Recapitulates Ontology
Phenex is an application for annotating character matrix files with ontology terms. Character states can be annotated using the Entity-Quality syntax for ontologically describing phenotypes. In addition, taxon entries can be annotated with identifiers from a taxonomy ontology. Phenex saves...
Platforms: Windows
License: Freeware | Size: 28.4 MB | Download (696): Phenex 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....
Platforms: Windows
License: Freeware | Download (466): MEFIT 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
Platforms: Windows
License: Freeware | Download (382): FastSemSim Download |
Prot+eg+e is an ontology editor and a knowledge-base editor.Prot+eg+e is also an open-source, Java tool that provides an extensible architecture for the creation of customized knowledge-based applications.
Platforms: Mac
License: Freeware | Size: 23.4 MB | Download (314): Protege Download |
openDICOM.NET software implements a new approach towards DICOM (Digital Imaging and Communications in Medicine) libraries. DICOM is a worldwide standard in Medical IT and is provided by the National Electrical Manufacturers Assocation (NEMA). This standard specifies the way medical images and...
Platforms: *nix
License: Freeware | Download (160): openDICOM.NET 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...
Platforms: *nix
License: Freeware | Size: 870.4 KB | Download (128): GO::View 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...
Platforms: *nix
License: Freeware | Size: 4.7 MB | Download (109): Bio::Ontology::Relationship Download |
Vector Visuals provides an easy-to-use, object-based API for creating and manipulating Java2D-rendered shapes and images. The project features object embedding, dynamic connectors, and multithreaded task support. Vector Visuals has been downloaded thousands of times, and is already in use in a...
Platforms: *nix
License: Freeware | Size: 39.94 KB | Download (100): Vector Visuals Download |
Platypus Wiki provides a semantic Wiki Wiki Web. Platypus Wiki is an enhanced Wiki Wiki Web with ideas taken from Semantic Web. It offers a simple user interface for creating Wiki page plus metadata according to W3C standards. Weve chosen HTMLarea v3.0rc1 as a WYSIWYG editor for creating...
Platforms: *nix
License: Freeware | Size: 9.5 MB | Download (98): Platypus Wiki 0.5 Download |
GO::Model::Term is a term or concept in an ontology. SYNOPSIS # From a file use GO::Parser; my $parser = new GO::Parser({handler=>obj}); # create parser object $parser->parse("gene_ontology.obo"); # parse file -> objects my $graph = $parser->handler->graph; # get L object my $term =...
Platforms: *nix
License: Freeware | Size: 593.92 KB | Download (97): GO::Model::Term 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(...
Platforms: *nix
License: Freeware | Size: 4.7 MB | Download (95): 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 =...
Platforms: *nix
License: Freeware | Size: 4.7 MB | Download (92): Bio::Ontology::Ontology 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...
Platforms: *nix
License: Freeware | Size: 4.7 MB | Download (90): Bio::Ontology::OntologyEngineI Download |
Bio::OntologyIO::simplehierarchy is a base class parser for simple hierarchy-by-indentation type formats. SYNOPSIS use Bio::OntologyIO; # do not use directly -- use via Bio::OntologyIO my $parser = Bio::OntologyIO->new ( -format => "simplehierarchy", -file => "pathology_terms.csv",...
Platforms: *nix
License: Freeware | Size: 4.7 MB | Download (86): Bio::OntologyIO::simplehierarchy Download |
Amine is a Multi-Layer Java Open Source Platform dedicated to the development of various kinds of Intelligent Systems (Knowledge-Based, Ontology-Based, Conceptual Graph Based, NLP, etc.) and Intelligent Agents. See: //amine-platform.sourceforge.net/
Platforms: Windows, Mac, Linux
License: Freeware | Size: 23.23 MB | Download (58): AminePlatform 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 (57): Experimental Factor Ontology Download |
ONTODerm is a specialty specific ontology for dermatology to integrate dermatology with medical software systems.
Platforms: Windows, Mac, Linux
License: Freeware | Size: 29.23 KB | Download (57): ONTODerm - Ontology for Dermatology Download |
Some More Individual - Yes! A couple of projects around Semantic Web technologies to help to establish a better accessible Web and personalize this access. Features - Semantic Web Ontologies - The Counter Ontology - The Ordered List Ontology - Some More Individual - The Association...
Platforms: *nix
License: Freeware | Size: 20.48 KB | Download (54): Some More Individual Download |
ROO is an (OWL) ontology construction tool based on Protégé 4. ROO makes the ontology building process easier as it provides guidance about the steps involved and it allows to enter knowledge using an easy to learn controlled natural language.
Platforms: Windows, Mac, Linux
License: Freeware | Size: 32.61 MB | Download (52): ROO Rabbit to OWL Ontology construction Download |
WSMO Studio is a Semantic Web Service and Semantic Business Process modelling environment based on the Web Services Modelling Ontology (WSMO). WSMO Studio is available as a set of Eclipse plug-ins that can be extended and customised by 3rd parties.
Platforms: Windows, Mac, Linux
License: Freeware | Size: 92.05 KB | Download (51): WSMO Studio Download |