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knotview 0.2.0rc1 (Default branch)
02-21-2008
Knotview is a crossing between a concept mapper, a wiki, and a database. The main idea behind it is to split information into small chunks (knots) and make links between them. Visual organisation is not enforced: links can be drawn arbitrarily. With Knotview, only the user decides how the information must be shown. Creating links pointing towards files or URLs is possible, and make it very easy to gather scattered information into a single place. Knotview can be used as a powerful bookmark manager, a mind mapper, a small database, and much more. License: GNU General Public License (GPL) Changes:|
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Bio::IdentifiableI(3pm) User Contributed Perl Documentation Bio::IdentifiableI(3pm) NAME
Bio::IdentifiableI - interface for objects with identifiers SYNOPSIS
# to test this is an identifiable object $obj->isa("Bio::IdentifiableI") || $obj->throw("$obj does not implement the Bio::IdentifiableI interface"); # Accessors $object_id = $obj->object_id(); $namespace = $obj->namespace(); $authority = $obj->authority(); $version = $obj->version(); # Gets authority:namespace:object_id $lsid = $obj->lsid_string(); # Gets namespace:object_id.version $ns_string = $obj->namespace_string(); DESCRIPTION
This interface describes methods expected on identifiable objects, i.e. ones which have identifiers expected to make sense across a number of instances and/or domains. This interface is modeled after pretty much ubiquitous ideas for names in bioinformatics being databasename:object_id.version Example: swissprot:P012334.2 or: GO:0007048 The object will also work with LSID proposals which adds the concept of an authority, being the DNS name of the organisation assigning the namespace. See <http://lsid.sourceforge.net/>. Helper functions are provided to make useful strings: lsid_string - string complying to the LSID standard namespace_string - string complying to the usual convention of namespace:object_id.version 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 one of the Bioperl mailing lists. 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 the bugs and their resolution. Bug reports can be submitted via the web: https://redmine.open-bio.org/projects/bioperl/ AUTHOR - Ewan Birney Email birney@ebi.ac.uk Implementation Specific Functions These functions are the ones that a specific implementation must define. object_id Title : object_id Usage : $string = $obj->object_id() Function: a string which represents the stable primary identifier in this namespace of this object. For DNA sequences this is its accession_number, similarly for protein sequences Returns : A scalar Status : Virtual version Title : version Usage : $version = $obj->version() Function: a number which differentiates between versions of the same object. Higher numbers are considered to be later and more relevant, but a single object described the same identifier should represent the same concept Returns : A number Status : Virtual authority Title : authority Usage : $authority = $obj->authority() Function: a string which represents the organisation which granted the namespace, written as the DNS name for organisation (eg, wormbase.org) Returns : A scalar Status : Virtual namespace Title : namespace Usage : $string = $obj->namespace() Function: A string representing the name space this identifier is valid in, often the database name or the name describing the collection Returns : A scalar Status : Virtual Implementation optional functions These functions are helper functions that are provided by the interface but can be overridden if so wished lsid_string Title : lsid_string Usage : $string = $obj->lsid_string() Function: a string which gives the LSID standard notation for the identifier of interest Returns : A scalar namespace_string Title : namespace_string Usage : $string = $obj->namespace_string() Function: a string which gives the common notation of namespace:object_id.version Returns : A scalar perl v5.14.2 2012-03-02 Bio::IdentifiableI(3pm)