Changes between Initial Version and Version 1 of DespoinaLog/2010/04/28


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Timestamp:
2010-10-01T23:19:13+02:00 (14 years ago)
Author:
trac
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  • DespoinaLog/2010/04/28

    v1 v1  
     1= HVP pilot & Lucene on Ontologies  =
     2== HVP pilot add functionality for retrieving from !OntoCat ==
     3 * Added function for inserting an element (li) for each result returned form ontocat (hvp_pilot: search module).
     4 * 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)."
     5   * Delete "Clean Tomcat Work Directory" , "Delete Server", Restart, does work
     6     * Need or a Line Port scanner
     7       * Available in macox in command line ! : /Applications/Utilities/Network Utility.app/Contents/Resources/stroke       * or open from Applications :
     8         * enter 127.0.0.1 & number of ports (not necessary)
     9     * ..or
     10       * ps -ax | grep apache
     11       * kill -9 <process_number>
     12 * Other functionality added. (svn commit)
     13== Links ==
     14 * http://www.ebi.ac.uk/Rebholz/
     15   * http://www.ebi.ac.uk/webservices/whatizit/info.jsf
     16   * http://www.ebi.ac.uk/Rebholz-srv/ebimed/index.jsp
     17   * http://www.ebi.ac.uk/Rebholz-srv/pcorral/advancedSearch.jsp
     18 * http://genomebiology.com/2005/6/7/224
     19
     20== Ontology resources in files : ==
     21   * http://www.semanticdesktop.org/ontologies/nfo/
     22   * http://dev.nepomuk.semanticdesktop.org/wiki/LuceneSail
     23     * Tool: LuceneSail: http://dev.nepomuk.semanticdesktop.org/wiki/LuceneSail
     24 * http://bioportal.bioontology.org/ontologies/39002 & owl ---> protege
     25 * * http://www.sequenceontology.org/resources/faq.html#ovcv
     26 * The feature vector : http://www.ncbi.nlm.nih.gov/collab/FT/index.html
     27
     28== Resources : ==
     29http://www.berkeleybop.org/ontologies/
     30
     31http://www.obofoundry.org/index.cgi?show=mappings
     32
     33http://www.obofoundry.org/
     34
     35== Create a Lucene Index (command line) using on the above ontologies ==
     36Test : Create an index with lucene in parent directory : Ontologies  : ontologies & mappings between ontologies :
     37
     38 * * java org.apache.lucene.demo.!IndexFiles /Users/despoina/Documents/Ontologies/
     39 * OK index build
     40 * *  java org.apache.lucene.demo.!SearchFiles
     41 * Enter query:
     42   * glioblastoma
     43   * Searching for: glioblastoma
     44   * 2 total matching documents
     45   * 1. /Users/despoina/Documents/Ontologies/ontologies/BrendaTissueOBO.txt
     46   * 2. /Users/despoina/Documents/Ontologies/ontologies/pro.obo.txt
     47   * Press (q)uit or enter number to jump to a page. *