[Genbank-bb] GenBank Release 197.0 Available : August 15 2013

Cavanaugh, Mark (NIH/NLM/NCBI) [E] via genbankb%40net.bio.net (by cavanaug from ncbi.nlm.nih.gov)
Thu Aug 15 17:06:16 EST 2013

Greetings GenBank Users,

  GenBank Release 197.0 is now available via FTP from the
National Center for Biotechnology Information (NCBI):

  Ftp Site           Directory   Contents
  ----------------   ---------   ---------------------------------------
  ftp.ncbi.nih.gov   genbank     GenBank Release 197.0 flatfiles
                     ncbi-asn1   ASN.1 data used to create Release 197.0

  Close-of-data for GenBank 197.0 occurred on 08/12/2013. Uncompressed,
the Release 197.0 flatfiles require roughly 607 GB (sequence files only).
The ASN.1 data require approximately 501 GB.

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

  Release  Date      Base Pairs    Entries

  196      Jun 2013  152599230112  165740164
  197      Aug 2013  154192921011  167295840

Recent statistics for WGS sequences:

  Release  Date      Base Pairs    Entries

  196    Jun 2013  453829752320  112488036
  197    Aug 2013  500420412665  124812020

  During the 60 days between the close dates for GenBank Releases 196.0
and 197.0, the non-WGS/non-CON portion of GenBank grew by 1,593,690,899
basepairs and by 1,555,676 sequence records. During that same period,
1,274,878 records were updated. An average of 47,176 non-WGS/non-CON
records were added and/or updated per day.

  Between releases 196.0 and 197.0, the WGS component of GenBank grew by
46,590,660,345 basepairs and by 12,323,984 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 197.0 and Upcoming Changes) have been appended
below for your convenience.

                    * * * Important * * *

  A significant change is described in Section 1.4.1 of the release
notes: An anticipated phasing-out of NCBI GI sequence identifiers.
We urge users who make use of GIs in their information systems and
analysis pipelines to review that section.

  Release 197.0 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: August 15 2013, 197.0). 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

Or, if the files are compressed, perhaps:

        gzcat $i | head -10 | grep Release

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

        info from ncbi.nlm.nih.gov

Mark Cavanaugh, Michael Kimelman, Ilya Dondoshansky, Sergey Zhdanov,

1.3 Important Changes in Release 197.0

1.3.1 Organizational changes

The total number of sequence data files increased by 25 with this release:

  - the BCT division is now composed of 106 files (+3)
  - the CON division is now composed of 215 files (+7)
  - the ENV division is now composed of  62 files (+1)
  - the EST division is now composed of 474 files (+1)
  - the GSS division is now composed of 278 files (+5)
  - the PLN division is now composed of  63 files (+1)
  - the PRI division is now composed of  46 files (+1)
  - the TSA division is now composed of 145 files (+4)
  - the VRL division is now composed of  26 files (+1)
  - the VRT division is now composed of  31 files (+1)

1.3.2 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 117
of the GSS flatfiles in Release 197.0. Consider gbgss162.seq :

GBGSS1.SEQ          Genetic Sequence Data Bank
                            June 15 2013

                NCBI-GenBank Flat File Release 196.0

                           GSS Sequences (Part 1)

   87041 loci,    63875275 bases, from    87041 reported sequences

  Here, the filename and part number in the header is "1", though the file
has been renamed as "162" 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

1.4.1 GI sequence identifiers to be phased out (slowly!) at NCBI

  The numeric GI sequence identifier that NCBI assigns to all nucleotide
and protein sequences were first made publicly available in GenBank Release
products as of GenBank 81.0, in February 1994. See:


 These simple, uniform, integer-based unique identifiers (which predated the
introduction of Accession.Version sequence identifiers) were crucial to the
development of NCBI's Entrez retrieval system, and have served their purpose
very well for nearly 20 years. 

  However, as NCBI considers how best to address the expected increase in the
volume of submitted sequence data, it is clear that prior practices will need
to be re-thought. As an example, imagine 100,000 pathogen-related
genomes/samples, each with 5000 proteins, most of which are common to all. We
will be moving toward solutions that represent each unique protein *once*.
The coding region protein products for each genome will likely continue to be
assigned their own Accession.Version identifiers, but (within the NCBI data
model) they will simply *reference* the unique proteins. And, they will no
longer be issued GIs of their own.

  Such a change will likely have a significant impact on NCBI users who utilize
GIs in their own information systems and analysis pipelines, so it will not be
introduced quickly. You can expect that a great deal of additional detail will
be made available via NCBI's various announcement mechanisms.

  *This* particular announcement is chiefly intended to provide some advance
warning to our users. There _will_ be classes of GenBank sequences that
are not assigned GIs in the not-too-distant future. If GIs are central to
your operations, then it might be appropriate to begin planning a switch to
the use of Accession.Version identifiers instead.

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