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

[Chris Fields]

Just to follow up, it appears to be a disparity between the efetch gene data and the summary information (via esummary).  The folks at NCBI are checking up on it.

chris

On Feb 2, 2010, at 8:34 AM, Chris Fields wrote:

> Michael,
> 
> 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.
> 
> chris
> 
> 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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> 
> 
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