ZOOMA

ZOOMA is an optimal ontology mapping application developed by the Functional Genomics Production team at the European Bioinformatics Institute.

This is the publicly available code repository for ZOOMA. Currently, this only includes the core libraries for ZOOMA - there are no generic user interface implementations available, only the EBI internal version that is visible at the homepage listed below. We're in the process of adding support for building customized versions of ZOOMA with your own data, and we will update these pages when this is available.

Developer documentation is available as part of the ZOOMA documentation at the link given below. If you can't find what you need there, feel free to email the lead developer, Tony Burdett, on tburdett@ebi.ac.uk.

Links

ZOOMA homepage

http://www.ebi.ac.uk/spot/zooma

ZOOMA documentation

http://www.ebi.ac.uk/spot/zooma/docs

EBI

http://www.ebi.ac.uk

Dependencies

Project Dependencies

ZOOMA depends on the lodestar project to produce it's SPARQL endpoint. The source for this project is embedded as a submodule, served from the GitHUb repository https://github.com/EBISPOT/lodestar. See this project for more details. When building from source, the latest version of this codebase will be incorporated into the build.

Software Dependencies

1. Java - Tested on Oracle JDK version 1.8
2. Maven - Tested using Maven 3.6
3. Virtuoso - Tested on the open source version of Virtuoso 7.2.5 which can be downloaded from http://vos.openlinksw.com/owiki/wiki/VOS/VOSDownload.
4. Solr

Building Zooma

Zooma requires ojdbc6.jar version 11.2.0.X for which there is no maven repository. Hence, one needs to download the file from Oracle and install it manually into a Maven repository. The steps to do this are:

1. Download ojdbc6.jar from http://www.oracle.com/technetwork/apps-tech/jdbc-112010-090769.html. The version number of the driver is given at the top of the page as 11.2.0.X. At the time of writing the actual value for X is 4. Thus the full version number is 11.2.0.4.

2. Install the ojdbc6.jar file into a Maven repository. The command below installs the file into the local Maven repository(Assuming X=4): mvn install:install-file -DgroupId=com.oracle -DartifactId=ojdbc6 -Dpackaging=jar -Dversion=11.2.0.4 -Dfile=PATH_TO_THE_JAR_YOU_DOWNLOADED/ojdbc6.jar

You should get a 'Build Success' message and the library should be installed under your mvn repository:

~/.m2/repository/com/oracle/ojdbc6/11.2.0.4/ojdbc6-11.2.0.4.jar

Once the ojdbc6.jar file has been installed into the Maven repository, Zooma can be built from its root directory be using:

mvn clean package

Configuring Zooma

Once Zooma has been built, a zooma-builder.zip can be found under /zooma/zooma-builder-app/target. This contains the application for setting up zooma. Extract zooma-builder.zip and navigate to /zooma-builder/bin/README. This file contains important information on configuring Zooma and the order in which various scripts must be run.

1. Add the environment variables as described in /zooma-builder/bin/README.

2. To deploy the zooma web application to Tomcat, navigate /zooma/zooma-ui/target and copy the zooma.war to the /webapps directory of Tomcat. This will create the template config under $ZOOMA_HOME. Stop Tomcat.

3. Run the scripts under Execution in /zooma-builder/bin/README.