Christopher Fields > BioPerl-1.6.923 > Bio::Phenotype::OMIM::OMIMparser

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NAME ^

Bio::Phenotype::OMIM::OMIMparser - parser for the OMIM database

SYNOPSIS ^

  use Bio::Phenotype::OMIM::OMIMparser;

  # The OMIM database is available as textfile at:
  # ftp://ncbi.nlm.nih.gov/repository/OMIM/omim.txt.Z
  # The genemap is available as textfile at:
  # ftp://ncbi.nlm.nih.gov/repository/OMIM/genemap

  $omim_parser = Bio::Phenotype::OMIM::OMIMparser->new( -genemap  => "/path/to/genemap",
                                                        -omimtext => "/path/to/omim.txt" );

  while ( my $omim_entry = $omim_parser->next_phenotype() ) {
    # This prints everything.
    print( $omim_entry->to_string() );
    print "\n\n";

    # This gets individual data (some of them object-arrays)
    # (and illustrates the relevant methods of OMIMentry).
    my $numb  = $omim_entry->MIM_number();                     # *FIELD* NO
    my $title = $omim_entry->title();                          # *FIELD* TI - first line
    my $alt   = $omim_entry->alternative_titles_and_symbols(); # *FIELD* TI - additional lines
    my $mtt   = $omim_entry->more_than_two_genes();            # "#" before title
    my $sep   = $omim_entry->is_separate();                    # "*" before title
    my $desc  = $omim_entry->description();                    # *FIELD* TX
    my $mm    = $omim_entry->mapping_method();                 # from genemap
    my $gs    = $omim_entry->gene_status();                    # from genemap
    my $cr    = $omim_entry->created();                        # *FIELD* CD
    my $cont  = $omim_entry->contributors();                   # *FIELD* CN
    my $ed    = $omim_entry->edited();                         # *FIELD* ED
    my $sa    = $omim_entry->additional_references();          # *FIELD* SA
    my $cs    = $omim_entry->clinical_symptoms_raw();              # *FIELD* CS
    my $comm  = $omim_entry->comment();                        # from genemap

    my $mini_mim   = $omim_entry->miniMIM();                   # *FIELD* MN
      # A Bio::Phenotype::OMIM::MiniMIMentry object.
      # class Bio::Phenotype::OMIM::MiniMIMentry
      # provides the following:
      # - description()
      # - created()
      # - contributors()
      # - edited() 
      #
    # Prints the contents of the MINI MIM entry (most OMIM entries do
    # not have MINI MIM entries, though).
    print $mini_mim->description()."\n";
    print $mini_mim->created()."\n";
    print $mini_mim->contributors()."\n";
    print $mini_mim->edited()."\n";

    my @corrs      = $omim_entry->each_Correlate();            # from genemap
      # Array of Bio::Phenotype::Correlate objects.
      # class Bio::Phenotype::Correlate
      # provides the following:
      # - name()
      # - description() (not used)
      # - species() (always mouse)
      # - type() ("OMIM mouse correlate")
      # - comment() 

    my @refs       = $omim_entry->each_Reference();            # *FIELD* RF
      # Array of Bio::Annotation::Reference objects.


    my @avs        = $omim_entry->each_AllelicVariant();       # *FIELD* AV
      # Array of Bio::Phenotype::OMIM::OMIMentryAllelicVariant objects.
      # class Bio::Phenotype::OMIM::OMIMentryAllelicVariant
      # provides the following:
      # - number (e.g ".0001" )
      # - title (e.g "ALCOHOL INTOLERANCE" )
      # - symbol (e.g "ALDH2*2" )
      # - description (e.g "The ALDH2*2-encoded protein has a change ..." )
      # - aa_ori  (used if information in the form "LYS123ARG" is found)
      # - aa_mut (used if information in the form "LYS123ARG" is found)
      # - position (used if information in the form "LYS123ARG" is found)
      # - additional_mutations (used for e.g. "1-BP DEL, 911T")

    my @cps        = $omim_entry->each_CytoPosition();         # from genemap
      # Array of Bio::Map::CytoPosition objects.

    my @gss        = $omim_entry->each_gene_symbol();          # from genemap
      # Array of strings.

    # do something ...
  }

DESCRIPTION ^

This parser returns Bio::Phenotype::OMIM::OMIMentry objects (which inherit from Bio::Phenotype::PhenotypeI). It parses the OMIM database available as ftp://ncbi.nlm.nih.gov/repository/OMIM/omim.txt.Z together with (optionally) the gene map file at ftp://ncbi.nlm.nih.gov/repository/OMIM/genemap.

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   : $omim_parser = Bio::Phenotype::OMIM::OMIMparser->new( -genemap  => "/path/to/genemap",
                                                                 -omimtext => "/path/to/omim.txt" );                      
 Function: Creates a new OMIMparser.
 Returns : A new OMIMparser object.
 Args    : -genemap  => the genemap file name (optional)
           -omimtext => the omim text file name

next_phenotype

 Title   : next_phenotype()
 Usage   : while ( my $omim_entry = $omim_parser->next_phenotype() ) {
               # do something with $omim_entry
           }    
 Function: Returns an Bio::Phenotype::OMIM::OMIMentry or
           undef once the end of the omim text file is reached.
 Returns : A Bio::Phenotype::OMIM::OMIMentry.
 Args    :

init

 Title   : init()
 Usage   : $omim_parser->init();   
 Function: Initializes this OMIMparser to all "".
 Returns : 
 Args    :

genemap_file_name

 Title   : genemap_file_name
 Usage   : $omimparser->genemap_file_name( "genemap" );
 Function: Set/get for the genemap file name.
 Returns : The genemap file name [string].
 Args    : The genemap file name [string] (optional).

omimtxt_file_name

 Title   : omimtxt_file_name
 Usage   : $omimparser->omimtxt_file_name( "omim.txt" );
 Function: Set/get for the omim text file name.
 Returns : The the omim text file name [string].
 Args    : The the omim text file name [string] (optional).
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