From cavanaug from ncbi.nlm.nih.gov Fri Oct 26 14:15:50 2007 From: cavanaug from ncbi.nlm.nih.gov (Cavanaugh, Mark (NIH/NLM/NCBI) [E]) Date: Fri Oct 26 14:16:02 2007 Subject: [Genbank-bb] GenBank 162.0 Close-of-Data Message-ID: <7F40ACD22B0A23448C4E8755E5875FE70E017ACB@NIHCESMLBX8.nih.gov> Greetings GenBank Users, Close-of-data for the upcoming GenBank Release 162.0 occurred on Friday October 19th at approximately 1:30am EDT. The subsequently generated GenBank Incremental Update files nc1019.aso, nc1019.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 162.0 release files, even though they are "post-close" . Our apologies for the lack of advanced notice about the close date. An initial attempt to send this announcement on Sunday, October 21 appears to have failed. Mark Cavanaugh GenBank NCBI/NLM/NIH/HHS From cavanaug from ncbi.nlm.nih.gov Fri Oct 26 23:54:18 2007 From: cavanaug from ncbi.nlm.nih.gov (Mark Cavanaugh) Date: Fri Oct 26 23:54:27 2007 Subject: [Genbank-bb] GenBank Release 162.0 Now Available Message-ID: <200710270454.l9R4sI9A020339@hyperion.ncbi.nlm.nih.gov> Greetings GenBank Users, GenBank Release 162.0 is now available via FTP from the National Center for Biotechnology Information (NCBI): Ftp Site Directory Contents ---------------- --------- --------------------------------------- ftp.ncbi.nih.gov genbank GenBank Release 162.0 flatfiles ncbi-asn1 ASN.1 data used to create Release 162.0 Close-of-data for GenBank 162.0 occured on 10/19/2007. Uncompressed, the Release 162.0 flatfiles require roughly 305 GB (sequence files only) or 325 GB (including the 'short directory', 'index' and the *.txt files). The ASN.1 data require approximately 281 GB. Recent statistics for non-WGS, non-CON sequences: Release Date Base Pairs Entries 161 Aug 2007 79525559650 76146236 162 Oct 2007 81563399765 77632813 Recent statistics for WGS sequences: Release Date Base Pairs Entries 161 Aug 2007 101964323738 25384475 162 Oct 2007 102003045298 25354041 During the 66 days between the close dates for GenBank Releases 161.0 and 162.0, the non-WGS/non-CON portion of GenBank grew by 2,037,840,115 basepairs and by 1,486,577 sequence records. During that same period, 608,147 records were updated. An average of about 31,738 non-WGS records were added and/or updated per day. Between releases 161.0 and 162.0, the WGS portion of GenBank grew by 38,721,560 basepairs and the number of sequence records declined by 30,434 . 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 162.0 and Upcoming Changes) have been appended below. ** Important Note ** GenBank 'index' files are now provided without any EST content, and without most GSS content. See Section 1.3.9 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 162.0 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 2007, 162.0). 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 162.0, 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 162.0 1.3.1 Sequences moved from SYN division to GSS division Due to a timing problem in the deployment of a software change, 264,607 GSS (Genome Survey Sequence) sequences were mistakenly included in the SYN-division sequence files for GenBank Release 161.0 . The GSS sequences involved are labelled with a /transgenic qualifier on their source features (see EF711103 for an example). The presence of that qualifier normally indicates that the SYN division is the most appropriate place for a record. But this is not the case for GSS records. Although a software change was made to accomodate transgenic GSS records on July 2, the flatfiles had already been generated and stored in the database that is used to build GenBank releases. Hence they were dumped to the SYN-division files for August's Release 161.0. We have resolved this problem for Release 162.0, and as a result, the number of SYN-division sequence files has decreased from five back to two. All the records involved are now in the GSS-division sequence files. Our thanks to the informatics group at The Jackson Laboratory for reporting this problem. 1.3.2 CON division organizational changes As mentioned in the release notes for GenBank 161.0, procedures for processing the ASN.1 version of CON ('constructed') division records have been updated such that a much larger number (119) of smaller (approximately 260MB) gbcon*.aso files are now generated. This change parallels a similar change which was made for the processing of CON division flatfiles (gbcon*.seq) for Release 161.0. For further details, please see the GenBank 161.0 release notes: ftp://ftp.ncbi.nih.gov/genbank/release.notes/gb161.release.notes 1.3.3 Organizational changes The total number of sequence data files increased by 25 with this release: - the BCT division is now comprised of 25 files (+1) - the CON division is now comprised of 83 files (+1) - the ENV division is now comprised of 7 files (+1) - the EST division is now comprised of 649 files (+14) - the GSS division is now comprised of 269 files (+5) - the HTG division is now comprised of 102 files (+4) - the MAM division is now comprised of 4 files (+1) - the PAT division is now comprised of 31 files (+1) - the SYN division is now comprised of 2 files (-3) (See Section 1.3.1) The total number of index files increased by 1 with this release: - the AUT (Author Name) index is now comprised of 48 files (+1) 1.3.4 Structured /specimen_voucher qualifiers As of October 2007, the content of the /specimen_voucher qualifier can support a structured value consisting of an institution code, a collection code, and a specimen identifier, as well as the existing unstructured values. Here is the new definition of the qualifier: Qualifier /specimen_voucher= Definition identifier for the specimen from which the nucleic acid sequenced was obtained Value format /specimen_voucher="[:[:]]" Example /specimen_voucher="UAM:Mamm:52179" /specimen_voucher="AMCC:101706" /specimen_voucher="USNM:field series 8798" /specimen_voucher="personal collection:Dan Janzen:99-SRNP-2003" /specimen_voucher="99-SRNP-2003" Comment the /specimen_voucher qualifier is intended to annotate a reference to the physical specimen that remains after the sequence has been obtained; if the specimen was destroyed in the process of sequencing, electronic images (e-vouchers) are an adequate substitute for a physical voucher specimen; ideally the specimens will be deposited in a curated museum, herbarium, or frozen tissue collection, but often they will remain in a personal or laboratory collection for some time before they are deposited in a curated collection; there are three forms of specimen_voucher qualifiers; if the text of the qualifier includes one or more colons it is a 'structured voucher'; structured vouchers include institution-codes (and optional collection-codes) taken from a controlled vocabulary that denotes the museum or herbarium collection where the specimen resides; 1.3.5 /operon qualifiers for protein_bind features Due to an oversight, the /operon qualifier was not listed as a legal qualifier for the protein_bind feature. This has been corrected as of October 2007, with an update to the Feature Table document which includes the qualifier among those that are legal for protein_bind. 1.3.6 Alignment as EVIDENCE_BASIS for the /inference qualifier Several algorithms exist which allow mRNAs to be aligned to genomic sequence, taking into account introns and splice signals. In order to document the use of such algorithms for the structured /inference qualifier, a new class of EVIDENCE_BASIS will be introduced: alignment This addition to the controlled vocabulary of the /inference qualifier is legal as of this October 2007 release. 1.3.7 New ncRNA feature A variety of new types of RNA features have been introduced in recent years. snRNA, snoRNA, and scRNA are some examples. Because the number of non-coding RNA families is quite likely to continue to expand, a new ncRNA feature has been created, so that they can be accomodated more flexibly. This new feature utilizes a new qualifier called /ncRNA_class, with a controlled vocabulary to indicate what type of non-coding RNA is being represented. Here are the definitions of the ncRNA feature and /ncRNA_class : Feature Key ncRNA Definition a non-protein-coding gene, other than ribosomal RNA and transfer RNA, the functional molecule of which is the RNA transcript; Mandatory qualifiers /ncRNA_class="TYPE" Optional qualifiers /allele="text" /citation=[number] /db_xref=":" /experiment="text" /function="text" /gene="text" /inference="TYPE[ (same species)][:EVIDENCE_BASIS]" /label=feature_label /locus_tag="text" (single token) /map="text" /note="text" /old_locus_tag="text" (single token) /product="text" /pseudo /standard_name="text" /trans_splicing /operon="text" Comment the ncRNA feature is not used for ribosomal and transfer RNA annotation, for which the rRNA and tRNA feature keys should be used, respectively; Qualifier /ncRNA_class= Definition a structured description of the classification of the non-coding RNA described by the ncRNA parent key Value format "TYPE" Example /ncRNA_class="miRNA" /ncRNA_class="siRNA" /ncRNA_class="scRNA" Comment TYPE is a term taken from the INSDC controlled vocabulary for ncRNA classes; on 15-Oct-2007, the following terms were valid: "antisense_RNA" "autocatalytically_spliced_intron" "hammerhead_ribozyme" "RNase_P_RNA" "RNase_MRP_RNA" "telomerase_RNA" "guide_RNA" "rasiRNA" "scRNA" "siRNA" "miRNA" "piRNA" "snoRNA" "snRNA" "SRP_RNA" "vault_RNA" "Y_RNA" "other" ncRNA classes not yet in the INSDC /ncRNA_class controlled vocabulary can be annotated by entering '/ncRNA_class="other"' with '/note="[brief explanation of novel ncRNA_class]"'; 1.3.8 /organism no longer to be used for misc_recomb The /organism qualifier had been legal for misc_recomb features. But a review of the existing cases in the database indicated that all could be better annotated through the use of multiple source features. That work was completed in October 2007, and at this point the /organism qualifier is no longer allowed for the misc_recomb feature key. 1.3.9 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. 1.3.10 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 from 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 forty-eight of the GSS flatfiles in Release 162.0. Consider gbgss222.seq : GBGSS1.SEQ Genetic Sequence Data Bank October 15 2007 NCBI-GenBank Flat File Release 162.0 GSS Sequences (Part 1) 86842 loci, 64244408 bases, from 86842 reported sequences Here, the filename and part number in the header is "1", though the file has been renamed as "222" 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 New /culture_collection and /bio_material qualifiers As of the December 2007 GenBank release, new qualifiers /culture_collection and /bio_material qualifiers will be legal for the source feature. These qualifiers will utilize the same format as /speciment_voucher (see Section 1.4.1 of these release notes). Their preliminary definitions are: Qualifier /culture_collection= Definition institution code and identifier for the culture from which the nucleic acid sequenced was obtained, with optional collection code. Value format ":[:]" Example /culture_collection="ATCC:26370" Comment the /culture_collection qualifier should be used to annotate live microbial and viral cultures, and cell lines that have been deposited in curated culture collections; microbial cultures in personal or laboratory collections should be annotated in strain qualifiers; annotation with a culture_collection qualifier implies that the sequence was obtained from a sample retrieved (by the submitter or a collaborator) from the indicated culture collection, or that the sequence was obtained from a sample that was deposited (by the submitter or a collaborator) in the indicated culture collection; annotation with more than one culture_collection qualifier indicates that the sequence was obtained from a sample that was deposited (by the submitter or a collaborator) in more than one culture collection. culture_id and institution_code are mandatory, collection_code is optional; the /culture_collection qualifier becomes legal on 15-Dec-2007; Qualifier /bio_material= Definition identifier for the biological material from which the nucleic acid sequenced was obtained, with optional institution code and collection code for the place where it is currently stored. Value format "[:[:]]" Example /bio_material="CGC:CB3912" <- Caenorhabditis stock centre Comment the bio_material qualifier should be used to annotate the identifiers of material in biological collections that are not appropriate to annotate as either /specimen_voucher or /culture_collection; these include zoos and aquaria, stock centres, seed banks, germplasm repositories and DNA banks; material_id is mandatory, institution_code and collection_code are optional; institution code is mandatory where collection code is present; the /bio_material qualifier becomes legal on 15-Dec-2007; 1.4.2 New tmRNA feature and /peptide_tag qualifier To support the annotation of a class of RNAs that have dual tRNA-like and mRNA-like behaviors, a new tmRNA feature will be legal for the Feature Table as of December 2007. The "tmRNA Website" at Indiana University provides some background information about the unusual biology of tmRNAs : http://www.indiana.edu/~tmrna/ Here is the definition of the new tmRNA feature: Feature Key tmRNA Definition transfer messenger RNA; tmRNA acts as a tRNA first, and then as an mRNA that encodes a peptide tag; the ribosome translates this mRNA region of tmRNA and attaches the encoded peptide tag to the C-terminus of the unfinished protein; this attached tag targets the protein for destruction or proteolysis; Optional qualifiers /allele="text" /citation=[number] /db_xref=":" /experiment="text" /function="text" /gene="text" /inference="TYPE[ (same species)][:EVIDENCE_BASIS]" /label=feature_label /locus_tag="text" (single token) /map="text" /note="text" /old_locus_tag="text" (single token) /product="text" /pseudo /standard_name="text" /tag_peptide= Comment the tmRNA feature key will become valid on 15-Dec-2007 To indicate the nucleotide region encoding the proteolysis tag peptide, a new /tag_peptide qualifier will be introduced for use with the tmRNA feature. The definition of /tag_peptide is: Qualifier /tag_peptide= Definition base location encoding the polypeptide for proteolysis tag of tmRNA and its termination codon; Value format Example /tag_peptide=90..122 Comment it is recommended that the amino acid sequence corresponding to the /tag_peptide be annotated by describing a 5' partial CDS feature; e.g. CDS <90..122; the /tag_peptide qualifier (and tmRNA feature) will become valid on 15-Dec-2007