[Genbank-bb] GenBank Release 176.0 Now Available

Cavanaugh, Mark (NIH/NLM/NCBI) [E] via genbankb%40net.bio.net (by cavanaug from ncbi.nlm.nih.gov)
Tue Feb 23 20:50:05 EST 2010


Greetings GenBank Users,

  GenBank Release 176.0 is now available via FTP from the National
Center for Biotechnology Information (NCBI):

  Ftp Site           Directory   Contents
  ----------------   ---------   ---------------------------------------
  ftp.ncbi.nih.gov   genbank     GenBank Release 176.0 flatfiles
                     ncbi-asn1   ASN.1 data used to create Release 176.0

  Close-of-data for GenBank 176.0 occurred on 02/19/2010. Uncompressed,
the Release 176.0 flatfiles require roughly 432 GB (sequence files only)
or 463 GB (including the 'short directory', 'index' and the *.txt
files). The ASN.1 data require approximately 354 GB.

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

  Release  Date      Base Pairs    Entries

  175      Dec 2009  110118557163  112910950
  176      Feb 2010  112326229652  116461672

Recent statistics for WGS sequences:

  Release  Date      Base Pairs    Entries

  175      Dec 2009  158317168385  54076973
  176      Feb 2010  163991858015  57134273

  During the 66 days between the close dates for GenBank Releases 175.0
and 176.0, the non-WGS/non-CON portion of GenBank grew by 2,207,672,489
basepairs and by 3,550,722 sequence records. During that same period,
938,827 records were updated. An average of about 68,000 non-WGS/non-CON
records were added and/or updated per day.

  Between releases 175.0 and 176.0, the WGS component of GenBank grew by
5,674,689,630 basepairs and by 3,057,300 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 176.0 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 176.0 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, 176.0). 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
176.0, 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 176.0

1.3.1 Organizational changes

The total number of sequence data files decreased by 619 with this release:

  - the BCT division is now composed of  52 files (+2)
  - the CON division is now composed of 134 files (+4)
  - the EST division is now composed of 410 files (-494)
  - the GSS division is now composed of 208 files (-148)
  - the MAM division is now composed of   6 files (+1)
  - the PAT division is now composed of 100 files (+12)
  - the TSA division is now composed of   4 files (+2)
  - the VRL division is now composed of  14 files (+1)
  - the VRT division is now composed of  21 files (+1)

  This is a planned decrease, see Section 1.3.2 for more information.

The total number of 'index' files increased by 3 with this release:

  - the AUT (author) index is now composed of 73 files (+2)
  - the JOU (journal) index is now composed of 8 files (+1)

1.3.2 Increase in the size of EST and GSS sequence files

  The average size of EST and GSS sequence files, uncompressed, was
approximately 222 MB prior to GenBank Release 176.0. But as of this
February 2010 GenBank release, we have increased the average 
uncompressed file size to about 500 MB. This has reduced the total
number of EST/GSS files by roughly 50% (from 1260 in Release 175.0 to
618 in Release 176.0).

  This change should make the FTP transfer of an entire release easier
to manage, because the number of files is reduced, and their compressed 
sizes remain fairly small (with a maximum of about 80MB). Although the
uncompressed files are larger than previously, 500MB should still be
tractable for most users, especially given the overall disk space needs
for an entire release.

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
eighty-seven of the GSS flatfiles in Release 176.0. Consider gbgss122.seq :

GBGSS1.SEQ          Genetic Sequence Data Bank
                        February 15 2010

                NCBI-GenBank Flat File Release 176.0

                           GSS Sequences (Part 1)

   87169 loci,    64174921 bases, from    87169 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

1.4.1 New /pseudogene and /non_functional qualifiers

  The GenBank 173.0 release notes described an anticipated conversion
of the /pseudo qualifer to /non_functional, based on the results of
the May 2009 INSDC annual meeting:

    "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 follow-up discussions, the INSDC members decided that existing
uses of /pseudo can include both of the possible meanings of the term,
and that a more conservative course would be to introduce two new
qualifiers:

    /pseudogene
    /non_functional

  Sequence submission tools will be updated to utilize these, and
the ambiguous /pseudo qualifier will be deprecated. If it is 
possible, existing instances of /pseudo would then be converted
to one of the two new qualifiers.

  /pseudogene and /non_functional will become legal for the Feature
Table as of the April 2010 GenBank Release.




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