David Gene Ontology
The home of the Gene Ontology project on SourceForge, including ontology requests, software downloads, bug trackers, and much, much more.
Platforms: Windows, Mac, Linux
|License: Freeware||Size: 44.5 MB||Download (29): Gene Ontology Download|
Each TS was tested for functional enrichment using annotation obtained from numerous ontologies or curated databases (Gene Ontology, KEGG, BioCarta, Swiss-Prot, BBID, SMART, NIH Genetic Association DB, COG/KOG, TargetScan, PicTar, TFBSConserved,...).
|License: Shareware||Cost: $0.00 USD||Size: 838 B||Download (16): TranscriptomeBrowser Download|
AGENDA (Application for mining Gene Ontology Data)
Platforms: Windows, Mac, Linux
|License: Freeware||Size: 59.32 KB||Download (27): BioAGENDA Download|
GO-Elite is a software tool designed to identify a minimal non-redundant set of Gene Ontology (GO) biological terms and pathways to describe a particular set of input identifiers. This tool calculates over-representation statistics similiar to the program MAPPFinder and subsequently produces...
|License: Shareware||Cost: $0.00 USD||Size: 15.17 MB||Download (18): GO-Elite Download|
ErmineJ performs analyses of gene sets in expression microarray data or other genome-wide data that results in rankings of genes. A typical goal is to determine whether particular biological pathways are "doing something interesting" in the data. The software is designed to be used by biologists...
|License: Freeware||Size: 21.13 MB||Download (16): ErmineJ Download|
Easily find and extract specific chemical reactions from the BioModels database. Features - Autosuggest for Gene Ontology terms - Update feature ensures access to the latest version of BioModels repository
|License: Shareware||Cost: $0.00 USD||Size: 11.18 MB||Download (31): SBML Reaction Finder Download|
FastSemSim is specially designed as a handy Python-based efficient implementation of a couple of semantic similarity measures.
The main target of the project is to enable fast and easy calculation of similarity between proteins and genes using the Gene Ontology
|License: Freeware||Download (38): FastSemSim Download|
GO::View is a Perl module that creates a gif or png image for visualizing the GO DAG. This perl module generates a graphic that displays the parent and child relationships of a selected GO term. It also provides the visualization for the GO::TermFinder perl module created by the Stanford...
|License: Freeware||Size: 870.4 KB||Download (105): GO::View Download|
MEFIT, also known as the Microarray Experiment Functional Integration Technology is developed as a system for microarray integration.
Given any amount of microarray data, it predicts the probability of pairwise functional relationship for any gene pair within individual biological functions....
|License: Freeware||Download (49): MEFIT Download|
Osprey is a software platform for visualization of complex interaction networks. Osprey builds data-rich graphical represetations from Gene Ontology (GO) annotated interactions maintained by the BioGRID.
Platforms: Windows, Mac, Solaris, Linux
|License: Freeware||Size: 8.32 MB||Download (31): Osprey Network Visualization System Download|
Blast2GO?*A* is an ALL in ONE tool for functional annotation of (novel) sequences and the analysis of annotation data. Main Application Features are: Easy start up and low maintenance. Make sure you have JAVA, download Blast2GO from this site and start using the application. Updates are...
|License: Freeware||Size: 4.1 KB||Download (19): Blast2GO Download|
EcoCyc is an electronic reference source for E. coli biologists and biologists who work with related microorganisms. EcoCyc Mobile provides a streamlined mobile interaction for EcoCyc, a bioinformatics database that describes the genome and the biochemical machinery of Escherichia coli K-12...
|License: Freeware||Size: 2.4 MB||Download (7): EcoCyc Download|
50 images of Egypt by David Roberts. Beautiful Pharaonic and Islamic scenes chosen from his six volumes of prints published in 1846. This screensaver includes a portrait of David Roberts plus scenes along the Nile of Abu Simbel, Karnak, the Temple of Luxor, the Colossus of Memnon, Temples of Kom...
|License: Demo||Cost: $11.00 USD||Size: 3.27 MB||Download (102): Egypt of David Roberts Download|
Bio::Ontology::Relationship is a relationship for an ontology. SYNOPSIS $rel = Bio::Ontology::Relationship->new( -identifier => "16847", -subject_term => $subj, -object_term => $obj, -predicate_term => $pred ); This is a basic implementation of Bio::Ontology::RelationshipI. The...
|License: Freeware||Size: 4.7 MB||Download (85): Bio::Ontology::Relationship Download|
Bio::Ontology::GOterm is a representation of GO terms. SYNOPSIS $term = Bio::Ontology::GOterm->new ( -go_id => "GO:0016847", -name => "1-aminocyclopropane-1-carboxylate synthase", -definition => "Catalysis of ...", -is_obsolete => 0, -comment => "" ); $term->add_definition_references(...
|License: Freeware||Size: 4.7 MB||Download (76): Bio::Ontology::GOterm Download|
Bio::Ontology::Ontology is a standard implementation of an Ontology. SYNOPSIS use Bio::Ontology::Ontology; # create ontology object my $ont = Bio::Ontology::Ontology->new(-name => "OBF"); # add terms, relationships ... my $bp = Bio::Ontology::Term->new(-name => "Bioperl"); my $obf =...
|License: Freeware||Size: 4.7 MB||Download (74): Bio::Ontology::Ontology Download|
GENE Graph Export Engine is an advanced XML exporter. GENE Graph Export Engine is a complex convertor/framework for multi-namespace XML transforming and exporting. It is able to convert various XML types including SVG, DocBook, MathML, XSL-FO, and their combinations into a wide area of output...
|License: Freeware||Size: 1.1 MB||Download (76): GENE Graph Export Engine Download|
OntologyEngineI is a Perl interface a minimal Ontology implementation should satisfy. This describes the minimal interface an ontology query engine should provide. It intentionally doesnt make explicit references to the ontology being a DAG, nor does it mandate that the ontology be a...
|License: Freeware||Size: 4.7 MB||Download (71): Bio::Ontology::OntologyEngineI Download|
Gene Visualizer is a small app designed to display an organism's genes visually. The program takes two sets of genes as input. One is a list of an organism's predicted genes, and the other is a list of an organism's known genes. It can be useful to compare how the two lists of genes match up,...
|License: Freeware||Download (49): Gene Visualizer Download|
It is an application focused on the ontology modeling ot the experimental factors in ArrayExpress.The application is used also in the constructing of mappings to multiple existing domain specific ontologies, such as Disease Ontology.
Platforms: Windows, Mac, *nix, Perl, BSD Solaris
|License: Freeware||Download (29): Experimental Factor Ontology Download|