The international nucleotide sequence database collaboration

Karsch-Mizrachi, Ilene; Takagi, Toshihisa; Cochrane, Guy

doi:10.1093/nar/gkx1097

Cited by 157 publications

(85 citation statements)

References 18 publications

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“…5.4.6;Gene Codes Corp.). Taxonomy was assigned by closest hits after manual BLAST runs against International Nucleotide Sequence Database** Collaboration (INSDC; http://www.insdc.org/ (Karsch-Mizrachi et al, 2018) and UNITE (Kõljalg et al, 2013). A representative sequence of each 99% OTU was submitted to GenBank (Supporting Information Table S3).…”

Section: Cultivation Of Soil Fungi From In-growth Mbsmentioning

confidence: 99%

Emerging from the ice‐fungal communities are diverse and dynamic in earliest soil developmental stages of a receding glacier

Dresch

Falbesoner

Ennemoser

et al. 2019

Environmental Microbiology

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SummaryWe used amplicon sequencing and isolation of fungi from in‐growth mesh bags to identify active fungi in three earliest stages of soil development (SSD) at a glacier forefield (0–3, 9–14, 18–25 years after retreat of glacial ice). Soil organic matter and nutrient concentrations were extremely low, but the fungal diversity was high [220 operational taxonomic units (OTUs)/138 cultivated OTUs]. A clear successional trend was observed along SSDs, and species richness increased with time. Distinct changes in fungal community composition occurred with the advent of vascular plants. Fungal communities of recently deglaciated soil are most distinctive and rather similar to communities typical for cryoconite or ice. This indicates melting water as an important inoculum for native soil. Moreover, distinct seasonal differences were detected in fungal communities. Some fungal taxa, especially of the class Microbotryomycetes, showed a clear preference for winter and early SSD. Our results provide insight into new facets regarding the ecology of fungal taxa, for example, by showing that many fungal taxa might have an alternative, saprobial lifestyle in snow‐covered, as supposed for a few biotrophic plant pathogens of class Pucciniomycetes. The isolated fungi include a high proportion of unknown species, which can be formally described and used for experimental approaches.

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Section: Cultivation Of Soil Fungi From In-growth Mbsmentioning

confidence: 99%

Emerging from the ice‐fungal communities are diverse and dynamic in earliest soil developmental stages of a receding glacier

Dresch

Falbesoner

Ennemoser

et al. 2019

Environmental Microbiology

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“…It should be obvious, then, that input and extraction of information from such diverse data collections will lead to widely different pathways to discovery. An inconspicuous but immense (ongoing) effort in this domain is undertaken by all participants of the INSDC (Karsch‐Mizrachi et al ., ), who endeavour to set up data structures in order to collect and make freely available nucleotide data sequences described in scientific articles, patents or deposited directly at one of its three entry points (DDBJ, ENA, GenBank). An important point here is that how data is structured has a far‐reaching impact on data annotation quality.…”

Section: Data Structuresmentioning

confidence: 99%

“…Their condition was that all molecular information would become publicly available so that data sharing would automatically feed into the collection process (Roberts and Koetzle, ; Blaxter et al ., ). After a long series of discussions and efforts, this resulted in the establishment of the International Nucleotide Sequence Database Collaboration [INSDC (Karsch‐Mizrachi et al ., )], exchanging and updating sequences on a daily basis between three entry points, DDBJ in Japan (Kodama et al ., ), ENA in Europe (Silvester et al ., ) and GenBank in the United States (Benson et al ., ).…”

Section: Introductionmentioning

confidence: 99%

No wisdom in the crowd: genome annotation in the era of big data – current status and future prospects

Danchin

Ouzounis

Tokuyasu

et al. 2018

Microbial Biotechnology

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SummaryScience and engineering rely on the accumulation and dissemination of knowledge to make discoveries and create new designs. Discovery‐driven genome research rests on knowledge passed on via gene annotations. In response to the deluge of sequencing big data, standard annotation practice employs automated procedures that rely on majority rules. We argue this hinders progress through the generation and propagation of errors, leading investigators into blind alleys. More subtly, this inductive process discourages the discovery of novelty, which remains essential in biological research and reflects the nature of biology itself. Annotation systems, rather than being repositories of facts, should be tools that support multiple modes of inference. By combining deduction, induction and abduction, investigators can generate hypotheses when accurate knowledge is extracted from model databases. A key stance is to depart from ‘the sequence tells the structure tells the function’ fallacy, placing function first. We illustrate our approach with examples of critical or unexpected pathways, using MicroScope to demonstrate how tools can be implemented following the principles we advocate. We end with a challenge to the reader.

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“…Unlike the International Nucleotide Sequence Database [4], these two databases for gene expression have not been exchanging data with each other. AE once had imported data from GEO, but stopped importing data in 2017 (https://www.ebi.ac.uk/arrayexpress/help/GEO_data.html).…”

Section: Introductionmentioning

confidence: 99%

All of gene expression (AOE): an integrated index for public gene expression databases

Bono

2019

Preprint

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Gene expression data have been archived as microarray and RNA-seq datasets in two public databases, Gene Expression Omnibus (GEO) and ArrayExpress (AE). In 2018, the DNA DataBank of Japan started a similar repository called the Genomic Expression Archive (GEA). These databases are useful resources for the functional interpretation of genes, but have been separately maintained and may lack RNA-seq data, while the original sequence data are available in the Sequence Read Archive (SRA).We constructed an index for those gene expression data repositories, called All Of gene Expression (AOE), to integrate publicly available gene expression data. The web interface of AOE can graphically query data in addition to the application programming interface. By collecting gene expression data from RNA-seq in the SRA, AOE also includes data not included in GEO and AE.AOE is accessible as a search tool from the GEA website and is freely available at https://aoe.dbcls.jp/.

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The international nucleotide sequence database collaboration

Cited by 157 publications

References 18 publications

Emerging from the ice‐fungal communities are diverse and dynamic in earliest soil developmental stages of a receding glacier

Emerging from the ice‐fungal communities are diverse and dynamic in earliest soil developmental stages of a receding glacier

No wisdom in the crowd: genome annotation in the era of big data – current status and future prospects

All of gene expression (AOE): an integrated index for public gene expression databases

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