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Table 2 Comparison of biological information integration softwares.

From: Biana: a software framework for compiling biological interactions and analyzing networks

  Feature BI PI AP AP2 BN UH MI ON iRI
Data types Supports multiple biomolecule types (protein, gene, compound...) X     X   X X  
  Supports multiple relation types (interaction, complex, pathway...) X     X X X X  
  Supports multiple data descriptor/identifiers types X X X X X X   X X
  User extensible to new user defined data types and attributes X         
Data Unification User specific data unification X        (1)  
  Standard user can extend to new data repositories X        (1)  
User Interface Standalone Graphical Interface      X    X  
  Scripting/Command line X X    X    X  
  Provides a webserver X   X   X X X   X
  Provides a plugin for Cytoscape X    X    X   X
Network analysis Adds network analysis methods X X    X    X  
Availability Open Source X X    X    X  
Installation Does not require additional software    X X   X X X X
  Standalone application (runs locally) X X    X    X  
  1. BIANA has been compared with other biological databases integration software/webservers. Compared software: PI, PIANA [13]; AP, APID [15]; AP2, APID2NET [66]; BN, BNDB [14]; UH, UniHI [67]; MI, MIMI [68], ON, ONDEX [18], iRI, iRefIndex [19]. (1)According to the original manuscript, "The installation and use of the data integration methods is still command line driven and requires technical expertise to install, configure and use this component of the ONDEX system".