Boulder::Medline - Fetch Medline 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::Medline(3pm)

       Boulder::Medline provides retrieval and parsing services for Medline records

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

       Access to Medline is provided by one accessors, which give access to  local Medline database.  When you
       create a new Boulder::Medline 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 Medline entries by reading from a flat file.  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 Medline entry from a text string stored in a scalar variable,
       returning a Stone object.

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

       new()
              # Local fetch via File
              $ml=new Boulder::Medline(-accessor  =>  'File',
                                       -param     =>  '/data/medline/medline.txt');

           The new() method creates a new Boulder::Medline 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 Medline entries from.

       get()
           The get() method is inherited from Boulder::Stream, and simply returns the next parsed Medline 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::Medline object back into Medline flatfile form.

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

       The tags returned by the parsing operation are taken from the MEDLARS definition file MEDDOC.DOC

   Top-LevelTags
       These are tags that appear at the top level of the parsed Medline entry.

           ABSTRACT
           ABSTRACT AUTHOR
           ADDRESS
           AUTHOR
           CALL NUMBER
           CAS REGISTRY/EC NUMBER
           CLASS UPDATE DATE
           COMMENTS
           COUNTRY
           DATE OF ENTRY
           DATE OF PUBLICATION
           ENGLISH ABSTRACT INDICATOR
           ENTRY MONTH
           GENE SYMBOL
           ID NUMBER
           INDEXING PRIORITY
           ISSN
           ISSUE/PART/SUPPLEMENT
           JOURNAL SUBSET
           JOURNAL TITLE CODE
           LANGUAGE
           LAST REVISION DATE
           MACHINE-READABLE IDENTIFIER
           MeSH HEADING
           NO-AUTHOR INDICATOR
           NOT FOR PUBLICATION
           NUMBER OF REFERENCES
           PAGINATION
           PERSONAL NAME AS SUBJECT
           PUBLICATION TYPE
           RECORD ORIGINATOR
           SECONDARY SOURCE ID
           SPECIAL LIST INDICATOR
           TITLE
           TITLE ABBREVIATION
           TRANSLITERATED/VERNACULAR  TITLE
           UNIQUE IDENTIFIER
           VOLUME ISSUE

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

           Example:

                 my $identifierNo = $s->Identifier;

       Title
           The Medline title for this entry.

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

       Boulder, Boulder::Blast, Boulder::Genbank

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

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