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[Genbank-bb] GenBank Release 198.0 Available : October 21 2013

Cavanaugh, Mark (NIH/NLM/NCBI) [E] via genbankb%40net.bio.net (by cavanaug from ncbi.nlm.nih.gov)
Mon Oct 21 19:18:13 EST 2013

Greetings GenBank Users,

  GenBank Release 198.0 is now available via FTP from the
National Center for Biotechnology Information (NCBI):

  Ftp Site           Directory   Contents
  ----------------   ---------   ---------------------------------------
  ftp.ncbi.nih.gov   genbank     GenBank Release 198.0 flatfiles
                     ncbi-asn1   ASN.1 data used to create Release 198.0

  Delivery of this release missed the normal target date of October 15th
due to a partial shutdown of the United States government which impacted
NCBI operations. When the shutdown ended on October 17th we expedited
release processing, such that we could deliver 198.0 only a week later
than usual. Our apologies for the delay.

  Close-of-data for GenBank 198.0 occurred on 10/17/2013. Uncompressed,
the Release 198.0 flatfiles require roughly 613 GB (sequence files only).
The ASN.1 data require approximately 504 GB.

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

  Release  Date      Base Pairs    Entries

  197      Aug 2013  154192921011  167295840
  198      Oct 2013  155176494699  168335396

Recent statistics for WGS sequences:

  Release  Date      Base Pairs    Entries

  197    Aug 2013  500420412665  124812020
  198    Oct 2013  535842167741  130203205

  During the 66 days between the close dates for GenBank Releases 197.0
and 198.0, the non-WGS/non-CON portion of GenBank grew by 983,573,688
basepairs and by 1,039,556 sequence records. During that same period,
503,602 records were updated. An average of 23,381 non-WGS/non-CON
records were added and/or updated per day.

  Between releases 197.0 and 198.0, the WGS component of GenBank grew by
35,421,755,076 basepairs and by 5,391,185 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 198.0 and Upcoming Changes) have been appended
below for your convenience.

                    * * * Important * * *

  Significant changes are described in Sections 1.4.1 and 1.4.3 of the
release notes: A new accession number format for WGS scaffolds, and
an anticipated phasing-out of NCBI GI sequence identifiers. Users who
make use of GIs in their information systems and analysis pipelines
should take particular note of section 1.4.3.

  Release 198.0 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 2013, 198.0). 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
198.0, 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 198.0

1.3.1 Delay in the availability of the catalog files for 198.0

  A last-minute problem was encountered in the generation of the
companion 'catalog' files for GenBank Release 198.0 . They are
normally provided in the genbank/catalog directory at the NCBI
FTP site:


We expect that this will be resolved very quickly on Tuesday October 22nd,
and the files will be made available shortly thereafter. Our apologies for
any inconvenience that might be caused by this delay.

1.3.2 Organizational changes

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

  - the BCT division is now composed of 112 files (+6)
  - the CON division is now composed of 226 files (+11)
  - the ENV division is now composed of  65 files (+3)
  - the INV division is now composed of  36 files (+1)
  - the PAT division is now composed of 197 files (+2)
  - the PLN division is now composed of  64 files (+1)
  - the VRL division is now composed of  27 files (+1)

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 117
of the GSS flatfiles in Release 198.0. Consider gbgss162.seq :

GBGSS1.SEQ          Genetic Sequence Data Bank
                         October 15 2013

                NCBI-GenBank Flat File Release 198.0

                           GSS Sequences (Part 1)

   87041 loci,    63875275 bases, from    87041 reported sequences

  Here, the filename and part number in the header is "1", though the file
has been renamed as "162" 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 accession format for CON-division WGS scaffold records

  WGS scaffolds that are constructed from WGS contigs currently
make use of a '2+6' accession number format, with two leading
alphabetic characters followed by six digits. Here is an example
of a WGS-master record that references two different ranges of
scaffold accession numbers:


LOCUS       AABR06000000          112651 rc    DNA     linear   ROD 16-MAR-2012
DEFINITION  Rattus norvegicus strain BN/SsNHsdMCW, whole genome shotgun
            sequencing project.
VERSION     AABR00000000.6  GI:380236478
DBLINK      BioProject: PRJNA10629
SOURCE      Rattus norvegicus (Norway rat)
  ORGANISM  Rattus norvegicus
WGS         AABR06000001-AABR06112651
WGS_SCAFLD  CM000072-CM000092
WGS_SCAFLD  JH612139-JH620698

  Many WGS projects have a large number of chromosome-specific scaffolds
(such as the JH accession range), and a much smaller number of scaffolds
that represent the entirety of the chromosomes (such as the the CM
accession range). Because of the former, we are consuming '2+6' prefixes,
like JH, at an unsustainable rate.

So we plan to introduce a new accession format for WGS scaffolds which
mirrors the format of the underlying WGS contigs:

  4 letter WGS project code
  2 digit assembly-version number
  "S" (for 'scaffold')
  Six or seven digits

So in the above example, the set of 'JH' scaffolds could make use of
accession numbers such as AABR06S000001 and AABR06S112651 :

WGS         AABR06000001-AABR06112651
WGS_SCAFLD  CM000072-CM000092
WGS_SCAFLD  AABR06S000001-AABR06S112651

  We do not currently plan to replace existing '2+6' accessions with
the new '4+2+S+6/7' accessions. However, as of the December 2013
GenBank release, the new format will begin to appear for newly-processed
WGS sequencing projects.

1.4.2 Support for higher-precision /collection_date values

  At the May 2013 meeting of the International Nucleotide Sequence Database 
Collaboration, it was agreed to provide support for collection dates that
include the time, and for collection date ranges.

  The new format for /collection_date will theoretically be legal as of
GenBank Release 199.0 in December 2013. However, given that a large 
number of submission tools and systems will have to be updated, it's 
possible that the new date/time format will not actually be encountered
until 2014.

  Here is a draft of the new /collection_date definition:

Qualifier       /collection_date= 

Definition      The date on which the specimen was collected.

                Date/time ranges are supported by providing two collection
                dates from among the supported value formats, delimited by a
                forward-slash character.

                Collection times are supported by adding "T", then the hour
                and minute, after the date. Collection times must be in
                Coordinated Universal Time (UTC), otherwise known as
                "Zulu Time" (Z).

Value format    "DD-Mmm-YYYY", "Mmm-YYYY", "YYYY"
                YYYY-MM-DDThh:mmZ, YYYY-MM-DDThhZ, YYYY-MM-DD, or YYYY-MM

Example         /collection_date="21-Oct-1952" 

Comment         'Mmm' represents a three-letter month abbreviation, and can
                be one of the following:
                Jan, Feb, Mar, Apr, May, Jun, Jul, Aug, Sep, Oct, Nov, Dec

                'YYYY' is a four-digit value representing the year. 'MM' is
                a two-digit value representing the month. 'DD' is a two-digit
                value representing the day of the month.

                'hh' is a two-digit value representing the hour of the day
                (00 to 23)

                'mm' is a two-digit value representing the minute of the hour
                (01 to 59)

                Within a date range, value formats that make use of 'Mmm'
                (month abbreviations) cannot be combined with value formats
                that make use of 'MM' (two-digit month number).

                Collection dates that are specified to at least the month,
                day, and year (DD-Mmm-YYYY or YYYY-MM-DD) are strongly
                encouraged. If the day and/or month of the collection date
                are not known, Mmm-YYYY or YYYY-MM or YYYY may be used.

                Within a collection date range, the first date (possibly
                including time) must be prior to the second date (possibly
                including time).

                Within a collection date range for which the day, month,
                and year are identical, the first time value must be prior
                to the second time value.

1.4.3 GI sequence identifiers to be phased out (slowly!) at NCBI

  The numeric GI sequence identifier that NCBI assigns to all nucleotide
and protein sequences was first introduced for GenBank Release products
as of GenBank 81.0, in February 1994. See:


 These simple, uniform, integer-based unique identifiers (which predated the
introduction of Accession.Version sequence identifiers) were crucial to the
development of NCBI's Entrez retrieval system, and have served their purpose
very well for nearly 20 years. 

  However, as NCBI considers how best to address the expected increase in the
volume of submitted sequence data, it is clear that prior practices will need
to be re-thought. As an example, imagine 100,000 pathogen-related
genomes/samples, each with 5000 proteins, most of which are common to all. We
will be moving toward solutions that represent each unique protein *once*.
The coding region protein products for each genome will likely continue to be
assigned their own Accession.Version identifiers, but (within the NCBI data
model) they will simply *reference* the unique proteins. And, they will no
longer be issued GIs of their own.

  Such a change will likely have a significant impact on NCBI users who utilize
GIs in their own information systems and analysis pipelines, so it will not be
introduced quickly. You can expect that a great deal of additional detail will
be made available via NCBI's various announcement mechanisms.

  *This* particular announcement is chiefly intended to provide some advance
warning to our users. There _will_ be classes of GenBank sequences that
are not assigned GIs in the not-too-distant future. If GIs are central to
your operations, then it might be appropriate to begin planning a switch to
the use of Accession.Version identifiers instead.

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