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The European Nucleotide Archive in 2017

Nicole Silvester, Blaise Alako, Clara Amid, Ana Cerdeño-Tarrága, Laura Clarke, Iain Cleland, Peter W Harrison, Suran Jayathilaka, Simon Kay, Thomas Keane, Rasko Leinonen, Xin Liu (+11 others)
2017 Nucleic Acids Research  
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

Done Stojanov
2017 Advanced Studies in Biology  
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]

Tomas Vetrovsky, Daniel Morais, Petr Kohout, Clementine Lepinay, Camelia Algora Gallardo, Sandra Awokunle Holla, Barbara Doreen Bahnmann, Kveta Bilohneda, Vendula Brabcova, Federica D'Alo, Zander Rainier Human, Mayuko Jomura (+21 others)
2020 bioRxiv   pre-print
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

Robert Petryszak
2017 Zenodo  
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  
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

Mariya Dimitrova, Raïssa Meyer, Pier Luigi Buttigieg, Teodor Georgiev, Georgi Zhelezov, Seyhan Demirov, Vincent Smith, Lyubomir Penev
2020 Biodiversity Information Science and Standards  
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

Shih Keng Loong, Kim-Kee Tan, Syuhaida Sulaiman, Pooi Fong Wong, Sazaly AbuBakar
2017 Genomics Data  
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

Yuichi Kodama, Jun Mashima, Takehide Kosuge, Eli Kaminuma, Osamu Ogasawara, Kousaku Okubo, Yasukazu Nakamura, Toshihisa Takagi
2017 Nucleic Acids Research  
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

Charles E Cook, Mary T Bergman, Guy Cochrane, Rolf Apweiler, Ewan Birney
2017 Nucleic Acids Research  
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

Cécile Baronti, Géraldine Piorkowski, Franck Touret, Rémi Charrel, Xavier de Lamballerie, Antoine Nougairede
2017 Genome Announcements  
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

C. Arango
2017 European Archives of Psychiatry and Clinical Neuroscience  
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

Florian Graef
2017 Zenodo  
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 ArchiveEuropean Variation ArchiveEuropean 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

Yuichi Kodama, Jun Mashima, Takehide Kosuge, Osamu Ogasawara
2018 Nucleic Acids Research  
), 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  
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

Géraldine Piorkowski, Lisandru Capai, Alessandra Falchi, François Casabianca, Oscar Maestrini, Pierre Gallian, Karine Barthélémy, Odile Py, Rémi Charrel, Xavier de Lamballerie, Irene L. G. Newton
2018 Microbiology Resource Announcements  
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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