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