[Genbank-bb] GenBank Release 194.0 Available : February 15 2013

Cavanaugh, Mark (NIH/NLM/NCBI) [E] via genbankb%40net.bio.net (by cavanaug from ncbi.nlm.nih.gov)
Sun Feb 17 03:09:15 EST 2013

Greetings GenBank Users,

  GenBank Release 194.0 is now available via FTP from the
National Center for Biotechnology Information (NCBI):

  Ftp Site           Directory   Contents
  ----------------   ---------   ---------------------------------------
  ftp.ncbi.nih.gov   genbank     GenBank Release 194.0 flatfiles
                     ncbi-asn1   ASN.1 data used to create Release 194.0

  Close-of-data for GenBank 194.0 occurred on 02/13/2013. Uncompressed,
the Release 194.0 flatfiles require roughly 587 GB (sequence files only)
or 632 GB (including the 'short directory', 'index' and the *.txt files).
The ASN.1 data require approximately 481 GB.

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

  Release  Date      Base Pairs    Entries

  193      Dec 2012  148390863904  161140325
  194      Feb 2013  150141354858  162886727

Recent statistics for WGS sequences:

  Release  Date      Base Pairs    Entries

  193    Dec 2012  356002922838   92767765
  194    Feb 2013  390900990416  103101291

  During the 63 days between the close dates for GenBank Releases 193.0
and 194.0, the non-WGS/non-CON portion of GenBank grew by 1,750,490,954
basepairs and by 1,746,402 sequence records. During that same period,
1,120,552 records were updated. An average of 45,507 non-WGS/non-CON
records were added and/or updated per day.

  Between releases 193.0 and 194.0, the WGS component of GenBank grew by
34,898,067,578 basepairs and by 10,333,526 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 194.0 and Upcoming Changes) have been appended
below for your convenience.

                    ** Important Note **

   New data products intended to replace the legacy 'index' files that
   accompany the sequence-data files of GenBank releases are being
   prepared, and will soon be made available at the NCBI FTP site.
   We will post to the GenBank newsgroup when they have been installed.
   See Section 1.3.4 of the release notes for further details about
   this change. We welcome your feedback about this change.

  Release 194.0 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: February 15 2013, 194.0). 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

Or, if the files are compressed, perhaps:

        gzcat $i | head -10 | grep Release

  If you encounter problems while ftp'ing or uncompressing Release
194.0, please send email outlining your difficulties to:

        info from ncbi.nlm.nih.gov

Mark Cavanaugh, Michael Kimelman, Ilya Dondoshansky, Sergey Zhdanov

1.3 Important Changes in Release 194.0

1.3.1 Organizational changes

The total number of sequence data files increased by 30 with this release:

  - the BCT division is now composed of  98 files (+4)
  - the CON division is now composed of 187 files (+8)
  - the ENV division is now composed of  59 files (+2)
  - the GSS division is now composed of 270 files (+4)
  - the INV division is now composed of  34 files (+1)
  - the PAT division is now composed of 190 files (+4)
  - the TSA division is now composed of 138 files (+5)
  - the VRT division is now composed of  30 files (+2)

The total number of 'index' files increased by 4 with this release:

  - the AUT (author name) index is now composed of 110 files (+4)

1.3.2 Release Catalog data files to replace old "index" files

  As described in Section 1.3.3, the legacy "index" files that accompany
the sequence data files of GenBank releases have limited utility. For the
past six years we have provided only partial support for them, and have
warned that we plan to cease support entirely. As of GenBank 193.0 we 
introduced experimental "release catalog" products that will eventually
replace the old "index" files. We expect to make the release catalog(s)
and other supplemental files for Release 194.0 available shortly after
the release has been installed at the NCBI FTP site.

  This is the last release for which the legacy index files will be

  Every GenBank sequence record will be represented in the new catalog
files by a 10-field, TAB-delimited row of data. The data fields are:

	Accession Number
	NCBI GI Identifier (if assigned)
	Molecule Type (dna, rna, mrna, etc)
	Sequence Length
	Organism Name
	NCBI Taxonomy Database Identifier
	Division Code
	BioProject Accession Number
	BioSample Accession Number

When a value does not exist for one of these fields, the field in the catalog
will be empty (eg, two sequential TAB characters can be present, with
nothing between them). Here is an example of the catalog data for CP003933:

CP003933	CP003933.1	429549985	dna	3618794	Sinorhizobium meliloti GR4	1235461	BCT	PRJNA175860 

It is our hope that the release catalog will be more useful than the current
accession number index files (gbacc*.idx).

  The author-name (gbaut*.idx) and keyword (gbkey*.idx) and secondary-accession
(gbsec*.idx) index files will be discontinued without replacements.

  However, new "PMID List" and "Gene List" TAB-delimited files will accompany
the release catalog. The format of the PubMed Identifier List is:

Accession1	Accession1.Version	PMID-1,PMID-2,PMID-3,.....
Accession2	Accession2.Version	PMID-1,PMID-2,PMID-3,.....

And the format of the Gene List is:

Accession1	Accession1.Version	Gene-Symbol-1	Locus-Tag-1
Accession1	Accession1.Version	Gene-Symbol-2	Locus-Tag-2
Accession1	Accession1.Version	Gene-Symbol-3	Locus-Tag-3
Accession2	Accession2.Version	Gene-Symbol-1	Locus-Tag-1
Accession2	Accession2.Version	Gene-Symbol-2	Locus-Tag-2
Accession2	Accession2.Version	Gene-Symbol-3	Locus-Tag-3

Note that either Gene Symbol or Locus Tag could be null for any given

  The "Short Directory" files (gbsdr*.txt), which provide the accession
and definition line (often truncated) for all sequence records, will 
be discontinued without a replacement.

  For now, we plan to provide the release catalog and accompanying lists
via files that are specific to EST, GSS, and non-EST/GSS (everything else).
And, initially, the catalogs and lists will not include the contig 
sequence records for WGS projects. The new files will be made available
in a new sub-directory of the GenBank FTP area:


And their names will be:




  Note that there is no Gene List for EST sequences. This is because
EST records in GenBank have no annotation other than source features.

  Our goal is to provide companion products for the release files which will
be of help for large-scale consumers of GenBank data. To that end, if you
have ideas for how to make the release catalog more useful, or have
suggestions for additional companion files like the PMID and Gene lists,
please let us know by contacting the NCBI Help Desk : info from ncbi.nlm.nih.gov .

  Be aware that these new products are still in the experimental stage.
If you encounter problems with their content, we would appreciate your
feedback (again, via the NCBI Help Desk).

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 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

  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.

1.3.4 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 115
of the GSS flatfiles in Release 194.0. Consider gbgss156.seq :

GBGSS1.SEQ          Genetic Sequence Data Bank
                        February 15 2013

                NCBI-GenBank Flat File Release 194.0

                           GSS Sequences (Part 1)

   87092 loci,    63916585 bases, from    87092 reported sequences

  Here, the filename and part number in the header is "1", though the file
has been renamed as "156" 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

  No changes impacting the flatfile format are expected between the
February 2013 and April 2013 GenBank releases.

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