NAME

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

SYNOPSIS

         # 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.
         }

DESCRIPTION

       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::Medline methods
       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.

OUTPUT TAGS

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

   Top-Level Tags
       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;

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.