Bio::Phenotype::OMIM::OMIMentry(3pm)			User Contributed Perl Documentation		      Bio::Phenotype::OMIM::OMIMentry(3pm)

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	:

perl v5.14.2							    2012-03-02				      Bio::Phenotype::OMIM::OMIMentry(3pm)