[ensembl-dev] Missing IDS in ENSEMBL database

Duarte Molha Duarte.Molha at ogt.co.uk
Fri May 25 12:02:11 BST 2012


Thanks Thibaut Hourlier

I just get very confused with all these IDS with the same format meaning different things!

Best regards

Duarte



From: dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] On Behalf Of Thibaut Hourlier
Sent: 25 May 2012 11:20
To: Ensembl developers list
Subject: Re: [ensembl-dev] Missing IDS in ENSEMBL database

Dear Duarte,
I went through the four first of your IDs:

On 25 May 2012, at 10:14, Duarte Molha wrote:


Dear Developers

I created a simple script to output the exons of specific transcripts with NM ids.
It works fine for all but a small list of IDS. The large majority of the failed IDS have been suppressed from NCBI
Because they were found to be a " nonsense-mediated mRNA decay (NMD) candidate" so I do not mind eliminating those records from my query.

However some of the ones that fail are in NCBI database and for some reason ENSEMBL is not able to query them:
NM_001040409.1
It is an NMD transcript.

NM_001167607.1
It is an exon supporting feature and not a transcript supporting feature, i think this is the reason you don't get it with your script
http://www.ensembl.org/Homo_sapiens/Transcript/SupportingEvidence?db=core;g=ENSG00000196743;r=5:150591711-150650001;t=ENST00000523466

NM_001199987.1
If you look in the Gene database at NCBI you will see that there is 2 other sequences for NDUFB6, which are the transcript supporting feature for the 2 transcripts in Ensembl for the gene.
http://www.ncbi.nlm.nih.gov/gene/?term=NM_001199987.1
http://www.ensembl.org/Homo_sapiens/Transcript/SupportingEvidence?db=core;g=ENSG00000165264;r=9:32552997-32573160;t=ENST00000379847

NM_001204090.1
Same problem as above, we did not use this sequence.

What you can do is to use the HGNC identifier of these failing IDs in the fetch_all_by_external_id method, i.e. NM_001199987.1 -> NDUFB6

Regards
Thibaut


NM_001242881.1
NM_014249.2
NM_015584.3
NM_024728.2

Can you tell me how to retrieve these from the database?

Here is the portion of my script I use to retrieve the data:

foreach my $query_transcript (@transcripts_of_interest) {
    chomp $query_transcript;
    my $transcript = "";
    if ($query_transcript =~ /ENST/i){
        $transcript =   $transcript_adaptor->fetch_by_stable_id("$query_transcript");
    }
    else{
        ($transcript) = @{ $transcript_adaptor->fetch_all_by_external_name("$query_transcript");
    }

    unless ($transcript){
        $progress->message("Query: $query_transcript failed");
        next;
    }
    foreach my $exon ( @{ $transcript->get_all_Exons() } ) {
        my $estring = feature2string($exon);
        print "$query_transcript:\t$estring\n";
    }
    $next_update = $progress->update() if (++$j > $next_update);

}

Best regards

Duarte Molha

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