[Genbank-bb] GenBank Release 192.0 Available : October 15 2012

Cavanaugh, Mark (NIH/NLM/NCBI) [E] via genbankb%40net.bio.net (by cavanaug from ncbi.nlm.nih.gov)
Thu Oct 11 14:04:28 EST 2012


Greetings GenBank Users,

  GenBank Release 192.0 is now available via FTP from the
National Center for Biotechnology Information (NCBI):

  Ftp Site           Directory   Contents
  ----------------   ---------   ---------------------------------------
  ftp.ncbi.nih.gov   genbank     GenBank Release 192.0 flatfiles
                     ncbi-asn1   ASN.1 data used to create Release 192.0

  Close-of-data for GenBank 192.0 occurred on 10/08/2012. Uncompressed,
the Release 192.0 flatfiles require roughly 569 GB (sequence files only)
or 612 GB (including the 'short directory', 'index' and the *.txt files).
The ASN.1 data require approximately 465 GB.

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

  Release  Date      Base Pairs    Entries

  191      Aug 2012  143081765233  156424033
  192      Oct 2012  145430961262  157889737

Recent statistics for WGS sequences:

  Release  Date      Base Pairs    Entries

  191    Aug 2012  308196411905   84020064
  192    Oct 2012  333881846451   86480509

  During the 56 days between the close dates for GenBank Releases 191.0
and 192.0, the non-WGS/non-CON portion of GenBank grew by 2,349,196,029
basepairs and by 1,465,704 sequence records. During that same period,
2,830,842 records were updated. An average of 76,724 non-WGS/non-CON
records were added and/or updated per day.

  Between releases 191.0 and 192.0, the WGS component of GenBank grew by
25,685,434,546 basepairs and by 2,460,445 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 192.0 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 192.0 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: October 15 2012, 192.0). 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
192.0, 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 192.0

1.3.1 Organizational changes

The total number of sequence data files increased by 33 with this release:

  - the BCT division is now composed of  91 files (+2)
  - the CON division is now composed of 176 files (+4)
  - the ENV division is now composed of  57 files (+2)
  - the HTG division is now composed of 141 files (+5)
  - the INV division is now composed of  33 files (+1)
  - the PLN division is now composed of  59 files (+2)
  - the TSA division is now composed of 112 files (+16)
  - the VRL division is now composed of  22 files (+1)

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

  - the AUT (author name) index is now composed of 102 files (+1)
  - the JOU (journal)     index is now composed of  14 files (+1)

1.3.2 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 is now 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

1.3.3 Modification of the /anticodon qualifier

  As of GenBank Release 192.0 in October 2012, the /anticodon qualifier
of tRNA features has been 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.

1.3.4 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, as of this GenBank Release 192.0 of October 2012, the value "pcr" is now
a legal value 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"

1.3.5 /frequency qualifier deprecated

  Note: This change was not announced in the August 2012 GenBank Release notes
  due to an oversight. Our apologies for the omission. 

  At the 2012 annual INSDC meeting, it was noted that the /frequency qualifier
was very rarely used, on fewer than 9000 records. It was also noted
that the qualifier has limited utility, given that relative frequencies will
evolve as additional sequencing of a given population occurs. Databases that
are dedicated to variation (dbSNP, DGVa, dbVAR, etc) provide far more accurate
frequency information than a little-used and never-updated text qualifier.

  So as of the October 2012 GenBank release, the /frequency qualifier has
been deprecated. Existing values for the qualifier are now presented via the
/note qualifier of source features, and GenBank submission tools are being
updated to cease support of /frequency. Here is an example of a record for
which frequency information is now presented via /note :

LOCUS       AJ631998                 673 bp    DNA     linear   BCT 10-JUN-2005
DEFINITION  Spiroplasma sp. MSRO partial 16S rRNA gene, strain MSRO.
ACCESSION   AJ631998
VERSION     AJ631998.1  GI:45720448
....
     source          1..673
                     /organism="Spiroplasma sp. MSRO"
                     /mol_type="genomic DNA"
                     /strain="MSRO"
                     /host="Drosophila melanogaster"
                     /db_xref="taxon:265049"
                     /country="Brazil:Campinas"
                     /note="natural symbiont of Drosophila melanogaster that
                     causes embryonic male lethality;
                     frequency: .23"

1.3.6 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.

1.3.7 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 192.0. Consider gbgss155.seq :

GBGSS1.SEQ          Genetic Sequence Data Bank
                          October 15 2012

                NCBI-GenBank Flat File Release 192.0

                           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

  No changes impacting the flatfile format are expected between the
October 2012 and February 2013 GenBank releases.






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