The Reports for International Collaborators Meetings

2018

31st ICM: May 15-17 2018, Bethesda, USA

International Nucleotide Sequence Database Collaboration (INSDC), consisted of DDBJ Center, EBI and NCBI, hold the international collaborators meeting every year.
In 2018, the meeting was held at NCBI, 15-17 May, to discuss practical matters to maintain and update nucleotide sequence data archives; DDBJENAGenBank and Sequence Read Archive (SRA).
The outcomes of the meeting are summarized below.

The Items; Discussed and To Be Studied

Format expansions for accession numbers and for /protein_id.
By the end of 2018, INSDC will expand the accession number formats as follows;
  • For bulk sequence data, WGS, TSA and TLS, currently using a “4+2+6/7/8” format ( four-letter prefix and two digits for set version followed by six digits), the expanded format will use a six-letter prefix and a two-digit set version number followed by 7, 8, or 9 digits (“6+2+7/8/9” format); for example, AAAAAA020000001.
  • For conventional sequence data, currently using a “2+6” format (two-letter prefix followed by six digits), the format will be expanded to eight digits (“2+8” format).
  • For /protein_id, currently using a “3+5” format (three-letter prefix followed by five digits), the format will be expanded to seven digits (“3+7” format).
International Protein Nomenclature Guidelines are introduced.
INSDC agreed to recommend the international protein nomenclature guidelines to submitters of DDBJ, ENA and GenBank. The guidelines were revised and reorganized from previous guidelines of UniPrott and NCBI by NCBI, EBI, the Protein Information Resource and the Swiss Institute for Bioinformatics. The guidelines are exclusively focused on nomenclature. The future changes of guidelines can be tracked in GitHub.See also NCBI Insights and Inside UniProt.
Increasing metagenomic data
Assembling/analysing methods for metagenomic approaches are progressed and data submissions of them are increased. We discussed to accommodate with metagenomic data. Both BioSample and flatfile will be expanded to deal with minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) as requested by the Genomic Standards Consortium.
See Nat. Biotechnol. 35:725-731 (2017) about MIMAG and MISAG in detail.
Forthcoming changes in The DDBJ/ENA/GenBank Feature Table: Definition
The following items will be applied after October 2018 with the next revision of Feature Table Definition, if not otherwise specified.
Data Access Policy
For COP14 and the Nagoya Protocol
DDBJ reported the results of the Conference of the Parties Convention on Biological Diversity 14 (COP14) for their opinion on whether “digital sequence information” should be included in the Nagoya Protocol. The Science Council of Japan and the International Chamber of Commerce do not favor this action.
We, INSDC, have an existing policy of free and unrestricted access to all of the data records.
For GDPR
In May 2018, the European General Data Protection Regulations (GDPR) have come into force. ENA presented the work and the changes that arise from these with respect to ENA operations.
NGS Quality Scores
Most of SRA storage is taken up by quality scores, however, the sequencing technologies are going to natural progression and precisions of base calling do not impact to assemblies or analyses. Besides, to save storage of users during analyses and to transfer SRA data from submitters and to users more easier, we consider that it is preferable to remove quality scores from SRA data. We would like to discuss about how to accept future NGS data with major research communities including vendors, tool maintainers and users.

2017

30th ICM: May 24-26 2017, Mishima, Japan

International Nucleotide Sequence Database Collaboration (INSDC), consisted of DDBJ, EBI and NCBI, hold the international collaborators meeting every year
In 2017, the meeting was held at DDBJ, 24-26 May, to discuss practical matters to maintain and update nucleotide sequence data archives; DDBJ, ENA, GenBank, Sequence Read Archive (SRA) and Trace Archive.
We also hold a symposium commemorating the 30th anniversary.
The outcomes of the meeting are summarized below.

The Items; Discussed and To Be Studied

Changes for organism names
Unidentified bacteria or fungi
In cases of sequence submissions derived from unidentified bacteria or fungi, we mainly requested to describe organism names (/organism qualifier) in the format, "[genus name] sp. [ID]" (e.g. "Acetobacter sp. ITDI2.1"). For the future submissions, describe in the simple format, "[genus name] sp." (e.g. "Acetobacter sp.").
In this regard, however, for whole genomes or proposing new species, describe organism names in the format, "[genus name] sp. [ID]", ongoingly.
See also here in detail.
Influenza viruses
In cases of sequence submissions derived from influenza viruses, we requested to describe virus names (/organism qualifiers) in the format, "Influenza [A/B/C/D] virus ([strain name]([serotype]))" (e.g. "Influenza A virus (A/chicken/Tokyo/2007(H7N7))").After January 2018, we accept them as "Influenza [A/B/C/D] virus" (e.g. "Influenza A virus").
See also here in detail.
Targeted Locus Study (TLS) data
Since 2016, INSDC has started to accept TLS data.
After discussion about some practical issues at the meeting, DDBJ will start accepting TLS data submission.
Targets of SRA storage
We confirmed each other the ways to accept data accompanied with read sequences, such as BioNano mapping data, methylation, antibiogram and so on.
INSDC annotation
We will start discussion to sort out relationship between annotation using features/qualifiers in INSDC and general format using Sequence Ontology/GFF3.
Assembly (Genome Collection)
To enhance the collaboration with Assembly since 2012, we discussed some practical issues.
Related to this, we confirmed that we should caution during sequence submissions when the sizes of genome sequences were deviated from the closely related species.

Forthcoming Changes in The DDBJ/ENA/GenBank Feature Table: Definition

The following items were proposed to be applied for Feature Table Definition from the next revision.

  • A new qualifier for source feature, /submitter_seqid will be available.
  • Addition of two controlled vocabularies, "scaRNA" and "pre_miRNA", for /ncRNA_class qualifier.
  • Addition of a controlled vocabulary, "contamination", for /gap_type qualifier.
  • Addition of some controlled vocabularies for /type_material qualifier.

2016

29th ICM: May 16-18 2016, Hinxton, UK

International Nucleotide Sequence Database Collaboration (INSDC), consisted of DDBJ, EBI and NCBI, hold the international collaborators meeting every year.
In 2016, the meeting was held at EBI, 16-18 May, to discuss practical matters to maintain and update nucleotide sequence data archives; DDBJ, ENA, GenBank, Sequence Read Archive (SRA) and Trace Archive.
The outcomes of the meeting are summarized below.

The Items; Discussed and To Be Studied

NGS Quality Scores
Currently, 70-80% of SRA storage is for quality scores, however, most of bioinformatic tools do not use them. For the long haul, we, INSDC, prefer to round down (i.e. binning or 8 binning) or to throw away quality scores for inhibition of SRA data increasing. But, the needs for quality scores might be different depending on research areas. We would like to discuss about how to accept future NGS data with major research communities, broadly.
SRA Objects VS BioProject/BioSample
The relationships between SRA study object and BioProject and between SRA sample object and BioSample were considered.
Introduction of Targeted Locus Study (TLS) data
GenBank has started to accept submissions of bulk sequence data including 16S rRNA or some other targeted loci to be clustered into operational taxonomic unit as TLS data with four-letter prefix accession numbers like as WGS.
INSDC Data Status
We discussed practical procedures about data exchange among databanks, especially, INSDC status for bulk data like WGS and TSA and also for SRA, BioProject and BioSample records.
Assembly (Genomic Collection)
To enhance the collaboration with Assembly since 2012, we discussed some practical issues.

Forthcoming Changes in The DDBJ/ENA/GenBank Feature Table: Definition

The following items were proposed to be applied for Feature Table Definition from the next revision or later.

  • For rep_origin feature, the /function qualifier will be available.
  • Expansion of definition of regulatory feature to describe regulation of replication.
  • Addition of some controlled vocabularies for /regulatory_class qualifier.
  • Addition of one feature key and one qualifier key to clarify current descriptions of miscellaneous features.
    • propeptide feature to describe intermediate of peptide maturation
    • /recombination_class qualifier for misc_recomb feature

2015

28th ICM: May 19-21 2015, Bethesda, USA

International Nucleotide Sequence Database Collaboration (INSDC), consisted of DDBJ, EBI and NCBI, hold the international collaborators meeting every year.
In 2015, the meeting was held at NCBI, 19-21 May, to discuss practical matters to maintain and update nucleotide sequence data archives; DDBJ, ENA, GenBank, Sequence Read Archive (SRA) and Trace Archive.
The outcomes of the meeting are summarized below.

The Items; Discussed and To Be Studied

Handling Human Data
Following kind introduction of recent activities at NIH; HeLa access, Genomic Data Sharing (GDS) policy, data analysis on cloud computing and so on, we discussed how to treat data submissions derived from human subjects at each databank.
INSDC Data Status
We discussed practical procedures about data exchange among databanks, especially, INSDC status, replaced data between databanks and suppressed data of SRA.
Assembly (Genomic Collection)
To enhance the collaboration with Assembly since 2012, we discussed some practical issues.
Rapid Growth of SRA Data
To accommodate rapid increase of SRA data, NCBI and EBI introduced their frameworks of data compression; cSRA (compressed SRA) and CRAM, respectively.
We discussed how to apply lossy/lossless compression appropriately.
Misidentification of Species of Microorganism Genomes
Following an academic paper, Federhen S (2015), and GenBank microbial genomic taxonomy workshop (12-13 May 2015), we discussed how to resolve the problem of misidentified genomes.

Forthcoming changes in The DDBJ/EMBL/GenBank Feature Table: Definition

The following items will be applied from October 2015 with the next revision of Feature Table Definition, if not otherwise specified.

  • The definition of unsure feature will be updated to distinguish clearly from sequencing gap.
  • We are discussing to add some terms for controlled vocabulary of /rpt_type qualifier.
    Accompanied with this modification, LTR feature will be merged into repeat_region feature.
  • Since 2013, a new qualifier, /type_material, is considered to specify type strains, type specimens and so on.
    It is not decided in details and officially applicable period of the qualifier at DDBJ.

2014

27th ICM: May 20-22 2014, Mishima, Japan

International Nucleotide Sequence Database Collaboration (INSDC), consisted of DDBJ, EBI and NCBI, hold the international collaborators meeting every year.
In 2014, the meeting was held at DDBJ, 20-22 May, to discuss practical matters to maintain and update nucleotide sequence data archives; DDBJ, ENA, GenBank, Sequence Read Archive (SRA) and Trace Archive.
The outcomes of the meeting are summarized below.

The Items; Discussed and To Be Studied

BioSample database
The BioSample database contains descriptions of biological source materials used in experimental assays.
DDBJ has also started accepting BioSample submissions in early 2014.
Following the meetings on 2012 and 2013, we discussed action items to collect and to share BioSample data at INSDC.
Issues about lots of genome submissions, WGS and so on
Data Exchange
We discussed new data formats and an effective way to exchange data each other.
Assembly (Genomic Collection)
Following the meeting on 2012, we continues collaboration with Assembly activities to collect genome sequences.
About /protein_id
Currently, we have so many submissions of similar genomes derived from multiple strains of a species etc. In those cases, there are many orthologs in CDS features, so, many /protein_ids seem to be redundantly assigned for them. We discussed possibilities about new ways of /protein_id assignment.

Changes in SRA XML schema

SRA XML schema version 2.0 continues to be discussed for refactoring SRA metadata with BioProject and BioSample data.

Forthcoming changes in The DDBJ/EMBL/GenBank Feature Table: Definition

The following items will be applied from October 2014 with the next revision of Feature Table Definition, if not otherwise specified.

  • A new feature, regulatory, and a new qualifier, /regulatory_class, will be available from December 2014.
    Following features will be replaced by the new feature; -35_signal, -10_signal, CAAT_signal, GC_signal, TATA_signal, polyA_signal, attenuator, terminator, promoter, enhancer, RBS.
  • A base code for 'dihydrouridine' of Modified Base Abbreviations and /mod_base qualifier, "d" will be replaced by "dhu".
  • To be sure using prim_transcript and precursor_RNA for RNA transcripts other than mRNA, their definitions will be updated appropriately.
  • Since 2013, a new qualifier, /type_material, is considered to specify type strains, type specimens and so on.
    It is not decided in details and applicable period of the qualifier.

2013

26th: May 21-23 2013, Hinxton, UK

International Nucleotide Sequence Database Collaboration (INSDC), consisted of DDBJ, EBI and NCBI, hold the international collaborators meeting every year.
In 2013, the meeting was held at EBI in UK, 21-23 May, to discuss practical matters to maintain and update nucleotide sequence data archives; DDBJ, EMBL-Bank, GenBank, Sequence Read Archive (SRA) and Trace Archive.
The outcomes of the meeting are summarized below.

The Items; Discussed and To Be Studied

BioSample database
The BioSample database contains descriptions of biological source materials used in experimental assays. The purpose of the BioSample database is to provide unified storage and access to information about biological samples. These samples may have investigation information stored in other databases (e.g. nucleotide sequence, expression).
Following the meeting on 2012, we discussed action items to collect and to share BioSample data at INSDC.
DDBJ started to accept BioSample submissions in 2014.
Strain level taxonomy ID assignment for microorganism genome submission
All organism names that are represented in the sequence data of INSDC are registered to the taxonomy database.
Since 2009, taxonomy database has considered to terminate assignment of strain level taxonomy ID for microorganism genomes.
From 2014, we will provide BioSample data instead of strain level taxonomy ID, and will terminate to assign strain level taxonomy ID for microorganism genomes
We reported in detail about this issue in an academic paper

Changes related to INSDC submission

Relaxation rules to accept WGS and scaffold data
Heretofore, INSDC accepted sequences of overlapping reads (not including any sequencing gaps) as WGS entries and accepted AGP format to indicate scaffolds (including sequencing gaps) as CON entries.
Recently, the policy seemed to be out of date, because some of software tools for genome assemble support to output scaffold only in sequences, not in AGP format. So, we decided to accept sequences of scaffolds with gap n's.
See also INSDC standards for genome assembly submission
Accepting submission of scaffolded TSA data
Recently, paired-end sequencing is fairly common not only for genomes but also for transcriptomes and some of the RNAseq assembly software packages have added scaffolding. So, we started accepting these scaffolded assemblies as TSA records with assembly_gap features and /linkage_evidence="paired-ends" or some.
Update guidelines for TPA submission
Guidelines for TPA submission will be updated to cope with the current status of data submission.See also TPA Submission Guidelines.
Major modification points are follows;
  • 1) TPA is renamed from "Third Party Annotation" to "Third Party Data".
  • 2) Specify to accept not only annotation but also assemble for TPA.
  • 3) A new subcategory, "TPA:specialist_db" will be added in TPA to accept submissions from expert databases.

Changes in SRA XML schema

SRA XML schema version 1.5 has been applied. The modification points are elimination and consolidation of redundant description items.

SRA XML schema version 2.0 continues to be discussed for refactoring SRA metadata with BioProject and BioSample data.

We decided to allow SRA accessions to have variable lengths after 6 digits have been used up, e.g. SRR1000000 would follow SRR999999.

Forthcoming changes in the DDBJ/EMBL/GenBank Feature Table: Definition

The following items will be applied from October 2013 with the revision of Feature Table Definition, if not otherwise specified.

  • It is reconfirmed that 5'UTR and 3'UTR features can be used for RNA viral genome. Their definitions will be updated appropriately
  • It is reconfirmed that 5'UTR and 3'UTR features can be used for RNA viral genome.
    It will be applied from December 2013
    • 1) Time (with time zone): in the ISO standard format
            i.e. "2007-04-05T14:30Z
    • 2) Range: in the format delimited by "/"
            i.e. "2007-03-01T13:00Z/2008-05-11T15:30Z""
  • A new value, "lncRNA", will be legal for /ncRNA_class qualifier.
  • The qualifier, /estimated_length, will be modified to allow different lengths for unknown length gaps.
  • A new qualifier, /type_material, will be considered to specify type strains, type specimens and so on.
    It is not decided in details and applicable period of the qualifier.

2012

25th ICM: June 11-13 2012, Bethesda, USA

International Nucleotide Sequence Database Collaboration (INSDC), consisted of DDBJ, EBI and NCBI, hold the international collaborators meeting every year.
In 2012, the meeting was held at NCBI in USA, 11-13 June, to discuss practical matters to maintain and update nucleotide sequence data archives; DDBJ, EMBL-Bank, GenBank, Sequence Read Archive (SRA) and Trace Archive
The outcomes of the meeting are summarized below.

The Items; Discussed and To Be Studied

BioSample database
The BioSample database contains descriptions of biological source materials used in experimental assays. The purpose of the BioSample database is to provide unified storage and access to information about biological samples. These samples may have investigation information stored in other databases (e.g. nucleotide sequence, expression).
Both EBI and NCBI have already been independently collecting BioSample at NCBI and BioSamples at EBI. Including DDBJ, we discussed how to collect and share BioSample data collaboratively as an INSDC activity.
The format of BioSample accession number is SAM[D|E|N]+ 8 digits; e.g. D=DDBJ; E=EBI; N=NCBI;
for example: SAMD01234567
Strain level taxonomy ID assignment for microorganism genome submission
All organism names that are represented in the sequence data of INSDC are registered to the taxonomy database.
Since 2009, taxonomy database has considered to terminate assignment of strain level taxonomy ID for microorganism genomes.
However, taxonomy database agreed not to stop assigning strain-level taxonomy IDs for prokaryotic strains with sequenced genomes until at least 2013. The change to the current practice will not be made until BioSamples has reached maturity and sample content is exchanged, and so the change may not take place until later in 2013 or beyond.
Genome scale submissions
Both submitters and users require INSDC to collect genome data varied in samples and study goals.
Especially in bulk (re)sequenced cases, INSDC should ask data providers to submit at least one set of assembled/annotated reference genome data, to accept only raw reads to SRA for other genomes with BAM, VCF, GFF in analysis object; i.e. without draft assembles of WGS and scaffold CON data.
While, in cases of genomes sequenced/assembled to finished level, i.e. possibly treated as a reference genome, INSDC should not label 'complete genome' in KEYWORDS for genome data without feature annotation. We should support submitters to annotate their sequences by providing tools and help documents for the minimal standards/requirements
NCBI introduced one of its activities, Assembly (Genome Collection) database. The Genome Collection database has information about the structure of assembled genomes as represented in an AGP file or as a collection of completely sequenced chromosomes. INSDC agreed to collaborate with this activity.

Changes related to INSDC submission

Termination of accepting new submission of MGA data
Since 2004, we have accepted the submission of MGA data. However, along with the popularization of new sequencing platforms, this data model seemed to be out of date. So, we decided to terminate accepting new submission of MGA data. For new submissions, please conact to DDBJ Sequence Read Archive (DRA) and DDBJ Omics Archive (DOR).

Changes in SRA XML schema

SRA XML schema version 1.4 has already been applied for SRA data since July 2012.

SRA XML schema version 1.5 will be applied in the near future. The modification points would be elimination and consolidation of redundant description items.

SRA SRA XML schema version 2.0 continues to be discussed for refactoring SRA metadata with BioProject and BioSample

Forthcoming changes in The DDBJ/EMBL/GenBank Feature Table: Definition

The following items will be applied from October 2012 with the revision of Feature Table Definition, if not otherwise specified.

  • Value format of /anticodon qualifier will be modified to include its sequence.
  • A new value, "pcr", will be legal for /linkage_evidence
  • The /frequency qualifier will be no more legal for source feature.
  • A new /altitude qualifier will be legal for source feature.
  • The controlled vocabularies for qualifier values will be reposited on INSDC web site to revise them more frequent than every 6 months, revision of Feature Table Definition.
  • Since controlled values of /mobile_element_type qualifier are not systematic and could not well cover some instances, INSDC will discuss to improve the controlled values. It will be revised in 2013.
  • To represent nonfunctional genes, /pseudo qualifier will be legal again.
    In ICM2011, INSDC adopted the new qualifier /pseudogene and deprecated the older /pseudo. The use of the /pseudogene qualifier indicates that the feature is a pseudogene of the type listed in the value.

    However, researchers still need to represent nonfunctional genes that are not formally described as pseudogenes. So, INSDC concluded to continue using /pseudo qualifier in parallel to /pseudogene qualifier would allow this.

2011

24th ICM: May 23-27 2011, Osaka, Japan

International Nucleotide Sequence Database Collaboration (INSDC), consisted of DDBJ, EBI and NCBI, hold the international collaborators meeting every year.
In 2011, the meeting was held at Osaka in Japan, 23-27 May, to discuss practical matters to maintain and update nucleotide sequence data archives; DDBJ, EMBL-Bank, GenBank, Sequence Read Archive (SRA) and Trace Archive.
Though there were still aftermaths of the Great East Japan Earthquake, DDBJ could host ICM2011 with understanding and cooperation of NCBI and EBI.
The outcomes of the meeting are summarized below.

The Items; Discussed and To Be Studied

NCBI continues SRA and Trace Archive repositories after October 1, 2011.
Recently, NCBI announced that due to budget constraints, it would be discontinuing its SRA and Trace Archive repositories for high-throughput sequence data. However, NIH has since committed interim funding for SRA in its current form until October 1, 2011. In addition, NCBI has been working with staff from other NIH Institutes and NIH grantees to develop an approach to continue archiving a widely used subset of next generation sequencing data after October 1, 2011.
In addition, NCBI will continue to provide access to existing SRA and Trace Archive data for the foreseeable future. NCBI is also continuing to discuss with NIH Institutes approaches for handling other next-generation sequencing data associated with specific large-scale studies.
BioProject database
Since 2005, INSDC has discussed project ID assignment as a flag to specify not only genomic and metagenomic sequencing projects but also many kinds of biological projects with considerable modifications.
In 2011, the schema of BioProject is introduced. See also DDBJ BioProject Database.
A BioProject is a collection of biological data related to a single initiative, originating from a single organization or from a consortium. A BioProject record provides users a single place to find links to the diverse data types generated for that project.
The format of BioProject accession numbers is PRJ[D|E|N][A-Z]+integer; e.g. D=DDBJ; E=EBI; N=NCBI;
for example: PRJNA38683

Changes related to INSDC submission

INSDC agreed with definitions of its common entry statuses in the following table;
* specific deadlines are available from INSDC partner.
Status name Causes Implications
Public Data are submitted with no request for confidential hold prior to publication or have reached an owner-agreed public release date. Data are fully available
Confidential Data owner requires and indicates to INSDC staff that confidentiality is required until a release date or publication in the literature, whichever comes earlier. Data are not available publicly through any means.

A data release date is recorded for the data, which are subsequently and automatically released as Public on reaching this date or being cited in a publication prior to this date. In the event that a release date must be extended, data owners are required to contact the INSDC partner responsible for the submission with sufficient notice*.
Suppressed
  • (1) Data are found by the owner to be incorrectly annotated or contaminated with no opportunity on the part of the owner to be updated.
  • (2) Data owners realise after sequences have been released that they failed to request a confidential status, either at the time of submission, or within the period between completion of submission processing and the date on which the submission is normally made available to the public (this time period can vary among the INSDC members).
Data are removed where possible from INSDC partner direct search tools (such as text and sequence similarity search) but remain available by accession number.
Replaced Data owners generate new data under new accession identifiers that directly replace existing data; this expected to be rare since replacement data normally use the existing accession identifiers for the records that they replace. Data are removed where possible from INSDC partner direct search tools (such as text and sequence similarity search) but remain available by accession number. Where possible, look-up by original accession identifiers leads to a re-direct to new records available under the new accession identifiers.
Killed
  • (1)The submitter has requested a Confidential status or an extension to an existing release date, but the INSDC partner, or their submissions brokering collaborator, has failed to apply the appropriate release date correctly.
  • (2) Data are found to have been submitted to the databases without the permission of the rightful owner; this is expected to be extremely rare and requires formal institutional contact with the submitting institution.
Data are not directly available publicly from INSDC partners through any means. However, because the data will have been distributed previously as Public, the INSDC partners cannot exercise any control on the resultant use of the data by third parties.
For submissions of CON division, AGP format version 2.0 will be applied from December 2011.

Changes in SRA XML schema

Forthcoming changes in The DDBJ/EMBL/GenBank Feature Table: Definition

  • Two new feature keys, centromere and telomere, will be legal from October 2011.
  • A new feature key, assembly_gap, will be legal from December 2011.
    The feature key is closely related to the modification of AGP format. With version up of AGP format, sequencing gaps of CON records will be described with assembly_gap features; i.e. not gap features.
  • Value format of /anticodon qualifier will be modified on April 2012.
  • Improvement of pseudogene annotation
    As mentioned in ICM2010 report, Prokaryotic Annotation Workshop requested INSDC to improve its pseudogene annotation. Also, to solve a problem of /pseudo qualifier usage in ICM2009, we discussed and decided following modification; A new qualifier key, /pseudogene, will be legal from April 2012, and an old qualifier key, /pseudo, will be no longer accepted in future submissions. The /pseudogene qualifier will be legal for only pseudogenes.
  • Implementation of /whole_replicon was cancelled.
    At ICM2010, we were to flag entries oriented to sequence whole replicon with /whole_replicon qualifier. However, we reconsidered that BioProject records would be more helpful to store representatives of whole genome data. INSDC will include a new item in BioProject records to flag representative data of 'genomic molecule' instead of addition to /whole_replicon qualifier.

    Subsequent to this discussion, INSDC partners agreed to the following definition of the INSDC meaning of 'genomic molecule'

    The submitter of a genomic assembly defines his/her INSDC sequence record as a 'genomic molecule', 
    meaning a chromosome, plasmid or linkage group, when it is the submitter's intention to use 
    that sequence record permanently as that biological molecule and the sequence is the current 
    reasonable model of the biological molecule. Whether the record shows a complete representation 
    of the molecule or not is not necessarily a factor under consideration for this submitter-declared 
    'genomic molecule'."

2010

23rd ICM: May 19-21 2010, Hinxton, UK

International Nucleotide Sequence Database Collaboration (INSDC), consisted of DDBJ, EBI and NCBI, hold the international collaborators meeting every year.
In 2010, the meeting was held at EBI in UK, 19-21 May, to discuss practical matters to maintain and update nucleotide sequence data archives; DDBJ, EMBL-Bank, GenBank, Sequence Read Archive and Trace Archive. As a result of travel disruptions relating to the Icelandic volcano, the meeting was shorter than expected. Despite these difficulties, we believe that we made significant progress at the meeting. The outcomes of the meeting are summarized below.

The Items; Discussed and To Be Studied

Current movements related to sequence data submission and standardized description formats for sampling information
Sampling information for genome scale data
According to the request from Genomic Standards Consortium (GSC), INSDC has discussed to include sampling information of genome scale data in complying with Minimum Information about a (Meta)Genome Sequence (MIGS/MIMS) and Minimum Information about an Environmental Sequence (MIENS) in sequence data records, since 2005
Since 2009, DDBJ, EMBL-Bank and GenBank have been using structured COMMENT/CC lines to describe this kind of extended metadata. However, making reference database for extensible metadata has some advantages; to maintain and to update independently; to reduce redundancy of contents. So, INSDC should consider to provide extensible metadata by some reference database
See also Genomic Standards Consortium on Wikipedia
Minimal submission requirements for INSDC
INSDC will register its minimal submission requirements into Minimum Information for Biological and Biomedical Investigations (MIBBI). MIBBI is a project to synthesize reporting guidelines from various communities into a suite of orthogonal standards.
Prokaryotic Annotation Workshop
Researchers participated Prokaryotic Annotation Workshop, hosted by NCBI, requested to INSDC some modifications for the description rules of features and qualifiers. The requests were mainly from J. Craig Venter Institute (JCVI).INSDC mainly discussed how to cite references for annotated features and a guideline for protein nomenclature for values of /product qualifiers in CDS features.
BioProject database
Since 2005, INSDC has discussed project ID assignment as a flag to specify many kinds of large scale sequencing projects with considerable modifications.
In 2010, the schema for project ID will be largely modified to extend its targets to many kinds of biological data other than nucleotide sequence, such as array, mass spectrometry, and so on. The database was renamed to BioProject database. BioProject database will be provided from NCBI near future.
Strain level taxonomy ID assignment for microorganism genome submission
All organism names that are represented in the sequence data of INSDC are registered to the taxonomy database.
Since 2009, taxonomy database has considered to terminate assignment of strain level taxonomy ID for microorganism genomes. However, since many institutes have already cited those strain level IDs, we will continue to add strain level taxids for prokaryotes at least for one more year.
European Nucleotide Archive (ENA) launched at EBI
From May 2010 at UK, the European Nucleotide Archive (ENA) has been launched, consolidating three major sequence resources in Europe, EMBL Nucleotide Sequence Database (EMBL-Bank), Trace Archive and Sequence Read Archive, to become Europe's primary access point to globally comprehensive nucleotide sequence information.

Names for activities of INSDC

Since 2009, new collaborators have joined to INSDC. So, some INSDC documents about policies and activities should be updated

  • INSDC is the official name for the entirety of the collaboration, including traditional sequence databases (DDBJ, EMBL-Bank and GenBank), the next-gen sequence databases and Trace Archive.
  • We agreed to call the international activities to archive raw sequencing data from next-generation sequencers "Sequence Read Archive". After the agreement, DRA has been renamed from "DDBJ Read Archive" to "DDBJ Sequence Read Archive".
  • The operations of INSDC to archive sequence chromatograms (traces) is named "Trace Archive".

Sequence Read Archive (SRA)

A paper for SRA introduction
We will prepare a joint SRA paper with details about the data model.
Dealing with data from new sequencing platforms
SRA schema will be updated to support new sequencing platforms;
  • Complete Genomics
  • Helicos
  • Pacific BioSciences
  • Ion Torrent

Changes in future revisions of the Feature Table Document: Features and Qualifiers

The following items will be applied from October 2010 with the revision of Feature Table Definition, if not otherwise specified.

  • The conflict feature will be no longer used.
    For data submitted to DDBJ, the conflict feature can be no longer used.
  • Three qualifiers, /codon, /label and /partial will be no longer used.
    For data submitted to DDBJ, the conflict feature can be no longer used.
  • The /gene_synonym qualifier will be legal when either /gene or /locus_tag is used in a feature.
  • The description rule for transposable element will be changed.
    Since 2006, transposable element has been described with repeat_region feature and /mobile_element qualifier. mobile_element feature and /mobile_element_type qualifier will be added and used to describe transposable element.
    This modification will be applied in December 2010.
  • A new qualifier, /whole_replicon, will be legal for source feature.
    To flag entries oriented to sequence whole replicon, we will use /whole_replicon qualifier.
    Time course for this addition has not yet been specified.
  • Improvement of format for /artificial_location qualifier.
    Since 2009, /artificial_location qualifier has been introduced as a valueless qualifier. To classify the reasons of its usages, the qualifier will have either of two controlled values; "heterogenous population sequenced" or "low-quality sequence region".
  • Improvement of formats for /experiment and /inference qualifiers.
    On the basis of requests from Prokaryotic Annotation Workshop, formats for /experiment and /inference qualifiers will be improved mainly to cite its support evidence in a feature.
    • header "COORDINATES", "DESCRIPTION", "EXISTS" による分類
    • description of PubMed ID (PMID) and Digital Object Identifier (DOI) to indicate cited publications
    Examples
                /experiment="COORDINATES: N-terminus verified by Edman degradation
                [PMID: 8096212]"
                /inference="DESCRIPTION: similar to AA sequence: INSDC: AAF23014.2"
    
  • How to improve pseudogene annotation?
    As mentioned above, Prokaryotic Annotation Workshop requested to improve description rules of features and qualifiers. One of their requests is improvement of pseudogene annotation. Also, to solve a problem of /pseudo qualifier usage in ICM2009, we discussed this issue. However, we could not reach any agreement in the meeting, mainly because of difficulties to keep integrity with existing records.
    This issue will be reconsidered.

2009

22nd ICM: May 12-15 2009, Bethesda, USA

International Nucleotide Sequence Database Collaboration (INSDC), the three data banks; DDBJ, EMBL-Bank/EBI, GenBank/NCBI hold the international collaborators meeting every year.
In 2009, the meeting was held at NCBI in USA, 12-13 May.

DDBJ, EMBL-Bank, GenBank reported each bank activities in the last year, discussed practical matters to maintain and update INSDC.

Also, since this year (2009), INSDC has added a coraborative meeting to deal with mass sequence data produced by the next generation sequencers (Short Read Archive) and traces produced by traditional sequencers (Trace Archive).
The first meeting for this collaboration was held at NCBI in USA, 14-15 May 2009.

Short Read Archive
Trace Archive

The outcomes of the two meetings are summarized below.

The Items; Discussed and To Be Studied

Sequence data from the next generation sequencers
As mentioned above, the databases collecting outputs from the next generation sequencers have joined INSDC since 2009.NSDC will request major scientific journals that DRA/ERA/SRA accession numbers for corresponding sequence data should be included in paper submissions.
DDBJ/EMBL-Bank/GenBank reject submissions of EST sequence data produced by 454 sequencers (GS-20, GS-FLX, etc.).In principle, only DRA/ERA/SRA should accept those kinds of EST data.
the database for project ID
Since 2005, INSDC has started to discuss project ID assignment as a flag to specify genome projects, and how to indicate project ID on flat files.
In 2008, INSDC decided to use project ID, not only for genome/metegenome projects, but also many kinds of large scale sequencing projects including transcriptomes.
DDBJ and GenBank indicate project ID at DBLINK line on flat files. EMBL-Bank indicate project IDs in PR line on flat files. For the genome/metagenome projects, we have almostly completed to assign project IDs.
DDBJ/EMBL-Bank/GenBank require to describe project IDs for TSA submissions and thier primary entries
Termination of strain level taxonomy ID assignment for microorganism genome submission
All organism names that are represented in the sequence data of DDBJ/EMBL-Bank/GenBank are registered to the taxonomy database.Taxonomy database assigned strain level taxonomy IDs for whole genome scale submissions of microorganisms, to flag those genome projects.
Since INSDC provided project IDs as a solution to index genome projects, we discussed to terminate assignment of strain level taxonomy ID for microorganism genomes. However, since many institutes have already cited those strain level IDs, we should carefully considrer that the policy change would cause confusion.
Frame mismatched candidates of protein coding regions of high-throughput sequence data
Increasing submissions of large scale draft sequence data, submitters often want to annotate frame mismatched candidates of protein coding regions with CDS features avoiding translation errors by operatively joined location.
To distinguish these kinds of CDS features, we will prepare a new qualifier, /artificial_location qualifier as a flag. In this regard, however DDBJ/EMBL-Bank/GenBank will accept only submissions from whole genome scaleprojects including large scale transcriptomes.
Structured COMMENT/CC line to capture metadata
Recently, GenBank started to use structured COMMENT approach to capture metadata related to a biological sample that has been sequenced.
The concept behind structured COMMENT is to provide submitters with a mechanism that allows them to supply a set of tag/value data elements that currently are not supported by the Feature Table.
DDBJ/EMBL-Bank/GenBank will discuss the format of structured COMMENT/CC line to use it in a formalized way.

Changes to the Feature Table Document: Features and Qualifiers

The following items will be applied from October 2009 with the revision of Feature Table Definition, if not otherwise specified.

  • Should /pseudo qualifier be renamed?

    "The word "pseudo" is likely to be associated with "pseudogene" but it is used for both putative pseudogenes and non-functional forms, so, the /pseudo qualifier should be separated and/or renamed to reflect their actual usages.
    This issue will be reconsidered.

  • The value, "annotated by transcript or proteomic data", will be legal for /exception qualifier
  • A new qualifier, /haplogroup, will be legal for source feature.
  • For the /strain qualifier, it is no more legal to describe multiple equivalent names.

    Previously (before May 2009), DDBJ accepted the sequence data with description of multiple-names in a /strain qualifier;

          /strain="ATCC #### (= JCM ### = NBRC ###)"

    To describe equivalent strain names, appropriate usage of /note qualifier is recommended.

          /note="strain coidentity: JCM ### = NBRC ###"
          /strain="ATCC ####"
  • A new qualifier, /artificial_location, will be legal for CDS and mRNA features, as mentioned above.

    The modification will be applied in December 2009.

  • Improvement of the format of /inference qualifier

    In order to describe inferential supports more effectively, format /inference qualifier will be improved.
    The discussion has been continued since 2008.

2008

21st ICM: May 20-22 2008, Mishima, Japan

International Nucleotide Sequence Database Collaboration (INSDC), the three data banks; DDBJ, EMBL-Bank/EBI, GenBank/NCBI hold the international collaborators meeting every year.
In 2008, the meeting was held at DDBJ in Japan, 20-22 May.

DDBJ, EMBL-Bank, GenBank reported each bank activities in the last year, discussed some practical matters to maintain and develop INSDC.

The Items; Discussed and To Be Studied

A new division, TSA (Transcriptome Shotgun Assembly)
From June 2008, INSDC introduce a new division for assembled mRNA sequences, TSA. Note that it is required that the TSA submission with the original sequence data of primary transcripts is classified into the EST division of INSDC, Trace Archive, or Short Read Archive. More information about how to submit the TSA entry will be provided via DDBJ website.
Sequence data from next generation sequencing
In principle, raw reads from next generation sequencing should be registered to Short Read Archive. Following the workshop on MINSEQE (Minimal Information about a High Throughput Sequencing Experiment), data from next generation sequencing not initially intended for INSD submissions might result in discoveries of variation or re-annotation that could be submitted to INSDC as TPA or TSA entries. The number of TPA entries is not expected to grow rapidly.
Representative submissions of identical sequences for variation studies
INSDC basically accept all sequence data, regardless of source and sequence identity. However, in order to take advantage of normalisation for variation studies, a single submission to represent multiple identical sequences is also acceptable with frequency and total sample number described by /frequency qualifier of source feature.
Removal of the frag for electronic publication, "(er)", in REFERENCE/JOURNAL lines
The electronic publication token in REFERENCE/JOURNAL lines, "(er)", will be removed. Old records will be retrofitted to conventional article citations where possible.

Changes to the Feature Table Document: Features and Qualifiers

The following items will be applied from October 2008 with the revision of Feature Table Definition, if not otherwise specified.

  • Modification of controlled vocabulary for /mol_type qualifier

    The /mol_type qualifier is used to indicate in vivo, synthetic or hypothetical molecule type in source feature. The vocabrary list for /mol_type qualifier will be modified as follows;

    • Addition: "transcribed RNA"
    • Removal: "snoRNA", "snRNA", "scRNA", "pre-RNA" and "tmRNA"
  • The value, "chromatophore", will be legal for /organelle qualifier
  • Modification of controlled vocabulary for /ncRNA_class qualifier

    The ncRNA feature utilizes a /ncRNA_class qualifier with a controlled vocabulary to indicate what type of non-protein-coding feature is being represented. The list for controlled vocabulary of /ncRNA_class qualifier will be modified as follows;

    • Addition: "6S/SsrS", "SraD RNA", "DsrA RNA", "SroC", "ribozyme"

    See also Controlled vocabulary for ncRNA classes.

  • A new qualifier, /satellite, will be legal for repeat_region feature.

    Format "<satellite_type>[:<class>][ <identifier>]"
       where satellite_type is one of the following;
       "satellite", "microsatellite", "minisatellite"

    Example
             /satellite="satellite: S1a"
             /satellite="satellite: gamma III"
             /satellite="minisatellite"
             /satellite="microsatellite: DC130"
  • Improvement of the format of the /frequency qualifier

    In order to represent a sample size, following descriptions will also be legal for the value formats of the /frequency qualifier in addition to decimal fractions;
    "[m] in [n]" or "[m] / [n]".

    Example
             /frequency="23/108"
             /frequency="1 in 12"
  • /specific_host qualifier will become /host qualifier.

    Both /host and /lab_host should be described with a binominal scientific name, if possible.

    Example
             /lab_host="Gallus gallus"
             /lab_host="Gallus gallus embryo"
             /lab_host="Escherichia coli strain DH5 alpha"
             /lab_host="Homo sapiens HeLa cells"
  • Removal of /virion qualifier

    Note: The /proviral qualifier will remain in use.

  • Removal of /cons_splice qualifier
  • Improvement of validation for both /rearranged and /germline qualifiers

    Basically, both /rearranged and /germline qualifiers should be used to indicate if the sequence has undergone somatic rearrangement as part of an adaptive immune response or not. However, since many of them have been wrongly used, we will correct them.

  • A new qualifier, /gene_synonym, will be legal for features that can use /gene qualifier.

    We also expect further minor changes in the usage of /gene qualifier. Details of changes will be made available shortly

  • Improvement of the format of /inference qualifier

    In order to describe inferential supports more effectively, format /inference qualifier will be improved. Details of changes will be made available shortly

  • A new qualifier, /mating_type, will be legal for source feature.

    The /sex qualifier will also remain in use. Guidelines of descriptions for both /mating_type and /sex will be made available shortly.

2007

20th ICM: May 21-23 2007, Hinxton, UK

International Nucleotide Sequence Database Collaboration (INSDC), the three data banks; DDBJ, EMBL-Bank/EBI, GenBank/NCBI hold the international collaborators meeting every year.
In 2007, the meeting was held at EMBL-Bank/EBI in UK, 21-23 May.

DDBJ, EMBL-Bank, GenBank reported each bank activities in the last year, discussed practical matters to maintain and to update INSDC. The outcomes of the meeting are summarized below.

The Items; Discussed and To Be Studied

INSDC web site
The three banks agree with that we are to add some samples for standardized submissions as the contents of the INSDC web site
Alternative assemblies
With large amount of reads of draft sequences available in the public, scientists are asking if they can submit assemblies of the reads to INSDC. We need to develop a policy for who can submit alternative assemblies and what we would do with the data once it is submitted i.e. would we start a TPA -like database for alternative assemblies? Three banks would ask to the advisors meeting.
GSC and MIGS
The Genomic Standards Consortium (GSC) is to support the community-based development of a standard datasets of information about complete genomes and metagenomic ones. It is currently working together towards the 'Minimal Information about a Genome Sequence(MIGS)' specification. Overall, the three banks agreed that a cooperative approach to GSC activities was preferred over a competitive approach.
EST/GSS clone library ID
A registration system to assign unique IDs for both academic and commercial EST and GSS libraries will be studied.
Controlled vocabulary in KEYWORDS line
The three banks agree to use following three keywords in common.
  • Two terms to describe the direction and location of EST
    "5'-end sequence (5'-EST)"
    "3'-end sequence (3'-EST)"
  • A term to indicate an entry belonging to a full length insert cDNA project
    "FLI_CDNA"

Changes to the Feature Table Document: Features and Qualifiers

The following items will be applied from October 2007 with the revision of Feature Table Definition, if not otherwise specified.

  • New ncRNA feature

    A variety of new types of RNA transcripts, "miRNA", "siRNA", and so on, have been introduced in recent years. Because the number of non protein coding RNA families is quite likely to continue to expand, a new ncRNA feature that can flexibly accommodate them will be introduced.
    Furthermore, snRNA, snoRNA, and scRNA features are merged into ncRNA feature by December 2007.

  • New /ncRNA_class qualifier

    The new feature, ncRNA, will utilize a new qualifier called /ncRNA_class, with a controlled vocabulary to indicate what type of non-protein-coding feature is being represented

    Format:  /ncRNA_class="<ncRNA_class_TYPE>"
    Example: /ncRNA_class="miRNA"
    <ncRNA_class_TYPE> should be selected from the following list;

    antisense_RNA", "autocatalytically_spliced_intron", "telomerase_RNA", 
    "hammerhead_ribozyme", "RNase_P_RNA", "RNase_MRP_RNA", "guide_RNA", 
    "rasiRNA", "scRNA", "siRNA", "miRNA", "snoRNA", "snRNA", "SRP_RNA", 
    "vault_RNA", "Y_RNA", "other" 
  • New tmRNA feature

    To support a class of RNA transcripts that have dual tRNA-like and mRNA-like behaviors, a new tmRNA feature will belegal. See tmRDB that provide some background information about the tmRNAs.

  • New /tag_peptide qualifier

    To indicate the nucleotide region encoding the proteolysis tag peptide of tmRNA, a new qualifier, /tag_peptide, will be used for the tmRNA feature.

    Format: /tag_peptide=<base_range>
    Example: /tag_peptide=90..122

  • "tmRNA" is added to the specified values for the /mol_type qualifier that indicates molecule type of the sequence in vivo on the source feature.
  • The value of /specimen_voucher qualifier will be become structured, consisting of an institution code, a collection code, and a specimen identifier, as well as the existing unstructured values.

    Format:
          /specimen_voucher="[<institution_code>:[<collection_code>:]]<specimen_id>"
          There are three forms of specimen_voucher qualifiers; 
          <specimen_id>
          <institution_code>:<specimen_id>
          <institution_code>:<collection_code>:<specimen_id>

    If the value of includes one or more colons, ":", it is 'structured'. Structured vouchers include institution_codes (and optional collection_codes) taken from a controlled vocabulary that denote the museum or herbarium collection where the specimen resides

    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"
  • The two new qualifiers, /culture_collection and /bio_material, will be legal for the source feature.

    These qualifiers will utilize the same format as /specimen_voucher.
    culture_collection; Institution code and identifier for the culture from which the nucleic acid sequenced was obtained.

    Format: 
            /culture_collection="<institution_code>:[<collection_code>:]<culture_id>"
    Example: 
            /culture_collection="ATCC:26370"

    bio_material; Identifier for the biological material from which the nucleic acid sequenced was obtained

    Format:  
            /bio_material="[<institution_code>:[<collection_code&'gt;:]]<material_id>"
    
    Example: 
            /bio_material="CGC:CB3912" 
                CGC; Caenorhabditis Genetics Center
  • The feature, old_sequence will be illegal for new entries.
  • At DDBJ, the two features, repeat_unit and satellite, will be illegal for new entries

    Both repeat_unit and satellite features will be merged into repeat_reigon feature.

  • The two features, 5'clip and 3'clip will be no longer used.
  • The /organism qualifier will be no longer used for misc_recomb.
  • The /operon qualifier will be legal on the protein_bind feature.
  • The term, "alignment", will be legal for [TYPE] of the /inference qualifier

2006

19th ICM: May 15-17 2006, Bethesda, USA

International Nucleotide Sequence Database Collaboration (INSDC), the three data banks; DDBJ, EMBL-Bank/EBI, GenBank/NCBI hold the international collaborators meeting every year.
In 2006, the meeting was held at GenBank in Bethesda, Maryland, USA, 15-17 May.

DDBJ, EMBL-Bank and GenBank reported each bank activities in the last year, discussed practical matters to maintain and to update INSDC.
The outcomes of the meeting are summarized below.

The Items; Discussed and To Be Studied

No restriction for using INSDC data
INSDC confirmed that we should not accept any submissions with restrictions in free public access.
Non-submission of data to INSDC
There are sequence and annotation data, although published, but not available at INSD. We will be in touch with authors and editors to remind them of the importance of submitting sequences and annotation to the databases.
INSDC homepage
Since 2005, INSDC has made public its web site; //www.insdc.org/.The three banks agreed with that we are to add more contents for the web site.
INSDSeq-XML
Since 2003, we have discussed the schema of this common XML description named INSDSeq-XML. Since 2005, three banks have trially exchanged data in INSDSeq-XML format. Thoroughly reviewing of the trial, we discussed some improvement of INSDSeq-XML to provide it as common XML description among three banks.
locus_tag
Since 2003, the /locus_tag qualifier has been used as the identifier for the tracking purpose by many genome projects. In the past, we allowed submitters to use the flexible prefixes for their locus_tag. Since 2005, to keep uniquness through INSDC, we have disccused to manage and to assign prefixes of locus_tag.The framework to assign the locus_tag prefixes will be available in the near future

Changes to the Feature Table Document: Features and Qualifiers

  • New amino acid abbreviations, "J" and "O"

    1) Pyl (O); Pyrrolysine
    The 22nd naturally encoded amino acid, pyrrolysine was discovered.
    The JCBN IUBMB-IUPAC (the Joint Commission on Biochemical Nomenclature of IUBMB and IUPAC) has agreed that Pyl (the three-letter abbreviation), O (the one-letter abbreviation) will be recommended for this amino acid.
    2) Xle (J); Leucine or Isoleucine
    The residue abbreviations, Xle (the three-letter abbreviation) and J (the one-letter abbreviation) are reserved for the case that cannot experimentally distinguish leucine from isoleucine.
    So, we are to add the following abbreviations;
    Abbreviation 1 letter abbreviation Amino acid name
    Xle J Leucine or Isoleucine
    Pyl O Pyrrolysine
    INSDC will use "J" and "O" for the amino acid sequences of /translation qualifiers in CDS features.
  • Two old qualifiers, /transposon and /insertion_seq, will be integrated into a new qualifier, /mobile_element. The qualifier will be legal on only repeat_region feature as below;

    Format:
              /mobile_element="<mobile_element_type>[:<mobile_element_name>]"
    Example:
              /mobile_element="transposon:Tnp9"

    The specified value for <mobile_element_type> is either of followings;

    • transposon
    • retrotransposon
    • integron
    • insertion sequence
    • non-LTR retrotransposon
    • SINE
    • MITE
    • LINE
    • other
  • "viral cRNA" is added to the specified values for the qualifier, /mol_type that indicates molecule type of the sequence in vivo on the source feature.

    Definition of "viral cRNA"
    cRNA is a plus-strand copy of a minus strand RNA genome which serves as a template to make viral progeny genomes

  • The /operon qualifier will be legal on rRNA feature.
  • /EC_number should be more controlled.

    Furthermore, we will accept the symbol "n" (initial of "new") to indicate that the code is not available now and will be assigned later.

  • For the values of /PCR_primers qualifier, modified base codes.

    Modified base codes (i.e. "i"; inosine) are required to be described with enclosing in the brackets; "<" and ">" for the values of /PCR_primers.

    Example:
              /PCR_primer="fwd_name; hoge1, fwd_seq;cgkgtgtatcttact
              rev_name; hoge2, rev_seq;cg<i>gtgtatcttact"
  • The rules for the description of location will be slightly changed.

    The use of range "(m.n)" descriptor will be discontinued.

2005

18th ICM: May 16-18 2005, Mishima, Japan

To operate and implement the collaborative construction of the international nucleotide sequence database, the three data banks; DDBJ, EMBL-Bank/EBI, GenBank/NCBI hold the international collaborators meeting every year.In 2005, the meeting was held at DDBJ in Mishima, 16-18 May.

DDBJ, EMBL-Bank, GenBank reported each databank activities in the last year, discussed practical matters to maintain and to update the nucleotide sequence database. The outcomes of the meeting are summarized below.

The Items; Discussed and To Be Studied

The international nucleotide sequence database constructed by the collaboration among DDBJ, EMBL-Bank and GenBank was agreed to be calledINSDC; International Nucleotide Sequence Database Collaboration. INSDC has made public its web site; //www.insdc.org/

Since 2003, we have discussed the format of INSDSeq-XML.DDBJ has made the trial data in INSDSeq-XML format available at its FTP site and its retrival tool, getentry, in advance of EMBL-Bank and GenBank

Since 2004, we have accepted the submission of MGA data. We reconsidered the rules for acceptance and the format for distribution.

Since 2002, we have accepted TPA submission. In the past, some biological evidence was required for the TPA submission. Now, we are planning to accept the inferred sequences by non-experimental evidence. We will continue to discuss the guideline for acceptance and classification of TPA submissions.

Since 2003, the /locus_tag qualifier has been used as the identifier for the tracking purpose by many genome projects. In the past, we allowed submitters to use the flexible prefixes for their locus_tag. However, since we are afraid that it would cause some disruption in the future, we will manage and assign prefixes of locus_tag to keep uniquness through the whole database. In association with it, we will improve our flat file format to include the project ID that can be utilized to specify the project (mainly for genome projects).

Relating to their strandness and partiality, rRNA sequences are not consistently annotated in the database. It was agreed that we should check them,and also that the same preference for plus stranded annotation should be applied to other single feature.

Changes to the Feature Table Document: Features and Qualifiers

For features, especially CDS, the database users demand the information if the feature description is based on some biological experiment or only inference based on sequence similarity or so.
To make the evidence information available, evidence qualifier will be split into two new qualifiers, /experiment and /inference;

a) An argument of the feature based on some biological experiment
  •      instead of /evidence=experimental
  • /experiment="free text" (less than 1000 letters)
b) An argument of the feature not based on any biological experiment
  •     instead of /evidence=not_experimental
  • /inference="[TYPE]( same species):[evidence basis]"
  • The values of [TYPE] will be controlled by the list.
- note -
The old qualifier, /evidence=experimental or not_experimental, will be replaced by folowings, respectively;
  • /experiment="experimental evidence, no additional details recorded"
  • /inference="non-experimental evidence, no additional details recorded"

Recently, the number of the entries for the research of environmental sampling and divergence of the life (e.g. the BARCODE project) is significantly increased. For these submission, it is important to describe the information on specification of the specimen from which the sequence is obtained. So, five new qualifiers will become legal on the source feature;

  • /collection_date="DD MMM YYYY", "MMM YYYY" or "YYYY"
    • DD ; two-digit for the date,
    • MMM ; three letter for the month abbreviation
    • YYYY; four-digit for the year
  • /lat_lon="###.## [N or S], ###.## [E or W]"
  • /collected_by="[Name of the person who collected the specimen.]""
  • /identified_by="[Name of the person who identified the specimen.]"
  • /PCR_primers="fwd_name:[name],fwd_seq:[sequence],rev_name:[name], rev_seq:[sequence]"

The /pseudo qualifier will be legal on intron and misc_RNA features.

The /rpt_unit qualifier will be split into two new qualifiers; /rpt_unit_range and /rpt_unit_seq will be introduced.

Two new qualifiers, /ribosomal_slippage and /trans_splicing will be valid on the CDS feature.

"hydrogenosome" will be added to the list of legal values for the /organelle qualifier.

Changes to Other Items

The rules for the description of location will be changed;

Combinations of "join" and "order" operators in one location will be illegal.

The use of two identical location construction operators within one location will be illegal.
     i.e. "100..100" will be illegal.

The usage of "^" will be restricted to adjacent nucleotides
     i.e. "100^200" will be illegal.

The use of range (m.n) descriptor within location spans will be illegal.
     i.e. "(5.10)..100" will be illegal.