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.
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 supportatpaccanarolabdotorg. 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
GOssTo with example data
Stable version (1.0) Source code GITHub source repo
Access GOssTo online
GOssTo manual in PDF
Bug reports, feedback
Something’s not working? Do you think you found an error? Do you want to contribute to the development of GOssTo? Contact us!