Tag: Semantic Similarity

FastSemSim 1.0 – Semantic Similarity Measures

FastSemSim 1.0

:: DESCRIPTION

FastSemSim is a package that implements several semantic similarity measures. It is both a library and an end-user application, featuring an intuitive graphical user interface (GUI). It has been implemented with the aim of being fast, expandable, and easy to use. It allows the user to work with the most updated version of GO database and customizable annotation corpora. It provides a set of logically-organized classes that can be easily exploited to both integrate semantic similarity into different analysis pipelines and extend the library with new measures.

::DEVELOPER

Marco Mina

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 FastSemSim

:: MORE INFORMATION

A-DaGO-Fun / DaGO-Fun – Gene Ontology Semantic Similarity based Functional Analysis

A-DaGO-Fun / DaGO-Fun

:: DESCRIPTION

A-DaGO-Fun is a python library that provides a comprehensive and customized set of Gene Ontology (GO) based functional analysis tools that exploit the biological knowledge that GO offers in describing genes or groups of genes through the use of GO semantic similarity measures for biological knowledge discovery.

The DaGO-Fun tool is a an integrated set of GO-based functional analysis tools incorporating the large amounts of biological knowledge that GO offers in describing genes or groups of genes.

::DEVELOPER

The UCT Computational Biology Group (CBIO)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

A-DaGO-Fun: An adaptable Gene Ontology semantic similarity based functional analysis tool.
Mazandu GK, Chimusa ER, Mbiyavanga M, Mulder NJ.
Bioinformatics. 2015 Oct 17. pii: btv590.

DaGO-Fun: tool for Gene Ontology-based functional analysis using term information content measures.
Mazandu GK, Mulder NJ.
BMC Bioinformatics. 2013 Sep 25;14:284. doi: 10.1186/1471-2105-14-284.

Argot2 – Functional Annotation of Proteins using the Semantic Similarity in the Gene Ontology

Argot2

:: DESCRIPTION

Argot2 (Annotation Retrieval of Genel Ontology Terms) is able to quickly process thousands of sequences for functional inference. The tool exploits a combined approach based on the clustering process of GO terms dependent on their semantic similarities and a weighting scheme which assesses retrieved hits sharing a certain degree of biological features with the sequence to annotate.

::DEVELOPER

Argot2 team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2012 Mar 28;13 Suppl 4:S14. doi: 10.1186/1471-2105-13-S4-S14.
Argot2: a large scale function prediction tool relying on semantic similarity of weighted Gene Ontology terms.
Falda M1, Toppo S, Pescarolo A, Lavezzo E, Di Camillo B, Facchinetti A, Cilia E, Velasco R, Fontana P.

GOssTo 1.01 – the Gene Ontology Semantic Similarity Tool

GOssTo 1.01

:: DESCRIPTION

GOssTo is a Java based semantic similarity calculator. Bundled in the software are the well-known Resnik, Lin, Jian, simUI, simGRASM similarity measures. It features powerful extension capabilities allowing the user to add as many similarity measures as needed.

::DEVELOPER

Paccanaro Lab

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

  GOssTo

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Mar 22. [Epub ahead of print]
GOssTo: a user-friendly stand-alone and web tool for calculating semantic similarities on the Gene Ontology.
Caniza H1, Romero AE, Heron S, Yang H, Devoto A, Frasca M, Mesiti M, Valentini G, Paccanaro A.

simDEF – Definition-based Semantic Similarity Measure of GO Terms for Functional Similarity Analysis of Genes

simDEF

:: DESCRIPTION

simDEF is an efficient method for measuring semantic similarity of GO terms using their GO definitions.

::DEVELOPER

Beiko lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

  simDEF

:: MORE INFORMATION

Citation:

simDEF: Definition-based Semantic Similarity Measure of Gene Ontology Terms for Functional Similarity Analysis of Genes.
Pesaranghader A, Matwin S, Sokolova M, Beiko RG.
Bioinformatics. 2015 Dec 26. pii: btv755.

SemanticSimilarity – Bien’s measure of Semantic Similarity for Gene Ontology

SemanticSimilarity

:: DESCRIPTION

SemanticSimilarity analysis facilitates automated semantic explanation of biological and clinical data annotated by biomedical ontologies. Gene Ontology (GO) becomes one of the most important biomedical ontologies with a set of controlled vocabularies, providing rich semantic annotations for genes and molecular phenotypes for diseases.

::DEVELOPER

SNUBI

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Java

:: DOWNLOAD

 SemanticSimilarity

:: MORE INFORMATION

Citation

Bien SJ, Park CH, Shim HJ, Yang W, Kim J, Kim JH.
Bi-directional semantic similarity for gene ontology to optimize biological and clinical analyses
J Am Med Inform Assoc (2012). doi:10.1136/amiajnl-2011-000659