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35th INSDC meeting report: May 23-27 2022, teleconference

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  • 35th INSDC meeting report: May 23-27 2022, teleconference

35th INSDC meeting report: May 23-27 2022, teleconference

International Nucleotide Sequence Database Collaboration (INSDC), consisted of DDBJ Center, EBI and NCBI, hold the international meeting every year.
In 2022, the meeting was to be held at NCBI. However, because of the influence of COVID-19, the meeting was held 23-27 May on a teleconference, to discuss practical matters to maintain and update nucleotide sequence data archives; DDBJ, ENA, GenBank, Sequence Read Archive (SRA), BioProject and BioSample.
The outcomes of the meeting are summarized below.

The Items Discussed and To Be Studied

For the INSDC operation

  • The status document was revised.
  • We discussed the challenges that will arise when migrating data to the cloud in the future.
    The strategies would be required non-reliance on a specific vendor, data kept at two or more sites, and so on.
  • The design of the INSDC site is improved.

SARS-CoV-2 Sequence Data Sharing

We consider that sharing sequence data related to SARS-CoV-2 is one of the most important task for INSDC.
We discussed some technical issues to accept SARS-CoV-2 sequences.
Continuing discussions in 2020 and 2021, we are encouraging the scientific communities to submit their SARS-CoV-2 sequences to INSDC databases.
We strongly recommend submitters of viral data provide following items

  • /isolate qualifier with the identifier in the recommended format by the International Committee on Taxonomy of Viruses
    See The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2
  • /host qualifier
  • /collection_date qualifier
  • /country qualifier

Verification for large scale data

NCBI introduced the following tools:

  • Foreign Contamination Screen (FCS)
  • Human read removal tool (HRRT)
  • SRA SARS-CoV-2 Detection Tool

Forthcoming Changes in The DDBJ/ENA/GenBank Feature Table Definition

  • Two new controlled vocabularies for /type_material qualifier will be introduced, “not verified as type” and “not considered type”, that are not so usually used.
  • By the end of 2022, we are planning to require that all new submissions include /country and /collection_date qualifiers for each entry.
    We are investigating operational issues for that.
    See Spatio-temporal annotation policy (18-11-2021).