[BioC] SRAdb: is the database missing some entries?

[Cook, Malcolm]

Hi,

In case it helps, I thought I might remind us of our prior similar
experience:

	https://stat.ethz.ch/pipermail/bioc-devel/2011-October/002849.html


Perhaps the solution this time will be similar..

Cheers,

~Malcolm




On 6/10/12 6:53 AM, "Sean Davis" <sdavis2 at mail.nih.gov> wrote:

>On Sat, Jun 9, 2012 at 8:20 PM, Ben Woodcroft <donttrustben at gmail.com>
>wrote:
>> Hi,
>>
>> Firstly thanks to the creators of this very useful package.
>>
>> I've come across SRA identifiers that don't appear to be in the
>>database (a
>> minority, but still). Here's a few:
>>
>> SRA036600
>> DRX001436
>> SRA049463
>> ERA062401
>> ERA062401
>>
>> For example:
>>> library(SRAdb)
>>> sra_con = dbConnect(SQLite(),'SRAmetadb.sqlite')
>>> sraConvert(c('SRA036600'), sra_con= sra_con)
>> [1] submission study      sample     experiment run
>> <0 rows> (or 0-length row.names)
>>
>> However this isn't a bogus accession because I can see it on the NCBI
>>SRA
>> website.
>>
>> I could be wrong but I don't think it is as simple as the metadata being
>> out of date because the submission dates are often relatively old
>> (SRA036600 was 2011-05-13) and there's metadata from more recent SRA
>> submissions in the SRAdb).
>
>Thanks, Ben.
>
>We'll look into it.  Sorry for the inconvenience.
>
>Sean
>
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