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Bio-GMOD-GenericGenePage-0.12
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/ Bio::GMOD::GenericGenePage

NAME

Bio::GMOD::GenericGenePage - Generic GMOD gene page base class

SYNOPSIS

my $page = Bio::GMOD::GenericGenePage->new( $gene_identifier );
my $xml = $page->render_xml();

DESCRIPTION

Bio::GMOD::GenericGenePage is an abstract class to make it easier for Model Organism Databases (MODs) to serve up a simple XML that describes attributes of their gene models. In order to implement this, the user needs to subclass Bio::GMOD::GenericGenePage and provide the methods listed below as abstract classes. These methods are then used by the render_xml method to create XML for a given gene.

There is one example implementation included with this distribution, Bio::GMOD::GenericGenePage::Chado, which is a Chado adapter for a yeast database derived from SGD's GFF3. In order to implement this for another Chado database it should be fairly easy to modify the provided methods to create your own adaptor. For example, ParameciumDB could subclass Bio::GMOD::GenericGenePage::Chado and create Bio::GMOD::GenericGenePage::Chado::ParameciumDB and only override the data_provider and organism methods to have a working adaptor. Databases not based on Chado will only have slightly more work, in order to implement all of the abstract classes in Bio::GMOD::GenericGenePage.

Another example implementation is included, CXGN::Phenome::GenericGenePage, however this is only a partial implementation and will not work with the current release of Bio::GMOD::GenericGenePage.

BASE CLASS(ES)

none

SUBCLASSES

Bio::GMOD::GenericGenePage::Chado CXGN::Phenome::GenericGenePage

BUGS AND SUPPORT

Please report bugs and make support requests on the GMOD developers list, gmod-devel@lists.sourceforge.net.

AUTHOR

Scott Cain
CPAN ID: SCAIN
Cold Spring Harbor Laboratory
scain@cpan.org
http://www.gmod.org/

and Robert Buels.

COPYRIGHT

Copyright (c) 2008 Scott Cain and Robert Buels. All rights reserved. This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself.

The full text of the license can be found in the LICENSE file included with this module.

SEE ALSO

perl(1).

PROVIDED METHODS

new

Usage: my $genepage = MyGenePage->new( -id => $gene_identifier );
Desc : create a new gene page object.  should be overridden
Args : not specified
Ret  : a new gene page object
Side Effects: none as implemented here, but subclass
              implementations may have side effects
Example:

render_xml

Usage: my $xml = $page->render_xml();
Desc : render the XML for this generic gene page
Args : none
Ret  : string of xml
Side Effects: none

render_html NOT IMPLEMENTED!

Usage: my $html = $page->render_html();
Desc : render HTML for this generic gene page.  you may want to
       override this method for your implementation
Args : none
Ret  : string of html
Side Effects: none

ABSTRACT METHODS

Methods below should be overridden by each GenericGenePage implementation.

name

Usage: my $name = $genepage->name();
Desc : get the string name of this gene
Args : none
Ret  : string gene name, e.g. 'Pax6'
Side Effects: none

accessions

Usage: my @accessions = $genepage->accessions();
Desc : get a list of local accession values
Args : none
Ret  : a list of local accessions
Side Effects: none

Note that these are the accessions that are used by the MOD providing the information, not accessions in external databases like GenBank.

data_provider

Usage: my $data_provider = $genepage->data_provider();
Desc : The name of the data providing authority (ie, WormBase, SGD, etc)
Args : none
Ret  : string, name of the data provider
Side Effects: none

synonyms

Usage: my @syn = $genepage->synonyms();
Desc : get a list of synonyms for this gene
Args : none

Ret : list of strings,
      e.g. (  '1500038E17Rik',
              'AEY11',
              'Dey',
              "Dickie's small eye",
              'Gsfaey11',
              'Pax-6',
           )
Side Effects: none

map_locations

Usage: my @locs = $genepage->map_locations()
Desc : get a list of known map locations for this gene
Args : none
Ret  : list of map locations, each a hashref as:
       {  map_name => string map name,
          chromosome => string chromosome name,
          marker     => (optional) associated marker name,
          position   => numerical position on the map,
          units      => map units, either 'cm', for centimorgans,
                        or 'b', for bases
       }
Side Effects: none

ontology_terms

Usage: my @terms = $genepage->ontology_terms();
Desc : get a list of ontology terms
Args : none
Ret  : hash-style list as:
         termname => human-readable description,
Side Effects: none
Example:

   my %terms = $genepage->ontology_terms()

   # and %terms is now
   (  GO:0016711 => 'F:flavonoid 3'-monooxygenase activity',
      ...
   )

Note that the value in that has is the the concatenation of F:, B: or C: for molecular_function, biological_process, or cellular_component GO terms respectively. If the term does not belong to GO, there is no prepended identifier.

dbxrefs

Usage: my @dbxrefs = $genepage->dbxrefs();
Desc : get a list of database cross-references for info related to this gene
Args : none
Ret  : list of strings, like type:id e.g. ('PFAM:00012')
Side Effects: none

comments

Usage: my @comments = $genepage->comments();
Desc : get a list of comments with types
Args : none
Ret  : a hash of comment=>type, where type is optional (empty string)
Side Effects: none

literature_references

Usage: my @refs = $genepage->lit_refs();
Desc : get a list of literature references for this gene
Args : none
Ret  : list of literature reference identifers, as type:id,
       like ('PMID:0023423',...)
Side Effects: none

summary_text

Usage: my $summary = $page->summary_text();
Desc : get a text string of plain-English summary text for this gene
Args : none
Ret  : string of summary text
Side Effects: none

organism

Usage: my $species_info = $genepage->organism
Desc : get a handful of species-related information
Args : none
Ret  : hashref as:
       { ncbi_taxon_id => ncbi taxon id, (e.g. 3702),
         binomial      => e.g. 'Arabidopsis thaliana',
         common        => e.g. 'Mouse-ear cress',
       }
Side Effects: none