NAME
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
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bioperl-l@bioperl.org - General discussion
http://bio.perl.org/MailList.html - About the mailing listsReporting 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/AUTHOR
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 92121APPENDIX
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 antryinit
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( "Patients with ..." );
or
print $omim->clinical_symptoms();
Function: Set/get for the clinical symptoms of this OMIM entry.
Returns : The clinical symptoms [scalar].
Args : The clinical symptoms [scalar] (optional).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 :