[Genbank-bb] GenBank Release 181.0 Now Available

Cavanaugh, Mark (NIH/NLM/NCBI) [E] via genbankb%40net.bio.net (by cavanaug from ncbi.nlm.nih.gov)
Fri Dec 17 17:46:58 EST 2010


Greetings GenBank Users,

  GenBank Release 181.0 is now available via FTP from the National
Center for Biotechnology Information (NCBI):

  Ftp Site           Directory   Contents
  ----------------   ---------   ---------------------------------------
  ftp.ncbi.nih.gov   genbank     GenBank Release 181.0 flatfiles
                     ncbi-asn1   ASN.1 data used to create Release 181.0

  Close-of-data for GenBank 181.0 occurred on 12/14/2010. Uncompressed,
the Release 181.0 flatfiles require roughly 468 GB (sequence files only)
or 503 GB (including the 'short directory', 'index' and the *.txt
files). The ASN.1 data require approximately 384 GB.

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

  Release  Date      Base Pairs    Entries

  180      Oct 2010  118551641086  125764384
  181      Dec 2010  122082812719  129902276

Recent statistics for WGS sequences:

  Release  Date      Base Pairs    Entries

  180    Oct 2010  175339059129   59397637
  181    Dec 2010  177385297156   59608311

  During the 60 days between the close dates for GenBank Releases 180.0
and 181.0, the non-WGS/non-CON portion of GenBank grew by 3,531,171,633
basepairs and by 4,137,892 sequence records. During that same period,
863,717 records were updated. An average of about 83,360 non-WGS/non-CON
records were added and/or updated per day.

  Between releases 180.0 and 181.0, the WGS component of GenBank grew by
2,046,238,027 basepairs and by 210,674 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 181.0 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 181.0 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: December 15 2010, 181.0). 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
181.0, 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 181.0

1.3.1 Organizational changes

The total number of sequence data files increased by 35 with this release:

  - the BCT division is now composed of  63 files (+3)
  - the CON division is now composed of 143 files (+1)
  - the ENV division is now composed of  33 files (+3)
  - the EST division is now composed of 427 files (+5)
  - the GSS division is now composed of 224 files (+7)
  - the INV division is now composed of  26 files (+1)
  - the PAT division is now composed of 138 files (+10)
  - the PLN division is now composed of  44 files (+1)
  - the TSA division is now composed of  15 files (+3)
  - the VRL division is now composed of  16 files (+1)

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

  - the AUT (author name)  index is now composed of 82 files (+2)
  - the KEY (keyword) index is now composed of 5 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
seemed 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.

1.3.3 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-four of the GSS flatfiles in Release 181.0. Consider gbgss131.seq :

GBGSS1.SEQ          Genetic Sequence Data Bank
                        December 15 2010

                NCBI-GenBank Flat File Release 181.0

                           GSS Sequences (Part 1)

   87140 loci,    64083567 bases, from    87140 reported sequences

  Here, the filename and part number in the header is "1", though the file
has been renamed as "131" 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 were 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.

  However, three of the planned changes could not be completed for the
October 15 GenBank 180.0 release:

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

b) 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.

c) 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.

  An investigation of (a) for older sequence records has thrown into question
whether the /partial qualifier can actually be done away with. On-going
review will determine whether this change will be implemented as agreed,
amended, or abandoned.

  The implementation of (b) has been delayed because of delays in software
development supporting the new classification system. We do not expect to
be able to deploy the new /inference and /experiment qualifiers until at
least February 2011.

  Specification of the conditions under which the /whole_replicon qualifier
is, and is not, allowed to be used for sequence records is not yet complete,
so implementation of (c) has likewise been delayed.

  We will inform GenBank users when the issues impacting these three changes
have been clarified.
  




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