[Genbank-bb] GenBank Release 173.0 Now Available

Cavanaugh, Mark (NIH/NLM/NCBI) [E] via genbankb%40net.bio.net (by cavanaug from ncbi.nlm.nih.gov)
Wed Aug 26 21:24:45 EST 2009


Greetings GenBank Users,

  GenBank Release 173.0 is now available via FTP from the National
Center for Biotechnology Information (NCBI):

  Ftp Site           Directory   Contents
  ----------------   ---------   ---------------------------------------
  ftp.ncbi.nih.gov   genbank     GenBank Release 173.0 flatfiles
                     ncbi-asn1   ASN.1 data used to create Release 173.0

  Close-of-data for GenBank 173.0 occured on 08/21/2009. Uncompressed,
the Release 173.0 flatfiles require roughly 408 GB (sequence files only)
or 437 GB (including the 'short directory', 'index' and the *.txt
files). The ASN.1 data require approximately 370 GB.

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

  Release  Date       Base Pairs   Entries

  172      Jun 2009  105277306080  106073709
  173      Aug 2009  106533156756   108431692

Recent statistics for WGS sequences:

  Release  Date       Base Pairs   Entries

  172      Jun 2009  145959997864  49063546
  173      Aug 2009  148165117763  48443067

  During the 72 days between the close dates for GenBank Releases 172.0
and 173.0, the non-WGS/non-CON portion of GenBank grew by 1,255,850,676
basepairs and by 2,357,983 sequence records. During that same period,
654,396 records were updated. An average of about 41,838
non-WGS/non-CON records were added and/or updated per day.

  Between releases 172.0 and 173.0, the WGS component of GenBank grew
by 2,205,119,899 basepairs, while the number of sequence records decreased
by 620,479 (due to some WGS projects being re-assembled into fewer,
but larger, 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 173.0 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 1.3.5 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 173.0 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: August 15 2009, 173.0). 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, 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
173.0, 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 173.0

1.3.1 Organizational changes

The total number of sequence data files increased by 28 with this release:

  - the BCT division is now composed of  48 files (+3)
  - the ENV division is now composed of  17 files (+1)
  - the EST division is now composed of 886 files (+11)
  - the GSS division is now composed of 340 files (+3)
  - the HTC division is now composed of  15 files (+1)
  - the HTG division is now composed of 134 files (+1)
  - the PAT division is now composed of  79 files (+6)
  - the PLN division is now composed of  38 files (-1)
  - the PRI division is now composed of  40 files (+1)
  - the TSA division is now composed of   2 files (+1)
  - the VRT division is now composed of  19 files (+1)

Note: The decline in the number of PLN division files is due to the fact that
twelve records representing the chromosomes of Oryza sativa Japonica Group
have been converted to a CON-division representation. See section 1.3.2 for
more details.

The total number of 'index' files increased by 1 with this release:

  - the AUT (author) index is now composed of 66 files (+1)

1.3.2 Twelve Oryza sativa Japonica Group records moved to CON division.

  Prior to Release 173.0, the sequence records for 12 Oryza sativa Japonica
Group chromosomes had been 'traditional' records, totalling over 382 Mbp of
sequence data.

  However, on August 7 2009, the records were converted to a CON-division
representation, with CONTIG-line join() statements that describe how the
chromosomes are constructed from underlying PAC and fosmid sequences. The
records involved are:

LOCUS       AP008207            45064769 bp    DNA     linear   CON 07-AUG-2009
LOCUS       AP008208            36823111 bp    DNA     linear   CON 07-AUG-2009
LOCUS       AP008209            37257345 bp    DNA     linear   CON 07-AUG-2009
LOCUS       AP008210            35863200 bp    DNA     linear   CON 07-AUG-2009
LOCUS       AP008211            30039014 bp    DNA     linear   CON 07-AUG-2009
LOCUS       AP008212            32124789 bp    DNA     linear   CON 07-AUG-2009
LOCUS       AP008213            30357780 bp    DNA     linear   CON 07-AUG-2009
LOCUS       AP008214            28530027 bp    DNA     linear   CON 07-AUG-2009
LOCUS       AP008215            23843360 bp    DNA     linear   CON 07-AUG-2009
LOCUS       AP008216            23661561 bp    DNA     linear   CON 07-AUG-2009
LOCUS       AP008217            30828668 bp    DNA     linear   CON 07-AUG-2009
LOCUS       AP008218            27757321 bp    DNA     linear   CON 07-AUG-2009

  Due to this change, these chromosomal records are now present in file
gbcon1.seq of the CON division. In addition, the total number of Oryza sativa
Japonica Group basepairs listed in the table in Section 2.2.7 has declined
by 370,461,808 bases, compared to Release 172.0. The table intentionally
excludes CON-division records, to avoid double-counting of underlying sequence
records and any larger-scale objects that are constructed from them.

1.3.3 File header problem for EST and GSS files

  A new method of generating the EST and GSS sequence files has been 
developed, which has reduced the time required to generate a GenBank
release by one day. However, a minor problem in the formatting of the
header of the sequence files was inadvertently introduced : a leading 
space exists before the filename on the very first line. For example:

 GBGSS100.SEQ          Genetic Sequence Data Bank                              
                         August 15 2009                                          
It should be:

GBGSS100.SEQ          Genetic Sequence Data Bank                              
                         August 15 2009                                          

The problem effects all EST files and most GSS files. We had hoped to
repair this formatting issue for Release 173.0, but the code changes
which were expected to fix the problem did not perform correctly. It
is hoped that this issue will be resolved for Release 174.0 .

1.3.4 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 of January 2005
seem 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.

1.3.5 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
seventy-two of the GSS flatfiles in Release 173.0. Consider gbgss269.seq :

GBGSS1.SEQ          Genetic Sequence Data Bank
                            August 15 2009

                NCBI-GenBank Flat File Release 173.0

                           GSS Sequences (Part 1)

   87186 loci,    64231458 bases, from    87186 reported sequences

  Here, the filename and part number in the header is "1", though the file
has been renamed as "269" 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 class of /exception value

  As of October 2009, a new class of /exception will be available for use
on coding region features:

   /exception="annotated by transcript or proteomic data"

  This exception will be used for situations in which: the protein sequence
(presented via the coding region's /translation qualifier) differs from the
conceptual translation; the quality of the DNA sequencing is high; and there
is evidence at the transcript or proteome level that the presented protein
*is* actually expressed by the organism.

  An inference qualifier of type "similar to" should be used in conjunction
with this new type of exception, to indicate the supporting EST/cDNA/protein
sequence.

  An updated definition of /exception, with examples for this new type
of exception value, will be provided via the GenBank newsgroup prior to
the October release.

1.4.2 /haplogroup qualifier introduced

  A haplotype is a combination of alleles at multiple loci that are transmitted
together on the same chromosome. A haplogroup is a group of similar haplotypes
that share a common ancestor with a single nucleotide polymorphism mutation.
The majority of submitters of complete human mitochondrial genomes provide
information about their haplogroup rather than their haplotype. Stable mtDNA
polymorphic variants clustered together in specific combination form a haplogroup. 

  To accomodate this need, a new /haplogroup qualifier will be introduced as
of GenBank Release 174.0 in October 2009.

  A formal definition of /haplogroup was not available as of the creation
of these release notes, so it will be provided via the GenBank newsgroup
prior to the October release.
  
1.4.3 /artificial_location qualifier introduced

  A new qualifier, intended for use in limited genome-scale annotation
contexts, will be introduced as of GenBank Release 175.0 in December 2009:

Qualifier	/artificial_location

Definition	indicates that location of the CDS or mRNA is modified to
		adjust for the presence of a frameshift or internal stop
		codon and not because of biological processing between the
		regions.  This is expected to be used only for genome-scale
		annotation, either because a heterogeneous population was
		sequenced, or because the feature is in a region of
		low-quality sequence.

1.4.4 /pseudo qualifier renamed as /non_functional

  Because the term "pseudo" is often assumed to mean "pseudogene", the
/pseudo qualifier will be renamed as /non_functional, to better reflect
its actual usage in the sequence databases. This change will take place
as of the April 2010 GenBank Release.



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