Thanks Jack ! Sent from my phone so apologies for my brevity and frequent typos. -------- Original message -------- From: Jack Zhu <zhujack@mail.nih.gov> Date: 17/06/2014 20:31 (GMT+00:00) To: Sean Davis <sdavis2@mail.nih.gov>,"Shanahan, Hugh" <hugh.shanahan@rhul.ac.uk>,bioconductor@r-project.org,Jamie.Al- Nasir.2012@live.rhul.ac.uk Subject: Re: [BioC] SRAmetadb Bioconductor package; study record count low for 2013 Hi Jamie and all, By modifying my codes and pulling data from a curated table (SRA_Accessions.tab) from the SRA, I think the missing 'submission_date' in the submission table have been fixed:   strftime('%Y', s.submission_date) count(*) 1                              2008      348 2                              2009     1260 3                              2010     2865 4                              2011     4276 5                              2012     6606 6                              2013   15309 7                              2014     7706 Please let me know if you still see any problems or have any questions.  Thanks. Jack ---- Yuelin Jack Zhu Genetics Branch/CCR/NCI/NIH Tel: (301)496-4527 FAX: (301) 402-3241 E-mail: zhujack@mail.nih.gov On Sun, Jun 8, 2014 at 11:11 AM, Jack Zhu <zhujack@mail.nih.gov> wrote: > Hi all, > > Regarding missing studies by submission_date for 2013 and 2014 in the > SRAdb SQLite database, I did some investigation and found the reason. > The metadata in the SRAdb is mainly parsed from the XML files of the > SRA submissions and it is true with the submission table.  But I see > quite some submission xml files don't have submission date, e.g. > > ftp://ftp-trace.ncbi.nih.gov/sra/Submissions/SRA157/SRA157949/ > >   SRA157949.experiment.xml >   SRA157949.submission.xml > > So it seem all the study and submission records are there, but some > submission records just don't submission date.  I am looking into the > possibility of adding dates for those records. > > Jamie, thanks for the finding and I will keep you updated. > > Jack > > > On Fri, Jun 6, 2014 at 3:49 PM, Sean Davis <sdavis2@mail.nih.gov> wrote: >> Hi, Jack. >> >> I took a look at this and it does appear that the number of >> submissions is very low for 2013.  Also, there are no 2014 submissions >> listed that I could find.  This was using the June 1, 2014 sqlite >> file. >> >> Sean >> >> >> >> ---------- Forwarded message ---------- >> From: Al-Nasir, Jamie (2012) <jamie.al-nasir.2012@live.rhul.ac.uk> >> Date: Thu, Jun 5, 2014 at 2:20 PM >> Subject: [BioC] SRAmetadb Bioconductor package; study record count low for 2013 >> To: "bioconductor@r-project.org" <bioconductor@r-project.org> >> Cc: "Shanahan, Hugh" <hugh.shanahan@rhul.ac.uk> >> >> >> Hello, >> >> >> I have been looking at the SRA (Sequence Read Archive) SQLite database >> >> provided as a Bioconductor package for R. >> >> >> My question concerns top-level studies, which are found in the study table >> >> and dated in the submissions table. >> >> >> The question is why are there so few entries for the top level studies for 2013 >> >> as compared with 2011 and 2012.... >> >> >> The SQL queries I have written, joining the Submission table and Study table >> >> in order to obtain the submission_date yield the following counts of top-level >> >> studies by year.... >> >> >> 2005|64 >> 2006|38 >> 2007|94 >> 2008|269 >> 2009|893 >> 2010|2631 >> 2011|4077 >> 2012|5208 >> 2013|724 >> >> >> As one can see the number of studies in the meta-data falls off on 2013. >> >> I have been using the sraDB bioconductor SQLite database which has >> >> the creation timestamp of 2013-12-03 08:29:26 in the metaInfo table. >> >> >> Would really appreciate if anyone has any useful thoughts on this. >> >> >> Best regards, >> >> Jamie >> >> Jamie Al-Nasir MPharm (Hons) >> Department of Computer Science >> Centre for Systems and Synthetic Biology >> Mobile: +44 (0)759 4800 229 >> Web: http://jamie.al-nasir.com/ >> >>         [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]