bio::ontology::pathi(3pm) [debian man page]
Bio::Ontology::PathI(3pm) User Contributed Perl Documentation Bio::Ontology::PathI(3pm) NAME
Bio::Ontology::PathI - Interface for a path between ontology terms SYNOPSIS
# see documentation of methods and an implementation, e.g., # Bio::Ontology::Path DESCRIPTION
This is the minimal interface for a path between two terms in an ontology. Ontology engines may use this. Essentially this is a very thin extension of the Bio::Ontology::RelationshipI interface. It basically adds an attribute distance(). For a RelationshipI, you can think of distance as equal to zero (subject == object) or 1 (subject != object). 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://redmine.open-bio.org/projects/bioperl/ AUTHOR - Hilmar Lapp Email hlapp at gmx.net APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ distance Title : distance Usage : $obj->distance($newval) Function: Get (and set if the implementation allows it) the distance between the two terms connected by this path. Example : Returns : value of distance (a scalar) Args : on set, new value (a scalar or undef, optional) Bio::Ontology::RelationshipI Methods subject_term Title : subject_term Usage : $subj = $rel->subject_term(); Function: Set/get for the subject term of this Relationship. The common convention for ontologies is to express relationships between terms as triples (subject, predicate, object). Returns : The subject term [Bio::Ontology::TermI]. Args : object_term Title : object_term Usage : $object = $rel->object_term(); Function: Set/get for the object term of this Relationship. The common convention for ontologies is to express relationships between terms as triples (subject, predicate, object). Returns : The object term [Bio::Ontology::TermI]. Args : predicate_term Title : predicate_term Usage : $type = $rel->predicate_term(); Function: Set/get for the predicate of this relationship. For a path the predicate (relationship type) is defined as the greatest common denominator of all predicates (relationship types) encountered along the path. I.e., if predicate A is-a predicate B, the greatest common denominator for a path containing both predicates A and B is B Returns : The predicate term [Bio::Ontology::TermI]. Args : ontology Title : ontology Usage : $ont = $obj->ontology() Function: Get the ontology that defined this relationship. Example : Returns : an object implementing Bio::Ontology::OntologyI Args : See Bio::Ontology::OntologyI. perl v5.14.2 2012-03-02 Bio::Ontology::PathI(3pm)
Check Out this Related Man Page
Bio::Ontology::RelationshipI(3pm) User Contributed Perl Documentation Bio::Ontology::RelationshipI(3pm) NAME
Bio::Ontology::RelationshipI - Interface for a relationship between ontology terms SYNOPSIS
# see documentation of methods and an implementation, e.g., # Bio::Ontology::Relationship DESCRIPTION
This is the minimal interface for a relationship between two terms in an ontology. Ontology engines will use this. The terminology we use here is the one commonly used for ontologies, namely the triple of (subject, predicate, object), which in addition is scoped in a namespace (ontology). It is called triple because it is a tuple of three ontology terms. There are other terminologies in use for expressing relationships. For those who it helps to better understand the concept, the triple of (child, relationship type, parent) would be equivalent to the terminology chosen here, disregarding the question whether the notion of parent and child is sensible in the context of the relationship type or not. Especially in the case of ontologies with a wide variety of predicates the parent/child terminology and similar ones can quickly become ambiguous (e.g., A synthesises B), meaningless (e.g., A binds B), or even conflicting (e.g., A is-parent-of B), and are therefore strongly discouraged. 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://redmine.open-bio.org/projects/bioperl/ AUTHOR - Peter Dimitrov Email dimitrov@gnf.org CONTRIBUTORS
Hilmar Lapp, email: hlapp at gmx.net APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ identifier Title : identifier Usage : print $rel->identifier(); Function: Set/get for the identifier of this Relationship. Note that this may not necessarily be used by a particular ontology. Returns : The identifier [scalar]. Args : subject_term Title : subject_term Usage : $subj = $rel->subject_term(); Function: Set/get for the subject term of this Relationship. The common convention for ontologies is to express relationships between terms as triples (subject, predicate, object). Returns : The subject term [Bio::Ontology::TermI]. Args : object_term Title : object_term Usage : $object = $rel->object_term(); Function: Set/get for the object term of this Relationship. The common convention for ontologies is to express relationships between terms as triples (subject, predicate, object). Returns : The object term [Bio::Ontology::TermI]. Args : predicate_term Title : predicate_term Usage : $type = $rel->predicate_term(); Function: Set/get for the relationship type of this relationship. The common convention for ontologies is to express relationships between terms as triples (subject, predicate, object). Returns : The relationship type [Bio::Ontology::TermI]. Args : ontology Title : ontology Usage : $ont = $obj->ontology() Function: Get the ontology that defined (is the scope for) this relationship. Example : Returns : an object implementing Bio::Ontology::OntologyI Args : See Bio::Ontology::OntologyI. perl v5.14.2 2012-03-02 Bio::Ontology::RelationshipI(3pm)