/ 
Bio-GMOD-GenericGenePage-0.11
River stage zero No dependents
/ Bio::GMOD::GenericGenePage::Chado

NAME

Bio::GMOD::GenericGenePage::Chado -

SYNOPSIS

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

#and then you can print the xml or html in your page

DESCRIPTION

BASE CLASS(ES)

none

SUBCLASSES

none yet

PROVIDED METHODS

new

Usage: my $genepage = MyGenePage->new( -id => $gene_identifier );
       my $genepage = Bio::GMOD::GenericGenePage::Chado->new( feature_id => $id);
Desc : create a new gene page object; overridden from abstract class.
Args : -id => $feature_id
Ret  : a new gene page object
Side Effects: Sets feature_id attribute, creates db connection

dbh

Usage: my $dbh = $obj->dbh();
Desc: Sets/Gets Chado database handle
Args: DBI database handle to set, none to get

feature_id

Usage: my $feature_id = $obj->feature_id();
Desc: Sets/Gets feature_id
Args: Integer to set, none to get

CHADO SPECIFIC METHODS

Methods below were overridden from the GenericGenePage abstract 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 accession the is used by the MOD providing the information.

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, with the canonical/official/approved gene
      name first.
      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',
      ...
   )

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

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

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

AUTHOR(S)

Robert Buels