Adding an extension for germplasm, GBIF IPT

The GBIF Provider Toolkit (IPT) is a database wrapper to help the provider of biodiversity information to set up and provide these data as a web service. The primary data exchange standard deployed by the GBIF IPT is the Darwin Core standard maintained by the Biodiversity Information Standards (TDWG).

http://code.google.com/p/gbif-providertoolkit/
http://code.google.com/p/darwincore/

Below are the steps I followed to develop a draft germplasm extension to the Darwin Core (DwC) standard, and next to add this draft DwC extension to the GBIF IPT software. You may follow the same steps to develop your own extension and to add this to the GBIF IPT.

If you are interested, you may visit the IPT from NordGen with a DEMO dataset mapped to terms from this DRAFT Darwin Core extension for germplasm at:
http://ipt.nordgen.org/ipt/occResource.html?resource_id=77

Summary of steps:

1. Schema
I built a suggestion to a DRAFT Darwin Core extension for germplasm
http://code.google.com/p/darwincore/source/browse/trunk/xsd/profiles/germplasm/dwc_germplasm_0_1.xsd
http://rs.nordgen.org/dwc/germplasm/0.1/dwc_germplasm_0_1.xsd

2. XML definition for IPT
Listing the terms to use from the suggested DRAFT DarwinCore extension
http://rs.nordgen.org/dwc/germplasm/0.1/ipt_germplasm_0_1.xml

3. Add this XML definition to a copy of extensions.json
Starting with: http://gbrds.gbif.org/registry/ipt/extensions.json
Add text {"title":"Germplasm","url":"http://rs.nordgen.org/dwc/germplasm/0.1/ipt_germplasm_0_1.xml","id":9}
Saved as: http://rs.nordgen.org/rs/ipt/extensions.json

4. Modify ipt.properties
PATH_TO_TOMCAT_WEBAPPS/ipt/WEB-INF/classes/ipt.properties
Line 7: "registryUrl=http://gbrds.gbif.org/registry" modified to
"registryUrl=http://rs.nordgen.org/rs"

5. Restart Tomcat (reload ipt)
The new ipt.properties settings does not seem to be loaded without restart of tomcat

6. Add/load the new extension to IPT
Login with admin permissions
http://your-ipt-service-url/ipt/admin/extensions.html
Click "Check for all available extensions"
Select the name of the new extension
Select "install" and "Done"

7. Mapping of terms to your data
Select the new extension under "Add New Mapping"
Click "Add" button to the right
Select and map terms

Remarks:

The IPT will contact the registry as defined in "ipt.properties". By default the GBIF registry in Copenhagen is defined here, but you may modify this to point to your own registry. I did not mimic the complete features of the registry - ONLY the list of extensions "extensions.json" to add the new draft germplasm extension I made. You may want to add your own thesaurus "thesauri.json" of controlled vocabulary or more features in the similar way. After loading my new extension to my IPT at NordGen, I modified the "properties.ipt" back to point to the GBIF registry in Copenhagen again.

To mimic the registry feature for adding the extension, I made a copy of the file from http://gbrds.gbif.org/registry/ipt/extensions.json and added my application schema from the extension as you will see at http://rs.nordgen.org/rs/ipt/extensions.json.

The application schema (as defined in "extensions.json") and online from: http://rs.nordgen.org/dwc/germplasm/0.1/ipt_germplasm_0_1.xml, creates a namespace (for the use by IPT) as well as includes the URL for the actual draft germplasm extension I made:

http://rs.nordgen.org/dwc/germplasm/0.1/ http://rs.nordgen.org/rs/dwc/germplasm/0.1/dwc_germplasm_0_1.xsd

The application schema itself (ipt_germplasm.xml) only lists the terms I want to use in IPT, with the property name to be displayed in the IPT mapping interface. To create this file I started with one of the other extensions http://gbrds.gbif.org/resources/extensions/vernacularName.xml. I just made a copy of this file and replaced the names and terms for vernacular name extension with the terms I wanted from the draft germplasm extension.

NB! This DRAFT extension for germplasm is still under development and I am sure that I still duplicate some terms from DarwinCore or perhaps other extensions! I did not yet work much with the terms for trait observations on germplasm, but added most of the terms from the new proposed draft standard for these data for the European genebank community.