Difference between revisions of "Main Page/Endnote"

Latest revision as of 16:51, 13 October 2009

Background

Term lists in Endnote v7 function as abbreviation lists for bibliographies. Some journals require full journal names in references, and some require abbreviations (and some that require abbreviations use dots, and others don't). E.g., one of these might be the format your journal is looking for:

• Abdominal Imaging
• Abdom Imaging
• Abdom. Imaging

Endnote comes out of the box with rather sparse term lists. This tutorial will describe how to make standardized and more comprehensive term lists.

Prerequisites

1. Endnote installed on the PC
2. perl installed on the PC (if you want to recreate the process), or the term list I generated

Fixing abbreviated journal names

Some of my references had the full journal name and others had abbreviations. This caused problems when I needed a bibliography in a specific format.

I got a copy of term lists from the University of Queensland. These term lists contain tab-separated full, abbreviated, and dot-abbreviated journal names. However, these term lists were haphazardly arranged with respect to the abbreviations (that is, some of the journals in the 2nd column had dots, and some in the 3rd column had dots). Therefore, the lists required some rearranging. Luckily, perl is very handy at string manipulations.

A perl script for creating a sed script to fix the term list

Creates the standardized column abbreviated term list:

#! /usr/bin/perl -W
use strict;
use warnings;

# construct sed scripts for fixing endnote

# args
if ($#ARGV == -1) {
  print "Usage: $0 <infile>\n";
  exit;
}

# does infile exist?
my $infile = $ARGV[0];
if (! -e $infile) {
  print "$infile does not exist\n";
  exit;
}

# output file
(my $outfile = $infile) =~ s/\.txt/_fixed\.txt/;
open (OUTTERM, ">$outfile");

# read input file
open (INFILE, "<$infile") or die "cannot open";
while (my $record = <INFILE>) {
    chomp $record;
    # split into pieces with tabs
    my @list = split(/\t/, $record);
    # how many substrings?
    my $count = @list;
    # extract the first 2 substrings
    my $ss1 = $list[0];
    my $ss2 = $list[1];
    # if 3 substrings
    if ($count == 3) {
        # get the 3rd substring
	my $ss3 = $list[2];
	# handle dots
	$ss3 =~ s/\./\./g;
	$ss2 =~ s/\./\./g;
	# if neither substring has a dot
	if (($ss2 !~ m/\./) && ($ss3 !~ m/\./)) {
	    print OUTTERM "$ss1\t$ss3\t$ss2\n";
	}
        # if the 2nd ss has a dot and the 3rd does not
	if (($ss2 =~ m/\./) && ($ss3 !~ m/\./)) {
	    print OUTTERM "$ss1\t$ss3\t$ss2\n";
	}
        # if the 3nd ss has a dot and the 2rd does not
    	if (($ss2 !~ m/\./) && ($ss3 =~ m/\./)) {
	    print OUTTERM "$ss1\t$ss2\t$ss3\n";
	}
        # if both ss have dots
    	if (($ss2 =~ m/\./) && ($ss3 =~ m/\./)) {
	    print OUTTERM "$ss1\t$ss2\t$ss3\n";
	}
    }
}
close INFILE;
close OUTTERM;
print "created $outfile\n";

which can be run as a command, e.g., construct_endnote_fix_sed.pl pmh_phd_journals_term.txt

To update the term list in Endnote

1. Open the library.
2. Click on Tools on the menu bar and choose Define Term Lists
3. Highlight Journals
4. Select all journals.
5. Delete (right-click/Cut). Do not remove the term list altogehter; there does not seem to be a way to add the journals term list back with all the fields in EndNote 7, contrary to the documentation.
6. Click on the Import List button.
7. Select the text file to be imported and click on the Open button (I used the Medical, Biosciences, and Chemistry lists that were rearranged with the perl script above). You can download this list if you want and use that in the process described here.

To create a series of XML files for import to EndNote

NOT NECESSARY Once Endnote has a term list containing the proper abbreviations, when a reference is added to a library, if the term list includes the abbreviation for that journal, it is possible to use any of the abbreviation styles in the term list.

#! /usr/bin/perl -w
use warnings;

# read the sed scripts to fix the endnote library

# open the xml library and read it all in
open (LIBRARY, "<pmh_phd.xml") or die "cannot open";
my $lines = <LIBRARY>;
close (LIBRARY);

# remove the header and trailer stuff
$lines =~ s/<XML><RECORDS>//;
$lines =~ s/<\/RECORDS><\/XML>//;

# open and start reading the list of journal names
open (SED, "<sed_nodots.sed") or die "cannot open sed_dots.sed";
$count = 0;
while (<SED>) {
    $count++;
    print "$count\n";
    $sedstr = $_;
    chomp $sedstr;
    @substr = split(/\|/, $sedstr);
    $sub1 = $substr[1];
    $sub2 = $substr[2];
    $sub2 =~ s/\&/\&amp\;/g;
    $lines =~ s/<SECONDARY_TITLE>$sub1<\/SECONDARY_TITLE>/<SECONDARY_TITLE>$sub2<\/SECONDARY_TITLE>/g;
}
close (SED);

# an array of lines
$lines =~ s/\/RECORD>/\/RECORD>\n/g;
@linelist = split(/\n/, $lines);

# process....
$outfile = "xml_0.xml";
open (OUT, ">$outfile");
$count = 0;
foreach $line (@linelist) {
    $count++;
    # substitute
    #$line =~ s/<\/(\w+)>/<\/$1>\n/g;
    $line =~ s/<styles><\/styles>//g;
    print OUT $line;
    $f = $count/100;
    $mod = $count%10;
    $r = (int($count/10))%10;
    if (($mod == 0) && ($r == 0)) {
       close (OUT);
       $outfile = join("\.", join("_", "xml", $f), "xml");
       open (OUT, ">$outfile");
    }
}
close (OUT);