutions for the Life Science

Logo silico.png


University of Minho

University of Minho

Uminho.gif 

CEB

Centre of Biological Engineering

Logo ceb.png

Powered By

Aibenchlogo.png www.aibench.org


Mysql.png www.mysql.com/


H2-logo-2.png www.h2database.com/


Gate.png www.gate.ac.uk


CArrot.gif http://project.carrot2.org/


150px‎ http://hibernate.org/


Download.png https://spring.io/


License


Copyright 2017
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
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU Public License for more details.

You should have received a copy of the GNU Public License
along with this code. If not, see http://www.gnu.org/licenses/

Created inside the BISBII Research Group (http://ceb.uminho.pt/biosystems)
Supported by SilicoLife Lda. (http://www.silicolife.com)


Gpl.png http://www.gnu.org/licenses/gpl-3.0.html