OMIMentry - represents OMIM (Online Mendelian Inheritance in Man) database entries $obj = Bio::Phenotype::OMIM::OMIMentry->new( -mim_number => 200000, -description => "This is ...", -more_than_two_genes => 1 ); 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.

Mailing Lists
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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 email or the web: bioperl-bugs@bio.perl.org http://bugzilla.bioperl.org/ Christian M. Zmasek Email: czmasek@gnf.org or cmzmasek@yahoo.com WWW: http://www.genetics.wustl.edu/eddy/people/zmasek/ Address: Genomics Institute of the Novartis Research Foundation 10675 John Jay Hopkins Drive San Diego, CA 92121 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

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

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 :