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.\" ========================================================================
.\"
.IX Title "Bio::Ontology::OntologyI 3pm"
.TH Bio::Ontology::OntologyI 3pm "2020-10-28" "perl v5.30.3" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
.if n .ad l
.nh
.SH "NAME"
Bio::Ontology::OntologyI \- Interface for an ontology implementation
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 1
\&    # see method documentation
.Ve
.SH "DESCRIPTION"
.IX Header "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.
.PP
This interface inherits from Bio::Ontology::OntologyEngineI.
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "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:
.PP
.Vb 1
\&  https://github.com/bioperl/bioperl\-live/issues
.Ve
.SH "AUTHOR \- Hilmar Lapp"
.IX Header "AUTHOR - Hilmar Lapp"
Email hlapp at gmx.net
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
.SH "Methods defined in this interface."
.IX Header "Methods defined in this interface."
.SS "name"
.IX Subsection "name"
.Vb 6
\& Title   : name
\& Usage   : $obj\->name($newval)
\& Function: Get/set the name of this ontology.
\& Example : 
\& Returns : value of name (a scalar)
\& Args    :
.Ve
.SS "authority"
.IX Subsection "authority"
.Vb 5
\& 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    :
.Ve
.SS "identifier"
.IX Subsection "identifier"
.Vb 3
\& 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\*(Aqs uniqueness may only hold within the scope of a
\&           particular application\*(Aqs run time, i.e., it may be a memory
\&           location.
\&
\& Example : 
\& Returns : value of identifier (a scalar)
\& Args    :
.Ve
.SS "definition"
.IX Subsection "definition"
.Vb 6
\& Title   : definition
\& Usage   : $def = $obj\->definition()
\& Function: Get a descriptive definition for this ontology.
\& Example : 
\& Returns : value of definition (a scalar)
\& Args    :
.Ve
.SS "close"
.IX Subsection "close"
.Vb 6
\& 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
.Ve
.SH "Methods inherited from Bio::Ontology::OntologyEngineI"
.IX Header "Methods 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 ...
.SS "add_term"
.IX Subsection "add_term"
.Vb 3
\& 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.
.Ve
.SS "add_relationship"
.IX Subsection "add_relationship"
.Vb 6
\& 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.
.Ve
.SS "get_relationships"
.IX Subsection "get_relationships"
.Vb 8
\& 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.
.Ve
.SS "get_predicate_terms"
.IX Subsection "get_predicate_terms"
.Vb 6
\& Title   : get_predicate_terms
\& Usage   : get_predicate_terms(): TermI[]
\& Function:
\& Example :
\& Returns :
\& Args    :
.Ve
.SS "get_child_terms"
.IX Subsection "get_child_terms"
.Vb 7
\& 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.
.Ve
.SS "get_descendant_terms"
.IX Subsection "get_descendant_terms"
.Vb 9
\& 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.
.Ve
.SS "get_parent_terms"
.IX Subsection "get_parent_terms"
.Vb 7
\& 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.
.Ve
.SS "get_ancestor_terms"
.IX Subsection "get_ancestor_terms"
.Vb 5
\& 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.
.Ve
.SS "get_leaf_terms"
.IX Subsection "get_leaf_terms"
.Vb 4
\& 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    :
.Ve
.SS "\fBget_root_terms()\fP"
.IX Subsection "get_root_terms()"
.Vb 4
\& 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    :
.Ve
.SS "get_all_terms"
.IX Subsection "get_all_terms"
.Vb 3
\& 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 = $obj\->get_all_terms()
\& Returns : Array of TermI objects.
\& Args    :
.Ve
.SS "find_terms"
.IX Subsection "find_terms"
.Vb 3
\& Title   : find_terms
\& Usage   : ($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
.Ve
.SH "Factory for relationships and terms"
.IX Header "Factory for relationships and terms"
.SS "relationship_factory"
.IX Subsection "relationship_factory"
.Vb 5
\& 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    :
.Ve
.SS "term_factory"
.IX Subsection "term_factory"
.Vb 5
\& 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    :
.Ve