== '''Primary goal: to have the semantic search available for BBMRI catalog''' ==
 * Get access to http://gbic.target.rug.nl:8080/ (DONE)
 * Added user at tomcat file , still cannot have access. Maybe should be in another file?
 * scheduled meeting with Eric to set it up through his account.
 * '''reintegrate the semantic search plugin and all dependencies - despoina'''

== Add the semantic plugin as a plugin inside the bbmri @pheno ==
 * First locally

 * In order to  generate bbmri  we encountered some problem with the Entities  :   name="Contact"   and "Institute" . Conflict with existing entities in pheno model : <entity name="Contact" implements="Identifiable" xref_label="!FirstName,!LastName"> and <entity name="Institute" implements="Identifiable,Nameable" xref_label="name">. (DONE, generate success)
 * Install semantic search in bbmri :
   * Check if plugin file  exists ...ok (DONE)
   * Check for configuration file if exists (DONE)
   * Adapt connection variables between code & configuration . Some removed , some added, some more documenattion added. (DONE) .
   * Check for configuration variables.
     * Change index location . (DONE)
     * Change the database field names that are used for the index . (DONE)
   * (check other dependencies for manual file ) (DONE)
   * when ready recreate both indexes to see if the are valid created. (DONE)
   * create ontocat index (by running particular java file) (DONE)

== '''search examples ''' ==
 * ''' search and ensure results make sense :Search for each table that have contents that make sense (to search) (DONE)'''
   * Biobank :
     * '''Agnes (a name),'''
     * '''HIV (from description),'''
     * '''musculoskeletal (word inside description),'''
     * '''"EU-PACT-NL" found only with quotes.'''
     * '''smoking behaviour  (found in several tables)'''
     * '''cohort'''
     * '''gwas'''
     * '''Utrecht'''
   * Contact table contents CANNOT be found ..(TODO):
     * variable (field name & table name are correctly loaded from configuration file )
   * Institute
     * '''AMC, UMCG , Sanquin'''
   * Observable feature
     * '''GWA'''
   * ObservationTarget
     * '''UMCG-Asthma'''
   * ObservedValue
     * '''Hap550'''
   * Ontologyterm
     * '''Schizophrenia, Stroke, "Type 2 diabetes"'''
   * 
 * then upload to gbic server .
 * '''make from each element in this list a link to the right biobank (if you get stuck wait) - despoina'''