[Genbank-bb] GenBank Release 168.0 Now Available

Cavanaugh, Mark (NIH/NLM/NCBI) [E] via genbankb%40net.bio.net (by cavanaug from ncbi.nlm.nih.gov)
Thu Oct 30 18:57:15 EST 2008


Greetings GenBank Users,

  GenBank Release 168.0 is now available via FTP from the National
Center for Biotechnology Information (NCBI):

  Ftp Site           Directory   Contents
  ----------------   ---------   ---------------------------------------
  ftp.ncbi.nih.gov   genbank     GenBank Release 168.0 flatfiles
                     ncbi-asn1   ASN.1 data used to create Release 168.0

  Close-of-data for GenBank 168.0 occured on 10/27/2008. Uncompressed,
the
Release 168.0 flatfiles require roughly 371 GB (sequence files only)
or 396 GB (including the 'short directory', 'index' and the *.txt
files). 
The ASN.1 data require approximately 338 GB.

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

  Release  Date       Base Pairs   Entries

  167      Aug 2008   95033791652  92748599
  168      Oct 2008   97381682336  96400790

Recent statistics for WGS sequences:

  Release  Date       Base Pairs   Entries

  167      Aug 2008  118593509342  40214247
  168      Oct 2008  136085973423  46108952

  During the 69 days between the close dates for GenBank Releases 167.0
and
168.0, the non-WGS/non-CON portion of GenBank grew by 2,347,890,684
basepairs
and by 3,652,191 sequence records. During that same period, 1,111,311
records
were updated. An average of about 69,036 non-WGS/non-CON records were
added
and/or updated per day.

  Between releases 167.0 and 168.0, the WGS component of GenBank grew by
17,492,464,081 basepairs and by 5,894,705 records.

  The combined WGS/non-WGS single-release increase of 19.84 Gbp for
Release 168.0 is the largest that GenBank has experienced, to date.

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

                ** Important Notes **

*  A number of changes have been implemented for the October 2008
   GenBank Release. Please see Section 1.3 for a complete list.

*  GenBank 'index' files are now provided without any EST content, and
   without most GSS content. See Section 1.3.12 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.

*  A new linetype ( DBLINK ) will be implemented as of the February 2009
   release. See Section 1.4.1 for information.

  Release 168.0 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: October 15 2008, 168.0). 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
168.0, please send email outlining your difficulties to:

        info from ncbi.nlm.nih.gov

Mark Cavanaugh, Michael Kimelman, Ilya Dondoshansky
GenBank
NCBI/NLM/NIH/HHS


1.3 Important Changes in Release 168.0

1.3.1 Organizational changes

  The total number of sequence data files increased by 60 with this
release:

  - the BCT division is now comprised of  32 files (+2)
  - the CON division is now comprised of 103 files (+6)
  - the EST division is now comprised of 802 files (+40)
  - the GSS division is now comprised of 309 files (+3)
  - the HTG division is now comprised of 122 files (+2)
  - the PAT division is now comprised of  47 files (+1)
  - the PLN division is now comprised of  32 files (+2)
  - the STS division is now comprised of  18 files (+4)

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

  - the JOU index is now comprised of 6 files (+1)

1.3.2 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, has been 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 have been 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 take effect with this October 2008 release.

1.3.3 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 are now 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 this October 2008 GenBank release, all satellite and repeat_unit
features have  been transformed into repeat_region features with an 
appropriate /satellite qualifier.
  
1.3.4 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 has been
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"

1.3.5 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'.

  A new qualifier has been made available for non-sexual reproductive
strategies as of October 2008:

Qualifier       /mating_type=
Definition      mating type of the organism from which the sequence was
                obtained; mating type is used for prokaryotes, and for
                eukaryotes that undergo meiosis without sexually
dimorphic
                gametes
Value format    "text"
Examples        /mating_type="MAT-1"
                /mating_type="plus"
                /mating_type="-"
                /mating_type="odd"
                /mating_type="even"
Comment         /mating_type="male" and /mating_type="female" are
                valid in the prokaryotes, but not in the eukaryotes;
                for more information, see the entry for /sex.

In light of the above, the definition for the /sex qualifier has been
refined:

Qualifier       /sex=
Definition      sex of the organism from which the sequence was
obtained;
                sex is used for eukaryotic organisms that undergo
meiosis
                and have sexually dimorphic gametes
Value format    "text"
Examples        /sex="female"
                /sex="male"
                /sex="hermaphrodite"
                /sex="unisexual"
                /sex="bisexual"
                /sex="asexual"
                /sex="monoecious" [or monecious]
                /sex="dioecious" [or diecious]
Comment         /sex should be used (instead of /mating_type)
                in the Metazoa, Embryophyta, Rhodophyta & Phaeophyceae;
                /mating_type should be used (instead of /sex)
                in the Bacteria, Archaea & Fungi;
                neither /sex nor /mating_type should be used
                in the viruses;
                outside of the taxa listed above, /mating_type
                should be used unless the value of the qualifier
                is taken from the vocabulary given in the examples
                above

  Records which inappropriately used the /sex qualifier have been
updated,
to utilize the new /mating_type qualifier.

1.3.6 Renaming of /specific_host as /host

  The /specific_host qualifier has been renamed as /host for Release
168.0 .
>From the Feature Table document:

Qualifier       /host=
Definition      natural (as opposed to laboratory) host to the organism
from
                which sequenced molecule was obtained
Value format    "text"
Example         /host="Homo sapiens"
                /host="Homo sapiens 12 year old girl"
                /host="Rhizobium NGR234"

In contrast:

Qualifier       /lab_host=
Definition      scientific name of the laboratory host used to propagate
the
                source organism from which the sequenced molecule was
obtained
Value format    "text"
Example         /lab_host="Gallus gallus"
                /lab_host="Gallus gallus embryo"
                /lab_host="Escherichia coli strain DH5 alpha"
                /lab_host="Homo sapiens HeLa cells"
Comment         the full binomial scientific name of the host organism
should
                be used when known; extra conditional information
relating to
                the host may also be included

1.3.7 New value for /organelle

  As of October 2008, the list of allowed values for /organelle has been
expanded
to include:

	/organelle="chromatophore"

1.3.8 Modification to value format for /frequency

  As of October 2008, the definition of /frequency has been expanded to
accomodate both the fraction of a population carrying a variation
expressed
as a decimal value, and as the number of observed instances vs. the
total
number of sequenced isolates:

Qualifier       /frequency=
Definition      frequency of the occurrence of a feature
Value format    text representing the proportion of a population
carrying the
                feature expressed as a fraction
Example         /frequency="23/108"
                /frequency="1 in 12"
                /frequency=".85"

1.3.9 /cons_splice qualifier 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 has been removed from sequence records, and the Feature Table
document, as of Release 168.0 .

1.3.10 /virion qualifier removed

  The intent of /virion was to indicate that a sequenced molecule
originates 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 be flagged with /virion, if it is believed that the sample
contained viral particles.

  However, a review of the database revealed that /virion was not
used consistently, and furthermore, submitters are often unable to
conclusively state that a virus sequence derives from the encapsidated
form. So the /virion qualifier has been removed from sequence records,
and the Feature Table document, as of Release 168.0 .

1.3.11 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 has been corrected, and the definition of the qualifier
is now:

Qualifier       /exception=
Definition      indicates that the coding region cannot be translated
using
                standard biological rules
Value format    "RNA editing", "reasons given in citation",
                "rearrangement required for product"
Example         /exception="RNA editing"
                /exception="reasons given in citation"
                /exception="rearrangement required for product"
Comment         only to be used to describe biological mechanisms such 
                as RNA editing;  where the exception cannot easily be
described 
                a published citation must be referred to; protein
translation of
                /exception CDS will be different from the according
conceptual 
                translation; 
                - must not be used where transl_except would be
adequate,
                  e.g. in case of stop codon completion use:
                /transl_except=(pos:6883,aa:TERM)
                /note="TAA stop codon is completed by addition of 3' A
residues to   
                mRNA".
                - must not be used for ribosomal slippage, instead use
join operator, 
                  e.g.: CDS   join(486..1784,1787..4810)
                              /note="ribosomal slip on tttt sequence at
1784..1787"

1.3.12 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.

1.3.13 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
sixty of the GSS flatfiles in Release 168.0. Consider gbgss250.seq :

GBGSS1.SEQ           Genetic Sequence Data Bank
                          October 15 2008

                NCBI-GenBank Flat File Release 168.0

                           GSS Sequences (Part 1)

   87217 loci,    64373883 bases, from    87217 reported sequences

  Here, the filename and part number in the header is "1", though the
file
has been renamed as "250" 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 PROJECT linetype to be replaced by DBLINK (April 2009)

  The PROJECT linetype allows a sequence record to be linked to
information
about the sequencing project that generated the data which ultimately
resulted in the record's submission to the International Nucleotide
Sequence
Database ( INSD; see http://www.insdc.org ) .

  This complete bacterial GenBank record illustrates the use of the
PROJECT
line:

LOCUS       CP000964             5641239 bp    DNA     circular BCT
24-SEP-2008
DEFINITION  Klebsiella pneumoniae 342, complete genome.
ACCESSION   CP000964
VERSION     CP000964.1  GI:206564770
PROJECT     GenomeProject:28471

  When viewed on the web in NCBI's Entrez:Nucleotide, the record's
project
identifier (28471) links to an entry in the Genome Project Database
(GPDB) :

 
http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=
Overview&uid=28471

where information about the sequencing center, the bacterium, and other
GenBank records (eg, plasmids) associated with the sequencing project
can be found.

  Since the introduction of PROJECT, the scope of the "Genome" Project
Database has expanded, to include projects that are not necessarily
targetted
to the sequencing of a complete genome.

  In addition, there can be other resources which underlie an INSD
sequence
record, such as the Trace Assembly Archive at the NCBI:

 
http://www.ncbi.nlm.nih.gov/Traces/assembly/assmbrowser.cgi?cmd=show&f=t
ree&m=main&s=tree

  Because of the expanded scope of the GPDB, and because we anticipate a
need
to link to more resources than just the GPDB, the PROJECT linetype is
going to
be replaced by a new linetype:

   DBLINK

  Modifications to linetypes can be disruptive, so the switch to DBLINK
will occur in several stages. Starting in October 2008, links to the
NCBI Trace Assembly Archive will be supported via a line of text in the
COMMENT section of sequence records. Here is a mock-up, based on
CP000964,
to illustrate this change:

LOCUS       CP000964             5641239 bp    DNA     circular BCT
24-SEP-2008
DEFINITION  Klebsiella pneumoniae 342, complete genome.
ACCESSION   CP000964
VERSION     CP000964.1  GI:206564770
PROJECT     GenomeProject:28471
....
COMMENT     Trace Assembly Archive:123456
            The source for the DNA and/or cells is:  Professor Eric W.
            Triplett, Chair, Department of Microbiology and Cell
Science,
            Institute of Food and Agricultural Sciences, University of
Florida,
            P.O. Box 110700, Gainesville, FL 32611-0700, ewt from ufl.edu.

Note: Use of the Trace Assembly Archive is still in its early stages, so
only
a few records are expected to have these links in the short term.

  The new DBLINK linetype will be introduced as of GenBank Release 170.0
,
on or near February 15, 2009 .

  The Genome Project ID and the Trace Assembly Archive ID will be
presented
via DBLINK, and the existing PROJECT line will continue to be displayed:

LOCUS       CP000964             5641239 bp    DNA     circular BCT
24-SEP-2008
DEFINITION  Klebsiella pneumoniae 342, complete genome.
ACCESSION   CP000964
VERSION     CP000964.1  GI:206564770
PROJECT     GenomeProject:28471
DBLINK      Project:28471
            Trace Assembly Archive:123456
....
COMMENT     The source for the DNA and/or cells is:  Professor Eric W.
            Triplett, Chair, Department of Microbiology and Cell
Science,
            Institute of Food and Agricultural Sciences, University of
Florida,
            P.O. Box 110700, Gainesville, FL 32611-0700, ewt from ufl.edu.

PROJECT and DBLINK will co-exist for one GenBank release, until Release
171.0
(April 15, 2009), at which point the PROJECT line will be removed. In
its final
state, our mock-up for CP000964 becomes:

LOCUS       CP000964             5641239 bp    DNA     circular BCT
24-SEP-2008
DEFINITION  Klebsiella pneumoniae 342, complete genome.
ACCESSION   CP000964
VERSION     CP000964.1  GI:206564770
DBLINK      Project:28471
            Trace Assembly Archive:123456
....
COMMENT     The source for the DNA and/or cells is:  Professor Eric W.
            Triplett, Chair, Department of Microbiology and Cell
Science,
            Institute of Food and Agricultural Sciences, University of
Florida,
            P.O. Box 110700, Gainesville, FL 32611-0700, ewt from ufl.edu.

  In summary: The PROJECT linetype will be replaced by DBLINK as of
Release 171.0 in April 2009.

  For those who process sequence data in NCBI's ASN.1 format: The
underlying representation for (Genome) Project IDs will remain
unchanged.
There will be no changes to the ASN.1 User-object that is used to store
them:

    user {
      type
        str "GenomeProjectsDB" ,
      data {
        {
          label
            str "ProjectID" ,
          data
            int 28471 } ,
        {
          label
            str "ParentID" ,
          data
            int 0 } } } ,

  However, to support linkages to other resources, such as the Trace
Assembly Archive, a new "DBLink" User-object will be introduced:

    user {
      type
        str "DBLink" ,
      data {
        {
          label
            str "Trace Assembly Archive" ,
          data
            ints { 123456 } } } }

  As new types of linkages are established, they will be added to
the DBLink User-object, and displayed via the DBLINK linetype in
the GenBank flatfile format. 

  There is a possibility that the GenomeProjectsDB User-object
might someday be incorporated into the new DBLink User-object.
But at the moment, there are no firm plans to do so.




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