Examples of using ONTO-PERL

• Finding and getting elements (e.g. terms, relationships)
  1. Find all the terms in a given ontology.
  2. Find all the relationships in a given ontology.
  3. Find all the terms using a regular expression for the ID.
  4. Get a specific term by name.
  5. Get a specific term by ID.
• Getting children terms and/or descendant ones
  1. Get all the descendant terms of a given term.
  2. Get only the child terms of a given term.
• Getting parent terms and/or ancestor ones
  1. Get all the ancestor terms of a given term.
  2. Get the only the parent terms of a given term.
• Intersection of ontologies
  1. Find out the intersection of two given ontologies o1 and o3.
• Getting a term by its features (e.g. synonyms, xref)
  1. Get a term by its name or any of its synonyms.
  2. Get a term by one of its xref's.
• Working with obsolete terms
  1. Get all the obsolete terms in a given ontology.
• Basic metrics in an ontology
  1. Get the total number of terms and relationships in a given ontology.
• Union of ontologies
  1. Find out the union of two given ontologies o1 and o4.
• Working with sub-ontologies
  1. Building an ontology from an existing sub-ontology.
• Ontology merging
  1. Simple merging of several and disjoint OBO ontologies from the same IDspace.
• Manipulating Ontology Terms
  1. Manipulating Ontology Terms (names, IDs, xref's, definitions, and so forth).
• Working with an Ontology
  1. Manipulating an Ontology.
  2. Getting sub-ontologies from a given ontology.
  3. Get paths from a given term A to a term B and/or from A to a set of given terms.
• Exporting ontologies into different formats
  1. Export a given ontology to OWL format (oboInOwl mapping).
  2. Export a given ontology to GML format.
  3. Export a given ontology to XML format.
  4. Export a given ontology to DOT format.
  5. Export a given ontology to OBO format (spec 1.2).
  6. Export a given ontology to RDF format.

More information:

ONTO-PERL: An API supporting the development and analysis of bio-ontologies
E. Antezana; M. Egana; B. De Baets; M. Kuiper; V. Mironov
Bioinformatics 2008; doi: 10.1093/bioinformatics/btn042