= 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
   * Press (q)uit or enter number to jump to a page. *