Christopher Fields > BioPerl-1.6.921 > Bio::Phenotype::OMIM::OMIMentry

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Module Version: 1.006921   Source   Latest Release: BioPerl-1.6.924

NAME ^

Bio::Phenotype::OMIM::OMIMentry - represents OMIM (Online Mendelian Inheritance in Man) database entries

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.

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.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

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

bioperl-l@bioperl.org

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://redmine.open-bio.org/projects/bioperl/

AUTHOR ^

Christian M. Zmasek

Email: czmasek-at-burnham.org or cmzmasek@yahoo.com

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::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

init

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

MIM_number

 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

 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).

alternative_titles_and_symbols

 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).

more_than_two_genes

 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).

is_separate

 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).

mapping_method

 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).

gene_status

 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).

clinical_symptoms

 Title   : clinical_symptoms
 Usage   : $omim->clinical_symptoms({});
 Function: Set/get for the clinical symptoms of this OMIM entry.
 Returns : [hash reference].
 Args    : [hash reference]. Suggested not to assign alone. Parser will do.

clinical_symptoms_raw

  Title     : clinical_symptoms_raw
  Usage     : $omim->clinical_symptoms( "Patients with ..." );
              print $omim->clinical_symptoms();
  Functions : Get/set for text information of clinical symptoms
  Returns   : The clinical symptoms [scalar].
  Args      : The clinical symptoms [scalar] (optional).

add_clinical_symptoms

  Title     : add_clinical_symptoms
  Usage     : $entry->add_clinical_symptoms('Ears', 'Floppy ears', 'Lop-ears');
  Function  : add one or more symptoms on one part of body.
  Returns   : [none]
  Args      : ($part, @symptoms)
              $part, the text name of part/organism of human
              @symptoms, an array of text description

query_clinical_symptoms

  Title     : get_clinical_symptoms
  Usage     : @symptoms = $self->query_clinical_symptoms('Ears');
  Function  : get all symptoms specific to one part/organism.
  Returns   : an array of text
  Args      : $organ

created

 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).

contributors

 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).

edited

 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).

additional_references

 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).

miniMIM

 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).

each_AllelicVariant

 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    :

add_AllelicVariants

 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).

remove_AllelicVariants

 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    :
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