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BioPerl-1.7.7
River stage two • 60 direct dependents • 65 total dependents
/ Bio::Ontology::SimpleOntologyEngine

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