[Genbank-bb] GenBank Release 184.0 Available : July 4 2011

Cavanaugh, Mark (NIH/NLM/NCBI) [E] via genbankb%40net.bio.net (by cavanaug from ncbi.nlm.nih.gov)
Mon Jul 4 14:42:25 EST 2011


Greetings GenBank Users,

  GenBank Release 184.0 is now available via FTP from the National
Center for Biotechnology Information (NCBI):

  Ftp Site           Directory   Contents
  ----------------   ---------   ---------------------------------------
  ftp.ncbi.nih.gov   genbank     GenBank Release 184.0 flatfiles
                     ncbi-asn1   ASN.1 data used to create Release 184.0

  Close-of-data for GenBank 184.0 occurred on 06/29/2011. Uncompressed,
the Release 184.0 flatfiles require roughly 506 GB (sequence files only)
or 543 GB (including the 'short directory', 'index' and the *.txt
files). The ASN.1 data require approximately 416 GB.

Recent statistics for non-WGS, non-CON sequences:

  Release  Date      Base Pairs    Entries

  183      Apr 2011  126551501141  135440924
  184      Jun 2011  129178292958  140482268

Recent statistics for WGS sequences:

  Release  Date      Base Pairs    Entries

  183    Apr 2011  191401393188   62715288
  184    Jun 2011  200487078184   63735078

  During the 79 days between the close dates for GenBank Releases 183.0
and 184.0, the non-WGS/non-CON portion of GenBank grew by 2,626,791,817
basepairs and by 5,041,344 sequence records. During that same period,
2,507,856 records were updated. An average of 95,559 non-WGS/non-CON
records were added and/or updated per day.

  Between releases 183.0 and 184.0, the WGS component of GenBank grew by
9,085,684,996 basepairs and by 1,019,790 sequence records.

  For additional release information, see the README files in either of
the directories mentioned above, and the release notes (gbrel.txt) in
the genbank directory. Sections 1.3 and 1.4 of the release notes
(Changes in Release 184.0 and Upcoming Changes) have been appended
below for your convenience.

                ** Important Notes **

*  GenBank 'index' files are now provided without any EST content, and
   without most GSS content. See Section 1.3.3 of the release notes for
   further details.

   NCBI is considering ceasing support for the index files, so we
   encourage affected users to review that section and provide feedback.

  Release 184.0 data, and subsequent updates, are available now via
NCBI's Entrez and Blast services.

  As a general guideline, we suggest first transferring the GenBank
release notes (gbrel.txt) whenever a release is being obtained. Check
to make sure that the date and release number in the header of the
release notes are current (eg: June 15 2011, 184.0). If they are
not, interrupt the remaining transfers and then request assistance from
the NCBI Service Desk.

  A comprehensive check of the headers of all release files after your
transfers are complete is also suggested. Here's how one might go about
this on a Unix or Linux platform, using csh/tcsh :

        set files = `ls gb*.*`
        foreach i ($files)
                head -10 $i | grep Release
        end

Or, if the files are compressed, perhaps:

        gzcat $i | head -10 | grep Release

  If you encounter problems while ftp'ing or uncompressing Release
184.0, please send email outlining your difficulties to:

        info from ncbi.nlm.nih.gov

Mark Cavanaugh, Michael Kimelman, Ilya Dondoshansky, Sergey Zhdanov
GenBank
NCBI/NLM/NIH/HHS

1.3 Important Changes in Release 184.0

1.3.1 Organizational changes

The total number of sequence data files increased by 60 with this release:

  - the BCT division is now composed of  72 files (+4)
  - the CON division is now composed of 149 files (+1)
  - the ENV division is now composed of  40 files (-1)
  - the EST division is now composed of 445 files (+10)
  - the GSS division is now composed of 247 files (+10)
  - the INV division is now composed of  30 files (+1)
  - the PAT division is now composed of 164 files (+23)
  - the PLN division is now composed of  48 files (+2)
  - the TSA division is now composed of  30 files (+8)
  - the VRL division is now composed of  18 files (+1)
  - the VRT division is now composed of  24 files (+1)

The decrease in the number of ENV division files was caused by the
removal of nearly 100,000 uncultured bacterial sequence records from
an environmental sampling sequence project, which had been redundantly
submitted to GenBank twice.

The total number of 'index' files decreased by 18 with this release:

  - the AUT (author name)  index is now composed of  88 files (-20)
  - the JOU (journal name)  index is now composed of 12 files (+2)

The decrease in the number of AUT index files was due to both the removal
of redundantly-submitted bacterial sequence records (mentioned above), and
to corrections in the database where author names are separately stored
for the purpose of generating the gbaut* index files.

1.3.2 Changes in the content of index files

  As described in the GB 153 release notes, the 'index' files which accompany
GenBank releases (see Section 3.3) are considered to be a legacy data product by
NCBI, generated mostly for historical reasons. FTP statistics from January 2005
seemed to support this: the index files were transferred only half as frequently as
the files of sequence records. The inherent inefficiencies of the index file
format also lead us to suspect that they have little serious use by the user
community, particularly for EST and GSS records.

  The software that generated the index file products received little
attention over the years, and finally reached its limitations in
February 2006 (Release 152.0). The required multi-server queries which
obtained and sorted many millions of rows of terms from several different
databases simply outgrew the capacity of the hardware used for GenBank
Release generation.

  Our short-term solution is to cease generating some index-file content
for all EST sequence records, and for GSS sequence records that originate
via direct submission to NCBI.

  The three gbacc*.idx index files continue to reflect the entirety of the
release, including all EST and GSS records, however the file contents are
unsorted.

  These 'solutions' are really just stop-gaps, and we will likely pursue
one of two options:

a) Cease support of the 'index' file products altogether.

b) Provide new products that present some of the most useful data from
   the legacy 'index' files, and cease support for other types of index data.

  If you are a user of the 'index' files associated with GenBank releases, we
encourage you to make your wishes known, either via the GenBank newsgroup,
or via email to NCBI's Service Desk:

   info from ncbi.nlm.nih.gov

  Our apologies for any inconvenience that these changes may cause.

1.3.3 GSS File Header Problem

  GSS sequences at GenBank are maintained in two different systems, depending
on their origin, and the dumps from those systems occur in parallel. Because
the second dump (for example) has no prior knowledge of exactly how many GSS
files will be dumped by the first, it does not know how to number its own
output files.

  There is thus a discrepancy between the filenames and file headers for
103 of the GSS flatfiles in Release 184.0. Consider gbgss145.seq :

GBGSS1.SEQ          Genetic Sequence Data Bank
                            June 15 2011

                NCBI-GenBank Flat File Release 184.0

                           GSS Sequences (Part 1)

   87117 loci,    64024027 bases, from    87117 reported sequences

  Here, the filename and part number in the header is "1", though the file
has been renamed as "145" based on the number of files dumped from the other
system.  We hope to resolve this discrepancy at some point, but the priority
is certainly much lower than many other tasks.

1.4 Upcoming Changes

  The May 2011 International Nucleotide Sequence Database Collaboration annual
meeting resolved a variety of outstanding issues related to changes for the
/partial qualifier, the /inference and /experiment qualifiers, and the
/whole_replicon qualifier. In addition, some new changes for 2011 were agreed
upon. A summary of these changes will be provided via the GenBank newsgroup
within two months.




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