Bio::Ontology OntologyI
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Summary
Bio::Ontology::OntologyI - Interface for an ontology implementation
Package variables
No package variables defined.
Inherit
Bio::Ontology::OntologyEngineI
Synopsis
    # see method documentation
Description
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.
Methods
nameDescriptionCode
authorityDescriptionCode
identifierDescriptionCode
definitionDescriptionCode
closeDescriptionCode
relationship_factoryDescriptionCode
term_factoryDescriptionCode
Methods description
namecode    nextTop
 Title   : name
Usage : $obj->name($newval)
Function: Get/set the name of this ontology.
Example :
Returns : value of name (a scalar)
Args :
authoritycodeprevnextTop
 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 :
identifiercodeprevnextTop
 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 :
definitioncodeprevnextTop
 Title   : definition
Usage : $def = $obj->definition()
Function: Get a descriptive definition for this ontology.
Example :
Returns : value of definition (a scalar)
Args :
closecodeprevnextTop
 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 : none
relationship_factorycodeprevnextTop
 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_factorycodeprevnextTop
 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 :
Methods code
namedescriptionprevnextTop
sub name {
    shift->throw_not_implemented();
}
authoritydescriptionprevnextTop
sub authority {
    shift->throw_not_implemented();
}
identifierdescriptionprevnextTop
sub identifier {
    shift->throw_not_implemented();
}
definitiondescriptionprevnextTop
sub definition {
    shift->throw_not_implemented();
}
closedescriptionprevnextTop
sub close {
    shift->throw_not_implemented();
}
relationship_factorydescriptionprevnextTop
sub relationship_factory {
    return shift->throw_not_implemented();
}
term_factorydescriptionprevnextTop
sub term_factory {
    return shift->throw_not_implemented();
}

1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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 Top
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 BugsTop
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://redmine.open-bio.org/projects/bioperl/
AUTHOR - Hilmar LappTop
Email hlapp at gmx.net
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
Methods defined in this interface.Top
Methods inherited from Bio::Ontology::OntologyEngineITop
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_termTop
 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_relationshipTop
 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_relationshipsTop
 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_termsTop
 Title   : get_predicate_terms
Usage : get_predicate_terms(): TermI[]
Function:
Example :
Returns :
Args :
get_child_termsTop
 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_termsTop
 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_termsTop
 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_termsTop
 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_termsTop
 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()Top
 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_termsTop
 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 = $obj->get_all_terms() Returns : Array of TermI objects. Args :
find_termsTop
 Title   : find_terms
Usage : ($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 name
Factory for relationships and termsTop