Provided by: libbio-perl-perl_1.7.2-2_all 
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:
https://github.com/bioperl/bioperl-live/issues
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: Retrieves 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