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onto-perl-1.04

Changes for version 1.04

Documentation

onto-perl
perl modules for CCO and OBO ontologies
get_ancestor_terms.pl
Collects the ancestor terms (list of IDs) from a given term (existing ID) in the given OBO ontology.
get_descendent_terms.pl
Collects the descendent terms (list of IDs) from a given term (existing ID) in the given OBO ontology.
go2owl.pl
Gene Ontology (in OBO) to OWL translator.
obo2owl.pl
OBO to OWL translator.
obsolete_term_id_vs_def_in_go.pl
Obsolete terms vs their definitions.
obsolete_term_id_vs_name_in_go.pl
Obsolete terms vs their names.
owl2obo.pl
OWL to OBO translator (oboinowl mapping).

Modules

CCO::Core::Dbxref
Reference structure.
CCO::Core::Def
A definition structure of the current term. A term must have zero or one instance of this type per term description.
CCO::Core::GoaAssociation
a GOA association record.
CCO::Core::IDspace
A mapping between a "local" ID space and a "global" ID space
CCO::Core::Interaction
An interaction from IntAct
CCO::Core::Interactor
An interactor from IntAct
CCO::Core::Ontology
An ontology holding terms and their relationships
CCO::Core::Relationship
A relationship between two terms or two relationships within an ontology.
CCO::Core::RelationshipType
A type of relationship type in an ontology
CCO::Core::Synonym
A term synonym
CCO::Core::SynonymTypeDef
A synonym type definition. It should contain a synonym type name, a space, a quote enclosed description, and an optional scope specifier.
CCO::Core::Term
A universal/term/class/concept in an ontology
CCO::Parser::GoaParser
A GOA associations to OBO translator.
CCO::Parser::IntActParser
An IntAct to OBO parser/filter.
CCO::Parser::InteractionManager
An IntAct to OBO parser/filter.
CCO::Parser::NCBIParser
A NCBI taxonomy to OBO translator.
CCO::Parser::NewIntActParser
An IntAct to OBO parser/filter.
CCO::Parser::OBOParser
An OBO (Open Biomedical Ontologies) file parser.
CCO::Parser::OWLParser
An OWL parser (oboInOwl mapping).
CCO::Parser::OrthoMCLParser
An orthoMCL data to OBO translator
CCO::Parser::UniProtParser
A UniProt to OBO translator.
CCO::Util::CCO_ID
A module for describing Cell Cycle Ontology (CCO) identifiers. Its namespace, subnamespace and number are stored.
CCO::Util::CCO_ID_Set
An implementation of a set of CCO::Util::CCO_ID objects.
CCO::Util::CCO_ID_Term_Map
a map between CCO IDs and term names.
CCO::Util::DbxrefSet
a DbxrefSet implementation
CCO::Util::GoaAssociationSet
a GoaAssociationSet implementation
CCO::Util::ObjectIdSet
A Set implementation of object Ids
CCO::Util::ObjectSet
An implementation of a set of ontology objects
CCO::Util::Ontolome
a set of ontologies
CCO::Util::Set
A Set implementation
CCO::Util::SynonymSet
A Set implementation of Synonyms
CCO::Util::SynonymTypeDefSet
A Set implementation of Synonym Types
CCO::Util::TermSet
A Set implementation

Provides

CCO::Util::XMLIntactParser
in CCO/Util/XMLIntactParser.pm

Other files