[Genbank-bb] GenBank Release 177.0 Now Available

Cavanaugh, Mark (NIH/NLM/NCBI) [E] via genbankb%40net.bio.net (by cavanaug from ncbi.nlm.nih.gov)
Fri Apr 16 16:32:58 EST 2010


Greetings GenBank Users,

  GenBank Release 177.0 is now available via FTP from the National
Center for Biotechnology Information (NCBI):

  Ftp Site           Directory   Contents
  ----------------   ---------   ---------------------------------------
  ftp.ncbi.nih.gov   genbank     GenBank Release 177.0 flatfiles
                     ncbi-asn1   ASN.1 data used to create Release 177.0

  Close-of-data for GenBank 177.0 occurred on 04/14/2010. Uncompressed,
the Release 177.0 flatfiles require roughly 439 GB (sequence files only)
or 471 GB (including the 'short directory', 'index' and the *.txt
files). The ASN.1 data require approximately 361 GB.

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

  Release  Date      Base Pairs    Entries

  176      Feb 2010  112326229652  116461672
  177      Apr 2010  114348888771  119112251

Recent statistics for WGS sequences:

  Release  Date      Base Pairs    Entries

  176      Feb 2010  163991858015  57134273
  177      Apr 2010  165536009514  58361599

  During the 54 days between the close dates for GenBank Releases 176.0
and 177.0, the non-WGS/non-CON portion of GenBank grew by 2,022,659,119
basepairs and by 2,650,579 sequence records. During that same period,
4,707,333 records were updated. An average of about 136,250 non-WGS/non-CON
records were added and/or updated per day.

  Between releases 176.0 and 177.0, the WGS component of GenBank grew by
1,544,151,499 basepairs and by 1,227,326 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 177.0 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 1.3.3 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 177.0 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 2010, 177.0). 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
        end

Or, if the files are compressed, perhaps:

        gzcat $i | head -10 | grep Release

  If you encounter problems while ftp'ing or uncompressing Release
177.0, 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 177.0

1.3.1 Organizational changes

The total number of sequence data files increased by 29 with this release:

  - the BCT division is now composed of  54 files (+2)
  - the CON division is now composed of 136 files (+2)
  - the ENV division is now composed of  24 files (+1)
  - the EST division is now composed of 413 files (+3)
  - the GSS division is now composed of 211 files (+3)
  - the INV division is now composed of  21 files (+2)
  - the PAT division is now composed of 115 files (+15)
  - the PLN division is now composed of  40 files (+1)

1.3.2 New /pseudogene and /non_functional qualifiers : Delayed!

  New /pseudogene and /non_functional qualifiers were scheduled to
become legal for the GenBank Feature Table as of this April 2010
GenBank release. The intial plan was to simply rename /pseudo :

    "Because the term "pseudo" is often assumed to mean 'pseudogene',
     the /pseudo qualifier will be renamed as /non_functional, to
     better reflect its actual usage in the sequence databases."

  During subsequent discussions among the INSDC members, it was
decided that a more conservative course would be to introduce two
new qualifiers:

    /pseudogene
    /non_functional

  However, implementation of this decision has proved to be complex
for two of the INSDC partners (including GenBank), and the costs of
the proposed change are quite high. So at the very least, implementation
will be further delayed, by at least two months. And the decision to
introduce the new qualifiers will be re-examined at the May 2010
INSDC collaborative meeting, to decide if the implementation costs
really warrant the change.

  In the meantime, the /pseudo qualifier will continue to be used, in
all the same contexts as previously.

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 from 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
ninety of the GSS flatfiles in Release 177.0. Consider gbgss122.seq :

GBGSS1.SEQ          Genetic Sequence Data Bank
                           April 15 2010

                NCBI-GenBank Flat File Release 177.0

                           GSS Sequences (Part 1)

   87168 loci,    64172121 bases, from    87168 reported sequences

  Here, the filename and part number in the header is "1", though the file
has been renamed as "122" 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

  There are no planned format changes for GenBank at the present time.





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