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 (Genome Collection)
- To enhance the collaboration with Assembly since 2012, we discussed some practical issues.
The following items were proposed to be applied for Feature Table Definition from the next revision or later.
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.