[Genbank-bb] GenBank Release 151.0 Now Available

Mark Cavanaugh cavanaug at ncbi.nlm.nih.gov
Wed Dec 14 02:34:33 EST 2005


Greetings GenBank Users,

  GenBank Release 151.0 is now available via FTP from the National
Center for Biotechnology Information (NCBI):

  Ftp Site           Directory   Contents
  ----------------   ---------   ---------------------------------------
  ftp.ncbi.nih.gov   genbank     GenBank Release 151.0 flatfiles
                     ncbi-asn1   ASN.1 data used to create Release 151.0

  Close-of-data was 12/09/2005. Four days of processing were required to build
Release 151.0. Uncompressed, the Release 151.0 flatfiles require approximately
196 GB (sequence files only) or 216 GB (including the 'short directory' and
'index' files).  The ASN.1 version requires approximately 170 GB.

Statistics for non-WGS sequences:

   Release  Date       Base Pairs   Entries

   150      Oct 2005   53655236500  49152445
   151      Dec 2005   56037734462  52016762

And for WGS sequences:

  Release  Date        Base Pairs   Entries

  150      Oct 2005    56162807647  11169448
  151      Dec 2005    59638900034  12088491

  During the 61 days between the close dates for GenBank Releases 150.0
and 151.0, the non-WGS portion of GenBank grew by 2,382,497,962 basepairs
and by 2,864,317 sequence records. During that same period, 477,766 records
were updated. Combined, this yields an average of about 54,800 new and/or
updated records per day.

  Between releases 150.0 and 151.0, the WGS component of GenBank grew by
3,476,092,387 basepairs and by 919,043 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 151.0 and Upcoming Changes) have been appended
below.
		** Important Note **

  Problems were encountered generating the gbacc.idx, gbkey.idx, and
gbaut*.idx 'index' files that 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 151.0 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 2005, 151.0). 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
151.0, 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 151.0

1.3.1 Problems generating accession, keyword, and author-name indexes

  The methods used to generate the 'index' files which accompany GenBank
releases (see Section 3.3) are no longer adequate to the task of generating
those products.

  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. For GenBank 151.0, the affected 'indexes' include:

	    gbacc.idx  (accession number index)
	    gbaut*.idx (author name index)
	    gbkey.idx  (keyword index)

  A version of gbacc.idx was built manually (but note that the first field
contains just an accession number, rather than Accession.Version). For
the author name index, only the first 26 of an expected 34 gbaut*.idx files
could be generated. The gbkey.idx file failed completely, and is absent from
this release.

  The 'index' files 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. For example, what value is there in a
triplet of data values for keyword "EST" in gbkey.idx, for each and every
one of the 32 *million* EST sequences in GenBank? That keyword could 
simply be assumed to apply to every sequence in the gbest*.seq sequence files.

  As a result, the software to generate the index file products has received
little attention over the years, and has finally reached its limitations. 
Several courses are now possible:

a) Cease support of the 'index' file products altogether.

b) Segment the index files by major functional categories (EST, GSS, and
   'other'), generating, for example, an EST-specific author-name index,
   a GSS-specific author-name index, and an author-name index for all
   other sequences.

c) Provide a new product that presents some of the most useful data from
   the legacy 'index' files, and cease support for other types index data.

  Our short-term choice will most likely be (b). But even that is a stop-gap,
and thus we are likely to pursue either (a) or (c) within the next year.

  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 BCT division is now comprised of  13 files (+1)
  - the ENV division is now comprised of   3 files (+1)
  - the EST division is now comprised of 464 files (+28)
  - the GSS division is now comprised of 164 files (+6)
  - the HTG division is now comprised of  69 files (+1)
  - the PAT division is now comprised of  19 files (+1)
  - the PLN division is now comprised of  17 files (+1)
  - the ROD division is now comprised of  23 files (+2)

  The total number of author-name 'index' files decreased by 6 with this
  release, for reasons described in Section 1.3.1 .

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 151.0. Consider gbgss133.seq :

GBGSS1.SEQ           Genetic Sequence Data Bank
                          December 15 2005

                NCBI-GenBank Flat File Release 151.0

                           GSS Sequences (Part 1)

   87159 loci,    64705276 bases, from    87159 reported sequences

  Here, the filename and part number in the header is "1", though the file
has been renamed as "133" 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 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 . 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     GENOME_PROJECT:12345

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

There is a possibility that the contents of the PROJECT line might change 
somewhat from this example by the time the new identifier is implemented.
We will keep you posted of any such changes via these release notes and the
GenBank listserv.

  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

  The earliest date on which this new linetype will appear in the GenBank
flatfile format is February 15 2006.



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