search

EBISPOT / zooma

ZOOMA - Optimal Ontology Mapping Application. http://www.ebi.ac.uk/spot/zooma.
Apache License 2.0
24 stars 11 forks source link

readme

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).

Deploying with Docker

The preferred method of deployment for ZOOMA is using Docker. If you would like to deploy the entire OntoTools stack (OLS, OxO, and ZOOMA), check out the OntoTools Docker Config repository. If you would like to deploy ZOOMA only, read on

First, create the necessary volumes:

docker volume create --name=zooma-config

Then, start ZOOMA:

docker run -d --name zooma -p 8009:8080 -v zooma-config:/root/.zooma/config ebispot/zooma:stable

You should now be able to access ZOOMA at http://localhost:8009.

To configure ZOOMA, first stop the docker container:

docker stop zooma

The configuration files will be located in the zooma-config volume on your filesystem. For Ubuntu, this will be located at /var/lib/docker/volumes/zooma-config/_data.

Once configured, start ZOOMA again:

docker start zooma

Building ZOOMA manually

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.