[Bioperl-l] pubmed

Brian Osborne brian_osborne at cognia.com
Mon Apr 4 16:07:54 EDT 2005


Only 1 of the 5 references in the 56961711 entry has a Pubmed id, the rest
will return nothing when you try $value->pubmed.

Brian O.

-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Qunfeng
Sent: Monday, April 04, 2005 2:58 PM
To: Bioperl
Subject: Re: [Bioperl-l] pubmed

so, I tried to use
                     my $authors = $hash_ref->{'authors'};
                     my $medline = $hash_ref->{'medline'};
                     my $pubmed = $hash_ref->{'pubmed'};

to parse out authors, medline, pubmed.

I was able to successfully parse out authors and medline but not pubmed.

Then I tried to use

                     my $authors = $value->authors();
                     my $medline = $value->medline();
                     my $pubmed = $value->pubmed();

and I got the same thing.


At 07:50 PM 4/2/2005, Hilmar Lapp wrote:
>So what is the result of this script that you wouldn't have expected or
>that is not giving you what you need?
>BTW annotation objects under the tagname 'reference' are usually
>Bio::Annotation::Reference objects and have methods $ref->authors(),
>$ref->pubmed(), $ref->medline, etc. Check the POD.
>         -hilmar
>On Friday, April 1, 2005, at 12:04  PM, Qunfeng wrote:
>>Hilmar and Paulo,
>>I apologize for that,
>>here is a snippet of my code, I must have missed something very simple.
>>Thanks for your help! -- Qunfeng
>>#!/usr/bin/perl -w
>>use strict;
>>use Bio::SeqIO;
>>my $inputGBfile = $ARGV[0];
>>my  $seqio_object = Bio::SeqIO->new('-file' => "$inputGBfile",
>>                                    '-format' => 'GenBank');
>>my $seq_object;
>>while (1){
>>         eval{
>>                 $seq_object = $seqio_object->next_seq;
>>         };
>>         if($@){
>>                 print STDERR "EXCEPTION FOUND; SKIP THIS OBJECT\n";
>>                 next;
>>         }
>>         last if(!defined $seq_object);
>>         my $gi = $seq_object->primary_id;
>>         my $anno_collection = $seq_object->annotation;
>>         foreach my $key ( $anno_collection->get_all_annotation_keys ) {
>>             my @annotations = $anno_collection->get_Annotations($key);
>>             foreach my $value ( @annotations ) {
>>                 if($value->tagname eq "reference"){
>>                     my $hash_ref = $value->hash_tree;
>>                     my $authors = $hash_ref->{'authors'};
>>                     my $medline = $hash_ref->{'medline'};
>>                     my $pubmed = $hash_ref->{'pubmed'};
>>                     print STDERR
>> "gi=$gi\nauthors=$authors\nmedline=$medline\npubmed=$pubmed\n\n";
>>                 }
>>             }
>>         }
>>At 03:10 AM 4/1/2005, you wrote:
>>>*please* people always post the code or ideally a small snippet that
>>>demonstrates what you were trying to do, and post the result and if it's
>>>not an exception why it is not the result you expected. DO NOT just say
>>>'blah doesn't work for me'. Whenever someone needs to guess what you
>>>probably did and what you probably mean you are wasting other people's
>>>The GI# you have has multiple refs with one having a pubmed ID and none
>>>having a medline ID. So, the one ref that has a pubmed ID should return
>>>it from $ref->pubmed() but without any code snippet it is impossible to
>>>tell what you actually did and what therefore might be the problem.
>>>         -hilmar
>>>On Thursday, March 31, 2005, at 03:15  PM, Qunfeng wrote:
>>>>Hi there,
>>>>I am not very familiar with BioPerl. I tried to follow the example
>>>>showing in the above page to retrieve pubmed ID under each Reference
>>>>tag , i.e., $value->pubmed(), but it doesn't work for me for the seq
>>>>gi#56961711. The authors() works for me.  Appreciate any >>>
>>>>Bioperl-l mailing list
>>>>Bioperl-l at portal.open-bio.org
>>>Hilmar Lapp                            email: lapp at gnf.org
>>>GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
>Hilmar Lapp                            email: lapp at gnf.org
>GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
>Bioperl-l mailing list
>Bioperl-l at portal.open-bio.org

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