[Genbank-bb] GenBank Release 170.0 Now Available

Cavanaugh, Mark (NIH/NLM/NCBI) [E] via genbankb%40net.bio.net (by cavanaug from ncbi.nlm.nih.gov)
Wed Feb 18 20:03:07 EST 2009


Greetings GenBank Users,

  GenBank Release 170.0 is now available via FTP from the National
Center for Biotechnology Information (NCBI):

  Ftp Site           Directory   Contents
  ----------------   ---------   ---------------------------------------
  ftp.ncbi.nih.gov   genbank     GenBank Release 170.0 flatfiles
                     ncbi-asn1   ASN.1 data used to create Release 170.0

  Close-of-data for GenBank 170.0 occured on 02/13/2009. Uncompressed,
the Release 170.0 flatfiles require roughly 390 GB (sequence files only)
or 417 GB (including the 'short directory', 'index' and the *.txt
files). The ASN.1 data require approximately 356 GB.

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

  Release  Date       Base Pairs   Entries

  169      Dec 2008   99116431942   98868465
  170      Feb 2009  101467270308  101815678

Recent statistics for WGS sequences:

  Release  Date       Base Pairs   Entries

  169      Dec 2008  141374971004  48394838
  170      Feb 2009  143797800446  49036947

  During the 64 days between the close dates for GenBank Releases 169.0
and 170.0, the non-WGS/non-CON portion of GenBank grew by 2,350,838,366
basepairs and by 2,947,213 sequence records. During that same period,
1,318,594 records were updated. An average of about 66,653
non-WGS/non-CON
records were added and/or updated per day.

  Between releases 169.0 and 170.0, the WGS component of GenBank grew by
2,422,829,442 basepairs and by 642,109 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 170.0 and Upcoming Changes) have been appended
below for your convenience.

                ** Important Notes **

*  A new linetype ( DBLINK ) has been implemented with this February
2009
   release. See Section 1.3.2 for information. Records with the DBLINK
   line will begin to appear via the GenBank Updates shortly after 
   February 18, 2009.

*  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 170.0 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: February 15 2009, 170.0). 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
170.0, please send email outlining your difficulties to:

        info from ncbi.nlm.nih.gov

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


1.3.1 Organizational changes

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

  - the BCT division is now composed of  38 files (+4)
  - the ENV division is now composed of  12 files (+1)
  - the EST division is now composed of 838 files (+16)
  - the GSS division is now composed of 322 files (+3)
  - the HTG division is now composed of 133 files (-1)
  - the PAT division is now composed of  65 files (+10)
  - the VRT division is now composed of  18 files (+1)

  Note that the HTG division has one less file than previously.
Occasional
decreases like this are now possible, given a new method of flatfile
processing that was adopted in December 2008. Essentially, records
within
a particular sequence file (eg, gbhtg134.seq) can become absorbed in a
different file, depending on the overall distribution of the number of
records in the files that make up a division. Such decreases are
reviewed,
to ensure that they do not indicate a loss of release content.

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

  - the AUT index is now composed of 65 files (+3)

1.3.2 New DBLINK linetype legal as of February 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=t
ree&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

  With this release, the new DBLINK linetype is now legal for GenBank
sequence
records, and it will begin to appear in GenBank Update files, soon after
GenBank 170.0 is made available.

  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,
as
illustrated in the below mock-up of CP000964 :

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.

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

  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.

1.3.3 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.

1.3.4 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 170.0. Consider gbgss254.seq
:

GBGSS1.SEQ          Genetic Sequence Data Bank
                        February 15 2009

                NCBI-GenBank Flat File Release 170.0

                           GSS Sequences (Part 1)

   87215 loci,    64322450 bases, from    87215 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

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

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

  Genome Project IDs and Trace Assembly Archive IDs can now be presented
via DBLINK, in conjunction with the legacy PROJECT linetype:

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 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 be replaced by DBLINK as of
GenBank
Release 171.0 in April 2009.




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