From cavanaug from ncbi.nlm.nih.gov Thu Aug 21 13:58:21 2008 From: cavanaug from ncbi.nlm.nih.gov (Cavanaugh, Mark (NIH/NLM/NCBI) [E]) Date: Thu Aug 21 13:59:34 2008 Subject: [Genbank-bb] GenBank 167.0 Close-of-Data Message-ID: <7B6F170840CA6C4DA63EE0C8A7BB43EC0217110A@NIHCESMLBX15.nih.gov> Greetings GenBank Users, Close-of-data for the upcoming GenBank Release 167.0 occurred on Tuesday August 19 at approximately 1:30am ET. The subsequently generated GenBank Incremental Update files nc0819.aso, nc0819,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 167.0 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 Fri Aug 22 18:00:06 2008 From: cavanaug from ncbi.nlm.nih.gov (Mark Cavanaugh) Date: Fri Aug 22 18:00:21 2008 Subject: [Genbank-bb] GenBank Release 167.0 Now Available Message-ID: <48AF44F6.mailOZI11JDIW@widget1.be-md.ncbi.nlm.nih.gov> A non-text attachment was scrubbed... Name: not available Type: application/octet-stream Size: 15827 bytes Desc: not available Url : http://www.bio.net/bionet/mm/genbankb/attachments/20080822/df55ca5e/attachment.exe From cavanaug from ncbi.nlm.nih.gov Fri Aug 22 18:12:51 2008 From: cavanaug from ncbi.nlm.nih.gov (Mark Cavanaugh) Date: Fri Aug 22 18:13:00 2008 Subject: [Genbank-bb] GenBank Release 167.0 Now Available Message-ID: <200808222312.m7MNCpxS007915@goliath.ncbi.nlm.nih.gov> [Apologies, the initial announcement was interpreted as an attachment. Re-sending because the listserv might not handle it gracefully.] Greetings GenBank Users, GenBank Release 167.0 is now available via FTP from the National Center for Biotechnology Information (NCBI): Ftp Site Directory Contents ---------------- --------- --------------------------------------- ftp.ncbi.nih.gov genbank GenBank Release 167.0 flatfiles ncbi-asn1 ASN.1 data used to create Release 167.0 Close-of-data for GenBank 167.0 occured on 08/19/2008. Uncompressed, the Release 167.0 flatfiles require roughly 357 GB (sequence files only) or 381 GB (including the 'short directory', 'index' and the *.txt files). The ASN.1 data require approximately 326 GB. Recent statistics for non-WGS, non-CON sequences: Release Date Base Pairs Entries 166 Jun 2008 92008611867 88554578 167 Aug 2008 95033791652 92748599 Recent statistics for WGS sequences: Release Date Base Pairs Entries 166 Jun 2008 113639291344 39163548 167 Aug 2008 118593509342 40214247 During the 69 days between the close dates for GenBank Releases 166.0 and 167.0, the non-WGS/non-CON portion of GenBank grew by 3,025,179,785 basepairs and by 4,194,021 sequence records. During that same period, 939,305 records were updated. An average of about 74,396 non-WGS/non-CON records were added and/or updated per day. Between releases 166.0 and 167.0, the WGS component of GenBank grew by 4,954,217,998 basepairs and by 1,050,699. 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 167.0 and Upcoming Changes) have been appended below for your convenience. ** Important Notes ** * Support for the single, comprehensive protein FASTA file which accompanies GenBank releases ceased as of the June 2008 release. See Section 1.3.3 of the release notes for details. * A number of changes are expected for October's GenBank Release 168.0 . Please see Section 1.4 for a complete list. * GenBank 'index' files are now provided without any EST content, and without most GSS content. See Section 1.3.4 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 167.0 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 2008, 167.0). 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 167.0, please send email outlining your difficulties to: info@ncbi.nlm.nih.gov Mark Cavanaugh, Vladimir Alekseyev, Michael Kimelman GenBank NCBI/NLM/NIH/HHS 1.3 Important Changes in Release 167.0 1.3.1 Announcements for upcoming changes absent from Release 166.0 An oversight during GenBank Release 166.0 processing resulted in the exclusion of several announcements for changes that will be implemented as of GenBank Release 168.0 in October 2008 (see section 1.4, below). This means that only two months advance notice can be provided for those changes, rather than the customary four months. Our apologies for this oversight and any inconvenience that it may cause. 1.3.2 Organizational changes The total number of sequence data files increased by 58 with this release: - the BCT division is now comprised of 30 files (+1) - the CON division is now comprised of 97 files (+6) - the ENV division is now comprised of 10 files (+1) - the EST division is now comprised of 762 files (+24) - the GSS division is now comprised of 306 files (+16) - the HTG division is now comprised of 120 files (+3) - the INV division is now comprised of 13 files (+1) - the PAT division is now comprised of 46 files (+4) - the PLN division is now comprised of 30 files (+1) - the VRL division is now comprised of 10 files (+1) - the VRT division is now comprised of 16 files (+1) The total number of index files increased by 5 with this release: - the AUT index is now comprised of 59 files (+5) 1.3.3 Comprehensive protein FASTA file has been discontinued 'Divisional' protein FASTA files : ftp://ftp.ncbi.nih.gov/ncbi-asn1/gbXXX.fsa_aa.gz where 'XXX' represents an alphanumeric GenBank division code (such as pri10) were made available starting with GenBank Release 164.0 . Given their availability, support for the single, comprehensive protein FASTA file: ftp://ftp.ncbi.nih.gov/genbank/relNNN.fsa_aa.gz (where 'NNN' represents a three-digit GenBank release number) was discontinued as of GenBank Release 166.0 in June 2008. The size of the comprehensive file had exceeded 4GB, which was unmanageable for many users. The final comprehensive protein FASTA file was: rel166.fsa_aa . 1.3.4 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. 1.3.5 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 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 fifty-nine of the GSS flatfiles in Release 167.0. Consider gbgss248.seq : GBGSS1.SEQ Genetic Sequence Data Bank August 15 2008 NCBI-GenBank Flat File Release 167.0 GSS Sequences (Part 1) 87184 loci, 64446495 bases, from 87184 reported sequences Here, the filename and part number in the header is "1", though the file has been renamed as "248" 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 Changes related to ncRNA features, /ncRNA_class, and /moltype The list of allowed values for the /ncRNA_class qualifier, which is mandatory for all ncRNA features, will be expanded to include: /ncRNA_class="ribozyme" Non-coding RNAs which are not yet in the INSDC's controlled vocabulary: http://www.insdc.org/page.php?page=rna_vocab previously required /ncRNA_class="other" plus an accompanying /note qualifer to describes the nature of the ncRNA. This requirement will be changed, such that *either* a /product or a /note qualifier must accompany "other" ncRNAs features. The list of allowed /mol_type qualifiers for the source feature currently includes: /mol_type="snoRNA" /mol_type="snRNA" /mol_type="scRNA" /mol_type="tmRNA" All of these molecule types will be collapsed into a single value: /mol_type="transcribed RNA" Sequence records which represent one of these four types of molecules will thus have: an ncRNA feature with /ncRNA_class of "snoRNA", "scRNA" or "snRNA" a source feature with /mol_type of "transcribed RNA" or a tmRNA feature a source feature with /mol_type of "transcribed RNA" All of these changes will take effect as of Release 169.0 in October 2008. 1.4.2 Merging the satellite and repeat_unit features into repeat_region Satellites, minisatellites and microsatellites are comprised of repetitive units of DNA, with a variety of lengths and repeat patterns. With the addition of a new qualifier (/satellite), the satellite and repeat_unit features can be represented by the repeat_region feature. Qualifier /satellite= Definition identifier for satellite DNA marker; many tandem repeats (identical or related) of a short basic repeating unit; many have a base composition or other property different from the genome average that allows them to be separated from the bulk genomic DNA; Value format "[:][ ]" where satellite_type is one of the following "satellite", "microsatellite", "minisatellite" Example /satellite="satellite: S1a" /satellite="satellite: alpha" /satellite="satellite: gamma III" /satellite="microsatellite: DC130" As of the October 2008 GenBank release, all satellite features will be transformed into repeat_region features with /satellite qualifiers of type "satellite", and all repeat_unit features will be transformed into repeat_region features. 1.4.3 New /gene_synonym qualifier Gene symbols are presented via the /gene qualifier. When synonymous or alternative gene symbols are available, they have often been presented via multiple /gene qualifiers. To distinguish what might be an approved or official gene symbol from its synonyms or alternatives, a new /gene_synonym qualifier will be introduced for GenBank Release 168.0 . Qualifier /gene_synonym= Definition synonymous or alternative symbol for a gene corresponding to a sequence region Value format "text" Examples /gene="CF" /gene="ABCC7" 1.4.4 New /mating_type qualifier Because the /sex qualifier has a free-text value format, is has been innapropriately utilized for certain organisms, such as bacteria, fungi, and some insects and worms. In such cases, a more appropriate term would be 'mating type'. In October 2008, a new qualifier will be made available for non-sexual reproductive strategies: Qualifier /mating_type= Definition mating type of the organism from which the sequence was obtained Value format "text" Example /mating_type="Mating type A" 1.4.5 Renaming of /specific_host as /host The definition of /specific_host in the Feature Table document is as follows: Qualifier /specific_host= Definition natural host from which the sequence was obtained Value format "text" Example /specific_host="Rhizobium NGR234" The usage of /specific_host, and particularly the distinction between it and /lab_host, is not made clear with this definition. So the qualifier is going to be renamed and redefined, starting with Release 168.0 in October 2008 : Qualifier /host= Definition Natural (as opposed to laboratory) host to the organism from which the sequenced molecule was obtained Value format "text" Example /host="Homo sapiens" /host="Homo sapiens 12 year old girl" 1.4.6 New value for /organelle In October 2008, the list of allowed values for /organelle will be expanded to include: /organelle="chromatophore" 1.4.7 Modification to value format for /frequency The current definition of /frequency is : Qualifier /frequency= Definition frequency of the occurrence of a feature Value format text representing the fraction of population carrying the variation expressed as a decimal fraction Example /frequency=".85" Although this format is appropriate and useful in some contexts (for example, within a global population of individuals), it does not convey the number of sequences that might have been included in a variation study. As of Release 168.0, the format of /frequency will be expanded: Value format text representing the fraction of population carrying the variation expressed as a decimal fraction, or the number observed instances vs the total number of sequenced isolates Example /frequency=".85" /frequency="23/108" /frequency="1 in 12" 1.4.8 /cons_splice qualifier to be removed The /cons_splice qualifier has almost no usage within the sequence database. In addition, it does not account for the variation in splice signals that might be used by different classes of introns. So this qualfier will be removed from sequence records, and the Feature Table document, as of Release 168.0 in October 2008. 1.4.9 /virion qualifier to be removed The intent of /virion is to indicate that a sequenced molecule is from an encapsidated viral particle (as opposed to the proviral form of a virus, integrated into the host's genome). Viral sequences derived from a blood sample taken from an infected organism might typically be flagged with /virion, if it is believed that the sample contained viral particles. However, a review of the database reveals that this qualifier is not used consistently, and furthermore, submitters often are unable to conclusively state that a virus sequence derives from the encapsidated form. So the /virion qualifier will be removed from sequence records, and the Feature Table document, as of Release 168.0 in October 2008. 1.4.10 Updated value format for /exception Only three values for the /exception qualifier have been approved for use by the INSDC : "rearrangement required for product" "RNA editing" "reasons given in citation" However, the definition of /exception in the Feature Table document does not indicate that the contents of /exception are controlled. This oversight will be corrected in October 2008.