GOssTo – the Gene Ontology Semantic Similarity Tool

What are GOssTo and GOssToWeb?

GOssTo and GOssToWeb are tools to calculate the semantic similarity between genes or terms in the Gene Ontology.

GOssTo is a command-line tool that can be run through an intuitive command-line interface or easily integrated as a library into a pipeline. It runs on Windows, GNU/Linux and MacOS. No installation is required. To use it, just download the file and run it.

GOssToWeb is a web enabled version of GOssTO – you can use it to calculate semantic similarities without the need to download and install the standalone version of GOssTO. Access GOssToWeb here.

Overview

Semantic similarity calculations aim to provide a quantifiable measure of functional relatedness of genes by assessing the similarity of the Gene Ontology terms with which they are annotated.

GOssTo and GOssTOweb implement an improved measure, developed by Yang et. al (Bioinformatics, 28, 10, 1383-1389, 2012) as well as several well-known measures, such as Resnik, Lin, Jiang, simUI.

Powerful extension capabilities were included in GOssTo, enabling the user to add new semantic similarity measures with little effort. If you have developed a new similarity measure for GOssTo, please submit it to support@paccanarolab.org. We will test it and include it in the next release. Please refer to the manual for an in-depth explanation on how to extend GOssTo.

GOssTo was developed in collaboration with Professor Valentini‘s group from the Informatics Department of the University of Milan.

The one-minute guide to using GOssTo

This is a small step-by-step guide to getting GOssTo up and running. For a full description of all available options, please refer to the manual.

1. Download and run GOssTo. Stable version (1.0)
2. Input the Gene Ontology OBO file and the desired organisms GOA annotation file.
3. Select “n” to load the default evidence codes “EXP, IDA, IPI, IMP, IGI, IEP, TAS, IC”.
4. Select “t” for termwise calculations.
5. Choose “1” for Resnik’s. This is the measure GOssTo will improve.
6. Select “4” to use all the ontologies (Biological Process, Molecular Function and Cellular Component)
7. Select “n” for the complete set of similarity measures
8. Select “n” to obtain the base similarity measure as well as the improved one.
9. Select the file names to store the results.

References

H. Caniza, A. E. Romero, S. Heron, H. Yang, A. Devoto, M. Frasca, M. Mesiti, G. Valentini, and A. Paccanaro
GOssTo: a user-friendly stand-alone and web tool for calculating semantic similarities on the Gene Ontology
Bioinformatics, vol. 30, iss. pp. 2235-2236, 2014.

H. Yang, T. Nepusz, and A. Paccanaro
Improving GO semantic similarity measures by exploring the ontology beneath the terms and modelling uncertainty
Bioinformatics, vol. 28, iss. 10, pp. 1383-1389, 2012.