[Genbank-bb] GenBank Release 160.0 Now Available

Mark Cavanaugh via genbankb%40net.bio.net (by cavanaug from ncbi.nlm.nih.gov)
Wed Jun 20 20:34:59 EST 2007


Greetings GenBank Users,

  GenBank Release 160.0 is now available via FTP from the National
Center for Biotechnology Information (NCBI):

  Ftp Site           Directory   Contents
  ----------------   ---------   ---------------------------------------
  ftp.ncbi.nih.gov   genbank     GenBank Release 160.0 flatfiles
                     ncbi-asn1   ASN.1 data used to create Release 160.0

  Close-of-data for GenBank 160.0 occured on 06/14/2007. Uncompressed, the
Release 160.0 flatfiles require roughly 280 GB (sequence files only)
or 293 GB (including the 'short directory', 'index' and the *.txt files). 
The ASN.1 data require approximately 237 GB.

Recent statistics for non-WGS sequences:

  Release  Date       Base Pairs   Entries

  159      Apr 2007   75742041056  71802595
  160      Jun 2007   77248690945  73078143

And for WGS sequences:

  Release  Date       Base Pairs   Entries

  159      Apr 2007   93022691867   23446831
  160      Jun 2007   97102606459   23718400

  During the 63 days between the close dates for GenBank Releases 159.0 and
160.0, the non-WGS/non-CON portion of GenBank grew by 1,506,649,889 basepairs
and by 1,275,548 sequence records. During that same period, 409,163 records
were updated. An average of about 26,740 non-WGS/non-CON records were added
and/or updated per day.

  Between releases 159.0 and 160.0, the WGS component of GenBank grew by
4,079,914,592 basepairs and by 271,569 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 160.0 and Upcoming Changes) have been appended
below.
		** Important Note **

  GenBank 'index' files are now provided without any EST content, and without
most GSS content. See Section 1.3.3 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 160.0 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: June 15 2007, 160.0). 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
160.0, 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 160.0

1.3.1 Organizational changes

  The total number of sequence data files increased by 20 with this release:

  - the BCT division is now comprised of  22 files (+1)
  - the CON division is now comprised of   8 files (+1)
  - the EST division is now comprised of 609 files (+5)
  - the GSS division is now comprised of 261 files (+9)
  - the HTG division is now comprised of  96 files (+3)
  - the PAT division is now comprised of  29 files (+1)

1.3.2 Several CON-division files significantly exceed 2GB

  Data generated by the AACY02 metagenomic WGS project:

    PubMed ID 17355176 
    http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=17355176

resulted in the addition of over 3 million CON-division records to GenBank.
Current procedures are not optimized for handling such a large influx, and
as a result, several of the CON-division sequence files exceed 2GB when
uncompressed. For example:

    gbcon6.seq : 7,261,904,050 bytes
    gbcon7.seq : 3,092,551,793 bytes
    gbcon8.seq : 5,859,018,078 bytes

During the next several months, we will work to enhance the processing of
the CON-division of GenBank, such that the records are provided via a
larger number of much smaller files. 

1.3.3 Multiple identifiers for the PROJECT line

  The recently-introduced PROJECT linetype (see Section 3.4.7.2) provides a
way to link GenBank sequences that are part of a sequencing project to the
Entrez Genome Project database, where further details about the project can
be obtained.

  As of June 2007, multiple identifiers are now valid for the PROJECT line.
Here is a mocked-up example of the expected usage:

LOCUS       AANA01000001               2 rc    DNA     linear   BCT 09-FEB-2007
DEFINITION  Polaribacter dokdonensis MED152 whole genome shotgun sequencing
            project.
ACCESSION   AANA01000001
VERSION     AANA01000001.1  GI:85822094
PROJECT     GenomeProject:13543  GenomeProject:99999

  There are several situations in which a record could be considered part
of two different Genome Projects. For example, consider an
environmental-sampling metagenomic WGS project for which the individual
sequence-overlap contigs are not attributed to a specific organism. An
associated Genome Project could exist which provides further details about
the sequencing effort, the centers involved, etc.

  If, in subsequent assembly and annotation phases, scaffold/super-contig/
chromosomal records are created which **are** attributed to a specific
organism, then those CON-division records could have two Genome Project IDs:
one for the WGS sequencing project as a whole; and a second for an
organism-specific Genome Project.

  Additional examples illustrating the use of multiple Genome Project IDs 
will be provided in future release notes, and via the GenBank listserv.

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 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
forty-three of the GSS flatfiles in Release 160.0. Consider gbgss219.seq :

GBGSS1.SEQ           Genetic Sequence Data Bank
                            June 15 2007

                NCBI-GenBank Flat File Release 160.0

                           GSS Sequences (Part 1)

   86834 loci,    64340568 bases, from    86834 reported sequences

  Here, the filename and part number in the header is "1", though the file
has been renamed as "219" 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 Structured /specimen_voucher qualifiers

  As of October 2007, the content of the /specimen_voucher qualifier will
be able to support a structured value consisting of an institution code,
a collection code, and a specimen identifier, as well as the existing
unstructured values. Here is the preliminary new definition of the qualifier:

Qualifier:
specimen_voucher

Definition:
Identifier for the specimen from which the nucleic acid sequenced was obtained.

Value format:
/specimen_voucher="[<institution-code>:[<collection-code>:]]<specimen_id>"

Example:
/specimen_voucher="UAM:Mamm:52179"
/specimen_voucher="AMCC:101706"
/specimen_voucher="USNM:field series 8798"
/specimen_voucher="personal collection:Dan Janzen:99-SRNP-2003"
/specimen_voucher="99-SRNP-2003"

Comment:
The specimen_voucher qualifier is intended to annotate a reference to the
physical specimen that remains after the sequence has been obtained. If the
specimen was destroyed in the process of sequencing, electronic images
(e-vouchers) are an adequate substitute for a physical voucher specimen.
Ideally the specimens will be deposited in a curated museum, herbarium, or
frozen tissue collection, but often they will remain in a personal or
laboratory collection for some time before they are deposited in a curated
collection.

There are three forms of specimen_voucher qualifiers. If the text of the
qualifier includes one or more colons it is a 'structured voucher'. Structured
vouchers include institution-codes (and optional collection-codes) taken from
a controlled vocabulary that denote the museum or herbarium collection where
the specimen resides.

   <specimen_id>
   <institution_code>:<specimen_id>
   <institution_code>:<collection_code>:<specimen_id>

1.4.2 New /culture_collection and /bio_material qualifiers

  As of the December 2007 GenBank release, new qualifiers /culture_collection
and /bio_material qualifiers will be legal for the source feature. These
qualifiers will utilize the same format as /speciment_voucher (see Section
1.4.1 of these release notes). Their preliminary definitions are:

Qualifier:
culture_collection

Definition:
Institution code and identifier for the culture from which the nucleic acid
sequenced was obtained, with optional collection code.

Value format:
/culture_collection="<institution-code>:[<collection-code>:]<culture_id>"

Example:
/culture_collection="ATCC:26370"

Comment:
01234567890123456789012345678901234567890123456789012345678901234567890123456789
The culture_collection qualifier should be used to annotate live microbial and
viral cultures, and cell lines that have been deposited in curated culture
collections. Microbial cultures in personal or laboratory collections should
be annotated in strain qualifiers.

Annotation with a culture_collection qualifier implies that the sequence was
obtained from a sample retrieved (by the submitter or a collaborator) from the
indicated culture collection, or that the sequence was obtained from a sample
that was deposited (by the submitter or a collaborator) in the indicated culture
collection. Annotation with more than one culture_collection qualifier
indicates that the sequence was obtained from a sample that was deposited
(by the submitter or a collaborator) in more than one culture collection.

Culture_id and institution_code are mandatory, collection_code is optional.
Institution code is mandatory where collection code is present.


Qualifier:
bio_material

Definition:
Identifier for the biological material from which the nucleic acid sequenced
was obtained, with optional institution code and collection code for the place
where it is currently stored.

Value format:
/bio_material="[<institution-code>:[<collection-code>:]]<material_id>"

Example:
/bio_material="CGC:CB3912"      <- Caenorhabditis stock center

Comment:
The bio_material qualifier should be used to annotate the identifiers of material
in biological collections that are not appropriate to annotate as either
/specimen_voucher or /culture_collection. These include zoos and aquaria,
stock centers, seed banks, germplasm repositories and DNA banks.

Material_id is mandatory, institution_code and collection_code are optional.
Institution code is mandatory where collection code is present.

1.4.3 /operon qualifiers for protein_bind features

  Due to an oversight, the /operon qualifier is not currently listed 
as a legal qualifier for the protein_bind feature. This will be 
corrected as of October 2007, with an update to the Feature Table
document which includes the qualifier among those that are legal
for protein_bind.

1.4.4 Alignment as EVIDENCE_BASIS for the /inference qualifier

  Several algorithms exist which allow mRNAs to be aligned to genomic
sequence, taking into account introns and splice signals. In order to
document the use of such algorithms for the structured /inference
qualifier, a new class of EVIDENCE_BASIS will be introduced:

	alignment

This addition to the controlled vocabulary of the /inference qualifier
will be legal as of October 2007.

1.4.5 New ncRNA feature 

  A variety of new types of RNA features have been introduced in 
recent years. snRNA, snoRNA, and scRNA are some examples.

  Because the number of non-coding RNA families is quite likely to
continue to expand, a new ncRNA feature that can flexibly 
accomodate them will be introduced as of October 2007.

  This new feature will utilize a new qualifier called
/ncRNA_class, with a controlled vocabulary to indicate what type
of non-coding feature is being represented.

  A complete description of the ncRNA feature and the new
qualifier are not yet available. When details are finalized,
hopefully by June 30, additional details will be distributed
via the GenBank listserv, and in future versions of these
release notes.

1.4.6 New tmRNA feature and /peptide_tag qualifier

  To support the annotation of a class of RNAs that have dual
tRNA-like and mRNA-like behaviors, a new tmRNA feature will be
legal for the Feature Table as of December 2007. The "tmRNA Website"
at Indiana University provides some background information about
the unusual biology of tmRNAs :

	http://www.indiana.edu/~tmrna/ 

Here is a preliminary definition of the new tmRNA feature:

Feature Key           tmRNA
Definition            transfer messenger RNA; tmRNA acts like a tRNA first, 
                      and then an mRNA that encodes a peptide tag. 
                      The ribosome translates this mRNA region of tmRNA and 
                      attaches the encoded peptide tag to the C-terminus of the 
                      unfinished protein. This attached tag targets the protein
                      for destruction or proteolysis
Optional qualifiers   /allele="text"
                      /citation=[number]
                      /db_xref="<database>:<identifier>"
                      /experiment="text"
                      /function="text"
                      /gene="text"
                      /inference="TYPE[ (same species)][:EVIDENCE_BASIS]"
                      /label=feature_label
                      /locus_tag="text" (single token)
                      /map="text"
                      /note="text"
                      /old_locus_tag="text" (single token)
                      /product="text"
                      /pseudo
                      /standard_name="text"

To indicate the nucleotide region encoding the proteolysis tag
peptide, a new /peptide_tag qualifier will be introduced for
the tmRNA feature.

Complete details about this new feature and qualifier will be
distributed via the GenBank listserv, and in future versions of
these release notes.

1.4.7 /organism no longer to be used for misc_recomb

  The /organism qualifier is currently legal for misc_recomb
features. A review of the existing cases in the database has
indicated that all could be better annotated through the use
of multiple source features.

  That work will be completed by October 2007, at which
point /organism will no longer be allowed for the misc_recomb
feature key.



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