Bio::Phenotype::OMIM
OMIMentry
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Summary
OMIMentry - represents OMIM (Online Mendelian Inheritance in Man) database entries
Package variables
No package variables defined.
Included modules
Inherit
Synopsis
$obj = Bio::Phenotype::OMIM::OMIMentry->new( -mim_number => 200000,
-description => "This is ...",
-more_than_two_genes => 1 );
Description
Inherits from Bio::Phenotype::PhenotypeI.
Bio::Phenotype::OMIM::OMIMparser parses the flat file representation
of OMIM (i.e. files "omim.txt" and "genemap") returning OMIMentry objects.
Methods
Methods description
Title : MIM_number
Usage : $omim->MIM_number( "100050" );
or
print $omim->MIM_number();
Function: Set/get for the MIM number of this OMIM entry.
Returns : The MIM number [an integer larger than 100000].
Args : The MIM number [an integer larger than 100000] (optional). |
Title : add_AllelicVariants
Usage : $obj->add_AllelicVariants( @avs );
or
$obj->add_AllelicVariants( $av );
Function: Pushes one or more OMIMentryAllelicVariant
into the list of OMIMentryAllelicVariants.
Returns :
Args : Bio::Phenotype::OMIM::OMIMentryAllelicVariant object(s). |
Title : additional_references
Usage : $omim->additional_references( "Miller er al." );
or
print $omim->additional_references();
Function: Set/get for the additional references of this OMIM antry
(see also).
Returns : additional reference [scalar].
Args : additional reference [scalar] (optional). |
Title : alternative_titles_and_symbols
Usage : $omim->alternative_titles_and_symbols( "AORTIC ANEURYSM, ABDOMINAL" );
or
print $omim->alternative_titles_and_symbols();
Function: Set/get for the "alternative titles and symbols" of this OMIM entry.
Currently, everything after the first line of title (TI) field is
considered "alternative titles and symbols".
Returns : "alternative titles and symbols" [scalar].
Args : "alternative titles and symbols" [scalar] (optional). |
Title : clinical_symptoms
Usage : $omim->clinical_symptoms( "Patients with ..." );
or
print $omim->clinical_symptoms();
Function: Set/get for the clinical symptoms of this OMIM entry.
Returns : The clinical symptoms [scalar].
Args : The clinical symptoms [scalar] (optional). |
Title : contributors
Usage : $omim->contributors( "Kelly A. Przylepa - revised: 03/18/2002" );
or
print $omim->contributors();
Function: Set/get for the contributors field of the OMIM database.
Returns : Name(s) and date(s) [scalar - free form].
Args : Name(s) and date(s) [scalar - free form] (optional). |
Title : created
Usage : $omim->created( "Victor A. McKusick: 6/4/1986" );
or
print $omim->created();
Function: Set/get for the created field of the OMIM database.
Returns : Name(s) and date(s) [scalar - free form].
Args : Name(s) and date(s) [scalar - free form] (optional). |
Title : each_AllelicVariant()
Usage : @avs = $obj->each_AllelicVariant();
Function: Returns a list of Bio::Phenotype::OMIM::OMIMentryAllelicVariant objects
associated with this OMIM entry.
Returns : A list of Bio::Phenotype::OMIM::OMIMentryAllelicVariant objects.
Args : |
Title : edited
Usage : $omim->edited( "alopez: 06/03/1997" );
or
print $omim->edited();
Function: Set/get for the edited field of the OMIM database.
Returns : Name(s) and date(s) [scalar - free form].
Args : Name(s) and date(s) [scalar - free form] (optional). |
Title : gene_status
Usage : $omim->gene_status( "C" );
or
print $omim->gene_status();
Function: Set/get for the gene status of this OMIM entry.
The certainty with which assignment of loci to chromosomes or the linkage
between two loci has been established has been graded into the following
classes:
<L>C = confirmed - observed in at least two laboratories or in several families.
<L>P = provisional - based on evidence from one laboratory or one family.
<L>I = inconsistent - results of different laboratories disagree.
<L>L = limbo - evidence not as strong as that provisional, but included for
heuristic reasons. (Same as `tentative'.)
Returns : [C, P, I, or L].
Args : [C, P, I, or L] (optional). |
Title : init()
Usage : $obj->init();
Function: Initializes this OMIMentry to all "" and empty lists.
Returns :
Args : |
Title : is_separate
Usage : $omim->is_separate( 1 );
or
print $omim->is_separate();
Function: This is true if the phenotype determined by the gene at
the given locus is separate from those represented by
other entries where "is_separate" is true and if the mode
of inheritance of the phenotype has been proved
(in the judgment of the authors and editors).
In OMIM, this is indicated by a asterisk (*)
before an entry number (e.g. *113705 BREAST CANCER,
TYPE 1; BRCA1).
Returns : [1 or 0].
Args : [1 or 0] (optional). |
Title : mapping_method
Usage : $omim->mapping_method( "PCR of somatic cell hybrid DNA" );
or
print $omim->mapping_method();
Function: Set/get for the mapping method of this OMIM entry.
Returns : The mapping method [scalar].
Args : The mapping method [scalar] (optional). |
Title : miniMIM
Usage : $omim->miniMIM( $MM );
or
$MM = $omim->miniMIM();
Function: Set/get for the Mini MIM associated with this OMIM antry
(see also).
Returns : [Bio::Phenotype::OMIM::MiniMIMentry].
Args : [Bio::Phenotype::OMIM::MiniMIMentry] (optional). |
Title : more_than_two_genes
Usage : $omim->more_than_two_genes( 1 );
or
print $omim->more_than_two_genes();
Function: This is true if this phenotype can be caused
by mutation in any of two or more genes.
In OMIM, this is indicated by a number symbol (#)
before an entry number (e.g. #114480 -- BREAST CANCER).
Returns : [1 or 0].
Args : [1 or 0] (optional). |
Title : new
Usage : $obj = Bio::Phenotype::OMIM::OMIMentry->new( -mim_number => 200000,
-description => "This is ...",
-more_than_two_genes => 1 );
Function: Creates a new OMIMentry object.
Returns : A new OMIMentry object.
Args : -mim_number => the MIM number
-title => the title or name
-alternative_titles_and_symbols => the "alternative titles and symbols"
-more_than_two_genes => can phenotype can be caused by mutation in any of two or more genes?
-is_separate => is this phenotype separate from those represented by other entries
-description => the description of this phenotype
-mapping_method => the mapping method
-gene_status => the gene status of this
-comment => a comment
-species => ref to the the species (human)
-created => created by whom/when
-edited => edited by whom/when
-contributors => contributed by whom/when
-additional_references => "see also"
-clinical_symptoms => the clinical symptoms
-minimim => the Mini MIM associated with this OMIM antry |
Title : remove_AllelicVariants
Usage : $obj->remove_AllelicVariants();
Function: Deletes (and returns) the list of OMIMentryAllelicVariant objects
associated with this OMIM entry.
Returns : A list of OMIMentryAllelicVariant objects.
Args : |
Title : title
Usage : $omim->title( "AARSKOG SYNDROME" );
or
print $omim->title();
Function: Set/get for the title or name of this OMIM entry.
This method is an alias to the method "name" of
Bio::Phenotype::PhenotypeI.
Returns : The title [scalar].
Args : The title [scalar] (optional). |
Methods code
sub MIM_number
{ my ( $self, $value ) = @_;
if ( defined $value ) {
if ( $value =~ /\D/
|| ( $value < 100000 && $value != DEFAULT_MIM_NUMER ) ) {
$self->throw( "Found [$value]"
. " where [integer larger than 100000] expected" );
}
$self->{ "_MIM_number" } = $value;
}
return $self->{ "_MIM_number" };
}
} | sub _array_to_string
{ my( $self, @value ) = @_;
my $s = "";
for ( my $i = 0; $i < scalar( @value ); ++$i ) {
if ( ! ref( $value[ $i ] ) ) {
$s .= "#" . $i . "\n-- Value:\n" . $value[ $i ] . "\n";
}
elsif ( $value[ $i ]->isa( "Bio::Phenotype::OMIM::OMIMentryAllelicVariant" )
|| $value[ $i ]->isa( "Bio::Phenotype::Correlate" ) ) {
$s .= "#" . $i . "\n" . ( $value[ $i ] )->to_string() . "\n";
}
elsif ( $value[ $i ]->isa( "Bio::Annotation::Reference" ) ) {
$s .= "#".$i."\n-- Authors:\n".( $value[ $i ] )->authors()."\n";
$s .= "-- Title:\n".( $value[ $i ] )->title()."\n";
$s .= "-- Location:\n".( $value[ $i ] )->location()."\n";
}
elsif ( $value[ $i ]->isa( "Bio::Map::CytoPosition" ) ) {
$s .= "#" . $i . "\n-- Value:\n" . ( $value[ $i ] )->value() . "\n";
}
}
return $s;
}
} | sub _is_true_or_false
{ my ( $self, $value ) = @_;
unless ( $value !~ /\D/ && ( $value == TRUE || $value == FALSE ) ) {
$self->throw( "Found [" . $value
. "] where " . TRUE . " or " . FALSE . " expected" );
}
}
1;} | sub add_AllelicVariants
{ my ( $self, @values ) = @_;
return unless( @values );
foreach my $value ( @values ) {
$self->_check_ref_type( $value, "Bio::Phenotype::OMIM::OMIMentryAllelicVariant" );
}
push( @{ $self->{ "_allelic_variants" } }, @values );
}
} | sub additional_references
{ my ( $self, $value ) = @_;
if ( defined $value ) {
$self->{ "_additional_references" } = $value;
}
return $self->{ "_additional_references" };
}
} | sub alternative_titles_and_symbols
{ my ( $self, $value ) = @_;
if ( defined $value ) {
$self->{ "_alternative_titles_and_symbols" } = $value;
}
return $self->{ "_alternative_titles_and_symbols" };
}
} | sub clinical_symptoms
{ my ( $self, $value ) = @_;
if ( defined $value ) {
$self->{ "_clinical_symptoms" } = $value;
}
return $self->{ "_clinical_symptoms" };
}
} | sub contributors
{ my ( $self, $value ) = @_;
if ( defined $value ) {
$self->{ "_contributors" } = $value;
}
return $self->{ "_contributors" };
}
} | sub created
{ my ( $self, $value ) = @_;
if ( defined $value ) {
$self->{ "_created" } = $value;
}
return $self->{ "_created" };
}
} | sub each_AllelicVariant
{ my ( $self ) = @_;
if ( $self->{ "_allelic_variants" } ) {
return @{ $self->{ "_allelic_variants" } };
}
else {
return my @a = ();
}
}
} | sub edited
{ my ( $self, $value ) = @_;
if ( defined $value ) {
$self->{ "_edited" } = $value;
}
return $self->{ "_edited" };
}
} | sub gene_status
{ my ( $self, $value ) = @_;
if ( defined $value ) {
unless ( $value eq "C"
|| $value eq "P"
|| $value eq "I"
|| $value eq "L"
|| $value eq "" ) {
$value = "";
}
$self->{ "_gene_status" } = $value;
}
return $self->{ "_gene_status" };
}
} | sub init
{
my( $self ) = @_;
$self->MIM_number( DEFAULT_MIM_NUMER );
$self->title( "" );
$self->alternative_titles_and_symbols( "" );
$self->more_than_two_genes( FALSE );
$self->is_separate( FALSE );
$self->description( "" );
$self->mapping_method( "" );
$self->gene_status( "" );
$self->comment( "" );
my $species = Bio::Species->new();
$species->classification( qw( sapiens Homo ) );
$self->species( $species );
$self->created( "" );
$self->edited( "" );
$self->contributors( "" );
$self->additional_references( "" );
$self->clinical_symptoms( "" );
$self->remove_Correlates();
$self->remove_References();
$self->remove_AllelicVariants();
$self->remove_CytoPositions();
$self->remove_gene_symbols();
$self->remove_Genotypes();
$self->remove_DBLinks();
$self->remove_keywords();
$self->remove_Variants();
$self->remove_Measures();
$self->miniMIM( Bio::Phenotype::OMIM::MiniMIMentry->new() );
}
} | sub is_separate
{ my ( $self, $value ) = @_;
if ( defined $value ) {
$self->_is_true_or_false( $value );
$self->{ "_is_separate" } = $value;
}
return $self->{ "_is_separate" };
}
} | sub mapping_method
{ my ( $self, $value ) = @_;
if ( defined $value ) {
$self->{ "_mapping_method" } = $value;
}
return $self->{ "_mapping_method" };
}
} | sub miniMIM
{
my ( $self, $value ) = @_;
if ( defined $value ) {
$self->_check_ref_type( $value, "Bio::Phenotype::OMIM::MiniMIMentry" );
$self->{ "_mini_mim" } = $value;
}
return $self->{ "_mini_mim" };} | sub more_than_two_genes
{ my ( $self, $value ) = @_;
if ( defined $value ) {
$self->_is_true_or_false( $value );
$self->{ "_more_than_two_genes" } = $value;
}
return $self->{ "_more_than_two_genes" };
}
} | sub new
{
my( $class,@args ) = @_;
my $self = $class->SUPER::new( @args );
my ( $mim_number,
$title,
$alternative_titles_and_symbols,
$more_than_two_genes,
$is_separate,
$description,
$mapping_method,
$gene_status,
$comment,
$species,
$created,
$edited,
$contributors,
$additional_references,
$clinical_symptoms,
$miniMIM )
= $self->_rearrange( [ qw( MIM_NUMBER
TITLE
ALTERNATIVE_TITLES_AND_SYMBOLS
MORE_THAN_TWO_GENES
IS_SEPARATE
DESCRIPTION
MAPPING_METHOD
GENE_STATUS
COMMENT
SPECIES
CREATED
EDITED
CONTRIBUTORS
ADDITIONAL_REFERENCES
CLINICAL_SYMPTOMS
MINIMIM ) ], @args );
$self->init();
$mim_number && $self->MIM_number( $mim_number );
$title && $self->title( $title );
$alternative_titles_and_symbols && $self->alternative_titles_and_symbols( $alternative_titles_and_symbols );
$more_than_two_genes && $self->more_than_two_genes( $more_than_two_genes );
$is_separate && $self->is_separate( $is_separate );
$description && $self->description( $description );
$mapping_method && $self->mapping_method( $mapping_method );
$gene_status && $self->gene_status( $gene_status );
$comment && $self->comment( $comment );
$species && $self->species( $species );
$created && $self->created( $created );
$edited && $self->edited( $edited );
$contributors && $self->contributors( $contributors );
$additional_references && $self->additional_references( $additional_references );
$clinical_symptoms && $self->clinical_symptoms( $clinical_symptoms );
$miniMIM && $self->miniMIM( $miniMIM );
return $self;
}
} | sub remove_AllelicVariants
{ my ( $self ) = @_;
my @a = $self->each_AllelicVariant();
$self->{ "_allelic_variants" } = [];
return @a;
}
} | sub title
{ my ( $self, $value ) = @_;
$self->name( $value );
}
} | sub to_string
{
my( $self ) = @_;
my $s = "";
$s .= "-- MIM number:\n";
$s .= $self->MIM_number()."\n\n";
$s .= "-- Title:\n";
$s .= $self->title()."\n\n";
$s .= "-- Alternative Titles and Symbols:\n";
$s .= $self->alternative_titles_and_symbols()."\n\n";
$s .= "-- Can be caused by Mutation in any of two or more Genes:\n";
$s .= $self->more_than_two_genes()."\n\n";
$s .= "-- Phenotype is separate:\n";
$s .= $self->is_separate()."\n\n";
$s .= "-- Description:\n";
$s .= $self->description()."\n\n";
$s .= "-- Species:\n";
$s .= $self->species()->binomial()."\n\n";
$s .= "-- Clinical Symptoms:\n";
$s .= $self->clinical_symptoms()."\n\n";
$s .= "-- Allelic Variants:\n";
$s .= $self->_array_to_string( $self->each_AllelicVariant() )."\n";
$s .= "-- Cyto Positions:\n";
$s .= $self->_array_to_string( $self->each_CytoPosition() )."\n";
$s .= "-- Gene Symbols:\n";
$s .= $self->_array_to_string( $self->each_gene_symbol() )."\n";
$s .= "-- Correlates:\n";
$s .= $self->_array_to_string( $self->each_Correlate() )."\n";
$s .= "-- References:\n";
$s .= $self->_array_to_string( $self->each_Reference() )."\n";
$s .= "-- Additional References:\n";
$s .= $self->additional_references()."\n\n";
$s .= "-- Mapping Method:\n";
$s .= $self->mapping_method()."\n\n";
$s .= "-- Gene status:\n";
$s .= $self->gene_status()."\n\n";
$s .= "-- Created:\n";
$s .= $self->created()."\n\n";
$s .= "-- Contributors:\n";
$s .= $self->contributors()."\n\n";
$s .= "-- Edited:\n";
$s .= $self->edited()."\n\n";
$s .= "-- Comment:\n";
$s .= $self->comment()."\n\n";
$s .= "-- MiniMIM:\n";
$s .= $self->miniMIM()->to_string()."\n\n";
return $s;
}
} | General documentation
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The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _