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ZOOMA

ZOOMA is an application for discovering optimal ontology mappings, developed by the Samples, Phenotypes and Ontologies Team at EMBL-EBI. It can be used to automatically annotate "properties" (plain text, descriptive values about biological entities) with "semantic tags" (ontology classes).

Links

ZOOMA homepage

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

ZOOMA documentation

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

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.