Table 1

Examples of ONTO-PERL functionalities

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)


The left column lists ONTO-PERL scripts available in ONTO-ToolKit, with their functionality described in the right column. *: Scripts written specifically for ONTO-ToolKit and included in the ONTO-ToolKit download package.

Antezana et al. BMC Bioinformatics 2010 11(Suppl 12):S8   doi:10.1186/1471-2105-11-S12-S8

Open Data