Table 1 Examples of ONTO-PERL functionalities
From: ONTO-ToolKit: enabling bio-ontology engineering via Galaxy
Scripts | Functionality |
|---|---|
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_subontology_from.pl | Extracts a sub-ontology (in OBO format) of a given ontology having the given term ID as the root. |
get_obsolete_terms.pl | Finds 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 | Finds all the relationship types in a given ontology. |
get_root_terms.pl | Finds all the root terms in a given ontology. |
get_term_synonyms.pl | Finds all the synonyms of a given term name in an ontology. |
get_terms.pl | Finds all the terms in a given ontology. |
get_terms_by_name.pl | Finds all the terms in a given ontology that have a given string in their names. |
obo2owl.pl | OBO to OWL translator. |
obo2rdf.pl | OBO to RDF translator. |
obo_trimming.pl | This script trims a given branch of OBO ontology. |
obo2cco.pl | Converts an ontology into another one which could be integrated into CCO. |
obo2tran.pl | OBOF into RDF translator. The resulting file has (full) transitive closure |
obo2xml.pl | OBO to XML translator (CCO scheme). |
go2owl.pl | Gene Ontology (in OBO) to OWL translator. |
goa2rdf.pl | Generates a simple RDF graph from a given GOA file |
owl2obo.pl | OWL to OBO 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 |
term_id_vs_term_def.pl | Gets the term IDs and term definitions 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 |
get_list_intersection_from.pl* | Collects common OBO terms from a given set of lists containing OBO terms |
get_intersection_ontology_from.pl* | Provides an intersection of the given ontologies (in OBO format) |