[Genbank-bb] GenBank Release 161.0 Now Available

Mark Cavanaugh via genbankb%40net.bio.net (by cavanaug from ncbi.nlm.nih.gov)
Tue Aug 21 02:35:01 EST 2007


Greetings GenBank Users,

  GenBank Release 161.0 is now available via FTP from the National
Center for Biotechnology Information (NCBI):

  Ftp Site           Directory   Contents
  ----------------   ---------   ---------------------------------------
  ftp.ncbi.nih.gov   genbank     GenBank Release 161.0 flatfiles
                     ncbi-asn1   ASN.1 data used to create Release 161.0

  Close-of-data for GenBank 161.0 occured on 08/14/2007. Uncompressed, the
Release 161.0 flatfiles require roughly 299 GB (sequence files only)
or 319 GB (including the 'short directory', 'index' and the *.txt files). 
The ASN.1 data require approximately 245 GB.

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

  Release  Date       Base Pairs   Entries

  160      Jun 2007   77248690945  73078143
  161      Aug 2007   79525559650  76146236

And for WGS sequences:

  Release  Date       Base Pairs   Entries

  160      Jun 2007   97102606459  23718400
  161      Aug 2007  101964323738  25384475

  During the 61 days between the close dates for GenBank Releases 160.0 and
161.0, the non-WGS/non-CON portion of GenBank grew by 2,276,868,705 basepairs
and by 3,068,093 sequence records. During that same period, 849,992 records
were updated. An average of about 64,231 non-WGS/non-CON records were added
and/or updated per day.

  Between releases 160.0 and 161.0, the WGS component of GenBank grew by
4,861,717,279 basepairs and by 1,666,075 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 161.0 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 161.0 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 2007, 161.0). 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
161.0, 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 161.0

1.3.1 CON division organizational changes

  As mentioned in the release notes for GenBank 160.0, the processing
for "constructed" CON division records has been changed so that they
are provided via a larger number of much smaller files. 

  Consequently, there are now 82 gbcon*.seq sequence files, in contrast
to the eight of Release 160.0. And there are other impacts:

  - accession numbers for CON records now appear in gbacc1.txt,
    gbnew.txt, gbchg.txt, and gbdel.txt 

  - the Author Index files (gbaut*.idx) now reflect the content of
    CON division records, and the number of those files has increased
    from 21 to 47

  These changes were necessitated by the influx of 3 million CON division
records from the AACY02 metagenomic WGS project:

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

  Although the CON division sequence files have headers which include
the number of records and basepairs in each file, CON records are
excluded from the statistics reported in Sections 2.2.6, 2.2.7, 2.2.8,
and the file header of the GenBank release notes.

  The reason for this is that CON division records are constructed by
referring to basepair intervals on other (non-CON) records. Hence, their
inclusion in overall release statistics would be a form of double-counting.

  The procedures for generating the ASN.1-format release files will be
similarly modified by October 2007, and a much larger number of smaller
gbcon*.aso files will result.

  The dramatic increase in the number of Author Index files illustrates
the inefficiencies of the current index file data products. Note the
discussion in Section 1.3.3, below.

1.3.2 Organizational changes

  The total number of sequence data files increased by 119 with this release:

  - the BCT division is now comprised of  24 files (+2)
  - the CON division is now comprised of  82 files (+74)
  - the EST division is now comprised of 635 files (+26)
  - the GSS division is now comprised of 264 files (+3)
  - the ENV division is now comprised of   6 files (+1)
  - the HTG division is now comprised of  98 files (+2)
  - the INV division is now comprised of  11 files (+1)
  - the PAT division is now comprised of  30 files (+1)
  - the PLN division is now comprised of  26 files (+1)
  - the PRI division is now comprised of  34 files (+1)
  - the ROD division is now comprised of  26 files (+1)
  - the SYN division is now comprised of   5 files (+4)
  - the VRL division is now comprised of   8 files (+1)
  - the VRT division is now comprised of  14 files (+1)

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

  - the AUT (Author Name) index is now comprised of 47 files  (+26)
  - the JOU (Journal Name) index is now comprised of 4 files   (+1)
  - the Key (Keyword Phrase) index is now comprised of 3 files (+1)

1.3.3 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:
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.

  Here is the preliminary definition 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.
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"
Mandatory qualifiers  /ncRNA_class="TYPE"
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-protein-coding RNA described by the ncRNA parent key
Value format   "TYPE"
where TYPE is one of the following terms:

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

Example         /ncRNA_class="miRNA"
                /ncRNA_class="siRNA"
                /ncRNA_class="scRNA"       

Comment         ncRNA classes not found in the restricted vocabulary list can be 
                annotated by entering '/ncRNA_class="other"' with
                '/note="[brief explanation of novel ncRNA_class]"'

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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