DSS: Data Source Selection Algorithm

Intoduction

Sarah Cohen Boulakia, Séverine Lair, Nicolas Stransky, Stéphane Graziani, François Radvanyi, Emmanuel Barillot and Christine Froidevaux
Selecting biomedical data sources according to user preferences
In Proc. of ISMB/ECCB 2004, Bioinformatics, Vol 20, Suppl.1, pp. i86-i93

Running Applet

• To use the applet, you have to accept our security certificate.This certificate is necessary to let you save your preferences in XML files.
• If you cannot see the "Demo button", you probably need to download Sun Java Machine.

Some Documentation

Using this Applet

• Do a query:
  Click on the underlying* entities of your query (they are highlighted in red). Then, click on "Query" to open the "results" window. You can visualise the list of path-results ordered (with by default criteria order).
  *Example: the underlying entities of the query "Where is localised the BAC identified by CTD-2015 ?", are "LOCALISATION" and "BAC".
  
  
• Filter and sort answers:
  
  • Filter: Click on "Change" to open the query's preferences window.
    In the "ConfigPref" panel, configure which are the preferences to be taken into account in the results:
    
    • Length of paths: click on the first "configure" button and indicate the maximum number of cross-references that each path-solution may contain.
      Warning: remember that path length is defined as beeing the number of cross-references (links between entities inside the same source are not taken into account).
    • Focus: click on the second "configure" button and indicate the maximum number of banks consulted for another entity than their focus.
      
    • Unreliable links: click on the third "configure" button and indicate the maximum number of unreliable cross-references that each path-solution may contain.
      
    • Reliable banks: click on the forth "configure" button and by using the cursors indicate which is the maximum number of banks-entities of level-1 each path-solution must contained. Do the same for the level 2 to 10.
      
  • Sort: Click on "Change" to open the query's preferences window.
    In the "SortOrder" panel, choose with the "up" and "down" buttons in which order the different criterias of preferences have to be taken into account in the sort.
    
    
• Configure data banks and links:
  • Banks: Choose the "Configure" menu and the "Configure Banks" item.
    In the left side of the window, double-click on the bank you want to configure. Then, you can set new levels of reliability for all entities of a source (General panel) or be more specific and affect different levels depending on entities (Detail panel).
    
  • Links: Choose the "Configure" menu and the "Configure Banks" item.
    In the right side of the window, double-click on the bank from which the link to configure starts. Then, you can check which are the reliable links. Links can be configured globally: from all the entities of the selected source to all the entities of the others sources in the list (General panel) or more specifically at a bank-entity level (Detail panel).
    
    
• Save/Load data:
  • Save: Click on the "File" menu and choose the "Save" item.
    You can then save your configuration for further queries into an XML file.
    
  • Load: Click on the "File" menu and choose the "Load" item.
    You can then load an XML file from a previous configuration or load a new one (containing new banks, new entities, new links)...

XML File

• the whole description of query's user preferences
  • name of the preference, textual description, type (maximum length of paths, number of sources of level i (i from 1 to 10), number of unreliable links.)
  • minimum, maximum values, rating (way of understing distincts values)
• the whole description of sources
  • name of each source
  • focus (main entity)
  • list of entities contained and level of reliability of these entities
• the whole list of cross-references from one source-entity to another and level of reliability of these cross-references