Bio::Ontology::OntologyEngineI.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

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:
   http://bugzilla.open-bio.org/
 
 

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.