The International Nucleotide Sequence Database Collaboration

By Guy Cochrane, Ilene Karsch-Mizrachi, Yasukazu Nakamura. Nucleic Acids Res., 2010

685 citations recorded by the source corpus.

Under the International Nucleotide Sequence Database Collaboration (INSDC; http://www.insdc.org), globally comprehensive public domain nucleotide sequence is captured, preserved and presented. The partners of this long-standing collaboration work closely together to provide data formats and conventions that enable consistent data submission to their databases and support regular data exchange around the globe. Clearly defined policy and governance in relation to free access to data and relationships with journal publishers have positioned INSDC databases as a key provider of the scientific record and a core foundation for the global bioinformatics data infrastructure. While growth in sequence data volumes comes no longer as a surprise to INSDC partners, the uptake of next-generation sequencing technology by mainstream science that we have witnessed in recent years brings a step-change to growth, necessarily making a clear mark on INSDC strategy. In this article, we introduce the INSDC, outline data growth patterns and comment on the challenges of increased growth.

Subfields: Cancer Research, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/fe134631e96a8937b1cc93952e895d882c536655

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Citations in the corpus

Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2022 (2021, background): “Additionally, we keep paying efforts to build close collaborations with INSDC (International Nucleotide Sequence Database Collaboration) (51), as testified by the open sharing of SARS-CoV-2 genome data with NCBI.”
The SILVA ribosomal RNA gene database project: improved data processing and web-based tools (2012, methodology): “Consequently, vast amounts of rRNA gene sequence data—more than 3.5 million sequences (July 2012)—have been accumulated and are publicly available via the International Nucleotide Sequence Database Collaboration (INSDC) databases (1).”
Five simple guidelines for establishing basic authenticity and reliability of newly generated fungal ITS sequences. (2012, background): “…authors have spent significant time pursuing compromised ITS sequences in the International Nucleotide Sequence Databases (INSD: GenBank, ENA, and DDBJ; Karsch-Mizrachi et al. 2012) and UNITE (Abarenkov et al. 2010a; http://unite.ut.ee) or have worked with sequence reliability in other respects.”
RefSeq microbial genomes database: new representation and annotation strategy (2013, background): “Genomic sequences (nucleotide) in prokaryotic RefSeqs are identical copies of the underlying primary INSDC records (5).”
A review of methods and databases for metagenomic classification and assembly (2019, methodology): “Every sequence deposited within an INSDC database has a taxon identifier based on species information provided by the depositor.”
Ensembl Genomes 2016: more genomes, more complexity (2015, methodology): “Previously, we reported (18) the introduction of a new procedure to automatically update Ensembl Bacteria with all annotated genome sequence present in the archives of the International Nucleotide Sequence Database Collaboration (19).”
RefSeq: an update on mammalian reference sequences (2013, background): “A gene may be represented by transcript, protein or genomic RefSeqs (with an NM, NR, NP or NG accession prefix, hereafter referred to as ‘known’ RefSeqs) generated by automatic and manual processing of public sequence data maintained by members of the International Nucleotide Sequence Database Conso”
MGnify: the microbiome analysis resource in 2020 (2019, positive): “Our ambition is to ensure that all of the assemblies generated by MGnify are submitted into the ENA, in line with our data policy that all sequence datasets we analyse must be appropriately archived within INSDC.”
Improving ITS sequence data for identification of plant pathogenic fungi (2014, background): “…:K. Abarenkov (*) Natural History Museum, University of Tartu, Vanemuise 46, Tartu 51014, Estonia e-mail: kessy.abarenkov@ut.ee GenBank, ENA, and DDBJ; Nakamura et al. 2013) for fungal ITS sequences and offers extensive capacities for analysis and third-party annotation of sequences to its users.”
Ensembl core software resources: storage and programmatic access for DNA sequence and genome annotation (2016, background): “The ‘assembly’ table defines a hierarchy of sequence regions: any sequence region can be decomposed into component sequence regions much like an AGP file (https://www.ncbi.nlm.nih.gov/as sembly/agp/AGP_Specification/) or a record from the INSDC CON division (21).”
BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata (2011, background): “The NCBI and International Nucleotide Sequence Database Collaboration (INSDC) (1) archival databases hosting these data include GenBank (2), SRA (3), GEO (4), Epigenomics (5), dbSNP (6), dbVar (7) and dbGaP (8).”