Primary goal: to have the semantic search available for BBMRI catalog

1. Get access to ​http://gbic.target.rug.nl:8080/ (DONE)
2. Added user at tomcat file , still cannot have access. Maybe should be in another file?
3. scheduled meeting with Eric to set it up through his account.

• reintegrate the semantic search plugin and all dependencies - despoina

1. Add the semantic plugin as a plugin inside the bbmri @pheno

1. First locally
   1. 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)
   2. Install semantic search in bbmri :
      1. Check if plugin file exists ...ok (DONE)
      2. Check for configuration file if exists (DONE)
      3. Adapt connection variables between code & configuration . Some removed , some added, some more documenattion added. (DONE) .
      4. Check for configuration variables.
         1. Change index location . (DONE)
         2. Change the database field names that are used for the index . (DONE)
      5. (check other dependencies for manual file ) (DONE)
      6. when ready recreate both indexes to see if the are valid created. (DONE)
      7. create ontocat index (by running particular java file) (DONE)
      8. === search examples : search and ensure results make sense :Search for each table that have contents that make sense (to search) ===

1. Biobank :
   • "Agnes" (a name),
   • "HIV" (from description),
   • "musculoskeletal" (word inside description),
   • "EU-PACT-NL" found only with quotes.

1. then upload to gbic server .

• make sure that the search results make sense, i.e., list of features | biobank name - despoina
• make from each element in this list a link to the right biobank (if you get stuck wait) - despoina