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

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.

perl v5.10.1							    2011-03-05						     Boulder::Medline(3pm)