Bio::Ontology::SimpleOntologyEngine.3pm

Langue: en

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

Section: 3 (Bibliothèques de fonctions)

NAME

Bio::Ontology::SimpleOntologyEngine - Implementation of OntologyEngineI interface

SYNOPSIS

   my $soe = Bio::Ontology::SimpleOntologyEngine->new;
 
 

DESCRIPTION

This is a ``simple'' implementation of 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 the web:
   http://bugzilla.open-bio.org/
 
 

AUTHOR - Peter Dimitrov

Email dimitrov@gnf.org

CONTRIBUTORS

Hilmar Lapp, 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   : $soe = Bio::Ontology::SimpleOntologyEngine->new;
  Function: Initializes the ontology engine.
  Example : $soe = Bio::Ontology::SimpleOntologyEngine->new;
  Returns : Object of class SimpleOntologyEngine.
  Args    :
 
 

_instantiated_terms_store

  Title   : _instantiated_terms_store
  Usage   : $obj->_instantiated_terms_store($newval)
  Function:
  Example :
  Returns : hash
  Args    : empty hash
 
 

mark_instantiated

  Title   : mark_instantiated
  Usage   : $self->mark_instantiated(TermI terms): TermI
  Function: Marks TermI objects as fully instantiated,
            allowing for proper counting of the number of terms in the term store.
            The TermI objects has to be already stored in the term store in order
            to be marked.
  Example : $self->mark_instantiated($term);
  Returns : its argument or throws an exception if a term is not
            in the term store.
  Args    : array of objects of class TermI.
 
 

mark_uninstantiated

  Title   : mark_uninstantiated
  Usage   : $self->mark_uninstantiated(TermI terms): TermI
  Function: Marks TermI objects as not fully instantiated,
  Example : $self->mark_uninstantiated($term);
  Returns : its argument or throws an exception if a term is not
            in the term store(if the term is not marked it does nothing).
  Args    : array of objects of class TermI.
 
 

_term_store

  Title   : term_store
  Usage   : $obj->_term_store($newval)
  Function:
  Example :
  Returns : reference to an array of Bio::Ontology::TermI objects
  Args    : reference to an array of Bio::Ontology::TermI objects
 
 

add_term

  Title   : add_term
  Usage   : add_term(TermI term): TermI
  Function: Adds TermI object to the ontology engine term store.
  Marks the term fully instantiated by default.
  Example : $soe->add_term($term)
  Returns : its argument.
  Args    : object of class TermI.
 
 

get_term_by_identifier

  Title   : get_term_by_identifier
  Usage   : get_term_by_identifier(String id): TermI
  Function: Retrieves terms from the term store by their identifier
            field, or an empty list if not there.
  Example : $term = $soe->get_term_by_identifier("IPR000001");
  Returns : An array of zero or more Bio::Ontology::TermI objects.
  Args    : An array of identifier strings
 
 

_get_number_rels

  Title   : get_number_rels
  Usage   :
  Function:
  Example :
  Returns : 
  Args    :
 
 

_get_number_terms

  Title   : _get_number_terms
  Usage   :
  Function:
  Example :
  Returns : 
  Args    :
 
 

_relationship_store

  Title   : _storerelationship_store
  Usage   : $obj->relationship_store($newval)
  Function: 
  Example : 
  Returns : reference to an array of Bio::Ontology::TermI objects
  Args    : reference to an array of Bio::Ontology::TermI objects
 
 

_inverted_relationship_store

  Title   : _inverted_relationship_store
  Usage   :
  Function:
  Example :
  Returns : reference to an array of Bio::Ontology::TermI objects
  Args    : reference to an array of Bio::Ontology::TermI objects
 
 

_relationship_type_store

  Title   : _relationship_type_store
  Usage   : $obj->_relationship_type_store($newval)
  Function: 
  Example : 
  Returns : reference to an array of Bio::Ontology::RelationshipType objects
  Args    : reference to an array of Bio::Ontology::RelationshipType objects
 
 

_add_relationship_simple

  Title   : _add_relationship_simple
  Usage   :
  Function:
  Example :
  Returns : 
  Args    :
 
 

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(): RelationshipI
  Function: Retrieves all relationship objects.
  Example :
  Returns : Array of RelationshipI objects
  Args    :
 
 

get_all_relationships

  Title   : get_all_relationships
  Usage   : get_all_relationships(): RelationshipI
  Function: Retrieves all relationship objects.
  Example :
  Returns : Array of RelationshipI objects
  Args    :
 
 

get_predicate_terms

  Title   : get_predicate_terms
  Usage   : get_predicate_terms(): TermI
  Function: Retrives all relationship types stored in the engine
  Example :
  Returns : reference to an array of Bio::Ontology::RelationshipType objects
  Args    :
 
 

_is_rel_type

  Title   : _is_rel_type
  Usage   :
  Function:
  Example :
  Returns : 
  Args    :
 
 

_typed_traversal

  Title   : _typed_traversal
  Usage   :
  Function:
  Example :
  Returns :
  Args    :
 
 

get_child_terms

  Title   : get_child_terms
  Usage   : get_child_terms(TermI term, TermI predicate_terms): TermI
            get_child_terms(TermI term, RelationshipType 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
            get_child_terms(TermI term, RelationshipType predicate_terms): 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. Uses
            _typed_traversal to find all descendants.
 
  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
            get_child_terms(TermI term, RelationshipType 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
            get_child_terms(TermI term, RelationshipType 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. Uses _typed_traversal to find
            all ancestors.
 
  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    :
 
 

_filter_repeated

  Title   : _filter_repeated
  Usage   : @lst = $self->_filter_repeated(@old_lst);
  Function: Removes repeated terms
  Example :
  Returns : List of unique TermI objects
  Args    : List of TermI objects
 
 

get_all_terms

  Title   : get_all_terms
  Usage   : get_all_terms(): TermI
  Function: Retrieves all terms currently stored in the ontology.
  Example : @all_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.
 
            This implementation can efficiently resolve queries by
            identifier.
 
  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
 
 

relationship_factory

  Title   : relationship_factory
  Usage   : $fact = $obj->relationship_factory()
  Function: Get/set 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    : on set, a Bio::Factory::ObjectFactoryI compliant object
 
 

term_factory

  Title   : term_factory
  Usage   : $fact = $obj->term_factory()
  Function: Get/set the object factory to be used when term objects are
            created by the implementation on-the-fly.
 
            Note that this ontology engine implementation does not
            create term objects on the fly, and therefore setting this
            attribute is meaningless.
 
  Example : 
  Returns : value of term_factory (a Bio::Factory::ObjectFactoryI
            compliant object)
  Args    : on set, a Bio::Factory::ObjectFactoryI compliant object
 
 

_filter_unmarked

  Title   : _filter_unmarked
  Usage   : _filter_unmarked(TermI terms): TermI
  Function: Removes the uninstantiated terms from the list of terms
  Example :
  Returns : array of fully instantiated TermI objects
  Args    : array of TermI objects
 
 

remove_term_by_id

  Title   : remove_term_by_id
  Usage   : remove_term_by_id(String id): TermI
  Function: Removes TermI object from the ontology engine using the
            string id as an identifier. Current implementation does not
            enforce consistency of the relationships using that term.
  Example : $term = $soe->remove_term_by_id($id);
  Returns : Object of class TermI or undef if not found.
  Args    : The string identifier of a term.
 
 

to_string

  Title   : to_string
  Usage   : print $sv->to_string();
  Function: Currently returns formatted string containing the number of
            terms and number of relationships from the ontology engine.
  Example : print $sv->to_string();
  Returns :
  Args    :
 
 

_unique_termid

  Title   : _unique_termid
  Usage   :
  Function: Returns a string that can be used as ID using fail-over
            approaches. 
 
            If the identifier attribute is not set, it uses the
            combination of name and ontology name, provided both are
            set. If they are not, it returns the name alone.
 
            Note that this is a private method. Call from inheriting
            classes but not from outside.
 
  Example :
  Returns : a string
  Args    : a Bio::Ontology::TermI compliant object