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 [suppre/insdc/insdc-status-e#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.
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
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.