Scott Cain > Bio-GMOD-GenericGenePage-0.12 > Bio::GMOD::GenericGenePage::Chado

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Bio-GMOD-GenericGenePage-0.12.tar.gz

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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

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