Difference between revisions of "What´s new"

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'''General:'''
 
'''General:'''
−
• Eliminates dependency on Perl; fully implemented in Java; easier to install and run in different platforms
+
*Run Text miming workflows
−
• MySql database used to store all relevant information (including annotations); data model extended and re-organized to provide the core of the application
 
−
• Organization in a set of plug-ins taking advantage of AI Bench plug-in system; improves modularity; makes easier adding new functionality and alternatives for different processes
 
−
• Code was re-organized using Java interfaces for all relevant concepts and processes, making easier the integration of third party applications; MVC notions from AI Bench are better used to provide organized GUIs; core plug-ins define basic data structures and the interface of basic processes
 
−
• Indication of progress in time consuming processes
 
  
−
PubMedSearch
+
*Eliminates dependency on Perl; fully implemented in Java; easier to install and run in different platforms;
−
• Now a plug-in; new implementation more efficient based on eUtils.
 
−
• Query management system; larger number of options available
 
−
• Possibility of including external publications
 
−
• Possibility of updating the results of queries
 
−
• System to avoid publication crawling
 
  
−
Resources
+
*MySql or H2 embedded database are used to store all relevant information (including annotations); data model extended and re-organized to provide the core of the application;
−
• Better management of lexical resources (dictionaries, lookup tables, etc)
 
−
• Introduction of rules and ontologies
 
−
• More loaders and an interface allowing the easy implementation of new loaders
 
  
−
Corpus / corpora
+
*Organization in a set of plug-ins taking advantage of AI Bench plug-in system; improves modularity; makes easier adding new functionality and alternatives for different processes;
−
• Notion of corpus/ corpora added to @Note in a new plug-in
 
−
• Allows creating corpus from the publication manager
 
−
• Information extraction processes are-organized over corpora
 
−
• Corpus loader: Allows creating corpus from other available corpora (Genia Events, AIMED Protein and @NoteV1).
 
  
−
NER Resources
+
*Code was re-organized using Java interfaces for all relevant concepts and processes, making easier the integration of third party applications; MVC notions from AI Bench are better used to provide organized GUIs; core plug-ins define basic data structures and the interface of basic processes;
−
• Developed fully in Java and adapted to the new resources
 
−
• External NERs can be added with an easier interface
 
  
−
Curator
+
*Indication of progress in time consuming processes.
−
• Organized in a new plug-in
 
−
• Uses only HTML
 
  
 +
*Statistics and reports for all operation and datatypes
  
−
Relation
+
*Settings configuration system
−
• New Plug-in for Relation Extraction based in Natural Language processing
+
 
−
• Supports RE over corpora annotated by any NER
+
*Update System
 +
 
 +
'''Publication Manager'''
 +
*Add Patent document and Patent search
 +
*Add Springer search
 +
*PDF Retrieval from multiple sources
 +
*Query Update
 +
*Query Management system; larger number of options available
 +
*Possibility of including external publications manually
 +
*Publication Labeling and notes
 +
 
 +
'''Resources Manager'''
 +
*Better lexical resources management(dictionaries, lookup tables, etc)
 +
*Add Ontologies, rules ageneral lexical words (Stop Words)
 +
*More loaders and an interface allowing the easy implementation of new loaders
 +
 
 +
'''Corpora'''
 +
*Notion of corpus/ corpora added to @Note
 +
*Allows creating corpus from the publication manager
 +
*Allows creating corpus from PDF list
 +
*Information extraction processes are-organized over corpora
 +
*Corpus loader: Allows creating corpus from other available corpora (Genia Events, AIMED Protein and @NoteV1).
 +
*Manual curation of Relations
 +
 
 +
'''NER'''
 +
*Add and adapt Linnaeus Tagger algorithm
 +
*Add ABNER and Chenistry tagger (From Gate8)
 +
*External NERs can be added with an easier interface
 +
 
 +
 
 +
'''Relation'''
 +
* Add RE algorithms
 +
*Supports RE over corpora annotated by any NER Process
 +
*Relation Extraction based in Natural Language processing
 +
*Relation Co-occurrence
 +
*Kinetic RE
 +
 
 +
'''Workflow'''
 +
*Run Biomedical Text Mining workflows

Latest revision as of 14:26, 5 July 2017

Short list of what's new in @ Note2

Summary of features - Anote2 vs Anote

General:

  • Run Text miming workflows
  • Eliminates dependency on Perl; fully implemented in Java; easier to install and run in different platforms;
  • MySql or H2 embedded database are used to store all relevant information (including annotations); data model extended and re-organized to provide the core of the application;
  • Organization in a set of plug-ins taking advantage of AI Bench plug-in system; improves modularity; makes easier adding new functionality and alternatives for different processes;
  • Code was re-organized using Java interfaces for all relevant concepts and processes, making easier the integration of third party applications; MVC notions from AI Bench are better used to provide organized GUIs; core plug-ins define basic data structures and the interface of basic processes;
  • Indication of progress in time consuming processes.
  • Statistics and reports for all operation and datatypes
  • Settings configuration system
  • Update System

Publication Manager

  • Add Patent document and Patent search
  • Add Springer search
  • PDF Retrieval from multiple sources
  • Query Update
  • Query Management system; larger number of options available
  • Possibility of including external publications manually
  • Publication Labeling and notes

Resources Manager

  • Better lexical resources management(dictionaries, lookup tables, etc)
  • Add Ontologies, rules ageneral lexical words (Stop Words)
  • More loaders and an interface allowing the easy implementation of new loaders

Corpora

  • Notion of corpus/ corpora added to @Note
  • Allows creating corpus from the publication manager
  • Allows creating corpus from PDF list
  • Information extraction processes are-organized over corpora
  • Corpus loader: Allows creating corpus from other available corpora (Genia Events, AIMED Protein and @NoteV1).
  • Manual curation of Relations

NER

  • Add and adapt Linnaeus Tagger algorithm
  • Add ABNER and Chenistry tagger (From Gate8)
  • External NERs can be added with an easier interface


Relation

  • Add RE algorithms
  • Supports RE over corpora annotated by any NER Process
  • Relation Extraction based in Natural Language processing
  • Relation Co-occurrence
  • Kinetic RE

Workflow

  • Run Biomedical Text Mining workflows
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