Here is an XML::Twig that will be easy on your RAM (only one journal is in mem at any given time).

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

use XML::Twig;

# you will actually get the list from a file
my %to_remove= map { $_ => 1 } ( "1742-7061");

XML::Twig->new( twig_roots => { journal => \&journal },
                pretty_print => 'indented',
              )
         ->parse( \*DATA)  # replace by parsefile( "file.xml")
         ->flush;

sub journal 
  { my( $t, $journal)= @_;
    # this works if the ISSN is a child of journal,
    # otherwise it might be a little more tricky.
    if( $to_remove{$journal->field( 'ISSN')})
      { $journal->delete }
    else
      { $t->flush; } # ouput and cleanup memory
  }

__DATA__
<bulk>
  <journal>
    <full-title>Acta Biomaterialia</full-title>
    <alternate-title></alternate-title>
    <ISSN>1742-7061</ISSN>
    <E-ISSN></E-ISSN>
    <vol-year></vol-year>
    <iss-vol>1</iss-vol>
    <start-date>01-01-1974</start-date>
    <target>
      <siteID>1</siteID>
      <rank>200</rank>
      <activate></activate>
    </target>
  </journal>
  <journal>
    <full-title>Acta Biomaterialia</full-title>
    <alternate-title></alternate-title>
    <ISSN>1743-7061</ISSN>
    <E-ISSN></E-ISSN>
    <vol-year></vol-year>
    <iss-vol>1</iss-vol>
    <start-date>01-01-1974</start-date>
    <target>
      <siteID>1</siteID>
      <rank>200</rank>
      <activate></activate>
   </target>
  </journal>
</bulk>
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use strict;
use XML::Simple;

my @list; #read in your list into this array
my $infile ; #name of the file of your original xml
my $outfile; # name of the output file

my $parser = XML::Simple->new(rootname=>"bulk-load",noattr=>1,keyattr=
+>['ISSN']);
my $xml = $parser->XMLin($infile);
foreach my $issn (@list){
    delete $xml->{journal}->{$issn};
}
$parser->XMLout($xml,outputfile=>$outfile);
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Do you have the structure you have shown in a larger document, with enclosing elements? If so it would be possible to use, say, XML::DOM to find all the ISSN nodes and if they match the requirement then you can delete the parents.

/J\

The root element of the document is <bulk-load> the document is made up of the <journal> elements. The entire document is close to 3 MB. I am looking into XML::DOM, since I am unfamiliar with XML modules used in Perl. I appreciate your advice..thanks.

IN that case you can do something like:

use XML::DOM;
                                                                      
+              
                                                                      
+              
my $xml = 'jj.xml';
my $parser = new XML::DOM::Parser;
my $doc = $parser->parsefile($xml);
                                                                      
+              
my $nodes = $doc->getElementsByTagName ("ISSN");
                                                                      
+              
foreach my $node (@{$nodes})
{
   if ( $node->getFirstChild()->toString() eq '1742-7061' )
   {
      my $parent = $node->getParentNode();
      $doc->getFirstChild()->removeChild($parent);
   }
                                                                      
+              
}
                                                                      
+              
print $doc->toString();
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Of course in your production code you will want to have all the ISSN numbers you want removed in a hash and do exists rather than the single comparison I have there.

/J\

  use XML::Smart ;
  
  my $xml = new XML::Smart(q`
<root>
  <journal>
    <full-title>Acta Biomaterialia</full-title>
    <alternate-title></alternate-title>
    <ISSN>1742-7061</ISSN>
    <E-ISSN></E-ISSN>
    <vol-year></vol-year>
    <iss-vol>1</iss-vol>
    <start-date>01-01-1974</start-date>
    <target>
      <siteID>1</siteID>
      <rank>200</rank>
      <activate></activate>
    </target>
  </journal>
  <journal>
    <full-title>Acta Biomaterialia</full-title>
    <alternate-title></alternate-title>
    <ISSN>1742-7062</ISSN>
    <E-ISSN></E-ISSN>
    <vol-year></vol-year>
    <iss-vol>1</iss-vol>
    <start-date>01-01-1974</start-date>
    <target>
      <siteID>1</siteID>
      <rank>200</rank>
      <activate></activate>
    </target>
  </journal>
</root>
  `);
  
  my @jornals = @{ $xml->{root}{journal} } ;
  
  foreach my $jornals_i ( @jornals ) {
    if ( $jornals_i->{ISSN} eq '1742-7061' ) {
      my $i = $jornals_i->i() ;
      delete $xml->{root}{journal}[$i] ;
    }
  }
  
  print $xml->data ;
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