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Bio::Ontology::OntologUseriContributed Perl DBio::Ontology::OntologyEngineI(3)

NAME
       Bio::Ontology::OntologyEngineI -	Interface a minimal Ontology
       implementation should satisfy

SYNOPSIS
	   # see documentation of methods

DESCRIPTION
       This describes the minimal interface an ontology	query engine should
       provide.	 It intentionally does not make	explicit references to the
       ontology	being a	DAG, nor does it mandate that the ontology be a
       vocabulary. Rather, it tries to generically express what	should be
       accessible (queriable) about an ontology.

       The idea	is to allow for	different implementations for different
       purposes, which may then	differ as to which operations are efficient
       and which are not, and how much richer the functionality	is on top of
       this minimalistic set of	methods. Check modules in the Bio::Ontology
       namespace to find out which implementations exist. At the time of
       writing,	there is a SimpleOntologyEngine	(which does not	use Graph.pm),
       and a Graph.pm-based implementation in SimpleGOEngine.

       Ontology	parsers	in Bio::OntologyIO are required	to return an
       implementation of this interface.

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

APPENDIX
       The rest	of the documentation details each of the object	methods.
       Internal	methods	are usually preceded with a _

   add_term
	Title	: add_term
	Usage	: add_term(TermI term):	TermI
	Function: Adds TermI object to the ontology engine term	store
	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.

   add_relationship_type
	Title	: add_relationship_type
	Usage	: add_relationship_type(scalar,OntologyI ontology)
	Function: Adds a relationshiptype object to the	ontology engine.
	Example	:
	Returns	: 1 on success,	undef on failure
	Args	: The name(scalar) of the relationshiptype, and	the OntologyI
		  it is	to be added to.

   get_relationship_type
	Title	: get_relationship_type
	Usage	: get_relationship_type(scalar): RelationshipTypeI
	Function: Get a	relationshiptype object	from the ontology engine.
	Example	:
	Returns	: A RelationshipTypeI object.
	Args	: The name (scalar) of the RelationshipTypeI object desired.

   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 ancestors.

	Example	: @root_terms =	$obj->get_root_terms()
	Returns	: Array	of TermI objects.
	Args	:

Factory	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::ObjectFactory
		  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::ObjectFactory
		  compliant object)
	Args	:

Decorator Methods
	These methods come with	a default implementation that uses the
	abstract methods defined for this interface. This may not be very
	efficient, and hence implementors are encouraged to override these
	methods	if they	can provide more efficient implementations.

   get_all_terms
	Title	: get_all_terms
	Usage	: get_all_terms: TermI
	Function: Retrieves all	terms from the ontology.

		  This is more a decorator method. We provide a	default
		  implementation here that loops over all root terms and gets
		  all descendants for each root	term. The overall union	of
		  terms	is then	made unique by name and	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.

		  Engine implementations that can provide a more efficient
		  method for obtaining all terms should	definitely override
		  this.

	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 name

Experimental API method	proposals
	Ontologies are a very new domain in bioperl, and we are	not sure yet
	what we	will want to do	on and with ontologies in which
	situation. The methods from here on downwards are solely API
	descriptions to	solicit	comment	and feedback; the chance of any	of
	those being actually implemented already is very slim.

	Disclaimer: As long as an API method stays in this section, it is
	subject	to change, possibly even radical change	or complete
	deletion. If it's not implemented yet (most likely it isn't),
	implement yourself at your own risk.

	So far for the disclaimer. The reason the API description is here,
	however, is to solicit feedback. Please	feel encouraged	to share your
	opinion, regardless of what it is (a notable difference	of this	API
	method to others is that there is actually no working code behind it
	- so the defense line is non-existent for practical purposes).

   common_ancestor_path
	Title	: common_ancestor_path
	Usage	:
	Function: Get the paths	from two terms A and B to term C, such that
		  there	is no other term D to which A and B would have a shorter
		  path,	provided there is a term C to which both A and B are
		  connected by a path.

		  Note that the	path to	the common ancestor between A and A
		  exists, has distance zero, and predicate "identity".

		  The search for the common ancestor C can be further
		  constrained by supplying a predicate term. If	supplied, the
		  predicates of	the two	paths (A,C) and	(B,C) must have	a
		  common ancestor identical to the predicate, or that has a
		  path to the predicate.

	Example	:
	Returns	: The path of the first	term to	the common ancestor in scalar
		  context, and both paths in list context. Paths are
		  Bio::Ontology::PathI compliant objects.
	Args	: The two terms	(Bio::Ontology::TermI objects),	and optionally
		  a constraining common	predicate (Bio::Ontology::TermI	object).
		  The latter may also be given as a scalar, in which case it
		  is treated as	a boolean that,	if TRUE, means that the	two paths
		  must have identical predicates in order to be	returned.

perl v5.32.1			  2019-12-07 Bio::Ontology::OntologyEngineI(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Peter Dimitrov | APPENDIX | Factory for relationships and terms | Decorator Methods | Experimental API method proposals

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