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README.md

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Introduction

Welcome to GOssTo, the Gene Ontology Semantic Similarity Tool!

GOssTo is a software system for calculating semantic similarities between gene products in the Gene Ontology. GOssTo implements the Random Walk Contribution, improving the accuracy of similarity measures. For Yang's et. al description of the method:

  • Improving GO semantic similarity measures by exploring the ontology beneath the terms and modelling uncertainty, Bioinformatics, 28(10), pp. 1383-1389, 2012.

If you use GOssTo, please cite it.

  • GOssTo: an extendable stand-alone and web tool for calculating semantic similarities on the Gene Ontology, Bioinformatics, 30(15), pp. 2235-2236, 2014.

Also, check the Gossto paper website (https://paccanarolab.org/gossto) to get a thorough documentation, and to download a bundle with the jar a several example dataset (Gene Ontology, etc.).

Author labs' websites

These are the websites of the labs that contributed to Gossto.

Getting started

You can choose to run Gossto from the provided jar file (dist/Gossto.jar) or build it yourself. You can also download the jar file from the paper website.

Building Gossto

Prerequisites

Gossto was designed without many dependencies. If you want to build it from sources you will need:

  • Java (Java 5 or higher).
  • Ant (version 1.9 or higher).

There is one additional dependency (Apache Commons Cli), which will be resolved by the use of Apache Ivy. In the Gossto source we also included a modified version of Jama (https://math.nist.gov/javanumerics/jama/), using single float precision, as this is allowed by its public-domain license.

Using ant to build Gossto

In order to build Gossto, type

ant jar

This will first fetch all dependencies, compile the sources, and then build build/gossto.jar. That jar file is a 'fat jar', meaning that the generated file will not have any external dependency, and then, it will be easy to run in any system where a Java VM is available.

Running Gossto

Gossto can be run via the Gossto.jar file in two different manners:

  • Interactive way: just run
java -jar Gossto.jar

and follow the instructions.

  • Command-line way: options can be added after the Gossto.jar, such as:
java -jar Gossto.jar -calculationdata termwise -calculationtype ism -evidencecodes EXP,IDA,IPI,IMP,IGI,IEP,TAS,IC -goapath gene association.goa yeast -obopath gene ontology ext.obo -hsm Resnik -hsmoutput demo hsm output -ismoutput demo ism output -ontology all -relations is a,part of -weightedJaccard true -terms all

A full list of options can be checked via the java -jar Gossto.jar -help option.

Manual

There is a detailed manual on how to use Gossto, a FAQ, a list of possible errors, and several examples in the Gossto paper website: https://paccanarolab.org/gossto

License

Gossto is free software, released under the GNU General Public License (GPL) v3.0. A copy of it is made available in the LICENSE file.

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