28th: 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.