[Genbank-bb] GenBank Release 162.0 Now Available

Mark Cavanaugh via genbankb%40net.bio.net (by cavanaug from ncbi.nlm.nih.gov)
Fri Oct 26 23:54:18 EST 2007


Greetings GenBank Users,

  GenBank Release 162.0 is now available via FTP from the National
Center for Biotechnology Information (NCBI):

  Ftp Site           Directory   Contents
  ----------------   ---------   ---------------------------------------
  ftp.ncbi.nih.gov   genbank     GenBank Release 162.0 flatfiles
                     ncbi-asn1   ASN.1 data used to create Release 162.0

  Close-of-data for GenBank 162.0 occured on 10/19/2007. Uncompressed, the
Release 162.0 flatfiles require roughly 305 GB (sequence files only)
or 325 GB (including the 'short directory', 'index' and the *.txt files). 
The ASN.1 data require approximately 281 GB.

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

  Release  Date       Base Pairs   Entries

  161      Aug 2007   79525559650  76146236
  162      Oct 2007   81563399765  77632813

Recent statistics for WGS sequences:

  Release  Date       Base Pairs   Entries

  161      Aug 2007  101964323738  25384475
  162      Oct 2007  102003045298  25354041

  During the 66 days between the close dates for GenBank Releases 161.0 and
162.0, the non-WGS/non-CON portion of GenBank grew by 2,037,840,115 basepairs
and by 1,486,577 sequence records. During that same period, 608,147 records
were updated. An average of about 31,738 non-WGS records were added
and/or updated per day.

  Between releases 161.0 and 162.0, the WGS portion of GenBank grew by
38,721,560 basepairs and the number of sequence records declined by 30,434 .

  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 162.0 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 1.3.9 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 162.0 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 2007, 162.0). 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
162.0, 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 162.0

1.3.1 Sequences moved from SYN division to GSS division

  Due to a timing problem in the deployment of a software change,
264,607 GSS (Genome Survey Sequence) sequences were mistakenly
included in the SYN-division sequence files for GenBank Release 161.0 .

  The GSS sequences involved are labelled with a /transgenic qualifier
on their source features (see EF711103 for an example). The presence
of that qualifier normally indicates that the SYN division is the most
appropriate place for a record. But this is not the case for GSS records.

  Although a software change was made to accomodate transgenic GSS
records on July 2, the flatfiles had already been generated and stored
in the database that is used to build GenBank releases. Hence they
were dumped to the SYN-division files for August's Release 161.0.

  We have resolved this problem for Release 162.0, and as a result,
the number of SYN-division sequence files has decreased from five
back to two. All the records involved are now in the GSS-division
sequence files.

  Our thanks to the informatics group at The Jackson Laboratory for
reporting this problem.

1.3.2 CON division organizational changes

  As mentioned in the release notes for GenBank 161.0, procedures
for processing the ASN.1 version of CON ('constructed') division
records have been updated such that a much larger number (119) of
smaller (approximately 260MB) gbcon*.aso files are now generated.

  This change parallels a similar change which was made for the
processing of CON division flatfiles (gbcon*.seq) for Release 161.0.
For further details, please see the GenBank 161.0 release notes:

	ftp://ftp.ncbi.nih.gov/genbank/release.notes/gb161.release.notes

1.3.3 Organizational changes

  The total number of sequence data files increased by 25 with this release:

  - the BCT division is now comprised of  25 files (+1)
  - the CON division is now comprised of  83 files (+1)
  - the ENV division is now comprised of   7 files (+1)
  - the EST division is now comprised of 649 files (+14)
  - the GSS division is now comprised of 269 files (+5)
  - the HTG division is now comprised of 102 files (+4)
  - the MAM division is now comprised of   4 files (+1)
  - the PAT division is now comprised of  31 files (+1)
  - the SYN division is now comprised of   2 files (-3)  (See Section 1.3.1)

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

  - the AUT (Author Name) index is now comprised of 48 files (+1)

1.3.4 Structured /specimen_voucher qualifiers

  As of October 2007, the content of the /specimen_voucher qualifier can
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 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 denotes the museum or herbarium
                collection where the specimen resides;

1.3.5 /operon qualifiers for protein_bind features

  Due to an oversight, the /operon qualifier was not listed as a legal
qualifier for the protein_bind feature. This has been 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.

1.3.6 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
is legal as of this October 2007 release.

1.3.7 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 has been created, so that
they can be accomodated more flexibly.

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

  Here are the definitions of the ncRNA feature and /ncRNA_class :

Feature Key           ncRNA
Definition            a non-protein-coding gene, other than ribosomal RNA and
                      transfer RNA, the functional molecule of which is the RNA
                      transcript;
Mandatory qualifiers  /ncRNA_class="TYPE"
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"
                      /trans_splicing
                      /operon="text"
Comment               the ncRNA feature is not used for ribosomal and transfer
                      RNA annotation, for which the rRNA and tRNA feature keys
                      should be used, respectively;

Qualifier       /ncRNA_class=
Definition      a structured description of the classification of the
                non-coding RNA described by the ncRNA parent key
Value format   "TYPE"
Example         /ncRNA_class="miRNA"
                /ncRNA_class="siRNA"
                /ncRNA_class="scRNA"      
Comment         TYPE is a term taken from the INSDC controlled vocabulary for ncRNA
                classes; on 15-Oct-2007, the following terms were valid:

                      "antisense_RNA"
                      "autocatalytically_spliced_intron"
                      "hammerhead_ribozyme"
                      "RNase_P_RNA"
                      "RNase_MRP_RNA"
                      "telomerase_RNA"
                      "guide_RNA"
                      "rasiRNA"
                      "scRNA"
                      "siRNA"
                      "miRNA"
                      "piRNA"
                      "snoRNA"
                      "snRNA"
                      "SRP_RNA"
                      "vault_RNA"
                      "Y_RNA"
                      "other"

                ncRNA classes not yet in the INSDC /ncRNA_class controlled
                vocabulary can be annotated by entering
                '/ncRNA_class="other"' with '/note="[brief explanation of
                novel ncRNA_class]"';

1.3.8 /organism no longer to be used for misc_recomb

  The /organism qualifier had been legal for misc_recomb
features. But a review of the existing cases in the database
indicated that all could be better annotated through the use
of multiple source features.

  That work was completed in October 2007, and at this point
the /organism qualifier is no longer allowed for the misc_recomb
feature key.

1.3.9 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.

1.3.10 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-eight of the GSS flatfiles in Release 162.0. Consider gbgss222.seq :

GBGSS1.SEQ           Genetic Sequence Data Bank
                          October 15 2007

                NCBI-GenBank Flat File Release 162.0

                           GSS Sequences (Part 1)

   86842 loci,    64244408 bases, from    86842 reported sequences

  Here, the filename and part number in the header is "1", though the file
has been renamed as "222" 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 /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    "<institution-code>:[<collection-code>:]<culture_id>"
Example         /culture_collection="ATCC:26370"
Comment         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;
                the /culture_collection qualifier becomes legal on 15-Dec-2007;

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    "[<institution-code>:[<collection-code>:]]<material_id>"
Example         /bio_material="CGC:CB3912"      <- Caenorhabditis stock centre
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
                centres, 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;
                the /bio_material qualifier becomes legal on 15-Dec-2007;

1.4.2 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 the definition of the new tmRNA feature:

Feature Key           tmRNA
Definition            transfer messenger RNA; tmRNA acts as a tRNA first,
                      and then as 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"
                      /tag_peptide=<base_range>
Comment               the tmRNA feature key will become valid on 15-Dec-2007


To indicate the nucleotide region encoding the proteolysis tag
peptide, a new /tag_peptide qualifier will be introduced for
use with the tmRNA feature. The definition of /tag_peptide is:

Qualifier       /tag_peptide=
Definition      base location encoding the polypeptide for proteolysis tag of
                tmRNA and its termination codon;
Value format    <base_range>
Example         /tag_peptide=90..122
Comment         it is recommended that the amino acid sequence corresponding
                to the /tag_peptide be annotated by describing a 5' partial
                CDS feature; e.g. CDS    <90..122;
                the /tag_peptide qualifier (and tmRNA feature) will become
                valid on 15-Dec-2007



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