Boulder::Omim(3pm)					User Contributed Perl Documentation					Boulder::Omim(3pm)

NAME

       Boulder::Omim - Fetch Omim data records as parsed Boulder Stones

SYNOPSIS

	 # parse a file of Omim records
	 $om = new Boulder::Omim(-accessor=>'File',
				    -param => '/data/omim/omim.txt');
	 while (my $s = $om->get) {
	   print $s->Identifier;
	   print $s->Text;
	 }

	 # parse flatfile records yourself
	 open (OM,"/data/omim/omim.txt");
	 local $/ = "*RECORD*";
	 while (<OM>) {
	    my $s = Boulder::Omim->parse($_);
	    # etc.
	 }

DESCRIPTION

       Boulder::Omim provides retrieval and parsing services for OMIM records

       Boulder::Omim provides retrieval and parsing services for NCBI Omim records.  It returns Omim entries in Stone format, allowing easy access
       to the various fields and values.  Boulder::Omim is a descendent of Boulder::Stream, and provides a stream-like interface to a series of
       Stone objects.

       Access to Omim is provided by one accessors, which give access to  local Omim database.	When you create a new Boulder::Omim stream, you
       provide the accessors, along with accessor-specific parameters that control what entries to fetch.  The accessors is:

       File
	 This provides access to local Omim entries by reading from a flat file (typically omim.txt file downloadable from NCBI's Ftp site).  The
	 stream will return a Stone corresponding to each of the entries in the file, starting from the top of the file and working downward.  The
	 parameter is the path to the local file.

       It is also possible to parse a single Omim entry from a text string stored in a scalar variable, returning a Stone object.

   Boulder::Omim methods
       This section lists the public methods that the Boulder::Omim class makes available.

       new()
	      # Local fetch via File
	      $om=new Boulder::Omim(-accessor  =>  'File',
				       -param	  =>  '/data/omim/omim.txt');

	   The new() method creates a new Boulder::Omim stream on the accessor provided.  The only possible accessors is File.	If successful, the
	   method returns the stream object.  Otherwise it returns undef.

	   new() takes the following arguments:

		   -accessor	   Name of the accessor to use
		   -param	   Parameters to pass to the accessor

	   Specify the accessor to use with the -accessor argument.  If not specified, it defaults to File.

	   -param is an accessor-specific argument.  The possibilities is:

	   For File, the -param argument must point to a string-valued scalar, which will be interpreted as the path to the file to read Omim
	   entries from.

       get()
	   The get() method is inherited from Boulder::Stream, and simply returns the next parsed Omim Stone, or undef if there is nothing more to
	   fetch.  It has the same semantics as the parent class, including the ability to restrict access to certain top-level tags.

       put()
	   The put() method is inherited from the parent Boulder::Stream class, and will write the passed Stone to standard output in Boulder
	   format.  This means that it is currently not possible to write a Boulder::Omim object back into Omim flatfile form.

OUTPUT TAGS

       The tags returned by the parsing operation are taken from the names shown in the network Entrez interface to Omim.

   Top-Level Tags
       These are tags that appear at the top level of the parsed Omim entry.

       Identifier
	   The Omim identifier of this entry.  Identifier is a single-value tag.

	   Example:

		 my $identifierNo = $s->Identifier;

       Title
	   The Omim title for this entry.

	   Example:
		 my $titledef=$s->Title;

       Text The Text of this Omim entry
	   Example:
		 my $thetext=$s->Text;

       Mini The text condensed version, also called "Mini" in Entrez interface
	   Example:
		 my $themini=$s->Mini;

       SeeAlso References to other relevant work.
	   Example:
		 my $thereviews=$s->Reviews;

       CreationDate This field contains the name of the person who originated the initial entry in OMIM and the date it appeared in the database.
       The entry may have been subsequently added to, edited, or totally rewritten by others, and their attribution is listed in the CONTRIBUTORS
       field.
	   Example:
		 my $theCreation=$s->CreationDate;

       Contributors This field contains a list, in chronological order, of the persons who have contributed significantly to the content of the
       MIM entry. The name is followed by "updated", "edited" or "re-created".
	   Example:
		 my @theContributors=$s->Contributors;

       History This field contains the edit history of this record, with an identifier and a date in which minor changes had been performed on the
       record.
	   Example:
		 my @theHistory=$s->History;

       References The references cited in the entry. Example: my @theReferences=$s->References;
       ClinicalSynopsis The content of the Clinical Synopsis data field. Example: my @theClinicalSynopsis=$s->ClinicalSynopsis;
       AllelicVariants The Allelic Variants Example: my @theAllelicVariants=$s->AllelicVariants;

SEE ALSO

       Boulder, Boulder::Blast, Boulder::Genbank

AUTHOR

       Lincoln Stein <lstein@cshl.org>.  Luca I.G. Toldo <luca.toldo@merck.de>

       Copyright (c) 1997 Lincoln D. Stein Copyright (c) 1999 Luca I.G. Toldo

       This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself.  See DISCLAIMER.txt for
       disclaimers of warranty.

perl v5.10.1							    2000-01-18							Boulder::Omim(3pm)