Recapitulates Ontology

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...

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(...

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

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

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

ORE (Ontology Rule Editor) is a platform-independent application to manage the use of inference rules defined on a model represented by an ontology. ORE offers a easy, well-guided and intiutive GUI to define and test these inference rules.


Platforms: *nix

The home of the Gene Ontology project on SourceForge, including ontology requests, software downloads, bug trackers, and much, much more.


Platforms: Windows, Mac, Linux

ONTODerm is a specialty specific ontology for dermatology to integrate dermatology with medical software systems.


Platforms: Windows, Mac, Linux

An open source common API tasks to query existing ontology resources in local files (OWL and OBO) as well as public repositories (Bioportal, OLS) using a standardised, uniform interface.


Platforms: Windows, Mac, Linux

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

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

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,...).


Platforms: Mac

Alignment API is a development tool that allows various ontology matchers to share the same format and interface for accessing matching results. Using ontologies is the privileged way to achieve interoperability among heterogeneous systems within the Semantic web. However, as the ontologies...


Platforms: *nix

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

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

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


Platforms: Mac

FluentEditor for OWL is comprehensive tool for editing and manipulating complex ontologies using Controlled Natural Language. Fluent editor provides alternative to XML-based OWL editors that is better suitable for human users. It's main feature is using Controlled English as a knowledge...


Platforms: Windows

Vogon is a ontology-based text annotation instrument specially designed for creating relations between terms in a text. All the created relations can then be exported as RDF triples. Vogon was built using the Java programming language.


Platforms: Windows

AgentOWL library support RDF/OWL ontology models in JADE agent system. The library use Jena for ontology model manipulation.


Platforms: Windows, Mac, Linux

AKtive Media is an ontology based cross-media annotation (Images and Text) system. Our goal is to automate the process of annoation by suggesting knowledge to the user in an interactive way while the user is annotating and hence minimizing user effort.


Platforms: Windows, Mac, Linux