[Genbank-bb] GenBank Release 171.0 Now Available

Cavanaugh, Mark (NIH/NLM/NCBI) [E] via genbankb%40net.bio.net (by cavanaug from ncbi.nlm.nih.gov)
Tue Apr 14 18:14:06 EST 2009


Greetings GenBank Users,

  GenBank Release 171.0 is now available via FTP from the National
Center for Biotechnology Information (NCBI):

  Ftp Site           Directory   Contents
  ----------------   ---------   ---------------------------------------
  ftp.ncbi.nih.gov   genbank     GenBank Release 171.0 flatfiles
                     ncbi-asn1   ASN.1 data used to create Release 171.0

  Close-of-data for GenBank 171.0 occured on 04/10/2009. Uncompressed,
the Release 171.0 flatfiles require roughly 395 GB (sequence files only)
or 422 GB (including the 'short directory', 'index' and the *.txt
files). The ASN.1 data require approximately 360 GB.

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

  Release  Date       Base Pairs   Entries

  170      Feb 2009  101467270308  101815678
  171      Apr 2009  102980268709  103335421

Recent statistics for WGS sequences:

  Release  Date       Base Pairs   Entries

  170      Feb 2009  143797800446  49036947
  171      Apr 2009  144522542010  48948309

  During the 56 days between the close dates for GenBank Releases 170.0
and 171.0, the non-WGS/non-CON portion of GenBank grew by 1,512,998,401
basepairs and by 1,519,743 sequence records. During that same period,
1,040,778 records were updated. An average of about 45,723
non-WGS/non-CON records were added and/or updated per day.

  Between releases 170.0 and 171.0, the WGS component of GenBank grew
by 724,741,564 basepairs and the number of records **decreased** by
88,638. A decrease in the overall number of WGS records can
occasionally occur, as a result of genome re-assemblies which yield
larger (but fewer) records, and due to the submission of completed
genomes which supercede WGS projects.

  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 171.0 and Upcoming Changes) have been appended
below for your convenience.

                ** Important Notes **

*  This is the final release for which the PROJECT linetype
   will be present in GenBank flatfiles. The new DBLINK linetype
   replaces PROJECT. Post-171.0 GenBank Update files will
   have only the new DBLINK linetype within about two weeks,
   and the same will be true of all future complete releases.
   See Section 1.3.1 for more information.

*  GenBank 'index' files are now provided without any EST content, and
   without most GSS content. See Section 1.3.5 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 171.0 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: April 15 2009, 171.0). 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 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
171.0, 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 171.0

1.3.1 PROJECT linetype to be replaced by DBLINK (April 2009)

  The new DBLINK linetype was introduced as of the February 2009
GenBank Release 170.0.

  Genome Project IDs and Trace Assembly Archive IDs are now presented
via DBLINK, in conjunction with the legacy PROJECT linetype, as this
mock-up for CP000964 illustrates:

LOCUS       CP000964             5641239 bp    DNA     circular BCT
24-SEP-2008
DEFINITION  Klebsiella pneumoniae 342, complete genome.
ACCESSION   CP000964
VERSION     CP000964.1  GI:206564770
PROJECT     GenomeProject:28471
DBLINK      Project:28471
            Trace Assembly Archive:123456
....
COMMENT     The source for the DNA and/or cells is:  Professor Eric W.
            Triplett, Chair, Department of Microbiology and Cell
Science,
            Institute of Food and Agricultural Sciences, University of
Florida,
            P.O. Box 110700, Gainesville, FL 32611-0700, ewt from ufl.edu.

PROJECT and DBLINK have co-existed for GenBank releases 170.0 and 171.0
.
But subsequent to this April release, the PROJECT line will be removed
from the
flatfile format. In its final state, the above mock-up for CP000964
becomes:

LOCUS       CP000964             5641239 bp    DNA     circular BCT
24-SEP-2008
DEFINITION  Klebsiella pneumoniae 342, complete genome.
ACCESSION   CP000964
VERSION     CP000964.1  GI:206564770
DBLINK      Project:28471
            Trace Assembly Archive:123456
....
COMMENT     The source for the DNA and/or cells is:  Professor Eric W.
            Triplett, Chair, Department of Microbiology and Cell
Science,
            Institute of Food and Agricultural Sciences, University of
Florida,
            P.O. Box 110700, Gainesville, FL 32611-0700, ewt from ufl.edu.

  In summary: The PROJECT linetype will cease to be displayed in
post-171.0
GenBank Update data products within the next two weeks. The same will be
true of all future complete GenBank releases.

1.3.2 Organizational changes

The total number of sequence data files increased by 34 with this
release:

  - the BCT division is now composed of  40 files (+2)
  - the CON division is now composed of 131 files (+3)
  - the ENV division is now composed of  13 files (+1)
  - the EST division is now composed of 860 files (+22)
  - the GSS division is now composed of 335 files (+13)
  - the INV division is now composed of  15 files (+1)
  - the MAM division is now composed of   5 files (+1)
  - the PAT division is now composed of  67 files (+2)
  - the PLN division is now composed of  38 files (+1)

1.3.3 CON-division records for 'segmented sets' restored.

  A previously overlooked problem in Release 170.0 processing resulted
in
the exclusion of roughly 14,000 CON-division entries for a type of
record
referred to as a 'segmented set'. Segmented sets consist of small
sequence
fragments of an incompletely sequenced molecule, packaged together, with
a
top-level sequence that specifies the order of the underlying fragments.
That top-level sequence can be displayed as a CON division record.
AH000819
is an example:

ASN.1 for AH000819:

 
http://www.ncbi.nlm.nih.gov/nuccore/405204?report=asn1&log$=seqview

Flatfile view of the nine sequenced fragments:

	 http://www.ncbi.nlm.nih.gov/nuccore/405204

These (largely legacy) CON-division records have been restored in
Release 171.0 and can be found in gbcon131.seq .

1.3.4 File header problem for EST and GSS files

  A new method of generating the EST and GSS sequence files has been 
developed, which has reduced the time required to generate a GenBank
release by one day. However, a minor problem in the formatting of the
header of the sequence files was inadvertently introduced : a leading 
space exists before the filename on the very first line. For example:

 GBGSS100.SEQ          Genetic Sequence Data Bank

                         April 15 2009


It should be:

GBGSS100.SEQ          Genetic Sequence Data Bank

                         April 15 2009


The problem effects all EST files and most GSS files. We doubt that it
will cause significant problems for users, however the problem will be
corrected for our next release.

1.3.5 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 of January
2005
seem 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.

1.3.6 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
seventy-two of the GSS flatfiles in Release 171.0. Consider gbgss264.seq
:

GBGSS1.SEQ          Genetic Sequence Data Bank
                           April 15 2009

                NCBI-GenBank Flat File Release 171.0

                           GSS Sequences (Part 1)

   87206 loci,    64290178 bases, from    87206 reported sequences

  Here, the filename and part number in the header is "1", though the
file
has been renamed as "254" based on the number of files dumped from the
other
system.  We will work to resolve this discrepancy in future releases,
but the
priority is certainly much lower than many other tasks.

1.4 Upcoming Changes

  There are no scheduled format changes for GenBank.




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