Changes between Version 2 and Version 3 of SeedPod


Ignore:
Timestamp:
03/14/08 11:44:45 (11 years ago)
Author:
joshuadf
Comment:

--

Legend:

Unmodified
Added
Removed
Modified
  • SeedPod

    v2 v3  
    1 SeedPod is Hao's thesis project.  
     1= SeedPod =  
     2 
     3Seed``Pod is Hao's thesis project.  
    24 
    35It takes a [http://protege.stanford.edu/download/download.html Protégé] knowledge base  
    46and creates an Experiment Mangement System (EMS) including a relational database 
    5 with a webapp frontend.  
     7with a webapp frontend. More information can be found in SIG project page at  
     8http://sig.biostr.washington.edu/projects/seedpod/ 
     9 
     10Latest code being worked on by joshuadf is at source:seedpod/trunk/seedpod. 
     11 
     12== Status == 
     13 
     14As of March 2008, the transformation works well but must be run from the 
     15command line.  
     16 
     17Unfortunately Protege has no "read-only" projects, so the files  
     18change whenever they are opened. For this reason I recommend 
     19copying a project from the `seedpod/Knowledge``Base/` directory  
     20so that the large project files are not frequently committed to SVN. 
     21 
     22Here is how from the command line: 
     23{{{ 
     24svn co svn+ssh://trac.biostr.washington.edu/src/seedpod/trunk/seedpod latestseedpod 
     25cd latestseedpod 
     26cp KnowledgeBase/test2* /tmp/ 
     27ant compile 
     28java -cp build/classes:WebContent/WEB-INF/lib/protege32b355.jar edu.washington.biostr.sig.seedpod.kb2db.Application /tmp/test2.pprj somename /tmp/ 
     29}}} 
     30 
     31You should end up with these SQL files which you can put in a PostgreSql database: 
     32{{{ 
     33/tmp/test2_metadata.sql 
     34/tmp/test2_postgresql.sql 
     35}}} 
     36 
     37If you want to edit the Protege project, I recommend using 
     38http://protege.stanford.edu/download/old-releases/3.2/full/ 
     39 
     40== Older Seedpod Versions == 
     41 
    642There is a [http://sphenoid.biostr.washington.edu:8080/EMS/ Single-Unit Recording EMS demo]. 
    743 
    8 The code is in two parts: 
    9  * [http://trac.biostr.washington.edu/trac/browser/KB2DB source:KBtoDB] converts the Protégé KB into a relational schema and a template for a webapp frontend 
    10  * [http://sig.biostr.washington.edu/viewcvs/viewcvs.cgi/src/brain/seedpod/ src/brain/seedpod] is the webapp 
     44Older code: 
     45 * 2007 December [source:seedpod2.0] - this is what Hao has on her laptop. She may commit something which joshuadf will port to the trunk. 
     46 * 2006 [http://trac.biostr.washington.edu/trac/browser/KB2DB source:KBtoDB] converts the Protégé KB into a relational schema and a template for a webapp frontend 
     47 * 2005 version in CVS: [http://sig.biostr.washington.edu/viewcvs/viewcvs.cgi/src/brain/seedpod/ src/brain/seedpod] 
    1148 
    12 More information can be found in SIG publications at  
    13 http://sigpubs.biostr.washington.edu/view/projects/Seedpod.html