From cavanaug from ncbi.nlm.nih.gov Thu Oct 30 16:49:45 2008 From: cavanaug from ncbi.nlm.nih.gov (Cavanaugh, Mark (NIH/NLM/NCBI) [E]) Date: Thu Oct 30 16:51:22 2008 Subject: [Genbank-bb] GenBank 168.0 Status Report Message-ID: <7B6F170840CA6C4DA63EE0C8A7BB43EC031BC1DC@NIHCESMLBX15.nih.gov> Dear GenBank Users, October's GenBank Release 168.0 has been significantly delayed by a multitude of factors, most of which were related to the Feature Table and other changes scheduled for implementation this month. An unusually large number of records were affected, which caused processing difficulties for one of our systems. The difficulties were finally resolved as of Monday October 27, and we anticipate that the release files will be made available later this evening (Thursday, October 30). Our apologies for both the two-week delay, and for the lack of prior status reports. Mark Cavanaugh GenBank NCBI/NLM/NIH/HHS From cavanaug from ncbi.nlm.nih.gov Thu Oct 30 16:54:12 2008 From: cavanaug from ncbi.nlm.nih.gov (Cavanaugh, Mark (NIH/NLM/NCBI) [E]) Date: Thu Oct 30 16:54:33 2008 Subject: [Genbank-bb] GenBank 168.0 Close-of-Data Message-ID: <7B6F170840CA6C4DA63EE0C8A7BB43EC031BC1DE@NIHCESMLBX15.nih.gov> Greetings GenBank Users, Close-of-data for the upcoming GenBank Release 168.0 occurred on Monday October 27 at approximately 1:30am EDT. The subsequently generated GenBank Incremental Update files nc1027.aso, nc1027.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 168.0 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 Thu Oct 30 18:57:15 2008 From: cavanaug from ncbi.nlm.nih.gov (Cavanaugh, Mark (NIH/NLM/NCBI) [E]) Date: Thu Oct 30 18:58:03 2008 Subject: [Genbank-bb] GenBank Release 168.0 Now Available Message-ID: <7B6F170840CA6C4DA63EE0C8A7BB43EC031BC1F3@NIHCESMLBX15.nih.gov> Greetings GenBank Users, GenBank Release 168.0 is now available via FTP from the National Center for Biotechnology Information (NCBI): Ftp Site Directory Contents ---------------- --------- --------------------------------------- ftp.ncbi.nih.gov genbank GenBank Release 168.0 flatfiles ncbi-asn1 ASN.1 data used to create Release 168.0 Close-of-data for GenBank 168.0 occured on 10/27/2008. Uncompressed, the Release 168.0 flatfiles require roughly 371 GB (sequence files only) or 396 GB (including the 'short directory', 'index' and the *.txt files). The ASN.1 data require approximately 338 GB. Recent statistics for non-WGS, non-CON sequences: Release Date Base Pairs Entries 167 Aug 2008 95033791652 92748599 168 Oct 2008 97381682336 96400790 Recent statistics for WGS sequences: Release Date Base Pairs Entries 167 Aug 2008 118593509342 40214247 168 Oct 2008 136085973423 46108952 During the 69 days between the close dates for GenBank Releases 167.0 and 168.0, the non-WGS/non-CON portion of GenBank grew by 2,347,890,684 basepairs and by 3,652,191 sequence records. During that same period, 1,111,311 records were updated. An average of about 69,036 non-WGS/non-CON records were added and/or updated per day. Between releases 167.0 and 168.0, the WGS component of GenBank grew by 17,492,464,081 basepairs and by 5,894,705 records. The combined WGS/non-WGS single-release increase of 19.84 Gbp for Release 168.0 is the largest that GenBank has experienced, to date. 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 168.0 and Upcoming Changes) have been appended below for your convenience. ** Important Notes ** * A number of changes have been implemented for the October 2008 GenBank Release. Please see Section 1.3 for a complete list. * 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. * A new linetype ( DBLINK ) will be implemented as of the February 2009 release. See Section 1.4.1 for information. Release 168.0 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: October 15 2008, 168.0). 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 168.0, 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 168.0 1.3.1 Organizational changes The total number of sequence data files increased by 60 with this release: - the BCT division is now comprised of 32 files (+2) - the CON division is now comprised of 103 files (+6) - the EST division is now comprised of 802 files (+40) - the GSS division is now comprised of 309 files (+3) - the HTG division is now comprised of 122 files (+2) - the PAT division is now comprised of 47 files (+1) - the PLN division is now comprised of 32 files (+2) - the STS division is now comprised of 18 files (+4) The total number of index files increased by 1 with this release: - the JOU index is now comprised of 6 files (+1) 1.3.2 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, has been 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 have been 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 take effect with this October 2008 release. 1.3.3 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 are now 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 this October 2008 GenBank release, all satellite and repeat_unit features have been transformed into repeat_region features with an appropriate /satellite qualifier. 1.3.4 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 has been 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" 1.3.5 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'. A new qualifier has been made available for non-sexual reproductive strategies as of October 2008: Qualifier /mating_type= Definition mating type of the organism from which the sequence was obtained; mating type is used for prokaryotes, and for eukaryotes that undergo meiosis without sexually dimorphic gametes Value format "text" Examples /mating_type="MAT-1" /mating_type="plus" /mating_type="-" /mating_type="odd" /mating_type="even" Comment /mating_type="male" and /mating_type="female" are valid in the prokaryotes, but not in the eukaryotes; for more information, see the entry for /sex. In light of the above, the definition for the /sex qualifier has been refined: Qualifier /sex= Definition sex of the organism from which the sequence was obtained; sex is used for eukaryotic organisms that undergo meiosis and have sexually dimorphic gametes Value format "text" Examples /sex="female" /sex="male" /sex="hermaphrodite" /sex="unisexual" /sex="bisexual" /sex="asexual" /sex="monoecious" [or monecious] /sex="dioecious" [or diecious] Comment /sex should be used (instead of /mating_type) in the Metazoa, Embryophyta, Rhodophyta & Phaeophyceae; /mating_type should be used (instead of /sex) in the Bacteria, Archaea & Fungi; neither /sex nor /mating_type should be used in the viruses; outside of the taxa listed above, /mating_type should be used unless the value of the qualifier is taken from the vocabulary given in the examples above Records which inappropriately used the /sex qualifier have been updated, to utilize the new /mating_type qualifier. 1.3.6 Renaming of /specific_host as /host The /specific_host qualifier has been renamed as /host for Release 168.0 . >From the Feature Table document: Qualifier /host= Definition natural (as opposed to laboratory) host to the organism from which sequenced molecule was obtained Value format "text" Example /host="Homo sapiens" /host="Homo sapiens 12 year old girl" /host="Rhizobium NGR234" In contrast: Qualifier /lab_host= Definition scientific name of the laboratory host used to propagate the source organism from which the sequenced molecule was obtained Value format "text" Example /lab_host="Gallus gallus" /lab_host="Gallus gallus embryo" /lab_host="Escherichia coli strain DH5 alpha" /lab_host="Homo sapiens HeLa cells" Comment the full binomial scientific name of the host organism should be used when known; extra conditional information relating to the host may also be included 1.3.7 New value for /organelle As of October 2008, the list of allowed values for /organelle has been expanded to include: /organelle="chromatophore" 1.3.8 Modification to value format for /frequency As of October 2008, the definition of /frequency has been expanded to accomodate both the fraction of a population carrying a variation expressed as a decimal value, and as the number of observed instances vs. the total number of sequenced isolates: Qualifier /frequency= Definition frequency of the occurrence of a feature Value format text representing the proportion of a population carrying the feature expressed as a fraction Example /frequency="23/108" /frequency="1 in 12" /frequency=".85" 1.3.9 /cons_splice qualifier 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 has been removed from sequence records, and the Feature Table document, as of Release 168.0 . 1.3.10 /virion qualifier removed The intent of /virion was to indicate that a sequenced molecule originates 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 be flagged with /virion, if it is believed that the sample contained viral particles. However, a review of the database revealed that /virion was not used consistently, and furthermore, submitters are often unable to conclusively state that a virus sequence derives from the encapsidated form. So the /virion qualifier has been removed from sequence records, and the Feature Table document, as of Release 168.0 . 1.3.11 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 has been corrected, and the definition of the qualifier is now: Qualifier /exception= Definition indicates that the coding region cannot be translated using standard biological rules Value format "RNA editing", "reasons given in citation", "rearrangement required for product" Example /exception="RNA editing" /exception="reasons given in citation" /exception="rearrangement required for product" Comment only to be used to describe biological mechanisms such as RNA editing; where the exception cannot easily be described a published citation must be referred to; protein translation of /exception CDS will be different from the according conceptual translation; - must not be used where transl_except would be adequate, e.g. in case of stop codon completion use: /transl_except=(pos:6883,aa:TERM) /note="TAA stop codon is completed by addition of 3' A residues to mRNA". - must not be used for ribosomal slippage, instead use join operator, e.g.: CDS join(486..1784,1787..4810) /note="ribosomal slip on tttt sequence at 1784..1787" 1.3.12 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. 1.3.13 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 of the GSS flatfiles in Release 168.0. Consider gbgss250.seq : GBGSS1.SEQ Genetic Sequence Data Bank October 15 2008 NCBI-GenBank Flat File Release 168.0 GSS Sequences (Part 1) 87217 loci, 64373883 bases, from 87217 reported sequences Here, the filename and part number in the header is "1", though the file has been renamed as "250" 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=t ree&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. Starting in October 2008, links to the NCBI Trace Assembly Archive will be supported via a line of text in the COMMENT section of sequence records. Here is a mock-up, based on CP000964, to illustrate this 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 be introduced as of 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 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.