[Genbank-bb] GenBank Release 172.0 Now Available

Cavanaugh, Mark (NIH/NLM/NCBI) [E] via genbankb%40net.bio.net (by cavanaug from ncbi.nlm.nih.gov)
Fri Jun 12 14:41:53 EST 2009


Greetings GenBank Users,

  GenBank Release 172.0 is now available via FTP from the National
Center for Biotechnology Information (NCBI):

  Ftp Site           Directory   Contents
  ----------------   ---------   ---------------------------------------
  ftp.ncbi.nih.gov   genbank     GenBank Release 172.0 flatfiles
                     ncbi-asn1   ASN.1 data used to create Release 172.0

  Close-of-data for GenBank 172.0 occured on 06/10/2009. Uncompressed,
the Release 172.0 flatfiles require roughly 403 GB (sequence files only)
or 431 GB (including the 'short directory', 'index' and the *.txt
files). The ASN.1 data require approximately 366 GB.

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

  Release  Date       Base Pairs   Entries

  171      Apr 2009  102980268709  103335421
  172      Jun 2009  105277306080  106073709

Recent statistics for WGS sequences:

  Release  Date       Base Pairs   Entries

  171      Apr 2009  144522542010  48948309
  172      Jun 2009  145959997864  49063546

  During the 60 days between the close dates for GenBank Releases 171.0
and 172.0, the non-WGS/non-CON portion of GenBank grew by 2,297,037,371
basepairs and by 2,738,288 sequence records. During that same period,
3,680,844 records were updated. An average of about 106,985
non-WGS/non-CON records were added and/or updated per day.

  Between releases 171.0 and 172.0, the WGS component of GenBank grew
by 1,437,455,854 basepairs and by 115,237 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 172.0 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 1.3.5 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 172.0 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, 172.0). 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
172.0, 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 172.0

1.3.1 PROJECT linetype has been replaced by DBLINK

  The DBLINK linetype was introduced as of the February 2009
GenBank Release 170.0, to accomodate links to Project IDs and
the NCBI Trace Assembly Archive, and new types of links that
will arise in the future.

DBLINK co-existed with its predecessor linetype (PROJECT) for GenBank
releases 170.0 and 171.0 . With Release 172.0, however, the PROJECT
line has been completely removed, as this record illustrates:

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

1.3.2 Organizational changes

The total number of sequence data files increased by 36 with this
release:

  - the BCT division is now composed of  45 files (+5)
  - the ENV division is now composed of  16 files (+3)
  - the EST division is now composed of 875 files (+15)
  - the GSS division is now composed of 337 files (+2)
  - the INV division is now composed of  18 files (+3)
  - the PAT division is now composed of  73 files (+6)
  - the PLN division is now composed of  39 files (+1)
  - the VRL division is now composed of  12 files (+1)

The total number of 'index' files increased by 2 with this release:

  - the JOU (journal) index is now composed of 7 files (+1)
  - the KEY (keyword) index is now composed of 4 files (+1)

1.3.3 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

                         June 15 2009

It should be:

GBGSS100.SEQ          Genetic Sequence Data Bank

                         June 15 2009


The problem effects all EST files and most GSS files. We had hoped to
repair this formatting issue for Release 172.0, but the code changes
just missed the cut-off for release generation. The problem will
definitely be resolved for Release 173.0 .

1.3.4 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.

1.3.5 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 172.0. Consider gbgss266.seq
:

GBGSS1.SEQ          Genetic Sequence Data Bank
                            June 15 2009

                NCBI-GenBank Flat File Release 172.0

                           GSS Sequences (Part 1)

   87198 loci,    64267715 bases, from    87198 reported sequences

  Here, the filename and part number in the header is "1", though the
file
has been renamed as "266" 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 Qualifier changes from INSDC 2009

  Several qualifier changes for the Feature Table were agreed to at the
annual INSDC meeting in May 2009. Complete details and implementation
timelines will be made available in the August GenBank Release Notes.
In the meantime, here is an early preview of the changes that were
approved:

New value for /exception:

  /exception="annotated by transcript or proteomic data"

/pseudo qualifier to be re-named as /non_functional

  Because the term "pseudo" is often equated with "pseudogene", the
  /pseudo qualifier will be renamed as /non_functional, to better
  reflect its actual usage.

New /haplogroup qualifier defined for the source feature




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