Category: Publications || File ID: 50 || Last changed on: 2008-06-26 21:52:14+01

MOLGENIS integration demo for JAX Mouse Phenome Database

This page holds supplementary materials on the MOLGENIS web service wrappers for the JAX Mouse Phenome Database:
http://gbicserver1.biol.rug.nl:8080/molgenis4mpd/soap/api?wsdl

Introduction:

The MOLGENIS for the Mouse Phenome Database was created as part of a CASIMIR pilot studie to demonstrate how (parts of) existing databases can be made accessible in a standardized way using the MOLGENIS toolkit, BioMART and Taverna. The generation of MOLGENIS web services eases integration and interoperation using standard workflow tools like Taverna. The pilot has been described in a recently submitted paper (expect details soon).

Results:

The MOLGENIS wrapping resulted in the following results:

A standardized web service interface is generated using MOLGENIS: http://gbicserver1.biol.rug.nl:8080/molgenis4mpd/soap/api?wsdl
Also a graphical user interface is generated using MOLGENIS*: http://gbicserver1.biol.rug.nl:8080/molgenis4mpd/*.do
The MOLGENIS MPD has been integrated with BioMART and KEGG via an integrative Taverna workflow: http://www.myexperiment.org/workflows/126
A java server application WAR file for local installation is also available for download. See this myExperiment pack for more information: http://alpha.myexperiment.org/files/36

Materials:

The following materials have been used:

The original Mouse Phenome data from http://phenome.jax.org/phenome
MOLGENIS biological software generator from http://www.molgenis.org
The MPD database design described in MOLGENIS" domain specific language: http://gbicserver1.biol.rug.nl:8080/molgenis4mpd/mpd.xml

Procedure:

The MOLGENIS wrapper around the Mouse Phenome Data has been generated as follows:

The MPD data was downloaded as files from the MPD downloadcenter: http://phenome.jax.org/pub-cgi/phenome/mpdcgi?rtn=docs/downloadcenter

The structure of, and relationships between, these files was described in MOLGENIS little language as shown here: http://gbicserver1.biol.rug.nl:8080/molgenis4mpd/mpd.xml
This definition was checked against MPD documentation: http://phenome.jax.org/pub-cgi/phenome/mpdcgi?rtn=snps/download .

From this description the working software was generated using the open source MOLGENIS generator.

The principle of this strategy is described in Swertz & Jansen (2007) Nature Reviews Genetics 8, p235-243: http://www.nature.com/nrg/journal/v8/n3/abs/nrg2048.html

A simplified demonstrator (without "APIs") showing how that works is available here: http://gbic.biol.rug.nl/supplementary/2007/molgenis_showcase

The data was imported from files using the programmatic interface of the generated software.
This required a file like this: http://gbicserver1.biol.rug.nl:8080/molgenis4mpd/ImportFromFiles.java

Note: currently only the SNPs from the snp_48strains_b37.zip and Celera have been imported. Other SNP sources will follow.

NOTE: this tool is for demonstration purposes. It can be used to support your research but be aware that there may be errors. *The user interface was not designed to handle large data and can take up to a minute on first usage.

Email m.a.swertz@rug.nl for question and suggestions.