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The European Nucleotide Archive in 2017
2017
Nucleic Acids Research
Preserved Fulltext
For 35 years the European Nucleotide Archive (ENA; https://www.ebi.ac.uk/ena) has been responsible for making the world's public sequencing data available to the scientific community. ...
Here, we outline ENA services and content in 2017 and provide insight into a selection of current key areas of development in ENA driven by challenges arising from the above growth. ...
European Nucleotide Archive (ENA), maintained at the EMBL European Bioinformatics Institute (EMBL-EBI). ...
doi:10.1093/nar/gkx1125
pmid:29140475
pmcid:PMC5753375
fatcat:s2q7ka7s5nbufi7gnztodzyzym
C# desktop application with connection to the European Nucleotide Archive for fast identification of tandem repeats
2017
Advanced Studies in Biology
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This application works both with randomly provided content and real samples retrieved from the European Nucleotide Archive. ...
In order to facilitate the process of computational detection and analysis of tandem repeats in large DNA samples, a desktop application in C# was developed. ...
This study was supported by the research project Development of Secure and Reliable Techniques for Data Communication, funded by ,,Goce Delcev" University in Stip. ...
doi:10.12988/asb.2017.7926
fatcat:wn5easr3kbhgpdyli5lfhblkda
GlobalFungi: Global database of fungal records from high-throughput-sequencing metabarcoding studies
[article]
2020
bioRxiv
pre-print
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The high importance of fungi in the ecosystem processes contrasts with the incompleteness of understanding of the patterns of fungal biogeography and the environmental factors that drive it. ...
To close this gap of knowledge, we have here collected and validated data published on the composition of soil fungal communities in terrestrial environments including soil and plant-associated habitats ...
All corresponding authors of published studies that provided additional information on the samples included in the database are gratefully acknowledged. ...
doi:10.1101/2020.04.24.060384
fatcat:xg2234ejdvdcjhbdw53rueuszm
On The Way To Realising The Full Potential Of Pids In Biosciences: Thor Work At Embl-Ebi
2017
Zenodo
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EMBL-EBI -THOR participants Genes, genomes & variation European Nucleotide Archive Ensembl European Variation Archive Ensembl European Genome-phenome Archive Genomes Gene, protein & metabolite expression ...
• Part of the European Molecular Biology Laboratory, an intergovernmental research organisation • International: 570 members of staff from 57 nations • Home of the ELIXIR Technical hub Data resources at ...
doi:10.5281/zenodo.1064003
fatcat:liejbob3m5ggvmwrdnzsfmud6i
OUP accepted manuscript
2017
Nucleic Acids Research
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In this article, we reiterate the principles of the INSDC collaboration and briefly summarize the trends of the archival content. ...
Since 1987, the DNA Health in Bethesda, Maryland, USA have worked collaboratively to enable access to nucleotide sequence data in standardized formats for the worldwide scientific community. ...
The collaboration consists of three nodes: DNA Data Bank of Japan (DDBJ: http://www.ddbj. nig.ac.jp/) in Mishima, Japan (2); European Nucleotide Archive (ENA: http://www.ebi.ac.uk/ena/) in Hinxton, UK ...
doi:10.1093/nar/gkx1097
pmid:29190397
pmcid:PMC5753279
fatcat:aujil64o3zbkvpfa233kpi5pva
Streamlined Conversion of Omics Metadata into Manuscript Facilitates Publishing and Reuse of Omics Data
2020
Biodiversity Information Science and Standards
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The workflow streamlines automatic conversion and import of metadata from the European Nucleotide Archive (ENA) into an omics data paper manuscript created in the ARPHA Writing Tool (AWT), following a ...
three step procedure: mapping of the European Nucleotide Archive (ENA) metadata to the manuscript sections, extraction of the relevant metadata through the ENA project or study ID, and transforming the ...
This research has received partial funding from the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 764840. ...
doi:10.3897/biss.4.59041
fatcat:nfef2u26eng2tpj4suij3u3hjy
Draft genome of Bordetella pseudohinzii BH370 isolated from trachea and lung tissues of a laboratory mouse
2017
Genomics Data
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The nucleotide sequences of BH370 was deposited into the European Nucleotide Archive under the genome assembly accession number FPJN01000000. ...
In this study, we present the draft genome sequence of B. pseudohinzii BH370 recovered from the trachea and lung tissues of an ICR mouse in Malaysia. ...
Nucleotide accession number The genome sequences generated in this study are available from the European Nucleotide Archive under the genome assembly accession number FPJN01000000. 2017 The Authors. ...
doi:10.1016/j.gdata.2017.03.004
pmid:28377885
pmcid:PMC5369867
fatcat:gokvatfz5fh7dbakmp672khwme
DNA Data Bank of Japan: 30th anniversary
2017
Nucleic Acids Research
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We are collecting nucleotide sequence data and associated biological information from researchers as a member of the International Nucleotide Sequence Database Collaboration (INSDC), in collaboration with ...
the US National Center for Biotechnology Information and the European Bioinformatics Institute. ...
This endeavor has been conducted in collaboration with Gen-Bank (2) at the National Center for Biotechnology Information (NCBI) and with the European Nucleotide Archive (ENA) (3) at the European Bioinformatics ...
doi:10.1093/nar/gkx926
pmid:29040613
pmcid:PMC5753283
fatcat:3n45p6fz6bcfzgtv6j2prd44vq
The European Bioinformatics Institute in 2017: data coordination and integration
2017
Nucleic Acids Research
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This is reflected in our deep involvement in Open Targets, stewarding of plant phenotyping standards (MIAPPE) and partnership in the Human Cell Atlas data coordination platform, as well as the 2017 launch ...
The European Bioinformatics Institute (EMBL-EBI) supports life-science research throughout the world by providing open data, open-source software and analytical tools, and technical infrastructure (https ...
ChEBI (3), ChEMBL (4), the European Genome-phenome Archive (EGA) (5), the European Nucleotide Archive (ENA) (6), Ensembl (7), Ensembl Genomes (8), Europe PMC (9), IntAct (as part of the IMEx Consortium ...
doi:10.1093/nar/gkx1154
pmid:29186510
pmcid:PMC5753251
fatcat:ubzlegb2kjcltbtdftwsh6mlja
Complete Coding Sequences of Two Dengue Virus Type 2 Strains Isolated from an Outbreak in Burkina Faso in 2016
2017
Genome Announcements
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We report here the complete coding sequences of two strains of dengue virus type 2, isolated in France from patients returning from Burkina Faso in November 2016. ...
Both strains (cosmopolitan genotype) are almost identical (99.91% nucleotide identity) and closely related to a strain circulating in Burkina Faso in 1983. ...
This work was supported by the European Virus Archive goes Global project (EVAg; European Union-Horizon 2020 program under grant agreement no. 653316. ...
doi:10.1128/genomea.00209-17
pmid:28450505
pmcid:PMC5408103
fatcat:x6dkzq5g25awnoz4i4pxdhqgte
Candidate gene associations studies in psychiatry: time to move forward
2017
European Archives of Psychiatry and Clinical Neuroscience
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In the present issue, de Castro-Sala et al. report an association between two single-nucleotide polymorphisms in the regulator of G-protein signalling 4 (RGS4) gene, a candidate gene for schizophrenia ...
Recent papers in this journal have focused on the genetic association between polymorphisms in candidate genes and risk behaviour [2] or associations between polymorphisms of the dopamine transporter ...
doi:10.1007/s00406-016-0765-7
pmid:28070643
fatcat:cqp4hyemvrdn7hjspgwoewhd6y
Persistent Identifiers In The Life Sciences
2017
Zenodo
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Introduction to EMBL-EBI, integration of Persistent Identifiers in the life sciences information services, and the institution's cooperative efforts with project THOR and OpenAIRE. ...
• European Nucleotide Archive
• European Variation Archive
• European Genome-phenome Archive
• ArrayExpress
Database interactions
• Our collaborative community
facilitates social, scientific ...
in 2016
Scientists at over
3.2 million
unique IP addresses use
EMBL-EBI websites
Generic vs structured/specific data
archives
Biological metadata -critical
to scientific reuse
Generic: ...
doi:10.5281/zenodo.1004728
fatcat:qgvxaed6p5gftaxbc4n57ystcu
DDBJ update: the Genomic Expression Archive (GEA) for functional genomics data
2018
Nucleic Acids Research
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), which is a member of the International Nucleotide Sequence Database Collaboration (INSDC) with the US National Center for Biotechnology Information and the European Bioinformatics Institute. ...
The DDBJ Center collects nucleotide sequence data and associated biological information from researchers and also services the Japanese Genotype-phenotype Archive (JGA) with the National Bioscience Database ...
ACKNOWLEDGEMENTS We gratefully acknowledge Koji Watanabe, Naofumi Ishikawa, Yasukazu Nakamura, Kousaku Okubo, Toshihisa Takagi, Masanori Arita and all members of the DDBJ Center for their support in data ...
doi:10.1093/nar/gky1002
pmid:30357349
pmcid:PMC6323915
fatcat:3bgfc6a3lvf6fjavejrvwixzne
DDBJ Database updates and computational infrastructure enhancement
2019
Nucleic Acids Research
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Sequence Database Collaboration (INSDC) in partnership with the US National Center for Biotechnology Information and the European Bioinformatics Institute. ...
The Bioinformation and DDBJ Center (https://www.ddbj.nig.ac.jp) in the National Institute of Genetics (NIG) maintains a primary nucleotide sequence database as a member of the International Nucleotide ...
ACKNOWLEDGEMENTS We gratefully acknowledge the support of Koji Watanabe, Naofumi Ishikawa and all members of Bioinformation and DDBJ Center for their assistance in data collection, annotation, release ...
doi:10.1093/nar/gkz982
pmid:31724722
pmcid:PMC7145692
fatcat:uubxnpbeqvabrkkaw5ah4q7hzm
First Identification and Genomic Characterization of a Porcine Sapelovirus from Corsica, France, 2017
2018
Microbiology Resource Announcements
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We report the isolation and genomic characterization of a Sapelovirus A strain, or porcine sapelovirus (PSV), from a diarrheic Corsican piglet in France. ...
It shares 87% nucleotide identity with a 2014 German isolate. ...
This study was supported by the Corsica territorial collectivity and by the European Virus Archive goes Global (EVAg) project (European Union-Horizon 2020 program) under grant agreement no. 653316. ...
doi:10.1128/mra.01049-18
pmid:30533644
pmcid:PMC6256667
fatcat:p7tk2ywt7raazkcdx3zvhsoczu
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