[Genbank-bb] GenBank Release 178.0 Now Available

Cavanaugh, Mark (NIH/NLM/NCBI) [E] via genbankb%40net.bio.net (by cavanaug from ncbi.nlm.nih.gov)
Fri Jun 18 16:36:12 EST 2010

Greetings GenBank Users,

  GenBank Release 178.0 is now available via FTP from the National
Center for Biotechnology Information (NCBI):

  Ftp Site           Directory   Contents
  ----------------   ---------   ---------------------------------------
  ftp.ncbi.nih.gov   genbank     GenBank Release 178.0 flatfiles
                     ncbi-asn1   ASN.1 data used to create Release 178.0

  Close-of-data for GenBank 178.0 occurred on 06/11/2010. Uncompressed,
the Release 178.0 flatfiles require roughly 444 GB (sequence files only)
or 476 GB (including the 'short directory', 'index' and the *.txt
files). The ASN.1 data require approximately 364 GB.

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

  Release  Date      Base Pairs    Entries

  177      Apr 2010  114348888771  119112251
  178      Jun 2010  115624497715  120604423

Recent statistics for WGS sequences:

  Release  Date      Base Pairs    Entries

  177      Apr 2010  165536009514  58361599
  178      Jun 2010  167725292032  58592700

  During the 58 days between the close dates for GenBank Releases 177.0
and 178.0, the non-WGS/non-CON portion of GenBank grew by 1,275,608,944
basepairs and by 1,492,172 sequence records. During that same period,
11,534,642 records were updated. An average of about 224,600 non-WGS/non-CON
records were added and/or updated per day.

  Between releases 177.0 and 178.0, the WGS component of GenBank grew by
2,189,282,518 basepairs and by 231,101 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 178.0 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 178.0 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: June 15 2010, 178.0). 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

Or, if the files are compressed, perhaps:

        gzcat $i | head -10 | grep Release

  If you encounter problems while ftp'ing or uncompressing Release
178.0, please send email outlining your difficulties to:

        info from ncbi.nlm.nih.gov

Mark Cavanaugh, Michael Kimelman, Ilya Dondoshansky, Sergey Zhdanov

1.3 Important Changes in Release 178.0

1.3.1 Organizational changes

The total number of sequence data files increased by 15 with this release:

  - the BCT division is now composed of  57 files (+3)
  - the CON division is now composed of 137 files (+1)
  - the ENV division is now composed of  27 files (+3)
  - the GSS division is now composed of 212 files (+1)
  - the PAT division is now composed of 119 files (+4)
  - the PLN division is now composed of  42 files (+2)
  - the TSA division is now composed of   5 files (+1)

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

  - the AUT (author name) index is now composed of 74 files (+1)
  - the JOU (journal citation) index is now composed of 9 files (+1)

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 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

  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
ninety of the GSS flatfiles in Release 178.0. Consider gbgss123.seq :

GBGSS1.SEQ          Genetic Sequence Data Bank
                            June 15 2010

                NCBI-GenBank Flat File Release 178.0

                           GSS Sequences (Part 1)

   87164 loci,    64159197 bases, from    87164 reported sequences

  Here, the filename and part number in the header is "1", though the file
has been renamed as "123" 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

  A variety of changes affecting the GenBank flatfile format will be
implemented in October 2010, as a result of discussions among DDBJ, EBI,
and NCBI at the May 2010 International Nucleotide Sequence Database
Collaboration annual meeting. Full details of the changes will be made
available after the minutes have been finalized, but in the meantime
we can provide a brief summary:

* /artificial_location will become a controlled-vocabulary qualifier,
  with values of "heterogenous population sequenced" and
  "low-quality sequence region".

* The /codon qualifier will be discontinued, in favor of /transl_except .

* The /partial qualifier will be discontinued, given that 5' and 3'
  partiality can be indicated via a feature's location ('<' and '>').

* The /label qualifier will be discontinued.

* The conflict feature will be discontinued, with existing instances
  converted to to misc_difference features.

* A new mobile_element feature, with a /mobile_element_type qualifier,
  will be introduced for the annotation of gene cassettes, transposons,
  and insertion sequences.  Existing repeat_region features, with
  /mobile_element qualifiers, will be converted to mobile_element features.
  The /mobile_element qualifier will then be discontinued.

* A classification system will be introduced for the /inference and
  /experiment qualifiers, such that the inferential or experimental
  information can be associated with a feature's existence, location,
  or description.

* A /whole_replicon qualifier will be introduced, allowing records
  which represent the entirety of a replicon (a chromosome; an organelle;
  a mitochondrial plasmid) to be identified as such.

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