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[Genbank-bb] GenBank Release 187.0 Available : December 17 2011

Cavanaugh, Mark (NIH/NLM/NCBI) [E] via genbankb%40net.bio.net (by cavanaug from ncbi.nlm.nih.gov)
Sat Dec 17 18:13:55 EST 2011

Greetings GenBank Users,

  GenBank Release 187.0 is now available via FTP from the
National Center for Biotechnology Information (NCBI):

  Ftp Site           Directory   Contents
  ----------------   ---------   ---------------------------------------
  ftp.ncbi.nih.gov   genbank     GenBank Release 187.0 flatfiles
                     ncbi-asn1   ASN.1 data used to create Release 187.0

  Close-of-data for GenBank 187.0 occurred on 12/15/2011. Uncompressed,
the Release 187.0 flatfiles require roughly 518 GB (sequence files only)
or 557 GB (including the 'short directory', 'index' and the *.txt files).
The ASN.1 data require approximately 426 GB.

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

  Release  Date      Base Pairs    Entries

  186      Oct 2011  132067413372  144458648
  187      Dec 2011  135117731375  146413798

Recent statistics for WGS sequences:

  Release  Date      Base Pairs    Entries

  186    Oct 2011  218666368056   68330215
  187    Dec 2011  239868309609   73729553

  During the 63 days between the close dates for GenBank Releases 186.0
and 187.0, the non-WGS/non-CON portion of GenBank grew by 3,050,318,003
basepairs and by 1,955,150 sequence records. During that same period,
1,561,565 records were updated. An average of 55,821 non-WGS/non-CON
records were added and/or updated per day.

  Between releases 186.0 and 187.0, the WGS component of GenBank grew by
21,201,941,553 basepairs and by 5,399,338 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 187.0 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 187.0 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 2011, 187.0). 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
187.0, 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 187.0

1.3.1 Organizational changes

The total number of sequence data files increased by 38 with this release:

  - the BCT division is now composed of  80 files (+3)
  - the CON division is now composed of 162 files (+10)
  - the ENV division is now composed of  46 files (+3)
  - the EST division is now composed of 451 files (+1)
  - the GSS division is now composed of 251 files (+3)
  - the INV division is now composed of  32 files (+2)
  - the PAT division is now composed of 173 files (+2)
  - the PLN division is now composed of  52 files (+1)
  - the SYN division is now composed of   7 files (+4)
  - the TSA division is now composed of  51 files (+8)
  - the VRT division is now composed of  25 files (+1)

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

  - the AUT (author name)  index is now composed of 92 files (+1)
  - the JOU (journal name) index is now composed of 13 files (+1)

1.3.2 Project DBLINKs transitioning to BioProject

  The Genome Project Database resource at the NCBI was redesigned in
recent months, culminating in the implementation of a new BioProject


An article that describes the goals of BioProject is available:


BioProject is a collaborative effort of the International Nucleotide
Sequence Database Collaboration (INSDC), and project data are exchanged 
with NCBI's partner INSDC institutions, EBI and DDBJ. A BioProject
website is also available at DDBJ:


BioProjects are uniquely identified by BioProject Accession Numbers,
which utilize this format:

        "E" or "N" or "D"
        one letter
        one or more digits

Examples of valid BioProject accessions are PRJNA12521 and PRJEB1 .

With BioProject now in operation, we are preparing to implement links
from sequence records to the new resource. Previously, links to the
Genome Project Database were provided by numeric 'Project' DBLINKs .
Here's an example for a bacterial complete-genome record:

LOCUS       CP002497             1110245 bp    DNA     linear   PLN 14-NOV-2011
DEFINITION  Eremothecium cymbalariae DBVPG#7215 chromosome 1, complete
VERSION     CP002497.1  GI:356887709
DBLINK      Project: 60715

When this link is switched to a BioProject accession, the DBLINK
line will change slightly:

LOCUS       CP002497             1110245 bp    DNA     linear   PLN 14-NOV-2011
DEFINITION  Eremothecium cymbalariae DBVPG#7215 chromosome 1, complete
VERSION     CP002497.1  GI:356887709
DBLINK      BioProject: PRJNA60715

In the coming weeks, many millions of sequence records will gradually
be modified, to make use of the new BioProject DBLINK. They will not be
distributed via daily GenBank and RefSeq incremetal update products.
However, these new BioProject links *will* start to be seen in GenBank
and RefSeq release products as of December 2011. In addition, the new
BioProject links will become visible via NCBI's Entrez:Nucleotide
resource, as soon as the modification process begins. 

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
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

  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
103 of the GSS flatfiles in Release 187.0. Consider gbgss149.seq :

GBGSS1.SEQ          Genetic Sequence Data Bank
                        December 15 2011

                NCBI-GenBank Flat File Release 187.0

                           GSS Sequences (Part 1)

   87118 loci,    64000130 bases, from    87118 reported sequences

  Here, the filename and part number in the header is "1", though the file
has been renamed as "149" 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 changes scheduled for implementation in the April 2012
GenBank Release.

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