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