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).
- Java - Tested on Oracle JDK version 1.8
- Maven - Tested using Maven 3.6
- 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.
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:
ojdbc6.jarfrom 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 22.214.171.124.
ojdbc6.jarfile 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=126.96.36.199 -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:
ojdbc6.jar file has been installed into the Maven repository, Zooma can be built from its root directory be using:
mvn clean package
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.
Add the environment variables as described in
To deploy the zooma web application to Tomcat, navigate
/zooma/zooma-ui/targetand copy the
/webappsdirectory of Tomcat. This will create the template config under
$ZOOMA_HOME. Stop Tomcat.
Run the scripts under Execution in