INSD sequence record XML

Abbreviation: INSDSeq

General Information

The International Nucleotide Sequence Database Collaboration (INSDC) is a long-standing foundational initiative that operates between DDBJ, EMBL-EBI and NCBI. INSDC covers the spectrum of data raw reads, though alignments and assemblies to functional annotation, enriched with contextual information relating to samples and experimental configurations. The INSDSeq is the official supported XML format of the International Nucleotide Sequence Database Collaboration (INSDC). The current production version of the XML is INSDSeq v1.5.

Homepage http://www.insdc.org/documents/xml-status

Developed in China , France , Greece , Japan , United Kingdom , United States

Created in 1988

Taxonomic range

All

Knowledge Domains BETA

Subjects BETA

How to cite this record FAIRsharing.org: INSDSeq; INSD sequence record XML; DOI: https://doi.org/10.25504/FAIRsharing.tn873z; Last edited: Jan. 15, 2019, 1:59 p.m.; Last accessed: Mar 25 2019 6:16 p.m.

Record updated: Jan. 15, 2019, 1:58 p.m. by The FAIRsharing Team.

Show edit history

Edits to 'https://fairsharing.org/FAIRsharing.tn873z' by 'The FAIRsharing Team' at 13:58, 15 Jan 2019 (approved):

	'organizations' has been modified:
		Before:
			National Center for Biotechnology Information (NCBI), Rockville, MD, USA|http://www.ncbi.nlm.nih.gov/|Maintains
			National Institute of Genetics (NIG), Shizuoka, Japan|https://www.nig.ac.jp/nig/|Maintains
			Swiss Institute of Bioinformatics (SIB), Switzerland|https://www.sib.swiss|Maintains
			European Commission under FP7 Grant Agreement|http://ec.europa.eu/research/fp7/index_en.cfm?pg=documents|Undefined
		After:
			National Center for Biotechnology Information (NCBI), Rockville, MD, USA|http://www.ncbi.nlm.nih.gov/|Maintains
			National Institute of Genetics (NIG), Shizuoka, Japan|https://www.nig.ac.jp/nig/|Maintains
			European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, UK|https://www.ebi.ac.uk/|Maintains
			European Commission under FP7 Grant Agreement|http://ec.europa.eu/research/fp7/index_en.cfm?pg=documents|Funds
		Added:
			European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, UK|https://www.ebi.ac.uk/|Maintains
			European Commission under FP7 Grant Agreement|http://ec.europa.eu/research/fp7/index_en.cfm?pg=documents|Funds
		Removed:
			Swiss Institute of Bioinformatics (SIB), Switzerland|https://www.sib.swiss|Maintains
			European Commission under FP7 Grant Agreement|http://ec.europa.eu/research/fp7/index_en.cfm?pg=documents|Undefined

	'supportLinks' has been modified:
		Before:
			online documentation|http://www.insdc.org/documents
			online documentation|http://science.sciencemag.org/content/298/5597/1333.2
		After:
			online documentation|http://www.insdc.org/documents
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		Removed:
			online documentation|http://science.sciencemag.org/content/298/5597/1333.2

	'description' has been modified:
		Before: The International Nucleotide Sequence Database Collaboration (INSDC) is a long-standing foundational initiative that operates between DDBJ, EMBL-EBI and NCBI. INSDC covers the spectrum of data raw reads, though alignments and assemblies to functional annotation, enriched with contextual information relating to samples and experimental configurations.
		After: The International Nucleotide Sequence Database Collaboration (INSDC) is a long-standing foundational initiative that operates between DDBJ, EMBL-EBI and NCBI. INSDC covers the spectrum of data raw reads, though alignments and assemblies to functional annotation, enriched with contextual information relating to samples and experimental configurations. The INSDSeq is the official supported XML format of the International Nucleotide Sequence Database Collaboration (INSDC). The current production version of the XML is INSDSeq v1.5.

	'licences' has been modified:
		Before:
			EBI Terms of Use|http://www.ebi.ac.uk/about/terms-of-use|Data
			INSDC Data Policy|http://www.insdc.org/policy|Data
		After:
			EBI Terms of Use|http://www.ebi.ac.uk/about/terms-of-use|Data
			International Nucleotide Sequence Database Collaboration Policy|http://www.insdc.org/policy.html|Data
		Added:
			International Nucleotide Sequence Database Collaboration Policy|http://www.insdc.org/policy.html|Data
		Removed:
			INSDC Data Policy|http://www.insdc.org/policy|Data

	'dataProcesses' has been modified:
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			Download INSDSeq XML v1.5 DTD (in DOCX file)
		Added:
			Download INSDSeq XML v1.5 DTD (in DOCX file)
		Removed:

	'publications' has been modified:
		Before:
		After:
			Reminder to deposit DNA sequences.|Blaxter M,Danchin A,Savakis B,Fukami-Kobayashi K,Kurokawa K,Sugano S,Roberts RJ,Salzberg SL,Wu CI|Science|2016
			Databases: Reminder to deposit DNA sequences.|Salzberg SL|Nature|2016
		Added:
			Reminder to deposit DNA sequences.|Blaxter M,Danchin A,Savakis B,Fukami-Kobayashi K,Kurokawa K,Sugano S,Roberts RJ,Salzberg SL,Wu CI|Science|2016
			Databases: Reminder to deposit DNA sequences.|Salzberg SL|Nature|2016
		Removed:

Edits to 'https://fairsharing.org/FAIRsharing.tn873z' by 'The FAIRsharing Team' at 13:53, 21 May 2018 (approved):

	'homepage' has been modified:
		Before: http://www.insdc.org
		After: http://www.insdc.org/documents/xml-status

Edits to 'https://fairsharing.org/FAIRsharing.tn873z' by 'The FAIRsharing Team' at 20:09, 26 Nov 2016 (approved):

	'homepage' has been modified:
		Before: http://www.ebi.ac.uk/embl/Documentation/DTD/INSDSeq_v1.3.dtd.txt
		After: http://www.insdc.org

Edits to 'https://fairsharing.org/FAIRsharing.tn873z' by 'The FAIRsharing Team' at 16:43, 20 Oct 2016 (approved):

	'shortname' has been modified:
		Before: ISND sequence record XML
		After:

Support

General

online documentation

INSDC Documents

Tools

No tools defined

Schemas

No XSD schemas defined

Access / Retrieve Data

Conditions of Use

Applies to: Data use

Data Access

Download INSDSeq XML v1.5 DTD (in DOCX file)

http://www.insdc.org/sites/insdc.org/files/documents/INSD_v1.5.dtd.doc ...

Publications

Reminder to deposit DNA sequences.

Blaxter M,Danchin A,Savakis B,Fukami-Kobayashi K,Kurokawa K,Sugano S,Roberts RJ,Salzberg SL,Wu CI
Science 2016

View Paper (PubMed) View Publication

Databases: Reminder to deposit DNA sequences.

Salzberg SL
Nature 2016

View Paper (PubMed) View Publication

Related Standards

Reporting Guidelines

No guidelines defined

Terminology Artifacts

No semantic standards defined

Models and Formats

Extensible Markup Language

Identifier Schemas

No identifier schema standards defined

Metrics

No metrics standards defined

Implementing Databases (4)

GenBank
GenBank is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences. GenBank is part of the International Nucleotide Sequence Database Collaboration, which comprises the DNA DataBank of Japan (DDBJ), the European Molecular Biology Laboratory (EMBL), and GenBank at NCBI. These three organizations exchange data on a daily basis. The complete release notes for the current version of GenBank are available on the NCBI ftp site. A new release is made every two months. GenBank growth statistics for both the traditional GenBank divisions and the WGS division are available from each release.

DNA Data Bank of Japan
Annotated collection of all publicly available nucleotide and protein sequences. In Japan, Bioinformation and DDBJ Center internationally contributes as a member of INSDC to collect and to provide nucleotide sequence data with ENA/EBI in Europe and NCBI in USA. DDBJ collects sequence data mainly from Japanese researchers, as well as researchers in any other countries.

European Nucleotide Archive
The European Nucleotide Archive (ENA) is a globally comprehensive data resource for nucleotide sequence, spanning raw data, alignments and assemblies, functional and taxonomic annotation and rich contextual data relating to sequenced samples and experimental design. Serving both as the database of record for the output of the world's sequencing activity and as a platform for the management, sharing and publication of sequence data, the ENA provides a portfolio of services for submission, data management, search and retrieval across web and programmatic interfaces. The ENA is part of the International Nucleotide Sequence Database Collaboration.

Bacterial Diversity Metadatabase
BacDive—the Bacterial Diversity Metadatabase merges detailed strain-linked information on the different aspects of bacterial and archaeal biodiversity. BacDive contains entries for over 63,000 strains and provides information on their taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.

Implementing Policies

This record is not implemented by any policy.

Credit

Record Maintainer

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Funds

European Commission under FP7 Grant Agreement (Government body)

Maintains

National Center for Biotechnology Information (NCBI), Rockville, MD, USA (Research institute)
National Institute of Genetics (NIG), Shizuoka, Japan (Government body)
European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, UK (Research institute)

INSD sequence record XML

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