[Bioperl-l] Apparent disagreement between EUtilities and web page

Chris Fields cjfields at illinois.edu
Tue Feb 2 09:34:46 EST 2010


This is an unusual one and appears to be server-side.  I've seen this before with older obsoleted gene IDs (see: 435023, which is the older version of 100039753), so I'm wondering if an update going on that hasn't made it's way to the web interface yet.

I'm attempting to contact NCBI about the issue, so hopefully we'll hear back.


On Feb 2, 2010, at 6:14 AM, Michael Muratet wrote:

> Greetings
> I am using EUtilities for the first time to retrieve data from NCBI and I could use some help trying to isolate a problem I have. I was using a script I put together from examples in the How-To and email archives
>           $factory->set_parameters(-id => \@sub );
>           while ( my $docsum =$factory->next_DocSum ) {
>              my ($item) = $docsum->get_Items_by_name('GenomicInfoType');
>              my ( $chrloc, $acc, $start, $end) = (
>                                      $item->get_contents_by_name('ChrLoc'),
>                                      $item->get_contents_by_name('ChrAccVer'),
>                                      $item->get_contents_by_name('ChrStart'),
>                                      $item->get_contents_by_name('ChrStop'));
> and I found a record that has a suspect ChrStart field and no ChrStop field (using another example from the HowTo)
> ID: 100039753
> Name-Description-Orgname-Status-CurrentID-Chromosome-GeneticSource-MapLocation-OtherAliases-OtherDesignations-NomenclatureSymbol-NomenclatureName-NomenclatureStatus-TaxID-Mim-GenomicInfo-GeneWeight-Summary-ChrSort-ChrStart
> Name                :LOC100039753
> Description         :similar to putative
> Orgname             :Mus musculus
> Chromosome          :Y
> GeneticSource       :genomic
> MapLocation         :Y B
> OtherDesignations   :hypothetical protein LOC100039753
> TaxID               :10090
> GeneWeight          :401
> ChrSort             :~~last
> ChrStart            :999999999
> yet on the NCBI web page it shows a defined start and a stop for the locus.
> I can fix the perl code so that it won't barf when the field isn't defined, but I'd like to get all the data and I can't figure out if the problem is on the client side or the server side. All the data comes from the same source, doesn't it?
> Thanks
> Mike
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