Bio::Ontology::Ontology.3pm

Langue: en

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

Section: 3 (Bibliothèques de fonctions)

NAME

Bio::Ontology::Ontology - standard implementation of an Ontology

SYNOPSIS

     use Bio::Ontology::Ontology;
     use Bio::Ontology::Term;
 
     # create ontology object
     my $ont = Bio::Ontology::Ontology->new(-name => "OBF");
 
     # add terms, relationships ...
     my $bp = Bio::Ontology::Term->new(-identifier => '02', -name => "Bioperl");
     my $obf = Bio::Ontology::Term->new(-identifier => '01', -name => "OBF");
     my $partof = Bio::Ontology::RelationshipType->get_instance("PART_OF");
     $ont->add_term($bp);
     $ont->add_term($obf);
     $ont->add_relationship($bp, $obf, $partof);
 
     # then query
     my @terms = $ont->get_root_terms(); # "OBF"
     my @desc = $ont->get_descendant_terms($terms[0], $partof); # "Bioperl"
     # ... see methods for other ways to query
 
     # for advanced users, you can re-use the query engine outside of an
     # ontology to let one instance manage multiple ontologies
     my $ont2 = Bio::Ontology::Ontology->new(-name => "Foundations",
                                             -engine => $ont->engine());
 
 

DESCRIPTION

This is a no-frills implementation of Bio::Ontology::OntologyI.

The query functions are implemented by delegation to an OntologyEngineI implementation.

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 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 _

new

  Title   : new
  Usage   : my $obj = Bio::Ontology::Ontology->new();
  Function: Builds a new Bio::Ontology::Ontology object
  Returns : an instance of Bio::Ontology::Ontology
  Args    : any number of named arguments. The following names will be
            recognized by this module:
 
             -name         the name of the ontology
             -authority    the name of the authority for the ontology
             -identifier   an identifier for the ontology, if any
             -engine       the Bio::Ontology::OntologyEngineI
                           implementation that this instance should use;
                           default is Bio::Ontology::SimpleOntologyEngine
 
             See the corresponding get/set methods for further documentation
             on individual properties.
 
 

Methods from Bio::Ontology::OntologyI

name

  Title   : name
  Usage   : $obj->name($newval)
  Function: Get/set the name of the ontology.
  Example :
  Returns : value of name (a scalar)
  Args    : on set, new value (a scalar or undef, optional)
 
 

authority

  Title   : authority
  Usage   : $obj->authority($newval)
  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    : on set, new value (a scalar or undef, optional)
 
 

definition

  Title   : definition
  Usage   : $obj->definition($newval)
  Function: Get/set a descriptive definition of the ontology.
  Example :
  Returns : value of definition (a scalar)
  Args    : on set, new value (a scalar or undef, optional)
 
 

identifier

  Title   : identifier
  Usage   : $id = $obj->identifier()
  Function: Get an identifier for this ontology.
 
            This is primarily intended for look-up purposes. The value
            is not modifiable and is determined automatically by the
            implementation.  Also, the identifier's uniqueness will only
            hold within the scope of a particular application's run
            time since it is derived from a memory location.
 
  Example :
  Returns : value of identifier (a scalar)
  Args    :
 
 

close

  Title   : close
  Usage   :
  Function: Release any resources this ontology may occupy. In order
            to efficiently release unused 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
 
 

Implementation-specific public methods

engine

  Title   : engine
  Usage   : $engine = $obj->engine()
  Function: Get/set the ontology engine to which all the query methods
            delegate.
  Example :
  Returns : an object implementing Bio::Ontology::OntologyEngineI
  Args    : on set, new value (an object implementing
            Bio::Ontology::OntologyEngineI, or  undef)
 
 

See Bio::Ontology::OntologyEngineI.

Methods defined in Bio::Ontology::OntologyEngineI

add_term

  Title   : add_term
  Usage   : add_term(TermI term): TermI
  Function: Adds TermI object to the ontology engine term store
 
            If the ontology property of the term object was not set,
            this implementation will 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
            add_relatioship(TermI subject, TermI predicate, TermI object)
  Function: Adds a relationship object to the ontology engine.
  Example :
  Returns : Its argument.
  Args    : A RelationshipI object.
 
 

get_relationship_type

  Title   : get_relationship_type
  Usage   : get_relationship_type(scalar): RelationshipTypeI
  Function: Get a relationshiptype object from the ontology engine.
  Example :
  Returns : A RelationshipTypeI object.
  Args    : The name (scalar) of the RelationshipTypeI object desired.
 
 

get_relationships

  Title   : get_relationships
  Usage   : get_relationships(TermI term): RelationshipI[]
  Function: Retrieves all relationship objects in the ontology, or all
            relationships of a given term.
  Example :
  Returns : Array of Bio::Ontology::RelationshipI objects
  Args    : Optionally, a Bio::Ontology::TermI compliant object
 
 

get_predicate_terms

  Title   : get_predicate_terms
  Usage   : get_predicate_terms(): TermI
  Function: Retrieves all relationship types.
  Example :
  Returns : Array of TermI objects
  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.
 
            Note that a returned term may possibly be in another
            ontology than this one, because the underlying engine may
            manage multiple ontologies and the relationships of terms
            between them. If you only want descendants within this
            ontology, you need to filter the returned array.
 
  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.
 
            Note that a returned term may possibly be in another
            ontology than this one, because the underlying engine may
            manage multiple ontologies and the relationships of terms
            between them. If you only want descendants within this
            ontology, you need to filter the returned array.
 
  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.
 
            Note that a returned term may possibly be in another
            ontology than this one, because the underlying engine may
            manage multiple ontologies and the relationships of terms
            between them. If you only want descendants within this
            ontology, you need to filter the returned array.
 
  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.
 
            Note that a returned term may possibly be in another
            ontology than this one, because the underlying engine may
            manage multiple ontologies and the relationships of terms
            between them. If you only want descendants within this
            ontology, you need to filter the returned array.
 
  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 parents.
 
  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 implementations:
 
               -identifier    query by the given identifier
               -name          query by the given name
 
 

find_identical_terms

  Title   : find_identical_terms
  Usage   : ($term) = $oe->find_identical_terms($term0);
  Function: Find term instances where name or synonym
            matches the query exactly
  Example :
  Returns : an array of zero or more Bio::Ontology::TermI objects
  Args    : a Bio::Ontology::TermI object
 
 

find_similar_terms

  Title   : find_similar_terms
  Usage   : ($term) = $oe->find_similar_terms($term0);
  Function: Find term instances where name or synonym, or part of one,
            matches the query.
  Example :
  Returns : an array of zero or more Bio::Ontology::TermI objects
  Args    : a Bio::Ontology::TermI object
 
 

find_identically_named_terms

  Title   : find_identically_named_terms
  Usage   : ($term) = $oe->find_identically_named_terms($term0);
  Function: Find term instances where names match the query term
            name exactly
  Example :
  Returns : an array of zero or more Bio::Ontology::TermI objects
  Args    : a Bio::Ontology::TermI object
 
 

Factory for relationships and terms

relationship_factory

  Title   : relationship_factory
  Usage   : $fact = $obj->relationship_factory()
  Function: Get (and set, if the engine 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 engine 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    :
 
 

annotation

  Title   : annotation
  Usage   : $annos = $obj->annotation()
  Function: Get/Set the Bio::Annotation::Collection object
            The collection contains Bio::Annotation::SimpleValue
            objects to store header information like the version
            and date present in the header section of an Ontology
            file.
 
  Example :
  Returns : value of annotation (a Bio::Annotation::Collection
            compliant object)
  Args    : A Bio::Annotation::Collection object (Optional)