Morphbank LSID Resolver

Coordinator(s): GregRiccardi

Participants:

Description

Technical Information

• URL for prototype user interface: not ready yet
• *LSID authority(ies): morphbank.scs.fsu.edu, will eventually be morphbank.net
• *LSID namespace(s): morphbank, images
• Hardware platform: (Intel, Sun, etc - include complete specs: processors, amount of RAM, disk, SCSI, ATA, SATA, RAID, etc)
• Server platform: Linux w/ Tomcat 5.5.17
• LSID Software stack used: Java 5
• RDF/OWL ontology used for metadata: Using a prototype Darwin Core 2 vocabulary for specimen information.
• Approximate number of LSIDs stored: 30,000
• Other resources: Hibernate 3.1, Mysql, Jena RDF packages

Roadmap, Milestones, Timeline

(Enter one task per line with estimated time for completion. Check tasks when completed, but leave all entries for logging purposes) Example:

• Mar/06 - Set up webserver
• Apr/06 - Install LSID server stack and map data tables
• May/06 - Successful installation of LSID services for image metadata

Discussion, Implementation Issues

(List issues, readblocks, missing software components, etc)

The MorphBank? LSID authority is built using Java technologies.

• LSID services use the LSID server packages.
• Data access to the MorphBank? Mysql database uses the Hibernate object-relational mapping packages.
• Metadata generation uses the Jena RDF packages.
• The services are installed in Tomcat 5 on a Linux platform.

Lessons Learned, Conclusions, Recommendations

We initially had problems with the LSID Java system. Once we got it configured properly, with the correct jar files and services, it has worked well.

Similarly, the Hibernate tools for database access in Java have been a mixed blessing. Now that we understand how to create and manage the mapping files, we have an excellent foundation for providing LSID/Web service access to the entire MorphBank? repository.

Development was done using the Eclipse IDE on a Windows XP platform. Eclipse includes plugins to manage Tomcat installations, SVN code repositories, Hibernate tools. The Java development environment is truly excellent and and includes support for source code management including moving and renaming of methods, classes, and other Java objects.

The final movement of the code to the Linux Tomcat installation was held up by a problem with the interaction between Tomcat and Hibernate that does not occur on Windows.

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