Type material in the NCBI Taxonomy Database

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.

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

10.7287/peerj.preprints.3428v1 ◽

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.

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The NCBI Taxonomy database

Nucleic Acids Research ◽

10.1093/nar/gkr1178 ◽

2011 ◽

Vol 40 (D1) ◽

pp. D136-D143 ◽

Cited By ~ 595

Author(s):

S. Federhen

Keyword(s):

Ncbi Taxonomy ◽

Ncbi Taxonomy Database

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Taxallnomy: Closing gaps in the NCBI Taxonomy

10.1101/2020.05.28.119461 ◽

2020 ◽

Cited By ~ 1

Author(s):

Tetsu Sakamoto ◽

J. Miguel Ortega

Keyword(s):

Hierarchical Structure ◽

Ncbi Taxonomy ◽

Bioinformatics Analyses ◽

Taxonomic Rank ◽

Link Type ◽

Ncbi Taxonomy Database ◽

Hierarchical Levels ◽

Data Source ◽

Taxonomic Tree ◽

Parent Node

ABSTRACTNCBI Taxonomy is the main taxonomic source for several bioinformatics tools and databases since all organisms with sequence accessions deposited on INSDC are organized in its hierarchical structure. Despite the extensive use and application of this data source, taking advantage of its taxonomic tree could be challenging because (1) some taxonomic ranks are missing in some lineages and (2) some nodes in the tree do not have a taxonomic rank assigned (referred to as “no rank”). To address this issue, we developed an algorithm that takes the tree structure from NCBI Taxonomy and generates a hierarchically complete taxonomic tree. The procedures performed by the algorithm consist of attempting to assign a taxonomic rank to “no rank” nodes and of creating/deleting nodes throughout the tree. The algorithm also creates a name for the new nodes by borrowing the names from its ranked child or, if there is no child, from its ranked parent node. The new hierarchical structure was named taxallnomy and it contains 33 hierarchical levels corresponding to the 33 taxonomic ranks currently used in the NCBI Taxonomy database. From taxallnomy, users can obtain the complete taxonomic lineage with 33 nodes of all taxa available in the NCBI Taxonomy database. Taxallnomy is applicable to several bioinformatics analyses that depend on NCBI Taxonomy data. In this work, we demonstrate its applicability by embedding taxonomic information of a specified rank into a phylogenetic tree; and by making metagenomics profiles. Taxallnomy algorithm was written in PERL and all its resources are available at bioinfo.icb.ufmg.br/taxallnomy.Database URL: http://bioinfo.icb.ufmg.br/taxallnomy

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

10.7287/peerj.preprints.3428 ◽

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.

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Taxallnomy: an extension of NCBI Taxonomy that produces a hierarchically complete taxonomic tree

BMC Bioinformatics ◽

10.1186/s12859-021-04304-3 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Tetsu Sakamoto ◽

J. Miguel Ortega

Keyword(s):

Hierarchical Structure ◽

Ncbi Taxonomy ◽

Bioinformatics Analyses ◽

Taxonomic Rank ◽

Alternative Representation ◽

Ncbi Taxonomy Database ◽

Original Tree ◽

Data Source ◽

Taxonomic Tree ◽

Do So

Abstract Background NCBI Taxonomy is the main taxonomic source for several bioinformatics tools and databases since all organisms with sequence accessions deposited on INSDC are organized in its hierarchical structure. Despite the extensive use and application of this data source, an alternative representation of data as a table would facilitate the use of information for processing bioinformatics data. To do so, since some taxonomic-ranks are missing in some lineages, an algorithm might propose provisional names for all taxonomic-ranks. Results To address this issue, we developed an algorithm that takes the tree structure from NCBI Taxonomy and generates a hierarchically complete taxonomic table, maintaining its compatibility with the original tree. The procedures performed by the algorithm consist of attempting to assign a taxonomic-rank to an existing clade or “no rank” node when possible, using its name as part of the created taxonomic-rank name (e.g. Ord_Ornithischia) or interpolating parent nodes when needed (e.g. Cla_of_Ornithischia), both examples given for the dinosaur Brachylophosaurus lineage. The new hierarchical structure was named Taxallnomy because it contains names for all taxonomic-ranks, and it contains 41 hierarchical levels corresponding to the 41 taxonomic-ranks currently found in the NCBI Taxonomy database. From Taxallnomy, users can obtain the complete taxonomic lineage with 41 nodes of all taxa available in the NCBI Taxonomy database, without any hazard to the original tree information. In this work, we demonstrate its applicability by embedding taxonomic information of a specified rank into a phylogenetic tree and by producing metagenomics profiles. Conclusion Taxallnomy applies to any bioinformatics analyses that depend on the information from NCBI Taxonomy. Taxallnomy is updated periodically but with a distributed PERL script users can generate it locally using NCBI Taxonomy as input. All Taxallnomy resources are available at http://bioinfo.icb.ufmg.br/taxallnomy.

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An annotated checklist of mesoplodont whale species (Cetacea, Ziphiidae) discovered during the nineteenth century

Archives of Natural History ◽

10.3366/anh.2015.0307 ◽

2015 ◽

Vol 42 (2) ◽

pp. 226-235 ◽

Cited By ~ 2

Author(s):

G. N. H. Waller

Keyword(s):

Nineteenth Century ◽

Additional Data ◽

Original Description ◽

Type Specimen ◽

External Morphology ◽

Type Locality ◽

Type Material ◽

Beaked Whale ◽

Registration Number ◽

Annotated Checklist

Eight species of mesoplodont whales (genus Mesoplodon Gervais, 1850) named during the nineteenth century are based on valid descriptions. A checklist with the original description and type material for each of these species is provided. Additional data given may include type locality and illustrative sources, type material holding institution and type registration number(s). The only type specimen for which a record of external morphology was published relates to the 1803 stranding of Sowerby's beaked whale (Mesoplodon bidens).

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Making Graphene-type Material via Polymerization of Porphyrin

10.26434/chemrxiv.13041785.v1 ◽

2020 ◽

Author(s):

SANJIB KAR ◽

Sruti Mondal ◽

Kasturi Sahu ◽

Dilruba Hasina ◽

Tapobrata Som ◽

...

Keyword(s):

Layer Thickness ◽

Polymeric Material ◽

Single Layer ◽

Type Material ◽

Synthetic Pathway ◽

Simple Chemical ◽

Doped Graphene ◽

Ring Nitrogen ◽

2D Structure ◽

Porphyrin Macrocycles

The synthesis of new graphene-type materials (via polymerization of porphyrin macrocycles) through a simple chemical synthetic pathway (at RT) has been demonstrated. This newly synthesized material can be dispersed in water with an average sheet size of few microns and with single layer thickness. As the porphyrin contains four inner ring nitrogen atoms thus the presented polymeric material will be close analogous of N-doped graphene. Porphyrin as the key component to synthesize layered graphene type continuous 2D structure has never been attempted before.

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Review of Turkish crickets from the subfamily Gryllomorphinae (Orthoptera: Gryllidae)

Zoosystematica Rossica ◽

10.31610/zsr/2012.21.1.28 ◽

2012 ◽

Vol 21 (1) ◽

pp. 28-59

Author(s):

A.V. Gorochov ◽

M. Ünal

Keyword(s):

Type Material ◽

Southern Coast ◽

First Time

The fauna of Gryllomorphinae of Turkey is reviewed. Sixteen species and subspecies are established. Ovaliptila anamur sp. nov., O. anitli sp. nov., O. alanya sp. nov., O. alanya proxima subsp. nov., O. alara sp. nov., O. teke sp. nov., O. ibrahimi sp. nov., Glandulosa borisi sp. nov. and Gryllomorpha dalmatina minutissima subsp. nov. are described. Ovaliptila beroni (Popov, 1975), Glandulosa kinzelbachi Harz, 1979, G. harzi Gorochov, 1996 and Gryllomorpha Antalya Gorochov, 2009 are briefly characterized based on the type material. Ovaliptila buresi Mařan, 1958 is indicated as a rather widely distributed species in the western part of Anatolia (but not in the southern coast of this peninsula). Gryllomorpha dalmatina pieperi Harz, 1979, G. miramae Medvedev, 1933 and the nominotypical subspecies of G. miramae are recorded from Turkey for the first time, but both subspecies remain open to question.

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