Boulder::Medline(3) User Contributed Perl Documentation Boulder::Medline(3)NAMEBoulder::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.
}
DESCRIPTIONBoulder::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.
POD ERRORS
Hey! The above document had some coding errors, which are explained
below:
Around line 122:
You can't have =items (as at line 163) unless the first thing after
the =over is an =item
perl v5.14.1 2000-11-22 Boulder::Medline(3)
