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.
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.