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.