Provided by: libbio-perl-perl_1.6.923-1_all bug

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    :