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Gene Ontology terms semantic comparison software tools | Genome annotation

The semantic comparisons of Gene Ontology (GO) annotations provide quantitative ways to compute similarities between genes and gene groups, and have became important basis for many bioinformatics analysis approaches.Source text:(Yu et al., 2010)…
G-SESAME
Web

G-SESAME Gene Semantic Similarity Analysis and Measurement Tools

A set of online tools for measuring the semantic similarities of Gene Ontology…

A set of online tools for measuring the semantic similarities of Gene Ontology (GO) terms and the functional similarities of gene products, and for further discovering biomedical knowledge from the…

Word2vec
Desktop

Word2vec

Transforms similar words into similar vectors, thus enabling one to numerically…

Transforms similar words into similar vectors, thus enabling one to numerically quantify the similarity between two words by using Euclidean distance or cosine similarity. Using Word2vec as key…

SORA
Desktop

SORA Semantic Overlap Ratio of Annotations

Allows effective comparison of gene function. SORA employs semantic specificity…

Allows effective comparison of gene function. SORA employs semantic specificity and coverage to measure the information content (IC) of the term. It computes the IC of annotating term set by…

GOssTo
Desktop
Web

GOssTo Gene Ontology semantic similarity Tool

A user-friendly software system for calculating semantic similarities between…

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…

simDEF
Desktop

simDEF

An efficient method for measuring semantic similarity of GO terms using their…

An efficient method for measuring semantic similarity of GO terms using their GO definitions, which is based on the Gloss Vector measure commonly used in natural language processing. The simDEF…

A-DaGO-Fun
Desktop

A-DaGO-Fun ADaptable Gene Ontology semantic similarity based Functional analysis

A portable software package integrating all known GO information content-based…

A portable software package integrating all known GO information content-based semantic similarity measures and relevant biological applications associated with these measures. A-DaGO-Fun has the…

csbl.go
Desktop

csbl.go

An R package for computing semantic similarity between genes using Gene…

An R package for computing semantic similarity between genes using Gene Ontology annotation and for clustering genes based on the similarity measures. The methodology allows rapid identification of…

FunSimMat
Dataset

FunSimMat Functional Similarity Matrix

A comprehensive resource of semantic and functional similarity values.…

A comprehensive resource of semantic and functional similarity values. FunSimMat allows ranking disease candidate proteins for OMIM diseases and searching for functional similarity values for…

GOSemSim
Desktop

GOSemSim

An R package for semantic similarity computation among GO terms, sets of GO…

An R package for semantic similarity computation among GO terms, sets of GO terms, gene products and gene clusters. Four information content (IC)- and a graph-based methods are implemented in the…

SGFSC
Web

SGFSC Speeding Gene Functional Similarity Calculation

An online tool that is bundled with seven typical measures. SGFSC is able to…

An online tool that is bundled with seven typical measures. SGFSC is able to calculate two types of similarity: semantic similarity of Gene Ontology (GO) pairs and the functional similarity of genes…

GOToolBox
Web

GOToolBox

Provides a series of programs allowing the functional investigation of groups…

Provides a series of programs allowing the functional investigation of groups of genes, based on the Gene Ontology resource. GOToolBox allows 1) the identification of statistically relevant over- or…

WIS
Web

WIS Weighted Inherited Semantics

Allows to measure gene functional similarity based on gene ontology (GO). WIS…

Allows to measure gene functional similarity based on gene ontology (GO). WIS measures the information content (IC) of a term by considering its depth, the number of its ancestors and the topology of…

SML
Desktop

SML Semantic Measures Library

A generic and open source Java library dedicated to the computation and…

A generic and open source Java library dedicated to the computation and analysis of semantic measures. SML can be used to compute semantic similarities of concepts/terms defined in structured…

SML-Toolkit
Desktop

SML-Toolkit Semantic Measures Library Toolkit

A Java Toolkit dedicated to semantic measures computation and analysis.…

A Java Toolkit dedicated to semantic measures computation and analysis. SML-Toolkit is composed of various tools related to semantic measures computation and analysis. Those tools are provided…

clusterProfiler
Desktop

clusterProfiler

Automates the process of biological-term classification and the enrichment…

Automates the process of biological-term classification and the enrichment analysis of gene clusters. ClusterProfiler supports three species, including humans, mice, and yeast. Methods provided in…

GOSim
Desktop

GOSim

Allows to calculate the functional similarity of genes based on various…

Allows to calculate the functional similarity of genes based on various information theoretic similarity concepts for GO terms. GOSim extends existing tools by providing additional lately developed…

Meshes
Desktop

Meshes Medical Subject Headings

Allows users to manually index articles or publications for MEDLINE/PubMed.…

Allows users to manually index articles or publications for MEDLINE/PubMed. Terms of Meshes are combined by Entrez Gene ID by three methods: RBBH, gendoo, and gene2pubmed. This combination is very…

ProteInOn
Web

ProteInOn

A web tool focused on calculating Gene Ontology (GO)-based protein semantic…

A web tool focused on calculating Gene Ontology (GO)-based protein semantic similarity. ProteInOn features a stepwise query selection menu, which together with the possibility of selecting results as…

GS2
Desktop
Web

GS2 GO-based similarity of gene sets

A GO-based measure of gene set similarity that is computable in linear time in…

A GO-based measure of gene set similarity that is computable in linear time in the size of the gene set. The measure quantifies the similarity of the GO annotations among a set of genes by averaging…

KU GOAL
Web

KU GOAL University of Kansas Gene Ontology Analysis Layer

A web application designed for the people who are interested in discovering…

A web application designed for the people who are interested in discovering similar genes or gene products (GPs) as a drug target, validating drug targets by identifying known and similar drug…

DaGO-Fun
Web

DaGO-Fun

Incorporates many different Gene Ontology (GO) similarity measures for…

Incorporates many different Gene Ontology (GO) similarity measures for exploring, analyzing and comparing GO terms and proteins within the context of GO. DaGO-Fun uses GO data and UniProt proteins…

C-Hunter
Desktop

C-Hunter

Identifies gene clusters in eukaryotic genomes that utilizes functional…

Identifies gene clusters in eukaryotic genomes that utilizes functional categories defined in graph-based vocabularies such as the Gene Ontology (GO). C-Hunter is a clustering algorithm which…

InteGO2
Web

InteGO2 Inte Gene Ontology 2

Calculates the gene ontology (GO)-based gene semantic similarities using seven…

Calculates the gene ontology (GO)-based gene semantic similarities using seven widely used GO-based similarity measurements. InteGO2 is an integrative solution toward automatically choosing and…

Kerfuffle
Web

Kerfuffle

Provides genomic organizational information about a set of user-defined…

Provides genomic organizational information about a set of user-defined functionally related genes. Kerfuffle computes various summary statistics of gene clustering, compares significance of…

GFSST
Web

GFSST Gene Functional Similarity Search Tool

Identifies genes with related functions from annotated proteome databases.…

Identifies genes with related functions from annotated proteome databases. GFSST is a search engine that lets users design their search targets by gene functions. It provides functions not only for…

IntelliGO
Web

IntelliGO

Integrates several complementary properties in a novel vector space model.…

Integrates several complementary properties in a novel vector space model. IntelliGO provides a customizable and comprehensive method for quantifying gene similarity based on Gene Ontology (GO)…

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