| 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
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
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
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.
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://github.com/bioperl/bioperl-live/issues
Email birney@ebi.ac.uk
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
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
| 2018-10-27 | perl v5.26.2 |