International Nucleotide Sequence Database Collaboration
Encyclopedia
The International Nucleotide Sequence Database Collaboration (INSDC, http://insdc.org) consists of a joint effort to collect and disseminate database
s containing DNA
and RNA
sequences. It involves the following computerized database
s: DNA Data Bank of Japan
(Japan
), GenBank
(USA) and the EMBL (European Molecular Biology Laboratory
, Germany
). 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.
The DDBJ/EMBL/GenBank
synchronization is maintained according to a number of guidelines which are produced and published by an International Advisory Board http://insdc.org/page.php?page=advisors. The guidelines consist of a common definition of the feature
tables http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html for the databases, which regulate the content and syntax
http://www.ebi.ac.uk/embl/Documentation/DTD/INSDSeq_v1.3.dtd.txt of the database entries, in the form of a common DTD
or 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 http://www.ebi.ac.uk/cgi-bin/dbfetch?X56734 a DBFetch operation shows a typical INSD entry at the EBI database; the same entry at NCBI is here http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=21954.
Database
A database is an organized collection of data for one or more purposes, usually in digital form. The data are typically organized to model relevant aspects of reality , in a way that supports processes requiring this information...
s containing DNA
DNA
Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...
and RNA
RNA
Ribonucleic acid , or RNA, is one of the three major macromolecules that are essential for all known forms of life....
sequences. It involves the following computerized database
Database
A database is an organized collection of data for one or more purposes, usually in digital form. The data are typically organized to model relevant aspects of reality , in a way that supports processes requiring this information...
s: DNA Data Bank of Japan
DNA Data Bank of Japan
The DNA Data Bank of Japan is a biological database that collects DNA sequences. It is located at the National Institute of Genetics in the Shizuoka prefecture of Japan. It is also a member of the International Nucleotide Sequence Database Collaboration or INSDC...
(Japan
Japan
Japan is an island nation in East Asia. Located in the Pacific Ocean, it lies to the east of the Sea of Japan, China, North Korea, South Korea and Russia, stretching from the Sea of Okhotsk in the north to the East China Sea and Taiwan in the south...
), GenBank
GenBank
The GenBank sequence database is an open access, annotated collection of all publicly available nucleotide sequences and their protein translations. This database is produced and maintained by the National Center for Biotechnology Information as part of the International Nucleotide Sequence...
(USA) and the EMBL (European Molecular Biology Laboratory
European Molecular Biology Laboratory
The European Molecular Biology Laboratory is a molecular biology research institution supported by 20 European countries and Australia as associate member state. EMBL was created in 1974 and is an intergovernmental organisation funded by public research money from its member states...
, Germany
Germany
Germany , officially the Federal Republic of Germany , is a federal parliamentary republic in Europe. The country consists of 16 states while the capital and largest city is Berlin. Germany covers an area of 357,021 km2 and has a largely temperate seasonal climate...
). New and updated data on nucleotide
Nucleotide
Nucleotides are molecules that, when joined together, make up the structural units of RNA and DNA. In addition, nucleotides participate in cellular signaling , and are incorporated into important cofactors of enzymatic reactions...
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.
The DDBJ/EMBL/GenBank
GenBank
The GenBank sequence database is an open access, annotated collection of all publicly available nucleotide sequences and their protein translations. This database is produced and maintained by the National Center for Biotechnology Information as part of the International Nucleotide Sequence...
synchronization is maintained according to a number of guidelines which are produced and published by an International Advisory Board http://insdc.org/page.php?page=advisors. The guidelines consist of a common definition of the feature
Feature
A feature is a distinct property or piece, which may refer to:- Science and technology :* Feature is an intentional distinguishing characteristic of a software item ....
tables http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html for the databases, which regulate the content and syntax
Syntax
In linguistics, syntax is the study of the principles and rules for constructing phrases and sentences in natural languages....
http://www.ebi.ac.uk/embl/Documentation/DTD/INSDSeq_v1.3.dtd.txt of the database entries, in the form of a common DTD
Document Type Definition
Document Type Definition is a set of markup declarations that define a document type for SGML-family markup languages...
or Document Type Definition.
The syntax is called INSDSeq and its core consists of the letter sequence of the gene expression
Gene expression
Gene expression is the process by which information from a gene is used in the synthesis of a functional gene product. These products are often proteins, but in non-protein coding genes such as ribosomal RNA , transfer RNA or small nuclear RNA genes, the product is a functional RNA...
(amino acid
Amino acid
Amino acids are molecules containing an amine group, a carboxylic acid group and a side-chain that varies between different amino acids. The key elements of an amino acid are carbon, hydrogen, oxygen, and nitrogen...
sequence) and the letter sequence for nucleotide
Nucleotide
Nucleotides are molecules that, when joined together, make up the structural units of RNA and DNA. In addition, nucleotides participate in cellular signaling , and are incorporated into important cofactors of enzymatic reactions...
bases in the gene or decoded segment. In http://www.ebi.ac.uk/cgi-bin/dbfetch?X56734 a DBFetch operation shows a typical INSD entry at the EBI database; the same entry at NCBI is here http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=21954.
See also
- National Center for Biotechnology InformationNational Center for Biotechnology InformationThe National Center for Biotechnology Information is part of the United States National Library of Medicine , a branch of the National Institutes of Health. The NCBI is located in Bethesda, Maryland and was founded in 1988 through legislation sponsored by Senator Claude Pepper...
- Biological databaseBiological databaseBiological databases are libraries of life sciences information, collected from scientific experiments, published literature, high-throughput experiment technology, and computational analyses. They contain information from research areas including genomics, proteomics, metabolomics, microarray...
- Sequence databaseSequence databaseIn the field of bioinformatics, a sequence database is a large collection of computerized nucleic acid sequences, protein sequences, or other sequences stored on a computer...
- BioinformaticsBioinformaticsBioinformatics is the application of computer science and information technology to the field of biology and medicine. Bioinformatics deals with algorithms, databases and information systems, web technologies, artificial intelligence and soft computing, information and computation theory, software...
- DNA Data Bank of JapanDNA Data Bank of JapanThe DNA Data Bank of Japan is a biological database that collects DNA sequences. It is located at the National Institute of Genetics in the Shizuoka prefecture of Japan. It is also a member of the International Nucleotide Sequence Database Collaboration or INSDC...