[Genbank-bb] GenBank Release 167.0 Now Available

Mark Cavanaugh via genbankb%40net.bio.net (by cavanaug from ncbi.nlm.nih.gov)
Fri Aug 22 18:12:51 EST 2008


[Apologies, the initial announcement was interpreted as an attachment.
 Re-sending because the listserv might not handle it gracefully.]

Greetings GenBank Users,

  GenBank Release 167.0 is now available via FTP from the National
Center for Biotechnology Information (NCBI):

  Ftp Site           Directory   Contents
  ----------------   ---------   ---------------------------------------
  ftp.ncbi.nih.gov   genbank     GenBank Release 167.0 flatfiles
                     ncbi-asn1   ASN.1 data used to create Release 167.0

  Close-of-data for GenBank 167.0 occured on 08/19/2008. Uncompressed, the
Release 167.0 flatfiles require roughly 357 GB (sequence files only)
or 381 GB (including the 'short directory', 'index' and the *.txt files). 
The ASN.1 data require approximately 326 GB.

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

  Release  Date       Base Pairs   Entries

  166      Jun 2008   92008611867  88554578
  167      Aug 2008   95033791652  92748599

Recent statistics for WGS sequences:

  Release  Date       Base Pairs   Entries

  166      Jun 2008  113639291344  39163548
  167      Aug 2008  118593509342  40214247

  During the 69 days between the close dates for GenBank Releases 166.0 and
167.0, the non-WGS/non-CON portion of GenBank grew by 3,025,179,785 basepairs
and by 4,194,021 sequence records. During that same period, 939,305 records
were updated. An average of about 74,396 non-WGS/non-CON records were added
and/or updated per day.

  Between releases 166.0 and 167.0, the WGS component of GenBank grew by
4,954,217,998 basepairs and by 1,050,699.

  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 167.0 and Upcoming Changes) have been appended
below for your convenience.

                ** Important Notes **

*  Support for the single, comprehensive protein FASTA file which accompanies
   GenBank releases ceased as of the June 2008 release. See Section 1.3.3 of
   the release notes for details.

*  A number of changes are expected for October's GenBank Release 168.0 .
   Please see Section 1.4 for a complete list.

*  GenBank 'index' files are now provided without any EST content, and without
   most GSS content. See Section 1.3.4 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 167.0 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 2008, 167.0). 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
167.0, please send email outlining your difficulties to:

        info from ncbi.nlm.nih.gov

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


1.3 Important Changes in Release 167.0

1.3.1 Announcements for upcoming changes absent from Release 166.0

  An oversight during GenBank Release 166.0 processing resulted in the
exclusion of several announcements for changes that will be implemented
as of GenBank Release 168.0 in October 2008 (see section 1.4, below).

  This means that only two months advance notice can be provided for those
changes, rather than the customary four months. Our apologies for this
oversight and any inconvenience that it may cause.

1.3.2 Organizational changes

  The total number of sequence data files increased by 58 with this release:

  - the BCT division is now comprised of  30 files (+1)
  - the CON division is now comprised of  97 files (+6)
  - the ENV division is now comprised of  10 files (+1)
  - the EST division is now comprised of 762 files (+24)
  - the GSS division is now comprised of 306 files (+16)
  - the HTG division is now comprised of 120 files (+3)
  - the INV division is now comprised of  13 files (+1)
  - the PAT division is now comprised of  46 files (+4)
  - the PLN division is now comprised of  30 files (+1)
  - the VRL division is now comprised of  10 files (+1)
  - the VRT division is now comprised of  16 files (+1)

  The total number of index files increased by 5 with this release:

  - the AUT index is now comprised of  59 files  (+5)

1.3.3 Comprehensive protein FASTA file has been discontinued

  'Divisional' protein FASTA files :

	ftp://ftp.ncbi.nih.gov/ncbi-asn1/gbXXX.fsa_aa.gz

where 'XXX' represents an alphanumeric GenBank division code (such as
pri10) were made available starting with GenBank Release 164.0 . Given
their availability, support for the single, comprehensive protein FASTA
file:

	ftp://ftp.ncbi.nih.gov/genbank/relNNN.fsa_aa.gz

(where 'NNN' represents a three-digit GenBank release number) was
discontinued as of GenBank Release 166.0 in June 2008. The size of the
comprehensive file had exceeded 4GB, which was unmanageable for many users.

  The final comprehensive protein FASTA file was: rel166.fsa_aa .

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
fifty-nine of the GSS flatfiles in Release 167.0. Consider gbgss248.seq :

GBGSS1.SEQ           Genetic Sequence Data Bank
                           August 15 2008

                NCBI-GenBank Flat File Release 167.0

                           GSS Sequences (Part 1)

   87184 loci,    64446495 bases, from    87184 reported sequences

  Here, the filename and part number in the header is "1", though the file
has been renamed as "248" 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 Changes related to ncRNA features, /ncRNA_class, and /moltype

  The list of allowed values for the /ncRNA_class qualifier, which is
mandatory for all ncRNA features, will be expanded to include:

	/ncRNA_class="ribozyme"

Non-coding RNAs which are not yet in the INSDC's controlled vocabulary:

	http://www.insdc.org/page.php?page=rna_vocab

previously required /ncRNA_class="other" plus an accompanying /note
qualifer to describes the nature of the ncRNA. This requirement will
be changed, such that *either* a /product or a /note qualifier must
accompany "other" ncRNAs features.

  The list of allowed /mol_type qualifiers for the source feature
currently includes:

	/mol_type="snoRNA"
	/mol_type="snRNA"
	/mol_type="scRNA"
	/mol_type="tmRNA"

All of these molecule types will be collapsed into a single value:

	/mol_type="transcribed RNA"

Sequence records which represent one of these four types of molecules
will thus have:

	an ncRNA feature with /ncRNA_class of "snoRNA", "scRNA" or "snRNA"
	a source feature with /mol_type of "transcribed RNA"
or
	a tmRNA feature
	a source feature with /mol_type of "transcribed RNA"

All of these changes will take effect as of Release 169.0 in October 2008.

1.4.2 Merging the satellite and repeat_unit features into repeat_region

  Satellites, minisatellites and microsatellites are comprised of repetitive
units of DNA, with a variety of lengths and repeat patterns. With the 
addition of a new qualifier (/satellite), the satellite and repeat_unit
features can be represented by the repeat_region feature.

   Qualifier       /satellite=

   Definition      identifier for satellite DNA marker; many tandem repeats 
                   (identical or related) of a short basic repeating unit; many 
                   have a base composition or other property different from the 
                   genome average that allows them to be separated from the bulk 
                   genomic DNA;

   Value format    "<satellite_type>[:<class>][ <identifier>]" 

                   where satellite_type is one of the following 
                   "satellite", "microsatellite", "minisatellite"

   Example         /satellite="satellite: S1a"
                   /satellite="satellite: alpha"
                   /satellite="satellite: gamma III"
                   /satellite="microsatellite: DC130"

  As of the October 2008 GenBank release, all satellite features will be 
transformed into repeat_region features with /satellite qualifiers of
type "satellite", and all repeat_unit features will be transformed into
repeat_region features.
  
1.4.3 New /gene_synonym qualifier

  Gene symbols are presented via the /gene qualifier. When synonymous or 
alternative gene symbols are available, they have often been presented via
multiple /gene qualifiers.

  To distinguish what might be an approved or official gene symbol from its
synonyms or alternatives, a new /gene_synonym qualifier will be introduced
for GenBank Release 168.0 .

   Qualifier       /gene_synonym=

   Definition      synonymous or alternative symbol for a gene corresponding to
                   a sequence region
   Value format    "text"

   Examples        /gene="CF"
                   /gene="ABCC7"

1.4.4 New /mating_type qualifier

  Because the /sex qualifier has a free-text value format, is has been
innapropriately utilized for certain organisms, such as bacteria, fungi,
and some insects and worms. In such cases, a more appropriate term would
be 'mating type'.

In October 2008, a new qualifier will be made available for non-sexual
reproductive strategies:

   Qualifier       /mating_type=

   Definition      mating type of the organism from which the sequence was obtained
   Value format    "text"

   Example         /mating_type="Mating type A"

1.4.5 Renaming of /specific_host as /host

  The definition of /specific_host in the Feature Table document is as follows:

   Qualifier       /specific_host=

   Definition      natural host from which the sequence was obtained
   Value format    "text"

   Example         /specific_host="Rhizobium NGR234"

  The usage of /specific_host, and particularly the distinction between it and
/lab_host, is not made clear with this definition. So the qualifier is going
to be renamed and redefined, starting with Release 168.0 in October 2008 :

   Qualifier       /host=

   Definition      Natural (as opposed to laboratory) host to the organism from
                   which the sequenced molecule was obtained
   Value format    "text"

   Example         /host="Homo sapiens"
                   /host="Homo sapiens 12 year old girl"

1.4.6 New value for /organelle

  In October 2008, the list of allowed values for /organelle will be expanded
to include:

	/organelle="chromatophore"

1.4.7 Modification to value format for /frequency

  The current definition of /frequency is :

   Qualifier       /frequency=

   Definition      frequency of the occurrence of a feature

   Value format    text representing the fraction of population carrying the
                   variation expressed as a decimal fraction

   Example         /frequency=".85"

Although this format is appropriate and useful in some contexts (for 
example, within a global population of individuals), it does not convey
the number of sequences that might have been included in a variation
study. As of Release 168.0, the format of /frequency will be expanded:

   Value format    text representing the fraction of population carrying the
                   variation expressed as a decimal fraction, or the number
                   observed instances vs the total number of sequenced isolates

   Example         /frequency=".85"
                   /frequency="23/108"
                   /frequency="1 in 12"

1.4.8 /cons_splice qualifier to be removed

  The /cons_splice qualifier has almost no usage within the sequence
database. In addition, it does not account for the variation in splice
signals that might be used by different classes of introns. So this
qualfier will be removed from sequence records, and the Feature Table
document, as of Release 168.0 in October 2008.

1.4.9 /virion qualifier to be removed

  The intent of /virion is to indicate that a sequenced molecule
is from an encapsidated viral particle (as opposed to the proviral
form of a virus, integrated into the host's genome). Viral sequences
derived from a blood sample taken from an infected organism might
typically be flagged with /virion, if it is believed that the sample
contained viral particles.

  However, a review of the database reveals that this qualifier is
not used consistently, and furthermore, submitters often are unable
to conclusively state that a virus sequence derives from the 
encapsidated form. So the /virion qualifier will be removed from 
sequence records, and the Feature Table document, as of Release 168.0
in October 2008.

1.4.10 Updated value format for /exception

  Only three values for the /exception qualifier have been approved
for use by the INSDC : 

	"rearrangement required for product"
	"RNA editing"
	"reasons given in citation"

However, the definition of /exception in the Feature Table document
does not indicate that the contents of /exception are controlled.
This oversight will be corrected in October 2008.



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