title: GOssTo: a stand-alone application and a web tool for calculating semantic similarities on the Gene Ontology.
abstract: CONCLUSIONS
  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.
  
  
  BACKGROUND
  alberto@cs.rhul.ac.uk
  
  
  BACKGROUND
  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.
authors.affiliation: Department of Computer Science, Royal Holloway, University of London, Egham, TW200EX, UK, School of Mathematics, Statistics & Applied Mathematics, National University of Ireland, Galway, School of Biological Sciences, Royal Holloway, University of London, Egham, TW200EX, UK and Dipartimento di Informatica, Università degli Studi di Milano, via Comelico 39/41, 20135 Milano, Italy.
authors.forename: Horacio
authors.initials: H
authors.lastname: Caniza
authors.affiliation: Department of Computer Science, Royal Holloway, University of London, Egham, TW200EX, UK, School of Mathematics, Statistics & Applied Mathematics, National University of Ireland, Galway, School of Biological Sciences, Royal Holloway, University of London, Egham, TW200EX, UK and Dipartimento di Informatica, Università degli Studi di Milano, via Comelico 39/41, 20135 Milano, Italy.
authors.forename: Alfonso E
authors.initials: AE
authors.lastname: Romero
authors.affiliation: Department of Computer Science, Royal Holloway, University of London, Egham, TW200EX, UK, School of Mathematics, Statistics & Applied Mathematics, National University of Ireland, Galway, School of Biological Sciences, Royal Holloway, University of London, Egham, TW200EX, UK and Dipartimento di Informatica, Università degli Studi di Milano, via Comelico 39/41, 20135 Milano, Italy.
authors.forename: Samuel
authors.initials: S
authors.lastname: Heron
authors.affiliation: Department of Computer Science, Royal Holloway, University of London, Egham, TW200EX, UK, School of Mathematics, Statistics & Applied Mathematics, National University of Ireland, Galway, School of Biological Sciences, Royal Holloway, University of London, Egham, TW200EX, UK and Dipartimento di Informatica, Università degli Studi di Milano, via Comelico 39/41, 20135 Milano, Italy.
authors.forename: Haixuan
authors.initials: H
authors.lastname: Yang
authors.affiliation: Department of Computer Science, Royal Holloway, University of London, Egham, TW200EX, UK, School of Mathematics, Statistics & Applied Mathematics, National University of Ireland, Galway, School of Biological Sciences, Royal Holloway, University of London, Egham, TW200EX, UK and Dipartimento di Informatica, Università degli Studi di Milano, via Comelico 39/41, 20135 Milano, Italy.
authors.forename: Alessandra
authors.initials: A
authors.lastname: Devoto
authors.affiliation: Department of Computer Science, Royal Holloway, University of London, Egham, TW200EX, UK, School of Mathematics, Statistics & Applied Mathematics, National University of Ireland, Galway, School of Biological Sciences, Royal Holloway, University of London, Egham, TW200EX, UK and Dipartimento di Informatica, Università degli Studi di Milano, via Comelico 39/41, 20135 Milano, Italy.
authors.forename: Marco
authors.initials: M
authors.lastname: Frasca
authors.affiliation: Department of Computer Science, Royal Holloway, University of London, Egham, TW200EX, UK, School of Mathematics, Statistics & Applied Mathematics, National University of Ireland, Galway, School of Biological Sciences, Royal Holloway, University of London, Egham, TW200EX, UK and Dipartimento di Informatica, Università degli Studi di Milano, via Comelico 39/41, 20135 Milano, Italy.
authors.forename: Marco
authors.initials: M
authors.lastname: Mesiti
authors.affiliation: Department of Computer Science, Royal Holloway, University of London, Egham, TW200EX, UK, School of Mathematics, Statistics & Applied Mathematics, National University of Ireland, Galway, School of Biological Sciences, Royal Holloway, University of London, Egham, TW200EX, UK and Dipartimento di Informatica, Università degli Studi di Milano, via Comelico 39/41, 20135 Milano, Italy.
authors.forename: Giorgio
authors.initials: G
authors.lastname: Valentini
authors.affiliation: Department of Computer Science, Royal Holloway, University of London, Egham, TW200EX, UK, School of Mathematics, Statistics & Applied Mathematics, National University of Ireland, Galway, School of Biological Sciences, Royal Holloway, University of London, Egham, TW200EX, UK and Dipartimento di Informatica, Università degli Studi di Milano, via Comelico 39/41, 20135 Milano, Italy.
authors.forename: Alberto
authors.initials: A
authors.lastname: Paccanaro
mesh_terms: D057225:Data Mining / Q000379:methods*; D063990:Gene Ontology; D020407:Internet; D011506:Proteins / Q000235:genetics; D012660:Semantics; D012984:Software; D018875:Vocabulary, Controlled
chemical_list: D011506:Proteins