On this page you will find:

• For each menu item its documentation (Click on the menu item):
      
• The documentation for the entity popup menu
• The documentation for the entity-link (relation) popup menu
• The documentation for the source-entity popup menu
• The documentation for the source-entity link (cross-reference) popup menu

• Open: Allows you to load a new configuration file.
• Save As: Allows you to save your configuration in the BioGuide configuration file.
• Print entities graph: prints a picture of the graph of entities.
• Quit: Quit BioGuide.

• Query strategy: Please consult the querying process documentation.
• Run query: Run the query and open the results window
• Clear query: Erase all the selections, filters ... It will create a new query (but will keep all your preferences).
• BioGuide benchmarking: This menu item is dedicated to BioGuide advanced administrators.

• Filter on sources-entities: Set filters intervals based on sources-entities preferences. More information.
• Filter on path length: Set a minimum and maximum path length value. More information.
• Kind of links to follow: More information.

To understand how to use this menu, please consult the page dedicated to the querying process

• "Show non biological links?" allows you to see or not to see non-bio-links
• "Show tool links?," allows you to see or not to see tools-links
• "Show Sources internal links?" allows you to see or not to see links between sources-entities related to the same source (in the graph of sources-entities).
• "View full Sources-Entities graph": allows you to visualize the whole graph of sources-entities in a new frame.

• Entity: Allows you to manage an entity. You can
  • Add a new entity: specify its name.
  • Update an entity: click first on this entity and then modify its name.
  • Delete an entity: click first on this entity and then click on this menu to delete the corresponding entity.
• Entity Link: Allows you to manage a link between entity. You can
  • Add a new link: click on the two entities to be linked, then click on this item and specify the name of the link and its type.
  • Update a link: click first on the link and then on this menu for modifying its properties.
  • Delete a link: click first on the link and then click on this menu to delete the corresponding link.
• Source-Entity: Allows you to manage a source-entity. You can
  • Add a new source-entity: click on the entity first then click on this item and specify the name source.
  • Delete a source-entity: click first on the source-entity and then click on this menu to delete the source-entity.
• Source-Entity link: Allows you to manage a link between two sources-entities . You can
  • Add a new links: click on the two sources-entities and click on the entity link you want to consider. Then click on this item.
  • Delete a link of sources-entities: click on the link to delete and then click on this menu.

Need to add a new source?
This feature is currently not available using the Model menu but can easily be performed following these instructions:

1. Download the configuration file.
2. Edit this file and add a line  in the sources list (at the very beginning of the file). For example, to add the source Unilib just add 
   <SOURCE name="UNILIB" /> in the list. Please make sure that you spell the source name as it is spelt in the SRS server you use.
3. Save the file and open it in BioGuideSRS (see the File menu)
4. This source is now available for use, you can choose the entities it contains, add cross-references and/or preferences on it, as described in the Preferences and Model menus above.

See the list of the sources available at the SRS EBI server.
Want to use another SRS server? See the Option menu.

• Show reflexive entity links: You can choose to hide the relations that link an entity to itself in the entities graph.
• Popup messages: If this option is unchecked, error or warning messages will only be added to the "status bar" (no more popups).
  Remark: Due to some restrictions with Applets we can't force the popups to stay behind the main window if the user clicks in the main window.
• Graph layout algorithm: If the positions are not defined for sources-entities (when you change the model for example) or if you use the automatic positioning button, an layout algorithm is applied. Here you can switch between the complex layout algorithm (Organic) and a very basic one that will for a circle with sources-entities.
• Activate SRS: Whether the SRS extension to BioGuide must be activated
• Set SRS base URL: Set the SRS server to use.