NAME

OBO::APO::APO_ID - A module for describing Application Ontology (APO) identifiers. Its idspace, subnamespace and localID are stored.

SYNOPSIS

use OBO::APO::APO_ID;

$id = APO_ID->new();

$id->idspace("APO");

$id->subnamespace("X");

$id->localID("0000001");

$idspace = $id->idspace();

$subnamespace = $id->subnamespace();

$localID = $id->localID();

print $id->id_as_string();

$id->id_as_string("APO:P1234567");

DESCRIPTION

The OBO::APO::APO_ID class implements an Application Ontology identifier.

A APO ID holds: IDSPACE, SUBNAMESPACE and a NUMBER in the following form:

        APO:[A-Z][a-z]?nnnnnnn

For instance: APO:Pa1234567

The SUBNAMESPACE may be one of the following:

        C       Cellular component
        F       Molecular Function
        P       Biological Process
        B       Protein
        G       Gene
        I       Interaction
        R       Reference
        T       Taxon
        N       Instance
        U       Upper Level Ontology (APO)
        L       Relationship type (e.g. is_a)
        Y       Interaction type
        Z       Unknown

plus an extra (optional) qualifier could be added to explicitly capture the organism:

        a       Arabidopsis thaliana
        h       Homo sapiens
        y       Saccharomyces cerevisiae
        s       Schizosaccharomyces pombe
        c       Caenorhabditis elegans
        d       Drosophila melanogaster
        m       Mus musculus

AUTHOR

Erick Antezana, <erick.antezana -@- gmail.com>

COPYRIGHT AND LICENSE

This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself, either Perl version 5.8.7 or, at your option, any later version of Perl 5 you may have available.

subnamespace

  Usage    - print $id->subnamespace() or $id->subnamespace($name)
  Returns  - the subnamespace (string)
  Args     - the subnamespace (string)
  Function - gets/sets the subnamespace

id_as_string

  Usage    - print $id->id_as_string() or $id->id_as_string("APO:X0000001")
  Returns  - the id as string (scalar)
  Args     - the id as string
  Function - gets/sets the id as string

equals

  Usage    - print $id->equals($id)
  Returns  - 1 (true) or 0 (false)
  Args     - the other ID (OBO::APO::APO_ID)
  Function - tells if two IDs are equal

next_id

  Usage    - $id->next_id()
  Returns  - the next ID (OBO::APO::APO_ID)
  Args     - none
  Function - returns the next ID, which is new

previous_id

  Usage    - $id->previous_id()
  Returns  - the previous ID (OBO::APO::APO_ID)
  Args     - none
  Function - returns the previous ID, which is new

CPAN RT