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ONTO-PERL-1.21
River stage zero No dependents

Changes for version 1.21

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_child_terms.pl
Collects the child terms (list of term IDs and their names) 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.
get_obsolete_terms.pl
Find all the obsolete terms in a given ontology.
get_parent_terms.pl
Collects the parent terms (list of term IDs and their names) from a given term (existing ID) in the given OBO ontology.
get_relationship_types.pl
Find all the relationship types in a given ontology.
get_root_terms.pl
Find all the root terms in a given ontology.
get_subontology_from.pl
Extracts a subontology (in OBO format) of a given ontology having as root the given term ID.
get_terms.pl
Find all the terms in a given ontology.
get_terms_by_name.pl
Find all the terms in a given ontology having in their names a given string.
go2owl.pl
Gene Ontology (in OBO) to OWL translator.
goa2rdf.pl
Generates a simple RDF graph from a given GOA file.
obo2cco.pl
Converts an ontology into another one which could be integrated into CCO.
obo2owl.pl
OBO to OWL translator.
obo2rdf.pl
OBO to RDF translator.
obo2tran.pl
OBOF into RDF translator. The resulting file has (full) transitive closure.
obo2xml.pl
OBO to XML translator (CCO scheme).
obo_trimming.pl
This script trims a given branch of an OBO ontology.
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).
term_id_vs_term_def.pl
Gets the term IDs and term defintions of a given ontology.
term_id_vs_term_name.pl
Gets the term IDs and term names of a given ontology.
term_id_vs_term_namespace.pl
Gets the term IDs and its namespaces in a given ontology.

Modules

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

Other files