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International Nucleotide Sequence Database Collaboration

Topic: Biology

 From HandWiki - Reading time: 5 min

The International Nucleotide Sequence Database Collaboration (INSDC) consists of a joint effort to collect and disseminate databases containing DNA and RNA sequences.[1] It involves the following computerized databases: NIG's DNA Data Bank of Japan (Japan ), NCBI's GenBank (United States ) and the EMBL-EBI's European Nucleotide Archive (EMBL). New and updated data on nucleotide sequences contributed by research teams to each of the three databases are synchronized on a daily basis through continuous interaction between the staff at each the collaborating organizations.

All of the data in INSDC is available for free and unrestricted access, for any purpose, with no restrictions on analysis, redistribution, or re-publication of the data. This policy has been a foundational principle of the INSDC since its inception.[2] The official policy statement can be found at http://www.insdc.org/.[3] Since the 1990s, most of the world's major scientific journals have required that sequence data be deposited in an INSDC database as a pre-condition for publication.

The DDBJ/EMBL-EBI/GenBank synchronization is maintained according to a number of guidelines which are produced and published by an International Advisory Board.[4] The guidelines consist of a common definition of the feature tables [5] for the databases, which regulate the content and syntax of the database entries,[6] in the form of a common DTD (Document Type Definition).

The syntax is called INSDSeq and its core consists of the letter sequence of the gene expression (amino acid sequence) and the letter sequence for nucleotide bases in the gene or decoded segment. In a DBFetch operation shows a typical INSD entry at the EMBL-EBI database;[7] the same entry at NCBI.[8]

See also

References

  1. ↑ Karsch-Mizrachi, I.; Nakamura, Y.; Cochrane, G.; International Nucleotide Sequence Database Collaboration (2011). "The International Nucleotide Sequence Database Collaboration". Nucleic Acids Research 40 (Database issue): D33–D37. doi:10.1093/nar/gkr1006. PMID 22080546. 
  2. ↑ Brunak, Soren; Danchin, Antoine; Hattori, Masahira; Nakamura, Haruki; Shinozaki, Kazuo; Matise, Tara; Preuss, Daphne (15 November 2002). "Nucleotide sequence database policies". Science 298 (5597): 1333. doi:10.1126/science.298.5597.1333b. ISSN 1095-9203. PMID 12436968. https://pubmed.ncbi.nlm.nih.gov/12436968/. 
  3. ↑ "insdc.org". http://www.insdc.org/. 
  4. ↑ "INSDC :: Advisors". http://www.insdc.org/page.php?page=advisors. 
  5. ↑ "The DDBJ/ENA/GenBank Feature Table Definition". Ebi.ac.uk. http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html. 
  6. ↑ "European Nucleotide Archive < EMBL-EBI". https://www.ebi.ac.uk/ena. 
  7. ↑ "Database Browsing". http://www.ebi.ac.uk/cgi-bin/dbfetch?X56734. 
  8. ↑ USA (2019-05-06). "Trifolium repens mRNA for non-cyanogenic beta-glucosidase - Nucleotide - NCBI". Ncbi.nlm.nih.gov. https://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=21954. 



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