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      • Record: found
      • Abstract: found
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      SILVA, RDP, Greengenes, NCBI and OTT — how do these taxonomies compare?

      research-article
      Author(s): ,
      Publication date (Electronic):
      Journal: BMC Genomics
      Publisher: BioMed Central
      Conference name: The Fifteenth Asia Pacific Bioinformatics Conference (APBC 2017)
      Conference date: 16-18 January 2017
      Keywords: Metagenomics, Taxonomic classification, OTU assignment, NCBI, Silva, RDP, Greengenes, Open tree of life

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          Abstract

          Background

          A key step in microbiome sequencing analysis is read assignment to taxonomic units. This is often performed using one of four taxonomic classifications, namely SILVA, RDP, Greengenes or NCBI. It is unclear how similar these are and how to compare analysis results that are based on different taxonomies.

          Results

          We provide a method and software for mapping taxonomic entities from one taxonomy onto another. We use it to compare the four taxonomies and the Open Tree of life Taxonomy (OTT).

          Conclusions

          While we find that SILVA, RDP and Greengenes map well into NCBI, and all four map well into the OTT, mapping the two larger taxonomies on to the smaller ones is problematic.

          Electronic supplementary material

          The online version of this article (doi:10.1186/s12864-017-3501-4) contains supplementary material, which is available to authorized users.

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          Most cited references9

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          The new higher level classification of eukaryotes with emphasis on the taxonomy of protists.

          SINA M. ADL, ALASTAIR G. B. SIMPSON, MARK A. FARMER … (2005)
          This revision of the classification of unicellular eukaryotes updates that of Levine et al. (1980) for the protozoa and expands it to include other protists. Whereas the previous revision was primarily to incorporate the results of ultrastructural studies, this revision incorporates results from both ultrastructural research since 1980 and molecular phylogenetic studies. We propose a scheme that is based on nameless ranked systematics. The vocabulary of the taxonomy is updated, particularly to clarify the naming of groups that have been repositioned. We recognize six clusters of eukaryotes that may represent the basic groupings similar to traditional "kingdoms." The multicellular lineages emerged from within monophyletic protist lineages: animals and fungi from Opisthokonta, plants from Archaeplastida, and brown algae from Stramenopiles.
          Article 0 comments Cited 371 times – based on 0 reviews     Review now
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            The International Nucleotide Sequence Database Collaboration

            Guy Cochrane, Ilene Karsch-Mizrachi, Toshihisa Takagi … (2015)
            The International Nucleotide Sequence Database Collaboration (INSDC; http://www.insdc.org) comprises three global partners committed to capturing, preserving and providing comprehensive public-domain nucleotide sequence information. The INSDC establishes standards, formats and protocols for data and metadata to make it easier for individuals and organisations to submit their nucleotide data reliably to public archives. This work enables the continuous, global exchange of information about living things. Here we present an update of the INSDC in 2015, including data growth and diversification, new standards and requirements by publishers for authors to submit their data to the public archives. The INSDC serves as a model for data sharing in the life sciences.
            Article 0 comments Cited 98 times – based on 0 reviews     Review now
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              The Encyclopedia of Life v2: Providing Global Access to Knowledge About Life on Earth

              Cynthia S. Parr, Nathan Wilson, Patrick Leary … (2014)
              Abstract The Encyclopedia of Life (EOL, http://eol.org) aims to provide unprecedented global access to a broad range of information about life on Earth. It currently contains 3.5 million distinct pages for taxa and provides content for 1.3 million of those pages. The content is primarily contributed by EOL content partners (providers) that have a more limited geographic, taxonomic or topical scope. EOL aggregates these data and automatically integrates them based on associated scientific names and other classification information. EOL also provides interfaces for curation and direct content addition. All materials in EOL are either in the public domain or licensed under a Creative Commons license. In addition to the web interface, EOL is also accessible through an Application Programming Interface. In this paper, we review recent developments added for Version 2 of the web site and subsequent releases through Version 2.2, which have made EOL more engaging, personal, accessible and internationalizable. We outline the core features and technical architecture of the system. We summarize milestones achieved so far by EOL to present results of the current system implementation and establish benchmarks upon which to judge future improvements. We have shown that it is possible to successfully integrate large amounts of descriptive biodiversity data from diverse sources into a robust, standards-based, dynamic, and scalable infrastructure. Increasing global participation and the emergence of EOL-powered applications demonstrate that EOL is becoming a significant resource for anyone interested in biological diversity.
              Article 0 comments Cited 70 times – based on 0 reviews     Review now
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                Author and article information

                Contributors
                Monika Balvočiūtė: monika.balvociute@uni-tuebingen.de
                Daniel H. Huson: daniel.huson@uni-tuebingen.de
                Conference
                Journal ID (nlm-ta): BMC Genomics
                Journal ID (iso-abbrev): BMC Genomics
                Title: BMC Genomics
                Publisher: BioMed Central (London )
                ISSN (Electronic): 1471-2164
                Publication date (Electronic): 14 March 2017
                Publication date PMC-release: 14 March 2017
                Publication date Collection: 2017
                Volume: 18
                Issue : Suppl 2 Issue sponsor : Publication of this supplement has not been supported by sponsorship. Information about the source of funding for publication charges can be found in the individual articles. The articles have undergone the journal's standard peer review process for supplements. The Supplement Editors declare that they have no competing interests.
                Electronic Location Identifier: 114
                Affiliations
                University of Tübingen, Department of Computer Science, Sand 14, Tübingen, 72076 Germany
                Article
                Publisher ID: 3501
                DOI: 10.1186/s12864-017-3501-4
                PMC ID: 5374703
                PubMed ID: 28361695
                SO-VID: 1d401037-20e7-407d-9e31-e28a1bc8f2fd
                Copyright © © The Author(s) 2017
                License:

                Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

                Conference name: The Fifteenth Asia Pacific Bioinformatics Conference
                Conference acronym: APBC 2017
                Conference location: Shenzhen, China
                Conference date: 16-18 January 2017
                History
                Categories
                Subject: Research
                Custom metadata
                issue-copyright-statement © The Author(s) 2017

                ScienceOpen disciplines: Genetics
                Keywords: metagenomics,taxonomic classification,otu assignment,ncbi,silva,rdp,greengenes,open tree of life
                Data availability:
                ScienceOpen disciplines: Genetics
                Keywords: metagenomics, taxonomic classification, otu assignment, ncbi, silva, rdp, greengenes, open tree of life

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