Using taxonomic consistency with semi‐automated data pre‐processing for high quality DNA barcodes

  1. Rulik, Björn ORCID logo
  2. Eberle, Jonas
  3. Mark, Laura
  4. Thormann, Jana
  5. Jung, Manfred
  6. Köhler, Frank
  7. Apfel, Wolfgang
  8. Weigel, Andreas
  9. Kopetz, Andreas
  10. Köhler, Jonas
  11. Fritzlar, Frank
  12. Hartmann, Matthias
  13. Hadulla, Karl
  14. Schmidt, Joachim
  15. Hörren, Thomas
  16. Krebs, Detlef
  17. Theves, Florian
  18. Eulitz, Ute
  19. Skale, André
  20. Rohwedder, Dirk
  21. Kleeberg, Andreas
  22. Astrin, Jonas J.
  23. Geiger, Matthias F.
  24. Wägele, J. Wolfgang
  25. Grobe, Peter
  26. Ahrens, Dirk

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WeightNameValue
1000 Titel
  • Using taxonomic consistency with semi‐automated data pre‐processing for high quality DNA barcodes
1000 Autor/in
  1. Rulik, Björn |
  2. Eberle, Jonas |
  3. Mark, Laura |
  4. Thormann, Jana |
  5. Jung, Manfred |
  6. Köhler, Frank |
  7. Apfel, Wolfgang |
  8. Weigel, Andreas |
  9. Kopetz, Andreas |
  10. Köhler, Jonas |
  11. Fritzlar, Frank |
  12. Hartmann, Matthias |
  13. Hadulla, Karl |
  14. Schmidt, Joachim |
  15. Hörren, Thomas |
  16. Krebs, Detlef |
  17. Theves, Florian |
  18. Eulitz, Ute |
  19. Skale, André |
  20. Rohwedder, Dirk |
  21. Kleeberg, Andreas |
  22. Astrin, Jonas J. |
  23. Geiger, Matthias F. |
  24. Wägele, J. Wolfgang |
  25. Grobe, Peter |
  26. Ahrens, Dirk |
1000 Erscheinungsjahr 2017
1000 LeibnizOpen
1000 Art der Datei
1000 Publikationstyp
  1. Artikel |
1000 Online veröffentlicht
  • 2017-05-29
1000 Erschienen in
1000 Quellenangabe
  • 8(12):1878–1887
1000 FRL-Sammlung
1000 Copyrightjahr
  • 2017
1000 Lizenz
1000 Verlagsversion
  • https://doi.org/10.1111/2041-210X.12824 |
1000 Ergänzendes Material
  • https://besjournals.onlinelibrary.wiley.com/doi/abs/10.1111/2041-210X.12824 |
1000 Publikationsstatus
1000 Begutachtungsstatus
1000 Sprache der Publikation
1000 Abstract/Summary
  • 1. In recent years, large‐scale DNA barcoding campaigns have generated an enormous amount of COI barcodes, which are usually stored in NCBI's GenBank and the official Barcode of Life database (BOLD). BOLD data are generally associated with more detailed and better curated meta‐data, because a great proportion is based on expert‐verified and vouchered material, accessible in public collections. In the course of the initiative German Barcode of Life data were generated for the reference library of 2,846 species of Coleoptera from 13,516 individuals. 2. Confronted with the high effort associated with the identification, verification and data validation, a bioinformatic pipeline, “TaxCI” was developed that (1) identifies taxonomic inconsistencies in a given tree topology (optionally including a reference dataset), (2) discriminates between different cases of incongruence in order to identify contamination or misidentified specimens, (3) graphically marks those cases in the tree, which finally can be checked again and, if needed, corrected or removed from the dataset. For this, “TaxCI” may use DNA‐based species delimitations from other approaches (e.g. mPTP) or may perform implemented threshold‐based clustering. 3. The data‐processing pipeline was tested on a newly generated set of barcodes, using the available BOLD records as a reference. A data revision based on the first run of the TaxCI tool resulted in the second TaxCI analysis in a taxonomic match ratio very similar to the one recorded from the reference set (92% vs. 94%). The revised dataset improved by nearly 20% through this procedure compared to the original, uncorrected one. 4. Overall, the new processing pipeline for DNA barcode data allows for the rapid and easy identification of inconsistencies in large datasets, which can be dealt with before submitting them to public data repositories like BOLD or GenBank. Ultimately, this will increase the quality of submitted data and the speed of data submission, while primarily avoiding the deterioration of the accuracy of the data repositories due to ambiguously identified or contaminated specimens.
1000 Sacherschließung
lokal German Barcode of Life
lokal reference library
lokal data quality
lokal Coleoptera
lokal species identification
lokal DNA barcoding
lokal Germany
1000 Fachgruppe
  1. Biologie |
1000 Fächerklassifikation (DDC)
1000 Liste der Beteiligten
  1. http://orcid.org/0000-0002-2808-9305|https://frl.publisso.de/adhoc/creator/RWJlcmxlLCBKb25hcw==|https://frl.publisso.de/adhoc/creator/TWFyaywgTGF1cmE=|https://frl.publisso.de/adhoc/creator/VGhvcm1hbm4sIEphbmE=|https://frl.publisso.de/adhoc/creator/SnVuZywgTWFuZnJlZA==|https://frl.publisso.de/adhoc/creator/S8O2aGxlciwgRnJhbms=|https://frl.publisso.de/adhoc/creator/QXBmZWwsIFdvbGZnYW5n|https://frl.publisso.de/adhoc/creator/V2VpZ2VsLCBBbmRyZWFz|https://frl.publisso.de/adhoc/creator/S29wZXR6LCBBbmRyZWFz|https://frl.publisso.de/adhoc/creator/S8O2aGxlciwgSm9uYXM=|https://frl.publisso.de/adhoc/creator/RnJpdHpsYXIsIEZyYW5r|https://frl.publisso.de/adhoc/creator/SGFydG1hbm4sIE1hdHRoaWFz|https://frl.publisso.de/adhoc/creator/SGFkdWxsYSwgS2FybA==|https://frl.publisso.de/adhoc/creator/U2NobWlkdCwgSm9hY2hpbQ==|https://frl.publisso.de/adhoc/creator/SMO2cnJlbiwgVGhvbWFz|https://frl.publisso.de/adhoc/creator/S3JlYnMsIERldGxlZg==|https://frl.publisso.de/adhoc/creator/VGhldmVzLCBGbG9yaWFu|https://frl.publisso.de/adhoc/creator/RXVsaXR6LCBVdGU=|https://frl.publisso.de/adhoc/creator/U2thbGUsIEFuZHLDqQ==|https://frl.publisso.de/adhoc/creator/Um9od2VkZGVyLCBEaXJr|https://frl.publisso.de/adhoc/creator/S2xlZWJlcmcsIEFuZHJlYXM=|https://frl.publisso.de/adhoc/creator/QXN0cmluLCBKb25hcyBKLg==|https://frl.publisso.de/adhoc/creator/R2VpZ2VyLCBNYXR0aGlhcyBGLg==|https://frl.publisso.de/adhoc/creator/V8OkZ2VsZSwgSi4gV29sZmdhbmc=|https://frl.publisso.de/adhoc/creator/R3JvYmUsIFBldGVy|https://frl.publisso.de/adhoc/creator/QWhyZW5zLCBEaXJr
1000 Label
1000 Förderer
  1. German Federal Ministry of Education and Research (BMBF)
1000 Fördernummer
  1. 01LI1101A; 01LI1501A
1000 Förderprogramm
  1. German Barcode of Life 1 (GBOL 1)
1000 Dateien
1000 Objektart article
1000 Beschrieben durch
1000 @id frl:6408918.rdf
1000 Erstellt am 2018-07-19T14:20:49.351+0200
1000 Erstellt von 270
1000 beschreibt frl:6408918
1000 Bearbeitet von 25
1000 Zuletzt bearbeitet Thu Jan 30 19:05:46 CET 2020
1000 Objekt bearb. Fri Aug 03 08:50:31 CEST 2018
1000 Vgl. frl:6408918
1000 Oai Id
  1. oai:frl.publisso.de:frl:6408918 |
1000 Sichtbarkeit Metadaten public
1000 Sichtbarkeit Daten public
1000 Gegenstand von

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