bio::ontology::documentregistry(3pm) [debian man page]
Bio::Ontology::DocumentRegistry(3pm) User Contributed Perl Documentation Bio::Ontology::DocumentRegistry(3pm) NAME
Bio::Ontology::DocumentRegistry - Keep track of where to find ontologies. Allows lookups by name. SYNOPSIS
my $registry = Bio::Ontology::DocumentRegistry->get_instance(); my($ont,$def,$fmt) = $registry->documents('Sequence Ontology'); my $io = Bio::OntologyIO->new(-url => $ont, -defs_url => $def, -format => $fmt); my $so = $io->next_ontology(); #... DESCRIPTION
Do not use this directly, use Bio::Ontology::OntologyStore instead. Bio::Ontology::OntologyStore uses Bio::Ontology::DocumentRegistry to load and cache ontologies as object graphs, you can just ask it for what you want by name. See Bio::Ontology::OntologyStore for details. 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 - Allen Day Email allenday@ucla.edu APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ get_instance Title : get_instance Usage : my $singleton = Bio::Ontology::DocumentRegistry->get_instance(); Function: constructor Returns : The Bio::Ontology::DocumentRegistry singleton. Args : None Usage documents Title : documents Usage : my($ontology_url, $definitions_url, $format) = $obj->documents('Sequence Ontology'); Function: Maps an ontology name to a list of (local or) remote URIs where the files can be located. Returns : A 3-item list:(1) URI for the ontology file(2) URI for the ontology definitions file(3) format of the files (dagedit, obo, etc) Args : Name of an ontology, e.g. 'Sequence Ontology', or 'Cellular Component (Gene Ontology)' perl v5.14.2 2012-03-02 Bio::Ontology::DocumentRegistry(3pm)
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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)