wiki:BBMRI_task2

Version 28 (modified by antonak, 15 years ago) (diff)

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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

Add user authentication 

  • bbmri_ui : (done)  *