scholarly journals NCBI will no longer make taxonomy identifiers for individual influenza strains on January 15, 2018

2017 ◽  
Author(s):  
Eneida Hatcher ◽  
Yiming Bao ◽  
Paolo Amedeo ◽  
Olga Blinkova ◽  
Guy Cochrane ◽  
...  
Keyword(s):  
Influenza Virus ◽  
Data Processing ◽  
Virus Isolate ◽  
Ncbi Taxonomy ◽  
Virus Taxonomy ◽  
Previous Approach ◽  
Ncbi Taxonomy Database ◽  
Submission Process ◽  
Manual Processing ◽  
Manual Handling

Currently the National Center of Biotechnology Information (NCBI) assigns individual taxonomy identifiers to each distinct influenza virus isolate submitted to GenBank. To support this practice, individual flu isolates must be manually added to the NCBI taxonomy database and unique taxonomy identifiers generated. This added layer of manual processing is unique to influenza virus and prevents automatization of the flu sequence submission process. Here we outline a new NCBI policy that normalizes influenza virus taxonomy processing but maintains features supported by the previous approach. This change will reduce the amount of manual handling necessary for flu submissions and pave the way for increased automation of the submissions process. While this automation may disrupt some historic practices, it will better align influenza virus data processing with other viruses and ultimately lower the submission burden on data providers.

scholarly journals NCBI will no longer make taxonomy identifiers for individual influenza strains on January 15, 2018

2017 ◽  
Author(s):  
Eneida Hatcher ◽  
Yiming Bao ◽  
Paolo Amedeo ◽  
Olga Blinkova ◽  
Guy Cochrane ◽  
...  
Keyword(s):  
Influenza Virus ◽  
Data Processing ◽  
Virus Isolate ◽  
Ncbi Taxonomy ◽  
Virus Taxonomy ◽  
Previous Approach ◽  
Ncbi Taxonomy Database ◽  
Submission Process ◽  
Manual Processing ◽  
Manual Handling

Currently the National Center of Biotechnology Information (NCBI) assigns individual taxonomy identifiers to each distinct influenza virus isolate submitted to GenBank. To support this practice, individual flu isolates must be manually added to the NCBI taxonomy database and unique taxonomy identifiers generated. This added layer of manual processing is unique to influenza virus and prevents automatization of the flu sequence submission process. Here we outline a new NCBI policy that normalizes influenza virus taxonomy processing but maintains features supported by the previous approach. This change will reduce the amount of manual handling necessary for flu submissions and pave the way for increased automation of the submissions process. While this automation may disrupt some historic practices, it will better align influenza virus data processing with other viruses and ultimately lower the submission burden on data providers.

The disconnect between DNA and species names: lessons from reptile species in the NCBI taxonomy database

Zootaxa ◽  
2019 ◽  
Vol 4706 (3) ◽  
pp. 401-407 ◽  
Author(s):  
AKHIL GARG ◽  
DETLEF LEIPE ◽  
PETER UETZ
Keyword(s):  
Dna Sequence ◽  
Dna Sequences ◽  
Ncbi Taxonomy ◽  
Sequence Database ◽  
Ncbi Taxonomy Database ◽  
Reptile Species

We compared the species names in the Reptile Database, a dedicated taxonomy database, with those in the NCBI taxonomy database, which provides the taxonomic backbone for the GenBank sequence database. About 67% of the known ~11,000 reptile species are represented with at least one DNA sequence and a binary species name in GenBank. However, a common problem arises through the submission of preliminary species names (such as “Pelomedusa sp. A CK-2014”) to GenBank and thus the NCBI taxonomy. These names cannot be assigned to any accepted species names and thus create a disconnect between DNA sequences and species. While these names of unknown taxonomic meaning sometimes get updated, often they remain in GenBank which now contains sequences from ~1,300 such “putative” reptile species tagged by informal names (~15% of its reptile names). We estimate that NCBI/GenBank probably contain tens of thousands of such “disconnected” entries. We encourage sequence submitters to update informal species names after they have been published, otherwise the disconnect will cause increasing confusion and possibly misleading taxonomic conclusions.

scholarly journals Genetic Analyses of an H3N8 Influenza Virus Isolate, Causative Strain of the Outbreak of Equine Influenza at the Kanazawa Racecourse in Japan in 2007

2008 ◽  
Vol 70 (9) ◽  
pp. 899-906 ◽  
Author(s):  
Mika ITO ◽  
Makoto NAGAI ◽  
Yuji HAYAKAWA ◽  
Hirofumi KOMAE ◽  
Naruto MURAKAMI ◽  
...  
Keyword(s):  
Influenza Virus ◽  
Virus Isolate ◽  
Genetic Analyses ◽  
Equine Influenza

scholarly journals CYTOPATHOGENICITY OF INFLUENZA VIRUS (H4 N3)

2021 ◽  
Vol 25 (1) ◽  
pp. 181-193
Author(s):  
H. M. I. AL-HYALI
Keyword(s):  
Influenza Virus ◽  
Virus Isolate ◽  
Chicken Embryo Fibroblast ◽  
Post Inoculation ◽  
Tissue Cultures ◽  
Cytoplasmic Change ◽  
Infected Cells ◽  
Indirect Immunoperoxidase ◽  
Eosinophilic Inclusions ◽  
Cytopathogenic Effect

Monolayer tissue cultures of chicken embryo fibroblast ( CEF ) cells infected with avian influenza virus isolate were examined by the hematoxylie and eosin (H&E) staining and indirect immunoperoxidase test for studying the cytopathogenic effect of the virus. Cytopathological changes which occurred in the uncleus of infected cells included nuclear and nucleolar hypertropy, chromatin margination and intranuclear inclusions. The most striking cytoplasmic change were the presence of perinuclear. eosinophilic inclusions at 22-36 hours post inoculation ( p. i.). Vacuolization, and granulation were also observed. Indirect immunoperoxidase ( IP ) test demonstrated the localization of influenza virus antigens in infected cells. A positive peroxidase reaction observed in the nucleus and cytoplasm were similar to those shown hematoxyline and eosin staining.

scholarly journals Genetic Characteristics and Immunogenicity of Pandemic H1N1 Influenza Virus Isolate from Pig in Korea

2016 ◽  
Vol 16 (5) ◽  
pp. 311
Author(s):  
Hyoung Joon Moon ◽  
Jin Sik Oh ◽  
Woonsung Na ◽  
Minjoo Yeom ◽  
Sang Yoon Han ◽  
...  
Keyword(s):  
Influenza Virus ◽  
Virus Isolate ◽  
H1n1 Influenza ◽  
Pandemic H1n1 ◽  
H1n1 Influenza Virus ◽  
Genetic Characteristics ◽  
Pandemic H1n1 Influenza

scholarly journals Type material in the NCBI Taxonomy Database

2014 ◽  
Vol 43 (D1) ◽  
pp. D1086-D1098 ◽  
Author(s):  
Scott Federhen
Keyword(s):  
Type Material ◽  
Ncbi Taxonomy ◽  
Ncbi Taxonomy Database

WISDOM Calibration and Data Processing Pipeline for the ExoMars 2020 Mission

2020 ◽  
Author(s):  
Dirk Plettemeier ◽  
Christoph Statz ◽  
Yun Lu ◽  
Wolf-Stefan Benedix ◽  
Sebastian Hegler ◽  
...  
Keyword(s):  
Data Processing ◽  
Electromagnetic Waves ◽  
Continuous Wave ◽  
Field Measurements ◽  
Processing Pipeline ◽  
Martian Soil ◽  
Wave Radar ◽  
Past Life ◽  
Manual Processing ◽  
Ground Penetrating

<p>The WISDOM instrument is part of the 2020 ESA-Roscosmos ExoMars Rosalind-Franklin rover payload. It is a fully-polarimetric ground penetrating RADAR (GPR) operating as a stepped-frequency continuous-wave radar at frequencies between 500 MHz and 3 GHz yielding a centimetric resolution and a penetration depth of about 3 m in Martian soil. WISDOMs primary scientific objective is the detailed characterization the material distribution of the Martian subsurface as a contribution to the search for evidence of present and past life.</p><p>WISDOM  works by transmitting electromagnetic waves in the observable zone of the subsurface below the antenna. The transfer function of the observed zone is then recovered from the received signal. The processing of the WISDOM data involves several calibration steps, where environment and temperature as well as instrument influences are compensated in order to obtain interpretable results. The data processing involves several filters that are designed to extract and quantify features of interest w.r.t. the surface and subsurface. Calibration and processing are implemented in the WISDOM Data Processing Framework (WDPF). It can be operated manually (via GUI integration) as well as automatically as part of the ROCC processing pipeline yielding comparable and reproducible results from automatic and manual processing of WISDOM data. The capabilities of WDPF are validated on laboratory and field measurements performed with the WISDOM instrument.</p>

scholarly journals The NCBI Taxonomy database

2011 ◽  
Vol 40 (D1) ◽  
pp. D136-D143 ◽  
Author(s):  
S. Federhen
Keyword(s):  
Ncbi Taxonomy ◽  
Ncbi Taxonomy Database
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