PathwaysWeb provides publicly available information on genes, biological pathways, Gene Ontology terms, gene gene interaction networks with interaction directionality, and links to related PubMed documents.
Ontologizer is a Java webstart application for GO term enrichment analysis that provides browsing and graph visualization capabilities. The Ontologizer allows users to analyze data with the standard Fisher exact test and also the parent-child method and topology methods.
GOTreePlus is an interactive gene ontology visualization tool that can superimpose annotation information over gene ontology structures. GOTreePlus can facilitate the identification of important GO terms while visualizing them in the gene ontology structure. The interactive pie chart summary for a selected gene ontology term provides users with a succinct overview of their experimental results.
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.
Csbl.go is an R package for computing semantic similarity between genes using Gene Ontology annotation and for clustering genes based on the similarity measures. The package also includes GO enrichment analysis functionality.
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.
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.