[Genbank-bb] GenBank Release 179.0 Now Available

Cavanaugh, Mark (NIH/NLM/NCBI) [E] via genbankb%40net.bio.net (by cavanaug from ncbi.nlm.nih.gov)
Wed Aug 18 23:05:08 EST 2010


Greetings GenBank Users,

  GenBank Release 179.0 is now available via FTP from the National
Center for Biotechnology Information (NCBI):

  Ftp Site           Directory   Contents
  ----------------   ---------   ---------------------------------------
  ftp.ncbi.nih.gov   genbank     GenBank Release 179.0 flatfiles
                     ncbi-asn1   ASN.1 data used to create Release 179.0

  Close-of-data for GenBank 179.0 occurred on 08/16/2010. Uncompressed,
the Release 179.0 flatfiles require roughly 451 GB (sequence files only)
or 484 GB (including the 'short directory', 'index' and the *.txt
files). The ASN.1 data require approximately 370 GB.

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

  Release  Date      Base Pairs    Entries

  178      Jun 2010  115624497715  120604423
  179      Aug 2010  117476523128  122941883

Recent statistics for WGS sequences:

  Release  Date      Base Pairs    Entries

  178      Jun 2010  167725292032  58592700
  179      Aug 2010  169253846128  58994334

  During the 66 days between the close dates for GenBank Releases 178.0
and 179.0, the non-WGS/non-CON portion of GenBank grew by 1,852,025,413
basepairs and by 2,337,460 sequence records. During that same period,
709,945 records were updated. An average of about 46,172 non-WGS/non-CON
records were added and/or updated per day.

  Between releases 178.0 and 179.0, the WGS component of GenBank grew by
1,528,554,096 basepairs and by 401,634 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 179.0 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 179.0 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: August 15 2010, 179.0). 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
179.0, 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 179.0

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  59 files (+2)
  - the CON division is now composed of 140 files (+3)
  - the ENV division is now composed of  29 files (+2)
  - the EST division is now composed of 419 files (+6)
  - the GSS division is now composed of 215 files (+3)
  - the HTG division is now composed of 135 files (+1)
  - the INV division is now composed of  24 files (+3)
  - the PAT division is now composed of 121 files (+2)
  - the ROD division is now composed of  29 files (+1)
  - the TSA division is now composed of   8 files (+3)
  - the VRL division is now composed of  15 files (+1)

The total number of 'index' files increased by 1 with this release:

  - the AUT (author name) index is now composed of 75 files (+1)

1.3.2 Molecule type for non-coding RNAs on the LOCUS line

  The ncRNA feature was introduced in October 2007 (Release 162.) to
accomodate the growing number of regulatory non-coding RNAs that are
being discovered. 

  And as described in the October 2008 release notes for Release 168.0 ,
records that represent non-coding RNA molecules (as opposed to ncRNA
features annotated on genomic DNA), have these characteristics:

        an ncRNA feature, with an /ncRNA_class qualifier of the
        appropriate type, spanning the entire length of the sequence

        a source feature with /mol_type of "transcribed RNA"

  The domain of possible LOCUS-line molecule type values has now
been reduced to reflect our new approach to ncRNA annotation. Values
'snRNA', 'snoRNA', and 'scRNA' have all been replaced by 'RNA'.

  Although this is not a GenBank flatfile format change per-se, it
certainly could affect those who have been using the LOCUS line to
identify small nuclear RNAs, small nucleolar RNAs, and small cytoplasmic
RNAs. Please be aware that the discontinued LOCUS-line molecule types
are three of *many* possible non-coding RNA types, so an analysis of
ncRNA feature content is required if one is interested in ncRNAs.

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-three of the GSS flatfiles in Release 179.0. Consider gbgss123.seq :

GBGSS1.SEQ          Genetic Sequence Data Bank
                          August 15 2010

                NCBI-GenBank Flat File Release 179.0

                           GSS Sequences (Part 1)

   87143 loci,    64110475 bases, from    87143 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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