[Genbank-bb] GenBank Release 191.0 Available : August 15 2012

[Cavanaugh, Mark (NIH/NLM/NCBI) [E]]

Greetings GenBank Users,

  GenBank Release 191.0 is now available via FTP from the
National Center for Biotechnology Information (NCBI):

  Ftp Site           Directory   Contents
  ----------------   ---------   ---------------------------------------
  ftp.ncbi.nih.gov   genbank     GenBank Release 191.0 flatfiles
                     ncbi-asn1   ASN.1 data used to create Release 191.0

  Close-of-data for GenBank 191.0 occurred on 08/13/2012. Uncompressed,
the Release 191.0 flatfiles require roughly 561 GB (sequence files only)
or 604 GB (including the 'short directory', 'index' and the *.txt files).
The ASN.1 data require approximately 460 GB.

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

  Release  Date      Base Pairs    Entries

  190      Jun 2012  141343240755  154130210
  191      Aug 2012  143081765233  156424033

Recent statistics for WGS sequences:

  Release  Date      Base Pairs    Entries

  190    Jun 2012  287577367116   82076779
  191    Aug 2012  308196411905   84020064

  During the 61 days between the close dates for GenBank Releases 190.0
and 191.0, the non-WGS/non-CON portion of GenBank grew by 1,738,524,478
basepairs and by 2,293,823 sequence records. During that same period,
886,629 records were updated. An average of 52,138 non-WGS/non-CON
records were added and/or updated per day.

  Between releases 190.0 and 191.0, the WGS component of GenBank grew by
20,619,044,789 basepairs and by 1,943,285 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 191.0 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 191.0 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 2012, 191.0). 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
191.0, 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 191.0

1.3.1 Organizational changes

The total number of sequence data files increased by 25 with this release:

  - the BCT division is now composed of  89 files (+1)
  - the CON division is now composed of 172 files (+3)
  - the ENV division is now composed of  55 files (+1)
  - the EST division is now composed of 466 files (+2)
  - the GSS division is now composed of 260 files (+4)
  - the INV division is now composed of  32 files (+1)
  - the PAT division is now composed of 182 files (+2)
  - the TSA division is now composed of  96 files (+10)
  - the VRT division is now composed of  27 files (+1)

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

  - the AUT (author name) index is now composed of 101 files (+2)
  - the KEY (keyword)     index is now composed of   7 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
106 of the GSS flatfiles in Release 191.0. Consider gbgss155.seq :

GBGSS1.SEQ          Genetic Sequence Data Bank
                          August 15 2012

                NCBI-GenBank Flat File Release 191.0

                           GSS Sequences (Part 1)

   87101 loci,    63965498 bases, from    87101 reported sequences

  Here, the filename and part number in the header is "1", though the file
has been renamed as "155" 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 qualifier : /altitude

  Altitude information is an important component of an accurate environmental
sample description (see related qualifiers /lat_lon and /collection_date).
To capture altitude data, a new source-feature qualifier will be legal as of
October 15 2012 (GenBank 192.0) :

Qualifier       /altitude=
Definition      geographical altitude of the location from which the sample
                was collected
Value format    "text"
Example         /altitude="-256 m."
                /altitude="330.12 m."
Cardinality     1
Comment         Values indicate altitudes above or below nominal sea level 
                provided in metres

1.4.2 Modification of the /anticodon qualifier

  As of the October 15 2012 GenBank Release 192.0, the /anticodon qualifier
of tRNA features will be modified to include the sequence of the anticodon:

Qualifier       /anticodon=
Definition      location of the anticodon of tRNA and the amino acid for which
                it codes
Value format    (pos:<location>,aa:<amino_acid>,seq:<text>) where location
                is the position of the anticodon, amino_acid is the 
                abbreviation for the amino acid encoded and seq is the 
                sequence of the anticodon
Example         /anticodon=(pos:34..36,aa:Phe,seq:aaa)
                /anticodon=(pos:join(5,495..496),aa:Leu,seq:taa)
                /anticodon=(pos:complement(4156..4158),aa:Gln,seq:ttg)

Currently, only the 'pos' and 'aa' elements are supported. The addition
of 'seq' should make it more convenient for database users to process
tRNA features: It will no longer be necessary to analyze the 'pos' element
in order to obtain the anticodon sequence.

1.4.3 Expansion of the /linkage_evidence controlled vocabulary

  Genome centers sometimes have knowledge from PCR evidence that two contigs
are linked, and thus should be part of a CON-division/scaffold record, however
none of the values in the linkage_evidence controlled vocabulary are appropriate.

So, also as of GenBank Release 192.0 in October 2012, the value "pcr" will
be legal for the /linkage_evidence qualifier:

Qualifier       /linkage_evidence=
Value format    "paired-ends", "align genus", "align xgenus", "align trnscpt",
                "within clone", "clone contig", "map", "strobe", "pcr", and
                "unspecified"