wiki:DespoinaLog/2010/04/28

Version 1 (modified by trac, 14 years ago) (diff)

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HVP pilot & Lucene on Ontologies

HVP pilot add functionality for retrieving from OntoCat

  • Added function for inserting an element (li) for each result returned form ontocat (hvp_pilot: search module).
  • Problem with tomcat : "Several ports (8080, 8009) required by Tomcat v6.0 Server at localhost are already in use. The server may already be running in another process, or a system process may be using the port. To start this server you will need to stop the other process or change the port number(s)."
    • Delete "Clean Tomcat Work Directory" , "Delete Server", Restart, does work
      • Need or a Line Port scanner
        • Available in macox in command line ! : /Applications/Utilities/Network? Utility.app/Contents/Resources/stroke * or open from Applications :
          • enter 127.0.0.1 & number of ports (not necessary)
      • ..or
        • ps -ax | grep apache
        • kill -9 <process_number>
  • Other functionality added. (svn commit)

Ontology resources in files :

Resources :

http://www.berkeleybop.org/ontologies/

http://www.obofoundry.org/index.cgi?show=mappings

http://www.obofoundry.org/

Create a Lucene Index (command line) using on the above ontologies

Test : Create an index with lucene in parent directory : Ontologies : ontologies & mappings between ontologies :

  • * java org.apache.lucene.demo.IndexFiles /Users/despoina/Documents/Ontologies/
  • OK index build
  • * java org.apache.lucene.demo.SearchFiles
  • Enter query:
    • glioblastoma
    • Searching for: glioblastoma
    • 2 total matching documents
    • 1. /Users/despoina/Documents/Ontologies/ontologies/BrendaTissueOBO.txt
    • 2. /Users/despoina/Documents/Ontologies/ontologies/pro.obo.txt
    • Press (q)uit or enter number to jump to a page. *