| | 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 : == |
| | 29 | http://www.berkeleybop.org/ontologies/ |
| | 30 | |
| | 31 | http://www.obofoundry.org/index.cgi?show=mappings |
| | 32 | |
| | 33 | http://www.obofoundry.org/ |
| | 34 | |
| | 35 | == Create a Lucene Index (command line) using on the above ontologies == |
| | 36 | Test : 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. * |
