|Bio::IdentifiableI(3pm)||User Contributed Perl Documentation||Bio::IdentifiableI(3pm)|
Bio::IdentifiableI - interface for objects with identifiers
# 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();
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
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
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AUTHOR - Ewan Birney¶
Implementation Specific Functions¶
These functions are the ones that a specific implementation must define.
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
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
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
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
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
Title : namespace_string Usage : $string = $obj->namespace_string() Function: a string which gives the common notation of namespace:object_id.version Returns : A scalar