[Genbank-bb] GenBank Release 169.0 Now Available

Cavanaugh, Mark (NIH/NLM/NCBI) [E] via genbankb%40net.bio.net (by cavanaug from ncbi.nlm.nih.gov)
Tue Dec 16 04:17:17 EST 2008


Greetings GenBank Users,

  GenBank Release 169.0 is now available via FTP from the National
Center for Biotechnology Information (NCBI):

  Ftp Site           Directory   Contents
  ----------------   ---------   ---------------------------------------
  ftp.ncbi.nih.gov   genbank     GenBank Release 169.0 flatfiles
                     ncbi-asn1   ASN.1 data used to create Release 169.0

  Close-of-data for GenBank 169.0 occured on 12/11/2008. Uncompressed,
the Release 169.0 flatfiles require roughly 381 GB (sequence files only)
or 407 GB (including the 'short directory', 'index' and the *.txt
files). The ASN.1 data require approximately 349 GB.

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

  Release  Date       Base Pairs   Entries

  168      Oct 2008   97381682336  96400790
  169      Dec 2008   99116431942  98868465

Recent statistics for WGS sequences:

  Release  Date       Base Pairs   Entries

  168      Oct 2008  136085973423  46108952
  169      Dec 2008  141374971004  48394838

  During the 45 days between the close dates for GenBank Releases 168.0
and 169.0, the non-WGS/non-CON portion of GenBank grew by 1,734,749,606
basepairs and by 2,467,675 sequence records. During that same period,
4,183,486 records were updated. An average of about 147,803 non-WGS/non-CON
records were added and/or updated per day.

  Between releases 168.0 and 169.0, the WGS component of GenBank grew by
5,288,997,581 basepairs and by 2,285,886 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 169.0 and Upcoming Changes) have been appended
below for your convenience.

                ** Important Notes **

*  A new linetype ( DBLINK ) will be implemented as of the February 2009
   release. See Section 1.4.1 for information.

*  GenBank 'index' files are now provided without any EST content, and
   without most GSS content. See Section 1.3.12 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 169.0 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: December 15 2008, 169.0). 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
169.0, please send email outlining your difficulties to:

        info from ncbi.nlm.nih.gov

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


1.3 Important Changes in Release 169.0

1.3.1 Organizational changes

  As described in a post to the GenBank Newsgroup on December 11, 2008, the
number of sequence data files associated with this GenBank release has 
increased by a larger-than-usual amount, due to changes in the way that data
are processed and stored at NCBI. Thus the per-division increases described
below reflect both the storage-related changes *and* actual database growth.

  In addition, GenBank divisions which consist of a single data file now
include a number in their names:

     gbtsa.seq -> gbtsa1.seq
     gbuna.seq -> gbuna1.seq

The total number of sequence data files increased by 94 with this release:

  - the BCT division is now composed of  34 files (+2)
  - the CON division is now composed of 128 files (+25)
  - the ENV division is now composed of  11 files (+1)
  - the EST division is now composed of 822 files (+20)
  - the GSS division is now composed of 319 files (+10)
  - the HTC division is now composed of  13 files (+1)
  - the HTG division is now composed of 134 files (+12)
  - the INV division is now composed of  14 files (+1)
  - the PAT division is now composed of  55 files (+8)
  - the PLN division is now composed of  37 files (+5)
  - the PRI division is now composed of  39 files (+3)
  - the ROD division is now composed of  28 files (+2)
  - the STS division is now composed of  20 files (+2)
  - the VRL division is now composed of  11 files (+1)
  - the VRT division is now composed of  17 files (+1)

In addition, the total number of index files increased by 3 with this release:

  - the AUT index is now composed of 62 files (+3)

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 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.

1.3.3 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
sixty-nine of the GSS flatfiles in Release 169.0. Consider gbgss251.seq :

GBGSS1.SEQ          Genetic Sequence Data Bank
                        December 15 2008

                NCBI-GenBank Flat File Release 169.0

                           GSS Sequences (Part 1)

   87209 loci,    64341123 bases, from    87209 reported sequences

  Here, the filename and part number in the header is "1", though the file
has been renamed as "251" 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

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

  The PROJECT linetype allows a sequence record to be linked to information
about the sequencing project that generated the data which ultimately
resulted in the record's submission to the International Nucleotide Sequence
Database ( INSD; see http://www.insdc.org ) .

  This complete bacterial GenBank record illustrates the use of the PROJECT
line:

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

  When viewed on the web in NCBI's Entrez:Nucleotide, the record's project
identifier (28471) links to an entry in the Genome Project Database (GPDB) :

  http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&uid=28471

where information about the sequencing center, the bacterium, and other
GenBank records (eg, plasmids) associated with the sequencing project
can be found.

  Since the introduction of PROJECT, the scope of the "Genome" Project
Database has expanded, to include projects that are not necessarily targetted
to the sequencing of a complete genome.

  In addition, there can be other resources which underlie an INSD sequence
record, such as the Trace Assembly Archive at the NCBI:

  http://www.ncbi.nlm.nih.gov/Traces/assembly/assmbrowser.cgi?cmd=show&f=tree&m=main&s=tree

  Because of the expanded scope of the GPDB, and because we anticipate a need
to link to more resources than just the GPDB, the PROJECT linetype is going to
be replaced by a new linetype:

   DBLINK

  Modifications to linetypes can be disruptive, so the switch to DBLINK will occur
in several stages. As of October 2008, links to the NCBI Trace Assembly Archive are
displayed via a line of text in the COMMENT section of sequence records. Here is a
mock-up, based on CP000964, to illustrate that initial change:

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
....
COMMENT     Trace Assembly Archive:123456
            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.

Note: Use of the Trace Assembly Archive is still in its early stages, so only
a few records are expected to have these links in the short term.

  The new DBLINK linetype will then be introduced with GenBank Release 170.0 ,
on or near February 15, 2009 .

  The Genome Project ID and the Trace Assembly Archive ID will be presented
via DBLINK, and the existing PROJECT line will continue to be displayed:

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 will co-exist for one GenBank release, until Release 171.0
(April 15, 2009), at which point the PROJECT line will be removed. In its final
state, our 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 be replaced by DBLINK as of GenBank
Release 171.0 in April 2009.

  For those who process sequence data in NCBI's ASN.1 format: The
underlying representation for (Genome) Project IDs will remain unchanged.
There will be no changes to the ASN.1 User-object that is used to store them:

    user {
      type
        str "GenomeProjectsDB" ,
      data {
        {
          label
            str "ProjectID" ,
          data
            int 28471 } ,
        {
          label
            str "ParentID" ,
          data
            int 0 } } } ,

  However, to support linkages to other resources, such as the Trace
Assembly Archive, a new "DBLink" User-object will be introduced:

    user {
      type
        str "DBLink" ,
      data {
        {
          label
            str "Trace Assembly Archive" ,
          data
            ints { 123456 } } } }

  As new types of linkages are established, they will be added to
the DBLink User-object, and displayed via the DBLINK linetype in
the GenBank flatfile format. 

  There is a possibility that the GenomeProjectsDB User-object
might someday be incorporated into the new DBLink User-object.
But at the moment, there are no firm plans to do so.



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