NAME
Bio::Ontology::OntologyI - Interface for an ontology implementation
SYNOPSIS
# see method documentationDESCRIPTION
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
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bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing listsSupport
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:
https://github.com/bioperl/bioperl-live/issuesAUTHOR - 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 : noneMethods 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 nameFactory 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 :