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 three banks agree with that we are to add some samples for standardized submissions as the contents of the INSDC web site.
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.
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.
A registration system to assign unique IDs for both academic and commercial EST and GSS libraries will be studied.
The three banks agree to use following three keywords in common.
The following items will be applied from October 2007 with the revision of Feature Table Definition, if not otherwise specified.
<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"
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"
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
:[ :]] "
Example: /bio_material="CGC:CB3912" CGC; Caenorhabditis Genetics Center