[Genbank-bb] GenBank Release 190.0 Available : June 15 2012

Cavanaugh, Mark (NIH/NLM/NCBI) [E] via genbankb%40net.bio.net (by cavanaug from ncbi.nlm.nih.gov)
Mon Jun 18 22:03:32 EST 2012


Greetings GenBank Users,

  GenBank Release 190.0 is now available via FTP from the
National Center for Biotechnology Information (NCBI):

  Ftp Site           Directory   Contents
  ----------------   ---------   ---------------------------------------
  ftp.ncbi.nih.gov   genbank     GenBank Release 190.0 flatfiles
                     ncbi-asn1   ASN.1 data used to create Release 190.0

  Close-of-data for GenBank 190.0 occurred on 06/13/2012. Uncompressed,
the Release 190.0 flatfiles require roughly 553 GB (sequence files only)
or 595 GB (including the 'short directory', 'index' and the *.txt files).
The ASN.1 data require approximately 454 GB.

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

  Release  Date      Base Pairs    Entries

  189      Apr 2012  139266481398  151824421
  190      Jun 2012  141343240755  154130210

Recent statistics for WGS sequences:

  Release  Date      Base Pairs    Entries

  189    Apr 2012  272693351548   80905298
  190    Jun 2012  287577367116   82076779

  During the 59 days between the close dates for GenBank Releases 189.0
and 190.0, the non-WGS/non-CON portion of GenBank grew by 2,076,759,357
basepairs and by 2,305,789 sequence records. During that same period,
1,616,053 records were updated. An average of 66,472 non-WGS/non-CON
records were added and/or updated per day.

  Between releases 189.0 and 190.0, the WGS component of GenBank grew by
14,884,015,568 basepairs and by 1,171,481 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 190.0 and Upcoming Changes) have been appended
below for your convenience.

                ** Important Notes **

*  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 190.0 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 2012, 190.0). 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 or Linux 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
190.0, please send email outlining your difficulties to:

        info from ncbi.nlm.nih.gov

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


1.3 Important Changes in Release 190.0

1.3.1 New /pseudogene qualifier

  A new controlled-vocabulary /pseudogene qualifier which had been under
discussion within the INSDC since the May 2011 collaborative INSD meeting
is now supported as of the June 2012 GenBank release. The goal of the new
qualifier is to use it for the annotation of certain well-defined classes
of pseudogenes. The new qualifier's definition is as follows:

Qualifier       /pseudogene=
Definition      indicates that this feature is a pseudogene of the element
                named by the feature key
Value format    "TYPE"
                where TYPE is one of the following:
                processed, unprocessed, unitary, allelic, unknown

Example         /pseudogene="processed"
                /pseudogene="unprocessed"
                /pseudogene="unitary"
                /pseudogene="allelic"
                /pseudogene="unknown"

Comment         TYPE is a term taken from the INSDC controlled vocabulary for 
                pseudogenes:

                processed: the pseudogene has arisen by reverse transcription
                of a mRNA into cDNA, followed by reintegration into the genome. 
                Therefore, it has lost any intron/exon structure, and it might
                have a pseudo-polyA-tail.

                unprocessed: the pseudogene has arisen from a copy of the parent 
                gene by duplication followed by accumulation of random mutations. 
                The changes, compared to their functional homolog, include 
                insertions, deletions, premature stop codons, frameshifts and a 
                higher proportion of non-synonymous versus synonymous 
                substitutions.

                unitary: the pseudogene has no parent. It is the original gene, 
                which is functional is some species but disrupted in some way 
                (indels, mutation, recombination) in another species or strain.

                allelic: a (unitary) pseudogene that is stable in the population 
                but importantly it has a functional alternative allele also in
                the population. i.e., one strain may have the gene, another
                strain may have the pseudogene. MHC haplotypes have allelic
                pseudogenes.

                unknown: the submitter does not know the method of
                pseudogenisation.

1.3.2 Legacy /pseudo qualifier likely to remain in use

  In the Upcoming Changes announcement for the April 2012 GenBank 189.0
release, mention was made that the /pseudo qualifier would be deprecated,
given that a new /pseudogene qualifier would be available. However, in 
subsequent discussions during the June 2012 INSDC meeting, it was decided
that a mechanism is still needed to flag certain Gene and CDS features as
non-functional or problematic. Since agreement could not be reached for the
name of a qualifier, it was suggested that /pseudo should be preserved,
with an update to its definition in the Feature Table document.

  Although this is not a "change" in the normal sense, the fact that /pseudo
will be retained, and its usage clarified, seem important enough to 
warrant mention here.

1.3.3 New representation for Transcriptome Shotgun Assembly (TSA) records.

  As announced in the GenBank 189.0 release notes, the very first TSA
(Transcriptome Shotgun Assembly) project processed using a WGS-like
approach was made available by FTP between 189.0 and 190.0 . In the 
genbank/tsa directory of the NCBI FTP site you will now find these files:

-rw-r--r--  1 gbupdate gbproces       95 May 16 01:54 stats.tsa.GAAA
-rw-r--r--  1 gbupdate gbproces 18479033 May 16 01:53 tsa.GAAA.1.fsa_nt.gz
-rw-r--r--  1 gbupdate gbproces 31652938 May 16 01:53 tsa.GAAA.1.gbff.gz
-rw-r--r--  1 gbupdate gbproces     1057 May 16 01:53 tsa.GAAA.mstr.gbff.gz
-rw-r--r--  1 gbupdate gbproces       12 May 16 01:54 tsa.proj_list.2012.0516

And the ASN.1 version can be found in the ncbi-asn1/tsa FTP directory:

-rw-r--r-- 1 gbupdate gbproces       95 May 16 01:54 stats.tsa.GAAA
-rw-r--r-- 1 gbupdate gbproces 15773347 May 16 01:53 tsa.GAAA.1.bbs.gz
-rw-r--r-- 1 gbupdate gbproces     1081 May 16 01:53 tsa.GAAA.mstr.bse.gz
-rw-r--r-- 1 gbupdate gbproces       12 May 16 01:54 tsa.proj_list.2012.0516

  TSA projects are assigned a four-letter project code starting with
the letter "G" (for example, GAAA). Individual mRNA sequences within a 
project make use of the 4+2+6 accession number convention, familiar
to users of WGS data (for example, GAAA01000001). Unlike WGS, re-assembly
of the mRNAs for a TSA sequencing project is expected to be a very rare
occurrence, and we expect that the 2-digit assembly-version number will
almost always be "01" for TSA mRNAs. Similar to WGS, a TSA master record
provides a convenient overview of a TSA project, with an 'all-zeroes'
accession number (eg: GAAA00000000) . 

1.3.4 Organizational changes

The total number of sequence data files increased by 32 with this release:

  - the BCT division is now composed of  88 files (+3)
  - the CON division is now composed of 169 files (+2)
  - the ENV division is now composed of  54 files (+1)
  - the EST division is now composed of 464 files (+3)
  - the INV division is now composed of  31 files (+1)
  - the PAT division is now composed of 180 files (+2)
  - the PLN division is now composed of  57 files (+2)
  - the PRI division is now composed of  45 files (+1)
  - the TSA division is now composed of  86 files (+16)
  - the VRL division is now composed of  21 files (+1)

The total number of 'index' files increased by 2 with this release:

  - the AUT (author name) index is now composed of 99 files (+2)

1.3.5 Project DBLINKs transitioning to BioProject

  The Genome Project Database resource at the NCBI was redesigned in
recent months, culminating in the implementation of a new BioProject
resource:

        http://www.ncbi.nlm.nih.gov/bioproject

An article that describes the goals of BioProject is available:

        http://www.ncbi.nlm.nih.gov/books/NBK54015/

BioProject is a collaborative effort of the International Nucleotide
Sequence Database Collaboration (INSDC), and project data are exchanged 
with NCBI's partner INSDC institutions, EBI and DDBJ. A BioProject
website is also available at DDBJ:

        http://trace.ddbj.nig.ac.jp/bioproject/index_e.shtml

BioProjects are uniquely identified by BioProject Accession Numbers,
which utilize this format:

        "PRJ"
        "E" or "N" or "D"
        one letter
        one or more digits

Examples of valid BioProject accessions are PRJNA12521 and PRJEB1 .

With BioProject now in operation, we are implementing links from
sequence records to this new resource. Previously, links to the
Genome Project Database were provided by numeric 'Project' DBLINKs .
Here's an example for a bacterial complete-genome record:

LOCUS       CP002497             1110245 bp    DNA     linear   PLN 14-NOV-2011
DEFINITION  Eremothecium cymbalariae DBVPG#7215 chromosome 1, complete
            sequence.
ACCESSION   CP002497
VERSION     CP002497.1  GI:356887709
DBLINK      Project: 60715

As records like this are switched to BioProject accessions, the DBLINK
line will change slightly:

LOCUS       CP002497             1110245 bp    DNA     linear   PLN 14-NOV-2011
DEFINITION  Eremothecium cymbalariae DBVPG#7215 chromosome 1, complete
            sequence.
ACCESSION   CP002497
VERSION     CP002497.1  GI:356887709
DBLINK      BioProject: PRJNA60715

In the coming months, many millions of sequence records will gradually
be modified, to make use of the new BioProject DBLINK. These modifications
will not be distributed via daily GenBank and RefSeq incremental-update
products.

The new BioProject links are also appearing on newly-submitted sequence
records, and have been present in GenBank and RefSeq release and
incremental-update products since December 2011.

1.3.6 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 from January 2005
seemed 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.

1.3.7 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
103 of the GSS flatfiles in Release 190.0. Consider gbgss154.seq :

GBGSS1.SEQ          Genetic Sequence Data Bank
                            June 15 2012

                NCBI-GenBank Flat File Release 190.0

                           GSS Sequences (Part 1)

   87112 loci,    63991594 bases, from    87112 reported sequences

  Here, the filename and part number in the header is "1", though the file
has been renamed as "154" based on the number of files dumped from the other
system.  We hope to resolve this discrepancy at some point, but the priority
is certainly much lower than many other tasks.

1.4 Upcoming Changes

  There are no upcoming changes for GenBank flatfile format or content
currently scheduled.





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