GOssTo: A stand-alone application and a web tool for calculating semantic similarities on the Gene Ontology

Horacio Caniza; Alfonso E. Romero; Samuel Heron; Haixuan Yang; Alessandra Devoto; Marco Frasca; Marco Mesiti; Giorgio Valentini; Alberto Paccanaro

doi:10.1093/bioinformatics/btu144

GOssTo: A stand-alone application and a web tool for calculating semantic similarities on the Gene Ontology

Horacio Caniza, Alfonso E. Romero, Samuel Heron, Haixuan Yang, Alessandra Devoto, Marco Frasca, Marco Mesiti, Giorgio Valentini, Alberto Paccanaro

Mathematics

Research output: Contribution to a Journal (Peer & Non Peer) › Article › peer-review

43 Citations (Scopus)

Abstract

Summary: We present GOssTo, the Gene Ontology semantic similarity Tool, a user-friendly software system for calculating semantic similarities between gene products according to the Gene Ontology. GOssTo is bundled with six semantic similarity measures, including both term- and graph-based measures, and has extension capabilities to allow the user to add new similarities. Importantly, for any measure, GOssTo can also calculate the Random Walk Contribution that has been shown to greatly improve the accuracy of similarity measures. GOssTo is very fast, easy to use, and it allows the calculation of similarities on a genomic scale in a few minutes on a regular desktop machine. Availability: GOssTo is available both as a stand-alone application running on GNU/Linux, Windows and MacOS from www.paccanarolab.org/gossto and as a web application from www.paccanarolab.org/gosstoweb. The stand-alone application features a simple and concise command line interface for easy integration into high-throughput data processing pipelines.

Original language	English
Pages (from-to)	2235-2236
Number of pages	2
Journal	Bioinformatics
Volume	30
Issue number	15
DOIs	https://doi.org/10.1093/bioinformatics/btu144
Publication status	Published - 1 Aug 2014

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title = "GOssTo: A stand-alone application and a web tool for calculating semantic similarities on the Gene Ontology",

abstract = "Summary: We present GOssTo, the Gene Ontology semantic similarity Tool, a user-friendly software system for calculating semantic similarities between gene products according to the Gene Ontology. GOssTo is bundled with six semantic similarity measures, including both term- and graph-based measures, and has extension capabilities to allow the user to add new similarities. Importantly, for any measure, GOssTo can also calculate the Random Walk Contribution that has been shown to greatly improve the accuracy of similarity measures. GOssTo is very fast, easy to use, and it allows the calculation of similarities on a genomic scale in a few minutes on a regular desktop machine. Availability: GOssTo is available both as a stand-alone application running on GNU/Linux, Windows and MacOS from www.paccanarolab.org/gossto and as a web application from www.paccanarolab.org/gosstoweb. The stand-alone application features a simple and concise command line interface for easy integration into high-throughput data processing pipelines.",

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AU - Caniza, Horacio

AU - Romero, Alfonso E.

AU - Heron, Samuel

AU - Yang, Haixuan

AU - Devoto, Alessandra

AU - Frasca, Marco

AU - Mesiti, Marco

AU - Valentini, Giorgio

AU - Paccanaro, Alberto

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Y1 - 2014/8/1

N2 - Summary: We present GOssTo, the Gene Ontology semantic similarity Tool, a user-friendly software system for calculating semantic similarities between gene products according to the Gene Ontology. GOssTo is bundled with six semantic similarity measures, including both term- and graph-based measures, and has extension capabilities to allow the user to add new similarities. Importantly, for any measure, GOssTo can also calculate the Random Walk Contribution that has been shown to greatly improve the accuracy of similarity measures. GOssTo is very fast, easy to use, and it allows the calculation of similarities on a genomic scale in a few minutes on a regular desktop machine. Availability: GOssTo is available both as a stand-alone application running on GNU/Linux, Windows and MacOS from www.paccanarolab.org/gossto and as a web application from www.paccanarolab.org/gosstoweb. The stand-alone application features a simple and concise command line interface for easy integration into high-throughput data processing pipelines.

AB - Summary: We present GOssTo, the Gene Ontology semantic similarity Tool, a user-friendly software system for calculating semantic similarities between gene products according to the Gene Ontology. GOssTo is bundled with six semantic similarity measures, including both term- and graph-based measures, and has extension capabilities to allow the user to add new similarities. Importantly, for any measure, GOssTo can also calculate the Random Walk Contribution that has been shown to greatly improve the accuracy of similarity measures. GOssTo is very fast, easy to use, and it allows the calculation of similarities on a genomic scale in a few minutes on a regular desktop machine. Availability: GOssTo is available both as a stand-alone application running on GNU/Linux, Windows and MacOS from www.paccanarolab.org/gossto and as a web application from www.paccanarolab.org/gosstoweb. The stand-alone application features a simple and concise command line interface for easy integration into high-throughput data processing pipelines.

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JO - Bioinformatics

JF - Bioinformatics

IS - 15

ER -

GOssTo: A stand-alone application and a web tool for calculating semantic similarities on the Gene Ontology

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