SRAdb: is the database missing some entries?

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Ben Woodcroft ▴ 40

@ben-woodcroft-5327

Last seen 10.2 years ago

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 I could be wrong but I don't think it is as simple as the metadata being out of date because the submission dates are often relatively old (SRA036600 was 2011-05-13) and there's metadata from more recent SRA submissions in the SRAdb). Any ideas? Thanks in advance, ben [[alternative HTML version deleted]]

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ADD COMMENT • link updated 12.5 years ago by Sean Davis 21k • written 12.5 years ago by Ben Woodcroft ▴ 40

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Sean Davis 21k

@sean-davis-490

Last seen 3 months ago

United States

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 out of date because the submission dates are often relatively old 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

ADD COMMENT • link 12.5 years ago Sean Davis 21k

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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 > >_______________________________________________ >Bioconductor mailing list >Bioconductor at r-project.org >https://stat.ethz.ch/mailman/listinfo/bioconductor >Search the archives: >http://news.gmane.org/gmane.science.biology.informatics.conductor