.\" Automatically generated by Pod::Man 4.14 (Pod::Simple 3.40)
.\"
.\" Standard preamble:
.\" ========================================================================
.de Sp \" Vertical space (when we can't use .PP)
.if t .sp .5v
.if n .sp
..
.de Vb \" Begin verbatim text
.ft CW
.nf
.ne \\$1
..
.de Ve \" End verbatim text
.ft R
.fi
..
.\" Set up some character translations and predefined strings.  \*(-- will
.\" give an unbreakable dash, \*(PI will give pi, \*(L" will give a left
.\" double quote, and \*(R" will give a right double quote.  \*(C+ will
.\" give a nicer C++.  Capital omega is used to do unbreakable dashes and
.\" therefore won't be available.  \*(C` and \*(C' expand to `' in nroff,
.\" nothing in troff, for use with C<>.
.tr \(*W-
.ds C+ C\v'-.1v'\h'-1p'\s-2+\h'-1p'+\s0\v'.1v'\h'-1p'
.ie n \{\
.    ds -- \(*W-
.    ds PI pi
.    if (\n(.H=4u)&(1m=24u) .ds -- \(*W\h'-12u'\(*W\h'-12u'-\" diablo 10 pitch
.    if (\n(.H=4u)&(1m=20u) .ds -- \(*W\h'-12u'\(*W\h'-8u'-\"  diablo 12 pitch
.    ds L" ""
.    ds R" ""
.    ds C` ""
.    ds C' ""
'br\}
.el\{\
.    ds -- \|\(em\|
.    ds PI \(*p
.    ds L" ``
.    ds R" ''
.    ds C`
.    ds C'
'br\}
.\"
.\" Escape single quotes in literal strings from groff's Unicode transform.
.ie \n(.g .ds Aq \(aq
.el       .ds Aq '
.\"
.\" If the F register is >0, we'll generate index entries on stderr for
.\" titles (.TH), headers (.SH), subsections (.SS), items (.Ip), and index
.\" entries marked with X<> in POD.  Of course, you'll have to process the
.\" output yourself in some meaningful fashion.
.\"
.\" Avoid warning from groff about undefined register 'F'.
.de IX
..
.nr rF 0
.if \n(.g .if rF .nr rF 1
.if (\n(rF:(\n(.g==0)) \{\
.    if \nF \{\
.        de IX
.        tm Index:\\$1\t\\n%\t"\\$2"
..
.        if !\nF==2 \{\
.            nr % 0
.            nr F 2
.        \}
.    \}
.\}
.rr rF
.\" ========================================================================
.\"
.IX Title "Boulder::Medline 3pm"
.TH Boulder::Medline 3pm "2021-01-05" "perl v5.32.0" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
.if n .ad l
.nh
.SH "NAME"
Boulder::Medline \- Fetch Medline data records as parsed Boulder Stones
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 7
\&  # parse a file of Medline records
\&  $ml = new Boulder::Medline(\-accessor=>\*(AqFile\*(Aq,
\&                             \-param => \*(Aq/data/medline/medline.txt\*(Aq);
\&  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.
\&  }
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
Boulder::Medline provides retrieval and parsing services for Medline records
.PP
Boulder::Medline provides retrieval and parsing services for \s-1NCBI\s0
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.
.PP
Access to Medline is provided by one \fIaccessors\fR, 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:
.IP "File" 2
.IX Item "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.
.PP
It is also possible to parse a single Medline entry from a text string 
stored in a scalar variable, returning a Stone object.
.SS "Boulder::Medline methods"
.IX Subsection "Boulder::Medline methods"
This section lists the public methods that the \fIBoulder::Medline\fR
class makes available.
.IP "\fBnew()\fR" 4
.IX Item "new()"
.Vb 3
\&   # Local fetch via File
\&   $ml=new Boulder::Medline(\-accessor  =>  \*(AqFile\*(Aq,
\&                            \-param     =>  \*(Aq/data/medline/medline.txt\*(Aq);
.Ve
.Sp
The \fBnew()\fR method creates a new \fIBoulder::Medline\fR stream on the
accessor provided.  The only possible accessors is \fBFile\fR.  
If successful, the method returns the stream
object.  Otherwise it returns undef.
.Sp
\&\fBnew()\fR takes the following arguments:
.Sp
.Vb 2
\&        \-accessor       Name of the accessor to use
\&        \-param          Parameters to pass to the accessor
.Ve
.Sp
Specify the accessor to use with the \fB\-accessor\fR argument.  If not
specified, it defaults to \fBFile\fR.
.Sp
\&\fB\-param\fR is an accessor-specific argument.  The possibilities is:
.Sp
For \fBFile\fR, the \fB\-param\fR argument must point to a string-valued
scalar, which will be interpreted as the path to the file to read
Medline entries from.
.IP "\fBget()\fR" 4
.IX Item "get()"
The \fBget()\fR method is inherited from \fIBoulder::Stream\fR, 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.
.IP "\fBput()\fR" 4
.IX Item "put()"
The \fBput()\fR 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.
.SH "OUTPUT TAGS"
.IX Header "OUTPUT TAGS"
The tags returned by the parsing operation are taken from the \s-1MEDLARS\s0 definition file
\&\s-1MEDDOC.DOC\s0
.SS "Top-Level Tags"
.IX Subsection "Top-Level Tags"
These are tags that appear at the top level of the parsed Medline entry.
.PP
.Vb 10
\&    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
.Ve
.IP "Identifier" 4
.IX Item "Identifier"
The Medline identifier of this entry.  Identifier is a single-value tag.
.Sp
Example:
.Sp
.Vb 1
\&      my $identifierNo = $s\->Identifier;
.Ve
.IP "Title" 4
.IX Item "Title"
The Medline title for this entry.
.Sp
Example:
      my \f(CW$titledef\fR=$s\->Title;
.SH "SEE ALSO"
.IX Header "SEE ALSO"
Boulder, Boulder::Blast, Boulder::Genbank
.SH "AUTHOR"
.IX Header "AUTHOR"
Lincoln Stein <lstein@cshl.org>.
Luca I.G. Toldo <luca.toldo@merck.de>
.PP
Copyright (c) 1997 Lincoln D. Stein
Copyright (c) 1999 Luca I.G. Toldo
.PP
This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself.  See \s-1DISCLAIMER\s0.txt for
disclaimers of warranty.