From cavanaug from ncbi.nlm.nih.gov Thu Dec 11 18:57:09 2008 From: cavanaug from ncbi.nlm.nih.gov (Cavanaugh, Mark (NIH/NLM/NCBI) [E]) Date: Thu Dec 11 21:10:55 2008 Subject: [Genbank-bb] GenBank : Increase in number of release files planned Message-ID: <7B6F170840CA6C4DA63EE0C8A7BB43EC03C7F7EC@NIHCESMLBX15.nih.gov> Greetings GenBank Users, Due to changes in the method by which the flatfile representations of GenBank sequence records are stored at NCBI, there will be about a 10% increase in the overall number of files in GenBank Release 169.0, compared to Release 168.0 in October. This will be in addition to the normal increase in files caused by the addition of new records. The sizes of the files in each division will also vary more than previously (although most files will still be in the 250MB to 350MB size range). These changes are the costs of an improvement in overall flatfile processing. Among the benefits: large-scale changes which affect many records (flatfile format changes; changes to widely used organism names) can now be handled much more quickly, and the preparation of certain GB release files now requires much less time. These changes, and others that are underway, should ultimately translate into a much faster release generation process in 2009. Mark Cavanaugh GenBank NCBI/NLM/NIH/HHS From cavanaug from ncbi.nlm.nih.gov Thu Dec 11 19:00:19 2008 From: cavanaug from ncbi.nlm.nih.gov (Cavanaugh, Mark (NIH/NLM/NCBI) [E]) Date: Thu Dec 11 21:11:02 2008 Subject: [Genbank-bb] GenBank 169.0 Close-of-Data Message-ID: <7B6F170840CA6C4DA63EE0C8A7BB43EC03C7F7ED@NIHCESMLBX15.nih.gov> Greetings GenBank Users, Close-of-data for the upcoming GenBank Release 169.0 occurred on Thursday December 11 at approximately 1:30am EST. The subsequently generated GenBank Incremental Update files nc1211.aso, nc1211.flat, etc. contain data through the close. Note: Release processing often does not begin until sometime during business hours on the close date. As a result, a number of sequence records processed *after* 1:30am are likely to be present in the GenBank 169.0 release files, even though they are "post-close" . Similarly, the first GenBank Incremental Update that is generated after the close date is likely to contain a number of sequence records that are unchanged, compared to their appearance in the release files. Our apologies for the lack of advanced notice about the close date. Mark Cavanaugh GenBank NCBI/NLM/NIH/HHS From cavanaug from ncbi.nlm.nih.gov Tue Dec 16 04:17:17 2008 From: cavanaug from ncbi.nlm.nih.gov (Cavanaugh, Mark (NIH/NLM/NCBI) [E]) Date: Tue Dec 16 06:13:45 2008 Subject: [Genbank-bb] GenBank Release 169.0 Now Available Message-ID: <7B6F170840CA6C4DA63EE0C8A7BB43EC01666652@NIHCESMLBX15.nih.gov> Greetings GenBank Users, GenBank Release 169.0 is now available via FTP from the National Center for Biotechnology Information (NCBI): Ftp Site Directory Contents ---------------- --------- --------------------------------------- ftp.ncbi.nih.gov genbank GenBank Release 169.0 flatfiles ncbi-asn1 ASN.1 data used to create Release 169.0 Close-of-data for GenBank 169.0 occured on 12/11/2008. Uncompressed, the Release 169.0 flatfiles require roughly 381 GB (sequence files only) or 407 GB (including the 'short directory', 'index' and the *.txt files). The ASN.1 data require approximately 349 GB. Recent statistics for non-WGS, non-CON sequences: Release Date Base Pairs Entries 168 Oct 2008 97381682336 96400790 169 Dec 2008 99116431942 98868465 Recent statistics for WGS sequences: Release Date Base Pairs Entries 168 Oct 2008 136085973423 46108952 169 Dec 2008 141374971004 48394838 During the 45 days between the close dates for GenBank Releases 168.0 and 169.0, the non-WGS/non-CON portion of GenBank grew by 1,734,749,606 basepairs and by 2,467,675 sequence records. During that same period, 4,183,486 records were updated. An average of about 147,803 non-WGS/non-CON records were added and/or updated per day. Between releases 168.0 and 169.0, the WGS component of GenBank grew by 5,288,997,581 basepairs and by 2,285,886 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 169.0 and Upcoming Changes) have been appended below for your convenience. ** Important Notes ** * A new linetype ( DBLINK ) will be implemented as of the February 2009 release. See Section 1.4.1 for information. * GenBank 'index' files are now provided without any EST content, and without most GSS content. See Section 1.3.12 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 169.0 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: December 15 2008, 169.0). 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 169.0, please send email outlining your difficulties to: info@ncbi.nlm.nih.gov Mark Cavanaugh, Michael Kimelman, Ilya Dondoshansky GenBank NCBI/NLM/NIH/HHS 1.3 Important Changes in Release 169.0 1.3.1 Organizational changes As described in a post to the GenBank Newsgroup on December 11, 2008, the number of sequence data files associated with this GenBank release has increased by a larger-than-usual amount, due to changes in the way that data are processed and stored at NCBI. Thus the per-division increases described below reflect both the storage-related changes *and* actual database growth. In addition, GenBank divisions which consist of a single data file now include a number in their names: gbtsa.seq -> gbtsa1.seq gbuna.seq -> gbuna1.seq The total number of sequence data files increased by 94 with this release: - the BCT division is now composed of 34 files (+2) - the CON division is now composed of 128 files (+25) - the ENV division is now composed of 11 files (+1) - the EST division is now composed of 822 files (+20) - the GSS division is now composed of 319 files (+10) - the HTC division is now composed of 13 files (+1) - the HTG division is now composed of 134 files (+12) - the INV division is now composed of 14 files (+1) - the PAT division is now composed of 55 files (+8) - the PLN division is now composed of 37 files (+5) - the PRI division is now composed of 39 files (+3) - the ROD division is now composed of 28 files (+2) - the STS division is now composed of 20 files (+2) - the VRL division is now composed of 11 files (+1) - the VRT division is now composed of 17 files (+1) In addition, the total number of index files increased by 3 with this release: - the AUT index is now composed of 62 files (+3) 1.3.2 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@ncbi.nlm.nih.gov Our apologies for any inconvenience that these changes may cause. 1.3.3 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 sixty-nine of the GSS flatfiles in Release 169.0. Consider gbgss251.seq : GBGSS1.SEQ Genetic Sequence Data Bank December 15 2008 NCBI-GenBank Flat File Release 169.0 GSS Sequences (Part 1) 87209 loci, 64341123 bases, from 87209 reported sequences Here, the filename and part number in the header is "1", though the file has been renamed as "251" 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 PROJECT linetype to be replaced by DBLINK (April 2009) The PROJECT linetype allows a sequence record to be linked to information about the sequencing project that generated the data which ultimately resulted in the record's submission to the International Nucleotide Sequence Database ( INSD; see http://www.insdc.org ) . This complete bacterial GenBank record illustrates the use of the PROJECT line: LOCUS CP000964 5641239 bp DNA circular BCT 24-SEP-2008 DEFINITION Klebsiella pneumoniae 342, complete genome. ACCESSION CP000964 VERSION CP000964.1 GI:206564770 PROJECT GenomeProject:28471 When viewed on the web in NCBI's Entrez:Nucleotide, the record's project identifier (28471) links to an entry in the Genome Project Database (GPDB) : http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&uid=28471 where information about the sequencing center, the bacterium, and other GenBank records (eg, plasmids) associated with the sequencing project can be found. Since the introduction of PROJECT, the scope of the "Genome" Project Database has expanded, to include projects that are not necessarily targetted to the sequencing of a complete genome. In addition, there can be other resources which underlie an INSD sequence record, such as the Trace Assembly Archive at the NCBI: http://www.ncbi.nlm.nih.gov/Traces/assembly/assmbrowser.cgi?cmd=show&f=tree&m=main&s=tree Because of the expanded scope of the GPDB, and because we anticipate a need to link to more resources than just the GPDB, the PROJECT linetype is going to be replaced by a new linetype: DBLINK Modifications to linetypes can be disruptive, so the switch to DBLINK will occur in several stages. As of October 2008, links to the NCBI Trace Assembly Archive are displayed via a line of text in the COMMENT section of sequence records. Here is a mock-up, based on CP000964, to illustrate that initial change: LOCUS CP000964 5641239 bp DNA circular BCT 24-SEP-2008 DEFINITION Klebsiella pneumoniae 342, complete genome. ACCESSION CP000964 VERSION CP000964.1 GI:206564770 PROJECT GenomeProject:28471 .... COMMENT Trace Assembly Archive:123456 The source for the DNA and/or cells is: Professor Eric W. Triplett, Chair, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, P.O. Box 110700, Gainesville, FL 32611-0700, ewt@ufl.edu. Note: Use of the Trace Assembly Archive is still in its early stages, so only a few records are expected to have these links in the short term. The new DBLINK linetype will then be introduced with GenBank Release 170.0 , on or near February 15, 2009 . The Genome Project ID and the Trace Assembly Archive ID will be presented via DBLINK, and the existing PROJECT line will continue to be displayed: LOCUS CP000964 5641239 bp DNA circular BCT 24-SEP-2008 DEFINITION Klebsiella pneumoniae 342, complete genome. ACCESSION CP000964 VERSION CP000964.1 GI:206564770 PROJECT GenomeProject:28471 DBLINK Project:28471 Trace Assembly Archive:123456 .... COMMENT The source for the DNA and/or cells is: Professor Eric W. Triplett, Chair, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, P.O. Box 110700, Gainesville, FL 32611-0700, ewt@ufl.edu. PROJECT and DBLINK will co-exist for one GenBank release, until Release 171.0 (April 15, 2009), at which point the PROJECT line will be removed. In its final state, our mock-up for CP000964 becomes: LOCUS CP000964 5641239 bp DNA circular BCT 24-SEP-2008 DEFINITION Klebsiella pneumoniae 342, complete genome. ACCESSION CP000964 VERSION CP000964.1 GI:206564770 DBLINK Project:28471 Trace Assembly Archive:123456 .... COMMENT The source for the DNA and/or cells is: Professor Eric W. Triplett, Chair, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, P.O. Box 110700, Gainesville, FL 32611-0700, ewt@ufl.edu. In summary: The PROJECT linetype will be replaced by DBLINK as of GenBank Release 171.0 in April 2009. For those who process sequence data in NCBI's ASN.1 format: The underlying representation for (Genome) Project IDs will remain unchanged. There will be no changes to the ASN.1 User-object that is used to store them: user { type str "GenomeProjectsDB" , data { { label str "ProjectID" , data int 28471 } , { label str "ParentID" , data int 0 } } } , However, to support linkages to other resources, such as the Trace Assembly Archive, a new "DBLink" User-object will be introduced: user { type str "DBLink" , data { { label str "Trace Assembly Archive" , data ints { 123456 } } } } As new types of linkages are established, they will be added to the DBLink User-object, and displayed via the DBLINK linetype in the GenBank flatfile format. There is a possibility that the GenomeProjectsDB User-object might someday be incorporated into the new DBLink User-object. But at the moment, there are no firm plans to do so.