Bio::Ontology::OntologyI.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

NAME

Bio::Ontology::OntologyI - Interface for an ontology implementation

SYNOPSIS

     # see method documentation
 
 

DESCRIPTION

This describes the minimal interface an ontology implementation must provide. In essence, it represents a namespace with description on top of the query interface OntologyEngineI.

This interface inherits from Bio::Ontology::OntologyEngineI.

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.
   bioperl-l@bioperl.org                  - General discussion
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
 
 

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via email or the web:
   http://bugzilla.open-bio.org/
 
 

AUTHOR - Hilmar Lapp

Email hlapp at gmx.net

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

Methods defined in this interface.

name

  Title   : name
  Usage   : $obj->name($newval)
  Function: Get/set the name of this ontology.
  Example : 
  Returns : value of name (a scalar)
  Args    :
 
 

authority

  Title   : authority
  Usage   : $auth = $obj->authority()
  Function: Get/set the authority for this ontology, for instance the
            DNS base for the organization granting the name of the
            ontology and identifiers for the terms.
 
            This attribute is optional and should not generally
            expected by applications to have been set. It is here to
            follow the rules for namespaces, which ontologies serve as
            for terms.
 
  Example : 
  Returns : value of authority (a scalar)
  Args    :
 
 

identifier

  Title   : identifier
  Usage   : $id = $obj->identifier()
  Function: Get an identifier for this ontology.
 
            This is primarily intended for look-up purposes. Clients
            should not expect the value to be modifiable, and it may
            not be allowed to set its value from outside. Also, the
            identifier's uniqueness may only hold within the scope of a
            particular application's run time, i.e., it may be a memory
            location.
 
  Example : 
  Returns : value of identifier (a scalar)
  Args    :
 
 

definition

  Title   : definition
  Usage   : $def = $obj->definition()
  Function: Get a descriptive definition for this ontology.
  Example : 
  Returns : value of definition (a scalar)
  Args    :
 
 

close

  Title   : close
  Usage   :
  Function: Release any resources this ontology may occupy. In order
            to efficiently release used memory or file handles, you
            should call this method once you are finished with an
            ontology.
 
  Example :
  Returns : TRUE on success and FALSE otherwise
  Args    : none
 
 

Methods inherited from Bio::Ontology::OntologyEngineI

Their documentations are copied here for completeness. In most use cases, you will want to access the query methods of an ontology, not just the name and description ...

add_term

  Title   : add_term
  Usage   : add_term(TermI term): TermI
  Function: Adds TermI object to the ontology engine term store.
 
            For ease of use, if the ontology property of the term
            object was not set, an implementation is encouraged to set
            it to itself upon adding the term.
 
  Example : $oe->add_term($term)
  Returns : its argument.
  Args    : object of class TermI.
 
 

add_relationship

  Title   : add_relationship
  Usage   : add_relationship(RelationshipI relationship): RelationshipI
  Function: Adds a relationship object to the ontology engine.
  Example :
  Returns : Its argument.
  Args    : A RelationshipI object.
 
 

get_relationships

  Title   : get_relationships
  Usage   : get_relationships(TermI term): RelationshipI
  Function: Retrieves all relationship objects from this ontology engine,
            or all relationships of a term if a term is supplied.
  Example :
  Returns : Array of Bio::Ontology::RelationshipI objects
  Args    : None, or a Bio::Ontology::TermI compliant object for which
            to retrieve the relationships.
 
 

get_predicate_terms

  Title   : get_predicate_terms
  Usage   : get_predicate_terms(): TermI[]
  Function:
  Example :
  Returns :
  Args    :
 
 

get_child_terms

  Title   : get_child_terms
  Usage   : get_child_terms(TermI term, TermI predicate_terms): TermI
  Function: Retrieves all child terms of a given term, that satisfy a
            relationship among those that are specified in the second
            argument or undef otherwise. get_child_terms is a special
            case of get_descendant_terms, limiting the search to the
            direct descendants.
 
  Example :
  Returns : Array of TermI objects.
  Args    : First argument is the term of interest, second is the list
            of relationship type terms.
 
 

get_descendant_terms

  Title   : get_descendant_terms
  Usage   : get_descendant_terms(TermI term, TermI rel_types): TermI
  Function: Retrieves all descendant terms of a given term, that
            satisfy a relationship among those that are specified in
            the second argument or undef otherwise.
  Example :
  Returns : Array of TermI objects.
  Args    : First argument is the term of interest, second is the list
            of relationship type terms.
 
 

get_parent_terms

  Title   : get_parent_terms
  Usage   : get_parent_terms(TermI term, TermI predicate_terms): TermI
  Function: Retrieves all parent terms of a given term, that satisfy a
            relationship among those that are specified in the second
            argument or undef otherwise. get_parent_terms is a special
            case of get_ancestor_terms, limiting the search to the
            direct ancestors.
 
  Example :
  Returns : Array of TermI objects.
  Args    : First argument is the term of interest, second is the list
            of relationship type terms.
 
 

get_ancestor_terms

  Title   : get_ancestor_terms
  Usage   : get_ancestor_terms(TermI term, TermI predicate_terms): TermI
  Function: Retrieves all ancestor terms of a given term, that satisfy
            a relationship among those that are specified in the second
            argument or undef otherwise.
 
  Example :
  Returns : Array of TermI objects.
  Args    : First argument is the term of interest, second is the list
            of relationship type terms.
 
 

get_leaf_terms

  Title   : get_leaf_terms
  Usage   : get_leaf_terms(): TermI
  Function: Retrieves all leaf terms from the ontology. Leaf term is a
            term w/o descendants.
 
  Example : @leaf_terms = $obj->get_leaf_terms()
  Returns : Array of TermI objects.
  Args    :
 
 

get_root_terms()

  Title   : get_root_terms
  Usage   : get_root_terms(): TermI
  Function: Retrieves all root terms from the ontology. Root term is a
            term w/o descendants.
 
  Example : @root_terms = $obj->get_root_terms()
  Returns : Array of TermI objects.
  Args    :
 
 

get_all_terms

  Title   : get_all_terms
  Usage   : get_all_terms: TermI
  Function: Retrieves all terms from the ontology.
 
            We do not mandate an order here in which the terms are
            returned. In fact, the default implementation will return
            them in unpredictable order.
 
  Example : @terms = $obj->get_all_terms()
  Returns : Array of TermI objects.
  Args    :
 
 

find_terms

  Title   : find_terms
  Usage   : ($term) = $oe->find_terms(-identifier => "SO:0000263");
  Function: Find term instances matching queries for their attributes.
 
            An implementation may not support querying for arbitrary
            attributes, but can generally be expected to accept
            -identifier and -name as queries. If both are provided,
            they are implicitly intersected.
 
  Example :
  Returns : an array of zero or more Bio::Ontology::TermI objects
  Args    : Named parameters. The following parameters should be recognized
            by any implementation:
 
               -identifier    query by the given identifier
               -name          query by the given name
 
 

Factory for relationships and terms

relationship_factory

  Title   : relationship_factory
  Usage   : $fact = $obj->relationship_factory()
  Function: Get (and set, if the implementation supports it) the object
            factory to be used when relationship objects are created by
            the implementation on-the-fly.
 
  Example : 
  Returns : value of relationship_factory (a Bio::Factory::ObjectFactoryI
            compliant object)
  Args    :
 
 

term_factory

  Title   : term_factory
  Usage   : $fact = $obj->term_factory()
  Function: Get (and set, if the implementation supports it) the object
            factory to be used when term objects are created by
            the implementation on-the-fly.
 
  Example : 
  Returns : value of term_factory (a Bio::Factory::ObjectFactoryI
            compliant object)
  Args    :