SeedPod

SeedPod is Hao's thesis project.

It takes a Protégé knowledge base and creates an Experiment Mangement System (EMS) including a relational database with a webapp frontend. More information can be found in SIG project page at http://sig.biostr.washington.edu/projects/seedpod/

Latest code being worked on by joshuadf is at source:seedpod/trunk/seedpod.

Status

As of March 2008, the transformation works well but must be run from the command line.

Unfortunately Protege has no "read-only" projects, so the files change whenever they are opened. For this reason I recommend copying a project from the seedpod/KnowledgeBase/ directory so that the large project files are not frequently committed to SVN.

Here is how from the command line: 

svn co svn+ssh://trac.biostr.washington.edu/src/seedpod/trunk/seedpod latestseedpod
cd latestseedpod
cp KnowledgeBase/test2* /tmp/
ant compile
java -cp build/classes:WebContent/WEB-INF/lib/protege32b355.jar edu.washington.biostr.sig.seedpod.kb2db.Application /tmp/test2.pprj somename /tmp/

You should end up with these SQL files which you can put in a PostgreSql database: 

/tmp/test2_metadata.sql
/tmp/test2_postgresql.sql

If you want to edit the Protege project, I recommend using http://protege.stanford.edu/download/old-releases/3.2/full/

Development

What you need:

Add the location svn+ssh://trac.biostr.washington.edu/src/ then expand seedpod/trunk/seedpod and right-click to check out. Eclipse will find the project files and configure it in your workspace. Right click and go to Run->Run on Server... and tell it where your Tomcat installation is located. It should then start up at http://localhost:8080/seedpod/

Older Seedpod Versions

There is a Single-Unit Recording EMS demo.

Older code:

  • 2007 December seedpod2.0 - this is what Hao has on her laptop. She may commit something which joshuadf will port to the trunk.
  • 2006 source:KBtoDB converts the Protégé KB into a relational schema and a template for a webapp frontend
  • 2005 version in CVS: src/brain/seedpod