[Genbank-bb] GenBank Release 153.0 Now Available

Mark Cavanaugh cavanaug at ncbi.nlm.nih.gov
Fri Apr 14 20:47:44 EST 2006


Greetings GenBank Users,

  GenBank Release 153.0 is now available via FTP from the National
Center for Biotechnology Information (NCBI):

  Ftp Site           Directory   Contents
  ----------------   ---------   ---------------------------------------
  ftp.ncbi.nih.gov   genbank     GenBank Release 153.0 flatfiles
                     ncbi-asn1   ASN.1 data used to create Release 153.0

  Close-of-data was 04/11/2006. Three days of processing were required to build
Release 153.0. Uncompressed, the Release 153.0 flatfiles require approximately
215 GB (sequence files only) or 224 GB (including the 'short directory' and
'index' files).  The ASN.1 data require approximately 189 GB.

Statistics for non-WGS sequences:

   Release  Date       Base Pairs   Entries

   152      Feb 2006   59750386305  54584635
   153      Apr 2006   61582143971  56620500

And for WGS sequences:

  Release  Date        Base Pairs   Entries

  152      Feb 2006    63183065091  12465546
  153      Apr 2006    67488612571  13573144

  During the 58 days between the close dates for GenBank Releases 152.0
and 153.0, the non-WGS portion of GenBank grew by 1,831,757,666 basepairs
and by 2,035,865 sequence records. During that same period, 502,495 records
were updated. An average of about 43,700 records were added and/or updated
per day.

  Between releases 152.0 and 153.0, the WGS component of GenBank grew by
4,305,547,480 basepairs and by 1,107,598 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 153.0 and Upcoming Changes) have been appended
below.
		** Important Note **

  After recent problems generating the 'index' files which normally
accompany GenBank Releases, these files are once again being provided,
though without any EST content, and without most GSS content. 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 153.0 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: April 15 2006, 153.0). 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
153.0, 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 153.0

1.3.1 Changes in the content of index files

  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 since January 2005 seem to support this:
the index files are transferred only half as frequently as the files of
sequence records. The inherent inefficiencies 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.

  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 index-file content
for all EST sequence records, and for GSS sequence records that originate
via direct submission to NCBI. GenBank 153.0 thus contains these ten index
files:

	gbaut1.idx
	gbaut2.idx
	gbaut3.idx
	gbaut4.idx
	gbaut5.idx
	gbaut6.idx
	gbgen.idx
	gbjou.idx
	gbkey.idx
	gbsec.idx

  In addition, a version of gbacc.idx which encompasses the entirety of the
release was built manually, but note that the first field contains just an
accession number, rather than Accession.Version. We hope to have this last
discrepancy resolved by the June release.

  This current 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 these changes may cause.

1.3.2 Organizational changes

  The total number of sequence data files increased by 32 with this release:

  - the BCT division is now comprised of  14 files (+1)
  - the EST division is now comprised of 512 files (+25)
  - the GSS division is now comprised of 174 files (+2)
  - the HTG division is now comprised of  81 files (+2)
  - the PRI division is now comprised of  30 files (+1)
  - the ROD division is now comprised of  24 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 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 153.0. Consider gbgss143.seq :

GBGSS1.SEQ           Genetic Sequence Data Bank
                           April 15 2006

                NCBI-GenBank Flat File Release 153.0

                           GSS Sequences (Part 1)

   86907 loci,    64480328 bases, from    86907 reported sequences

  Here, the filename and part number in the header is "1", though the file
has been renamed as "143" 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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