[Genbank-bb] GenBank Release 152.0 Now Available

Mark Cavanaugh cavanaug at ncbi.nlm.nih.gov
Sat Feb 18 00:42:41 EST 2006


Greetings GenBank Users,

  GenBank Release 152.0 is now available via FTP from the National
Center for Biotechnology Information (NCBI):

  Ftp Site           Directory   Contents
  ----------------   ---------   ---------------------------------------
  ftp.ncbi.nih.gov   genbank     GenBank Release 152.0 flatfiles
                     ncbi-asn1   ASN.1 data used to create Release 152.0

  Close-of-data was 02/13/2006. Four days of processing were required to build
Release 152.0. Uncompressed, the Release 152.0 flatfiles require approximately
207 GB (sequence files only) or 216 GB (including the 'short directory' and
'index' files).  The ASN.1 version requires approximately 180 GB.

Statistics for non-WGS sequences:

   Release  Date       Base Pairs   Entries

   151      Dec 2005   56037734462  52016762
   152      Feb 2006   59750386305  54584635

And for WGS sequences:

  Release  Date        Base Pairs   Entries

  151      Dec 2005    59638900034  12088491
  152      Feb 2006    63183065091  12465546

  During the 66 days between the close dates for GenBank Releases 151.0
and 152.0, the non-WGS portion of GenBank grew by 3,712,651,843 basepairs
and by 2,567,873 sequence records. During that same period, 223,952 records
were updated. An average of about 42,300 records were added and/or updated
per day.

  Between releases 151.0 and 152.0, the WGS component of GenBank grew by
3,544,165,057 basepairs and by 377,055 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 152.0 and Upcoming Changes) have been appended
below.
		** Important Note **

  Problems were encountered generating the 'index' files that normally
accompany GenBank Releases. See Section 1.3.1 for further details. NCBI is
considering ceasing support for the index files, so we strongly encourage
affected users to review that section and provide feedback.

  Release 152.0 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 2006, 152.0). 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 platform with 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
152.0, please send email outlining your difficulties to:

	info at ncbi.nlm.nih.gov

Mark Cavanaugh, Vladimir Alekseyev, Aleksey Vysokolov, Michael Kimelman
GenBank
NCBI/NLM/NIH/HHS


1.3 Important Changes in Release 152.0

1.3.1 Problems generating index files

  The 'index' files which accompany GenBank releases (see Section 3.3) are
considered to be largely a legacy data product by NCBI, generated mainly for
historical reasons. FTP statistics since January 2005 seem to support this:
the index files are transferred only half as frequently as the files of
sequence records. The inherent inefficiency of the index file format also
leads us to suspect that they have little serious use by the user community,
particularly for EST and GSS records.

  As a result, the software that generates the index file products has received
little attention over the years, and has finally reached its limitations.
The required multi-server queries which obtain and sort many millions of
rows of terms from several different databases, with ever-growing RAM
requirements, have simply outgrown the capacity of the hardware used for
GenBank Release generation.

  Our short-term solution will be to cease generating index-file content
for EST and (most) GSS sequence records. We were able to do this for the author
name index, so GenBank 152.0 contains six gbaut*.idx files (down from what
would have been 34).

  In addition, a version of gbacc.idx was built manually (but note that the
first field contains just an accession number, rather than Accession.Version).

  The other four index files ( gbgen.idx, gbkey.idx, gbjou.idx, and gbsec.idx)
are absent from this release. We hope to be able to provide them for
GenBank 153.0, in a manner similar to the author index files (no EST or GSS
content).

  But even when we reach that point, this solution is likely to be only a
stop-gap, and we will probably pursue one of two options within the next
year:

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 index data.

  If you are a user of the 'index' files associated with GenBank files, we
encourage you to make your wishes known, either via the GenBank newsgroup,
or via email to NCBI's Service Desk:

   info at ncbi.nlm.nih.gov

  Our apologies for any inconvenience that this ongoing problem may cause.

1.3.2 Organizational changes

  The total number of sequence data files increased by 41 with this release:

  - the EST division is now comprised of 487 files (+23)
  - the GSS division is now comprised of 172 files (+8)
  - the HTG division is now comprised of  79 files (+10)
  - the PAT division is now comprised of  20 files (+1)

  The total number of author-name 'index' files decreased by 20 with this
  release, and the gbgen.idx, gbjou.idx, gbkey.idx, and gbsec.idx are
  absent for reasons described in Section 1.3.1 .

1.3.3 New Linetype for Genome Project Identifier

  DDBJ, EMBL, and GenBank are working to create a collaborative system that
will assign a unique numeric identifier to genome projects. The purpose of
this new identifier is to provide a link among sequence records that pertain
to a specific genome sequencing project.

  At GenBank, this new identifier will be presented in the flatfile format
via a new linetype : PROJECT . With GenBank 152.0, this new linetype is now
legal (though still unimplemented). Here is a mocked-up example demonstrating
the new linetype's use:

LOCUS       CH476840             1669278 bp    DNA     linear   CON 05-OCT-2005
DEFINITION  Magnaporthe grisea 70-15 supercont5.200 genomic scaffold, whole
            genome shotgun sequence.
ACCESSION   CH476840 AACU02000000
VERSION     CH476840.1  GI:77022292
PROJECT     GenomeProject:12345

The integer 12345 represents the value of a possible genome project
identifier.

  These Genome Project identifiers will be searchable within NCBI's
Entrez: Genome-Project database:

  http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj

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 from 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
thirty-two of the GSS flatfiles in Release 152.0. Consider gbgss141.seq :

GBGSS1.SEQ           Genetic Sequence Data Bank
                          February 15 2006

                NCBI-GenBank Flat File Release 152.0

                           GSS Sequences (Part 1)

   87168 loci,    64691174 bases, from    87168 reported sequences

  Here, the filename and part number in the header is "1", though the file
has been renamed as "141" based on the number of files dumped from the other
system.  We will work to resolve this discrepancy in future releases, but the
priority is certainly much lower than many other tasks.

1.4 Upcoming Changes

1.4.1 New JOURNAL token for Pre-Grant Patent Publications

  Sequences associated with granted patents from the US Patent and
Trademark Office (USPTO) typically have references that look like this:

  REFERENCE   1  (bases 1 to 22)
    AUTHORS   Stewart,L.J.
    TITLE     Screening methods for identifying ligands
    JOURNAL   Patent: US 6950757-A 2 27-SEP-2005;

The "Patent:" token indicates that the JOURNAL line pertains to a
patent document, as opposed to a published article in the scientific
literature.

But sequence data can be available well in advance of the point at which
an actual patent has been granted. As of GenBank Release 153 in June 2006,
we will indicate that a patent sequence is associated with a "Pre-Grant
Publication" via a slight change to the JOURNAL line:

  REFERENCE   1  (bases 1 to 190)
    AUTHORS   Xu,M. and Humphreys,R.
      TITLE   Inhibition of li expression in mammalian cells
     JOURNAL  Pre-Grant Patent: US 20060008448A1 1 12-JAN-2006;
              ^^^^^^^^^^^^^^^^^

The introduction of "Pre-Grant Patent:" at the start of the JOURNAL
line will distinguish sequences associated with these two different
states in USPTO's patenting process.

Note that pre-grant identifiers from the USPTO are alphanumeric, and
lack a document-type suffix ("-A" in the granted-patent example above).





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