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

       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 v5.34.0                                       2022-06-08                                 Boulder::Omim(3pm)

       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::Omimmethods
       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.

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

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

   Top-LevelTags
       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;

       Boulder, Boulder::Blast, Boulder::Genbank

         # 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.
         }