Boulder::Medline(3pm)

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
30       Medline 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
50       This section lists the public methods that the Boulder::Medline class
51       makes available.
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53       new()
54              # Local fetch via File
55              $ml=new Boulder::Medline(-accessor  =>  'File',
56                                       -param     =>  '/data/medline/medline.txt');
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58           The new() method creates a new Boulder::Medline stream on the
59           accessor provided.  The only possible accessors is File.  If
60           successful, the method returns the stream object.  Otherwise it
61           returns undef.
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63           new() takes the following arguments:
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65                   -accessor       Name of the accessor to use
66                   -param          Parameters to pass to the accessor
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68           Specify the accessor to use with the -accessor argument.  If not
69           specified, it defaults to File.
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71           -param is an accessor-specific argument.  The possibilities is:
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73           For File, the -param argument must point to a string-valued scalar,
74           which will be interpreted as the path to the file to read Medline
75           entries from.
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77       get()
78           The get() method is inherited from Boulder::Stream, and simply
79           returns the next parsed Medline Stone, or undef if there is nothing
80           more to fetch.  It has the same semantics as the parent class,
81           including the ability to restrict access to certain top-level tags.
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83       put()
84           The put() method is inherited from the parent Boulder::Stream
85           class, and will write the passed Stone to standard output in
86           Boulder format.  This means that it is currently not possible to
87           write a Boulder::Medline object back into Medline flatfile form.
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OUTPUT TAGS

90       The tags returned by the parsing operation are taken from the MEDLARS
91       definition file MEDDOC.DOC
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93   Top-Level Tags
94       These are tags that appear at the top level of the parsed Medline
95       entry.
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97           ABSTRACT ABSTRACT AUTHOR ADDRESS AUTHOR CALL NUMBER CAS REGISTRY/EC
98           NUMBER CLASS UPDATE DATE COMMENTS COUNTRY DATE OF ENTRY DATE OF
99           PUBLICATION ENGLISH ABSTRACT INDICATOR ENTRY MONTH GENE SYMBOL ID
100           NUMBER INDEXING PRIORITY ISSN ISSUE/PART/SUPPLEMENT JOURNAL SUBSET
101           JOURNAL TITLE CODE LANGUAGE LAST REVISION DATE MACHINE-READABLE
102           IDENTIFIER MeSH HEADING NO-AUTHOR INDICATOR NOT FOR PUBLICATION
103           NUMBER OF REFERENCES PAGINATION PERSONAL NAME AS SUBJECT
104           PUBLICATION TYPE RECORD ORIGINATOR SECONDARY SOURCE ID SPECIAL LIST
105           INDICATOR TITLE TITLE ABBREVIATION TRANSLITERATED/VERNACULAR  TITLE
106           UNIQUE IDENTIFIER VOLUME ISSUE
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108           Identifier
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110           The Medline identifier of this entry.  Identifier is a single-value
111           tag.
112
113           Example:
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115                 my $identifierNo = $s->Identifier;
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117           Title
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119           The Medline title for this entry.
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121           Example:
122                 my $titledef=$s->Title;
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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
134       disclaimers of warranty.
135

POD ERRORS

137       Hey! The above document had some coding errors, which are explained
138       below:
139
140       Around line 122:
141           You can't have =items (as at line 163) unless the first thing after
142           the =over is an =item
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146perl v5.32.1                      2021-01-26               Boulder::Medline(3)

NAME

SYNOPSIS

DESCRIPTION

OUTPUT TAGS

SEE ALSO

AUTHOR

POD ERRORS