== Biomart API for Cytoscape ==

=== Use Case ===

 * ''I have a network in Cytoscape session and want to import some attributes ONLY FOR genes which exists on current network.''
 * ''I want to import ID conversion table from Ensemble Gene ID to HGNC Symbol for all human genes'' 

=== Function Request ===
 
 * Cytoscape sends list of IDs/terms as a query.  This list should be included returned data table.  Otherwise, Cytoscape cannot map any attributes.
 * Cytoscape BioMart client needs nicer GUI just like ''MartView'' web UI.
    * Need to create category-oriented list of attributes.
    * Need to tell user Max-selectable value

=== Desired API ===
{{{
public interface BioMartUtil {
	

	public Collection<String> getMartList(URL martLocation);
	
	public Collection<String> getIDListFilter(String martName);
	public Collection<String> getBooleanListFilter(String martName);
	
        // Simply returns list of entry as table.  FIRST COLUMN IS ALWAYS ID LIST SENT AS QUERY.
	public Collection<String[]> getResult(Query query);
}

}}}

=== Implementation Plan ===
 * REST API does not support some of the metadata, such as sub-category of attributes and filters
 * To extract those metadata fields, I need to use SOAP.  However, SOAP has some overhead and not as efficient as REST.

==== Solution ====
 * For building user interface, use SOAP.  Then the client has full-access to the metadata.
 * Send actual Query through REST.  This is faster than SOAP.