## 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 1.4).
  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

    ONTO-Toolkit: A set of Galaxy tools to deal with OBO-formatted ontologies,
    Antezana E, Venkatesan A, Mungall C, Mironov V, Kuiper M.
    BMC Bioinformatics 2010, 11(Suppl 12):S8 doi:10.1186/1471-2105-11-S12-S8

Copyright (c) 2006-2015 by Erick Antezana. All rights reserved.