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://github.com/bioperl/bioperl-live/issues

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    :