SYNOPSIS

#get Bio::Phenotype::PhenotypeI somehow
print $phenotype->name(), "\n";
print $phenotype->description(), "\n";
my @keywords = ( "achondroplasia", "dwarfism" );
$phenotype->add_keywords( @keywords );
foreach my $keyword ( $phenotype->each_keyword() ) {
print $keyword, "\n";
}
$phenotype->remove_keywords();
foreach my $gene_symbol ( $phenotype->each_gene_symbol() ) {
print $gene_symbol, "\n";
}
foreach my $corr ( $phenotype->each_Correlate() ) {
# Do something with $corr
}
foreach my $var ( $phenotype->each_Variant() ) {
# Do something with $var (mutation)
}
foreach my $measure ( $phenotype->each_Measure() ) {
# Do something with $measure
}

DESCRIPTION

This superclass implements common methods for classes modelling phenotypes. Bio::Phenotype::OMIM::OMIMentry is an example of an instantiable phenotype class (the design of this interface was partially guided by the need to model OMIM entries). Please note. This class provides methods to associate mutations (methods ``each_Variant'', ...) and genotypes (methods ``each_Genotype'', ...) with phenotypes. Yet, these aspects might need some future enhancements, especially since there is no ``genotype'' class yet.

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing lists Your participation is much appreciated.

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

[email protected]

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.

Reporting Bugs

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

AUTHOR

Christian M. Zmasek

Email: czmasek-at-burnham.org or [email protected]

WWW: http://monochrome-effect.net/

Address:

  Genomics Institute of the Novartis Research Foundation
  10675 John Jay Hopkins Drive
  San Diego, CA 92121

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new

 Title   : new
 Usage   : $obj = Bio::Phenotype::Phenotype->new( -name         => "XY",
                                                  -description  => "This is ..." );
 Function: Creates a new Phenotype object.
 Returns : A new Phenotype object.
 Args    : -name                           => the name
           -description                    => the description of this phenotype
           -species                        => ref to the the species
           -comment                        => a comment

init

 Title   : init()
 Usage   : $obj->init();   
 Function: Initializes this OMIMentry to all "" and empty lists.
 Returns : 
 Args    :

name

 Title   : name
 Usage   : $obj->name( "r1" );
           or
           print $obj->name();
 Function: Set/get for the name or id of this phenotype.
 Returns : A name or id [scalar].
 Args    : A name or id [scalar] (optional).

description

 Title   : description
 Usage   : $obj->description( "This is ..." );
           or
           print $obj->description();
 Function: Set/get for the description of this phenotype.
 Returns : A description [scalar].
 Args    : A description [scalar] (optional).

species

 Title   : species
 Usage   : $obj->species( $species );
           or
           $species = $obj->species();
 Function: Set/get for the species of this phenotype.
 Returns : A species [Bio::Species].
 Args    : A species [Bio::Species] (optional).

comment

 Title   : comment
 Usage   : $obj->comment( "putative" );
           or
           print $obj->comment();
 Function: Set/get for a comment about this phenotype.
 Returns : A comment [scalar].
 Args    : A comment [scalar] (optional).

each_gene_symbol

 Title   : each_gene_symbol()
 Usage   : @gs = $obj->each_gene_symbol();
 Function: Returns a list of gene symbols [scalars, most likely Strings]
           associated with this phenotype.
 Returns : A list of scalars.
 Args    :

add_gene_symbols

 Title   : add_gene_symbols
 Usage   : $obj->add_gene_symbols( @gs );
           or
           $obj->add_gene_symbols( $gs );
 Function: Pushes one or more gene symbols [scalars, most likely Strings]
           into the list of gene symbols.
 Returns : 
 Args    : scalar(s).

remove_gene_symbols

 Usage   : $obj->remove_gene_symbols();
 Function: Deletes (and returns) the list of gene symbols [scalars,
           most likely Strings] associated with this phenotype.
 Returns : A list of scalars.
 Args    :

each_Variant

 Title   : each_Variant()
 Usage   : @vs = $obj->each_Variant();
 Function: Returns a list of Bio::Variation::VariantI implementing objects
           associated with this phenotype.
           This is for representing the actual mutation(s) causing this 
           phenotype.
           {* The "variants" data member and its methods will/might need to be
           changed/improved in one way or another, CZ 09/06/02 *}
 Returns : A list of Bio::Variation::VariantI implementing objects.
 Args    :

add_Variants

 Usage   : $obj->add_Variants( @vs );
           or
           $obj->add_Variants( $v );
 Function: Pushes one or more Bio::Variation::VariantI implementing objects
           into the list of Variants.
 Returns : 
 Args    : Bio::Variation::VariantI implementing object(s).

remove_Variants

 Title   : remove_Variants
 Usage   : $obj->remove_Variants();
 Function: Deletes (and returns) the list of Bio::Variation::VariantI implementing
           objects associated with this phenotype.
 Returns : A list of Bio::Variation::VariantI implementing objects.
 Args    :

each_Reference

 Title   : each_Reference()
 Usage   : @refs = $obj->each_Reference();                 
 Function: Returns a list of Bio::Annotation::Reference objects
           associated with this phenotype.
 Returns : A list of Bio::Annotation::Reference objects.
 Args    :

add_References

 Title   : add_References
 Usage   : $obj->add_References( @refs );
           or
           $obj->add_References( $ref );                  
 Function: Pushes one or more Bio::Annotation::Reference objects
           into the list of References.
 Returns : 
 Args    : Bio::Annotation::Reference object(s).

remove_References

 Title   : remove_References()
 Usage   : $obj->remove_References();
 Function: Deletes (and returns) the list of Bio::Annotation::Reference objects
           associated with this phenotype.
 Returns : A list of Bio::Annotation::Reference objects.
 Args    :

each_CytoPosition

 Title   : each_CytoPosition()
 Usage   : @cps = $obj->each_CytoPosition();                 
 Function: Returns a list of Bio::Map::CytoPosition objects
           associated with this phenotype.
 Returns : A list of Bio::Map::CytoPosition objects.
 Args    :

add_CytoPositions

 Title   : add_CytoPositions
 Usage   : $obj->add_CytoPositions( @cps );
           or
           $obj->add_CytoPositions( $cp );                  
 Function: Pushes one or more Bio::Map::CytoPosition objects
           into the list of CytoPositions.
 Returns : 
 Args    : Bio::Map::CytoPosition object(s).

remove_CytoPositions

 Title   : remove_CytoPositions
 Usage   : $obj->remove_CytoPositions();
 Function: Deletes (and returns) the list o fBio::Map::CytoPosition objects
           associated with this phenotype.
 Returns : A list of Bio::Map::CytoPosition objects.
 Args    :

each_Correlate

 Title   : each_Correlate()
 Usage   : @corrs = $obj->each_Correlate();                 
 Function: Returns a list of Bio::Phenotype::Correlate objects
           associated with this phenotype.
           (Correlates are correlating phenotypes in different species;
           inspired by mouse correlates of human phenotypes in the OMIM
           database.)
 Returns : A list of Bio::Phenotype::Correlate objects.
 Args    :

add_Correlates

 Title   : add_Correlates
 Usage   : $obj->add_Correlates( @corrs );
           or
           $obj->add_Correlates( $corr );                  
 Function: Pushes one or more Bio::Phenotype::Correlate objects
           into the list of Correlates.
 Returns : 
 Args    : Bio::Phenotype::Correlate object(s).

remove_Correlates

 Title   : remove_Correlates
 Usage   : $obj->remove_Correlates();
 Function: Deletes (and returns) the list of Bio::Phenotype::Correlate objects
           associated with this phenotype.
 Returns : A list of Bio::Phenotype::Correlate objects.
 Args    :

each_Measure

 Title   : each_Measure()
 Usage   : @ms = $obj->each_Measure();                 
 Function: Returns a list of Bio::Phenotype::Measure objects
           associated with this phenotype.
           (Measure is for biochemically defined phenotypes
           or any other types of measures.)
 Returns : A list of Bio::Phenotype::Measure objects.
 Args    :

add_Measures

 Title   : add_Measures
 Usage   : $obj->add_Measures( @ms );
           or
           $obj->add_Measures( $m );                  
 Function: Pushes one or more Bio::Phenotype::Measure objects
           into the list of Measures.
 Returns : 
 Args    : Bio::Phenotype::Measure object(s).

remove_Measures

 Title   : remove_Measures
 Usage   : $obj->remove_Measures();
 Function: Deletes (and returns) the list of Bio::Phenotype::Measure objects
           associated with this phenotype.
 Returns : A list of Bio::Phenotype::Measure objects.
 Args    :

each_keyword

 Title   : each_keyword()
 Usage   : @kws = $obj->each_keyword();                 
 Function: Returns a list of key words [scalars, most likely Strings]
           associated with this phenotype.
 Returns : A list of scalars.
 Args    :

add_keywords

 Title   : add_keywords
 Usage   : $obj->add_keywords( @kws );
           or
           $obj->add_keywords( $kw );                  
 Function: Pushes one or more keywords [scalars, most likely Strings]
           into the list of key words.
 Returns : 
 Args    : scalar(s).

remove_keywords

 Title   : remove_keywords
 Usage   : $obj->remove_keywords();
 Function: Deletes (and returns) the list of key words [scalars,
           most likely Strings] associated with this phenotype.
 Returns : A list of scalars.
 Args    :

each_DBLink

 Title   : each_DBLink()
 Usage   : @dbls = $obj->each_DBLink();                 
 Function: Returns a list of Bio::Annotation::DBLink objects
           associated with this phenotype.
 Returns : A list of Bio::Annotation::DBLink objects.
 Args    :

add_DBLinks

 Title   : add_DBLinks
 Usage   : $obj->add_DBLinks( @dbls );
           or
           $obj->add_DBLinks( $dbl );                  
 Function: Pushes one or more Bio::Annotation::DBLink objects
           into the list of DBLinks.
 Returns : 
 Args    : Bio::Annotation::DBLink object(s).

remove_DBLinks

 Title   : remove_DBLinks
 Usage   : $obj->remove_DBLinks();
 Function: Deletes (and returns) the list of Bio::Annotation::DBLink objects
           associated with this phenotype.
 Returns : A list of Bio::Annotation::DBLink objects.
 Args    :

each_Genotype

 Title   : each_Reference()
 Usage   : @gts = $obj->each_Reference();                 
 Function: Returns a list of "Genotype" objects
           associated with this phenotype.
           {* the "genotypes" data member and its methods certainly will/needs to be
           changed/improved in one way or another since there is
           no "Genotype" class yet, CZ 09/06/02 *}
 Returns : A list of "Genotype" objects.
 Args    :

add_Genotypes

 Title   : add_Genotypes
 Usage   : $obj->add_Genotypes( @gts );
           or
           $obj->add_Genotypes( $gt );                  
 Function: Pushes one or more "Genotypes"
           into the list of "Genotypes".
 Returns : 
 Args    : "Genotypes(s)".

remove_Genotypes

 Title   : remove_Genotypes
 Usage   : $obj->remove_Genotypes();
 Function: Deletes (and returns) the list of "Genotype" objects
           associated with this phenotype.
 Returns : A list of "Genotype" objects.
 Args    :

_check_ref_type

 Title   : _check_ref_type
 Usage   : $self->_check_ref_type( $value, "Bio::Annotation::DBLink" );
 Function: Checks for the correct type.
 Returns : 
 Args    : The value to be checked, the expected class.