| This Release | ONTO-PERL-1.38 | [Download] [Browse] | 06 Mar 2012 | ||||
| Latest Release | ONTO-PERL-1.40 | [Download] [Browse] | 09 Nov 2012 | ||||
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| CPAN Testers | FAIL (93) UNKNOWN (2) [ View Reports ] [ Perl/Platform Version Matrix ] | ||||||
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| License | The Perl 5 License (Artistic 1 & GPL 1) | ||||||
| Special Files |
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| 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. | 1.38 | |
| 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::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. |
| 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_get_obsolete_terms.pl | Find all the obsolete terms in a given 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_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). |
