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
- 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 )
-
- then upload to gbic server .
- make from each element in this list a link to the right biobank (if you get stuck wait) - despoina
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