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)

Links

• ​http://www.ebi.ac.uk/Rebholz/
  • ​http://www.ebi.ac.uk/webservices/whatizit/info.jsf
  • ​http://www.ebi.ac.uk/Rebholz-srv/ebimed/index.jsp
  • ​http://www.ebi.ac.uk/Rebholz-srv/pcorral/advancedSearch.jsp
• ​http://genomebiology.com/2005/6/7/224

Ontology resources in files :

• ​http://www.semanticdesktop.org/ontologies/nfo/
• ​http://dev.nepomuk.semanticdesktop.org/wiki/LuceneSail
  • Tool: LuceneSail?: ​http://dev.nepomuk.semanticdesktop.org/wiki/LuceneSail

• ​http://bioportal.bioontology.org/ontologies/39002 & owl ---> protege
• * ​http://www.sequenceontology.org/resources/faq.html#ovcv
• The feature vector : ​http://www.ncbi.nlm.nih.gov/collab/FT/index.html

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
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