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ReadMe.md

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Ontologizer

Ontologizer is a tool for identifying enriched Gene Ontology terms in lists of names of genes or gene products. It is available as a Java program for both UI and command line usage as well as JavaScript version that can be conveniently run in modern Web browsers. Look at http://ontologizer.de for details and binary distribution.

Building

Ontologizer's build process is driven by Maven. You also need to install '''pandoc''' (https://pandoc.org/) before proceeding, as this is not handled by Maven. After cloning and checking out the source repository via

$ git clone --recurse-submodules https://github.com/sba1/ontologizer

you can start the build procedure via

$ cd ontologizer.parent
$ mvn package

When the build breaks due to bugs in Javadocs, add -Dmaven.javadoc.skip=true to the previous command and file an Issue. Similiary, if tests break the build you can add -DskipTests to skip the execution of the tests.

If successful, the command line version can be found in ontologizer.cmdline and the UI version in the ontologizer.gui modules in the respective target folders.

For instance, still being in the ontologizer.parent folder, you can start the GUI version by

$ cd ../ontologizer.gui/target
$ java -jar Ontologizer-jar-with-dependencies.jar

The Ontologizer-jar-with-dependencies.jar includes all dependencies, incl. SWT for your platform.

API - ontologizerlib

The core of Ontologizer can be in principle used by other applications, although the API is rather dumb. Please have a look at the https://github.com/ontologizer/ontologizerlib for the library project. The project is currently used in Ontologizer via directly importing the source. This simplifies the coordinated development of both projects.

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Ontologizer is a tool for identifying enriched Gene Ontology terms in lists of names of genes or gene products.

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