1Boulder::Medline(3)   User Contributed Perl Documentation  Boulder::Medline(3)
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NAME

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

9         # parse a file of Medline records
10         $ml = new Boulder::Medline(-accessor=>'File',
11                                    -param => '/data/medline/medline.txt');
12         while (my $s = $ml->get) {
13           print $s->Identifier;
14           print $s->Abstract;
15         }
16
17         # parse flatfile  yourself
18         open (ML,"/data/medline/medline.txt");
19         local $/ = "*RECORD*";
20         while (<ML>) {
21            my $s = Boulder::Medline->parse($_);
22            # etc.
23         }
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DESCRIPTION

26       Boulder::Medline provides retrieval and parsing services for Medline
27       records
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29       Boulder::Medline provides retrieval and parsing services for NCBI Med‐
30       line records.  It returns Medline entries in Stone format, allowing
31       easy access to the various fields and values.  Boulder::Medline is a
32       descendent of Boulder::Stream, and provides a stream-like interface to
33       a series of Stone objects.
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35       Access to Medline is provided by one accessors, which give access to
36       local Medline database.  When you create a new Boulder::Medline stream,
37       you provide the accessors, along with accessor-specific parameters that
38       control what entries to fetch.  The accessors is:
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40       File
41         This provides access to local Medline entries by reading from a flat
42         file.  The stream will return a Stone corresponding to each of the
43         entries in the file, starting from the top of the file and working
44         downward.  The parameter is the path to the local file.
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46       It is also possible to parse a single Medline entry from a text string
47       stored in a scalar variable, returning a Stone object.
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49       Boulder::Medline methods
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51       This section lists the public methods that the Boulder::Medline class
52       makes available.
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54       new()
55              # Local fetch via File
56              $ml=new Boulder::Medline(-accessor  =>  'File',
57                                       -param     =>  '/data/medline/medline.txt');
58
59           The new() method creates a new Boulder::Medline stream on the
60           accessor provided.  The only possible accessors is File.  If suc‐
61           cessful, the method returns the stream object.  Otherwise it
62           returns undef.
63
64           new() takes the following arguments:
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66                   -accessor       Name of the accessor to use
67                   -param          Parameters to pass to the accessor
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69           Specify the accessor to use with the -accessor argument.  If not
70           specified, it defaults to File.
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72           -param is an accessor-specific argument.  The possibilities is:
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74           For File, the -param argument must point to a string-valued scalar,
75           which will be interpreted as the path to the file to read Medline
76           entries from.
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78       get()
79           The get() method is inherited from Boulder::Stream, and simply
80           returns the next parsed Medline Stone, or undef if there is nothing
81           more to fetch.  It has the same semantics as the parent class,
82           including the ability to restrict access to certain top-level tags.
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84       put()
85           The put() method is inherited from the parent Boulder::Stream
86           class, and will write the passed Stone to standard output in Boul‐
87           der format.  This means that it is currently not possible to write
88           a Boulder::Medline object back into Medline flatfile form.
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OUTPUT TAGS

91       The tags returned by the parsing operation are taken from the MEDLARS
92       definition file MEDDOC.DOC
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94       Top-Level Tags
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96       These are tags that appear at the top level of the parsed Medline
97       entry.
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99           ABSTRACT ABSTRACT AUTHOR ADDRESS AUTHOR CALL NUMBER CAS REGISTRY/EC
100           NUMBER CLASS UPDATE DATE COMMENTS COUNTRY DATE OF ENTRY DATE OF
101           PUBLICATION ENGLISH ABSTRACT INDICATOR ENTRY MONTH GENE SYMBOL ID
102           NUMBER INDEXING PRIORITY ISSN ISSUE/PART/SUPPLEMENT JOURNAL SUBSET
103           JOURNAL TITLE CODE LANGUAGE LAST REVISION DATE MACHINE-READABLE
104           IDENTIFIER MeSH HEADING NO-AUTHOR INDICATOR NOT FOR PUBLICATION
105           NUMBER OF REFERENCES PAGINATION PERSONAL NAME AS SUBJECT PUBLICA‐
106           TION TYPE RECORD ORIGINATOR SECONDARY SOURCE ID SPECIAL LIST INDI‐
107           CATOR TITLE TITLE ABBREVIATION TRANSLITERATED/VERNACULAR  TITLE
108           UNIQUE IDENTIFIER VOLUME ISSUE
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110       Identifier
111           The Medline identifier of this entry.  Identifier is a single-value
112           tag.
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114           Example:
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116                 my $identifierNo = $s->Identifier;
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118       Title
119           The Medline title for this entry.
120
121           Example:
122                 my $titledef=$s->Title;
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SEE ALSO

125       Boulder, Boulder::Blast, Boulder::Genbank
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AUTHOR

128       Lincoln Stein <lstein@cshl.org>.  Luca I.G. Toldo <luca.toldo@merck.de>
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130       Copyright (c) 1997 Lincoln D. Stein Copyright (c) 1999 Luca I.G. Toldo
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132       This library is free software; you can redistribute it and/or modify it
133       under the same terms as Perl itself.  See DISCLAIMER.txt for dis‐
134       claimers of warranty.
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138perl v5.8.8                       2000-06-08               Boulder::Medline(3)