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ONTO-PERL-1.39
River stage zero No dependents

Changes for version 1.39

Documentation

ONTO-PERL
PERL modules for OBO-formatted 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_lowest_common_ancestor.pl
the lowest common ancestor (LCA) of two terms in a given OBO ontology.
get_obsolete_term_id_vs_def_in_go.pl
Obsolete terms vs their definitions.
get_obsolete_term_id_vs_name_in_go.pl
Obsolete terms vs their names.
get_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_id_vs_relationship_def.pl
Gets the relationship IDs and relationship definitions of a given ontology.
get_relationship_id_vs_relationship_name.pl
Gets the relationship IDs and relationship names of a given ontology.
get_relationship_id_vs_relationship_namespace.pl
Gets the relationship IDs and its namespaces in a given 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_term_id_vs_term_def.pl
Gets the term IDs and term defintions of a given ontology.
get_term_id_vs_term_name.pl
Gets the term IDs and term names of a given ontology.
get_term_id_vs_term_namespace.pl
Gets the term IDs and its namespaces in a given ontology.
get_term_local_neighbourhood.pl
Gets the local neighbourhood of a given term (and over an optional relationship type) in a given OBO ontology.
get_term_synonyms.pl
Find all the synonyms of a given term name in an ontology.
get_terms.pl
Find all the terms in a given ontology.
get_terms_and_synonyms.pl
Find all the terms and synonyms in a given ontology.
get_terms_by_name.pl
Find all the terms in a given ontology that have a given string in their names.
go2owl.pl
Gene Ontology (in OBO) to OWL translator.
goa2rdf.pl
Generates a simple RDF graph from a given GOA file.
obo2apo.pl
Converts an ontology into another one which could be integrated into APO.
obo2owl.pl
OBO to OWL translator.
obo2rdf.pl
OBO to RDF translator.
obo2tran.pl
OBOF into RDF translator. The resulting file has (full) transitive closures over 'is_a' and 'part_of'.
obo2xml.pl
OBO to XML translator (APO scheme).
obo_intersection.pl
Finds the intersection of two OBO-formatted ontologies.
obo_transitive_reduction.pl
Finds the transitive reduction ontology of the given OBO-formatted ontology.
obo_trimming.pl
This script trims a given branch of an OBO ontology.
obo_union.pl
Finds the union of the given OBO-formatted ontologies.
owl2obo.pl
OWL to OBO translator (oboinowl mapping).

Modules

OBO::APO::APO_ID
A module for describing Application Ontology (APO) identifiers. Its idspace, subnamespace and localID are stored.
OBO::APO::APO_ID_Set
An implementation of a set of OBO::APO::APO_ID objects.
OBO::APO::APO_ID_Term_Map
A map between APO IDs and term names.
OBO::APO::GoaAssociation
A GOA association record.
OBO::APO::GoaAssociationSet
A GoaAssociationSet implementation
OBO::APO::GoaToRDF
A GOA associations to RDF converter.
OBO::APO::NCBIToRDF
A NCBI taxonomy dump to RDF converter.
OBO::APO::SwissProtToRDF
A SwissProt to RDF converter.
OBO::Core::Dbxref
A database reference structure.
OBO::Core::Def
A definition structure of a term. A term should 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::Instance
An instance in an ontology.
OBO::Core::Ontology
An ontology holding terms, instances and relationships.
OBO::Core::Relationship
A relationship between two terms or two relationships or an instance and a term within an ontology.
OBO::Core::RelationshipType
A type of relationship type in an ontology.
OBO::Core::SubsetDef
A description of a term subset. The value for this tag should contain a subset name and a subset description.
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::GoaParser
A GOA associations to OBO translator.
OBO::Parser::IntActParser
An IntAct to OBO parser/filter.
OBO::Parser::NCBIParser
A NCBI taxonomy to OBO translator.
OBO::Parser::OBOParser
An OBO (Open Biomedical Ontologies) file parser.
OBO::Parser::OWLParser
An OWL parser (oboInOwl mapping).
OBO::Parser::UniProtParser
A UniProt to OBO translator.
OBO::Util::DbxrefSet
A Dbxref set implementation.
OBO::Util::IDspaceSet
An implementation of a set of IDspace's.
OBO::Util::InstanceSet
A Set implementation.
OBO::Util::Map
An implementation of a map (key -> value).
OBO::Util::ObjectIdSet
A Set implementation of object IDs.
OBO::Util::ObjectSet
An implementation of a set of OBO ontology objects.
OBO::Util::Ontolome
A set of ontologies.
OBO::Util::RelationshipTypeSet
A Set implementation.
OBO::Util::Set
An implementation of a set of scalars (sensu PERL).
OBO::Util::SubsetDefMap
A Map implementation of a subset definition.
OBO::Util::SynonymSet
An implementation of a set of synonyms.
OBO::Util::SynonymTypeDefSet
A Set implementation of Synonym Types.
OBO::Util::TermSet
A Set implementation.
OBO::XO::OBO_ID
A module for describing identifiers of any OBO ontology (e.g. XO). Its IDSpace and LocalID are stored.
OBO::XO::OBO_ID_Set
An implementation of a set of OBO::XO::OBO_ID objects.
OBO::XO::OBO_ID_Term_Map
A map between OBO IDs and term names.

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