i'm able to refine the problem...
Statement of the Problem:
parse Medline/Pubmed file paths on a Unix system in order to finally pass the PMID from each path to a pmid2doi conversion website < http://www.pmid2doi.org/ > ... and output companion DOIs…
(1) parse this link and fetch the pmid;
"/xxxxx/xxxxx/xxxxx/xxxxx/xxxxx/UNC00000000000042/00223468/v45i3/S0022346809003820";
(2) submit a query to http://www.pmid2doi.org/, fetch the return contents and parse the DOI value.
If you simply point your browser to:
http://www.pmid2doi.org/rest/json/doi/18507872
then your browser will display the result in the form:
{"pmid":18507872,"doi":"10.1186/gb-2008-9-5-r89"}
and then you need to parse this JSON format.
Examples of how to do that are at:
http://beerpla.net/2008/03/27/parsing-json-in-perl-by-example-southparkstudioscom-south-park-episodes/
#!/usr/local/bin/perl
use strict;
use warnings;
use 5.010;
use LWP::Simple;
# Fetch line from <DATA>
while ( <DATA> ) {
# PMID is an 8-digit string, surrounded by "/" and "/"
my $pmid = $1 if ( /\/(\d{8})\// );
# Query pmid in http://www.pmid2doi.org/
my $ret = get("http://www.pmid2doi.org/rest/json/doi/$pmid");
unless (defined $ret) {
warn "Failed to get doi for '$pmid': $!\n";
next;
}
# Parse query result, which would be like:
# {"pmid":18507872,"doi":"10.1186/gb-2008-9-5-r89"}
if ( $ret =~ /"doi":"(.*?)"}/ ) {
my $doi = $1;
# Output
say $pmid, "\t=>\t", $doi;
}
else {
say "doi not found in '$ret'";
}
}
exit 0;
__DATA__
/xxxxx/xxxxx/xxxxx/xxxxx/xxxxx/UNC00000000000042/00223468/v45i3/S00223
+46809003820
i'd appreciate any critiques/insights -- thx!
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