دورية أكاديمية

BOLD v4: A Centralized Bioinformatics Platform for DNA-Based Biodiversity Data.

التفاصيل البيبلوغرافية
العنوان: BOLD v4: A Centralized Bioinformatics Platform for DNA-Based Biodiversity Data.
المؤلفون: Ratnasingham S; Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada. sratnasi@uoguelph.ca., Wei C; Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada., Chan D; Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada., Agda J; Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada., Agda J; Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada., Ballesteros-Mejia L; Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada., Boutou HA; Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada., El Bastami ZM; Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada., Ma E; Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada., Manjunath R; Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada., Rea D; Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada., Ho C; Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada., Telfer A; Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada., McKeowan J; Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada., Rahulan M; Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada., Steinke C; Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada., Dorsheimer J; Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada., Milton M; Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada., Hebert PDN; College of Biological Science, University of Guelph, Guelph, ON, Canada.
المصدر: Methods in molecular biology (Clifton, N.J.) [Methods Mol Biol] 2024; Vol. 2744, pp. 403-441.
نوع المنشور: Journal Article; Research Support, Non-U.S. Gov't
اللغة: English
بيانات الدورية: Publisher: Humana Press Country of Publication: United States NLM ID: 9214969 Publication Model: Print Cited Medium: Internet ISSN: 1940-6029 (Electronic) Linking ISSN: 10643745 NLM ISO Abbreviation: Methods Mol Biol Subsets: MEDLINE
أسماء مطبوعة: Publication: Totowa, NJ : Humana Press
Original Publication: Clifton, N.J. : Humana Press,
مواضيع طبية MeSH: Biodiversity* , DNA Barcoding, Taxonomic*/methods , Computational Biology*/methods, Software ; DNA/genetics
مستخلص: BOLD, the Barcode of Life Data System, supports the acquisition, storage, validation, analysis, and publication of DNA barcodes, activities requiring the integration of molecular, morphological, and distributional data. Its pivotal role in curating the reference library of DNA barcodes, coupled with its data management and analysis capabilities, makes it a central resource for biodiversity science. It enables rapid, accurate identification of specimens and also reveals patterns of genetic diversity and evolutionary relationships among taxa.Launched in 2005, BOLD has become an increasingly powerful tool for advancing the understanding of planetary biodiversity. It currently hosts 17 million specimen records and 14 million barcodes that provide coverage for more than a million species from every continent and ocean. The platform has the long-term goal of providing a consistent, accurate system for identifying all species of eukaryotes.BOLD's integrated analytical tools, full data lifecycle support, and secure collaboration framework distinguish it from other biodiversity platforms. BOLD v4 brought enhanced data management and analysis capabilities as well as novel functionality for data dissemination and publication. Its next version will include features to strengthen its utility to the research community, governments, industry, and society-at-large.
(© 2024. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)
References: Sayers EW, Cavanaugh M, Clark K, Pruitt KD, Sherry ST, Yankie L, Karsch-Mizrachi I (2023) GenBank 2023 update. Nucleic Acids Res 51:D141–D144. (PMID: 10.1093/nar/gkac101236350640)
Edwards JL, Lane MA, Nielsen ES (2000) Interoperability of biodiversity databases: biodiversity information on every desktop. Science 289:2312–2314. (PMID: 10.1126/science.289.5488.231211009409)
Hobern D, Barik SK, Christidis L et al (2021) Towards a global list of accepted species VI: the catalogue of life checklist. Org Divers Evol 21:677–690. (PMID: 10.1007/s13127-021-00516-w)
Ratnasingham S, Hebert PDN (2007) The barcode of life data system. Mol Ecol Notes 7:355–364. (PMID: 10.1111/j.1471-8286.2007.01678.x187847901890991)
Ratnasingham S, Hebert PDN (2013) A DNA-based registry for all animal species: the barcode index number (BIN) system. PLoS One 8:e66213. https://doi.org/10.1371/journal.pone.0066213. (PMID: 10.1371/journal.pone.0066213238617433704603)
Sonet G, Jordaens K, Braet Y, Bourguignon L, Dupont E, Backeljau T, de Meyer M, Desmyter S (2013) Utility of GenBank and the barcode of life data systems (BOLD) for the identification of forensically important Diptera from Belgium and France. Zookeys 365:307–328. (PMID: 10.3897/zookeys.365.6027)
DeSalle R, Goldstein P (2019) Review and interpretation of trends in DNA barcoding. Front Ecol Evol 7. https://doi.org/10.3389/fevo.2019.00302.
Hebert PDN, Gregory TR (2005) The promise of DNA barcoding for taxonomy. Syst Biol 54:852–859. (PMID: 10.1080/1063515050035488616243770)
CBOL Plant Working Group, Hollingsworth PM, Forrest LL et al (2009) A DNA barcode for land plants. Proc Natl Acad Sci U S A 106:12794–12797. (PMID: 10.1073/pnas.09058451062722355)
Seifert KA (2009) Progress towards DNA barcoding of fungi. Mol Ecol Resour 9:83–89. (PMID: 10.1111/j.1755-0998.2009.02635.x21564968)
Min XJ, Hickey DA (2007) Barcoding: assessing the effect of varying sequence length on DNA barcoding of fungi. Mol Ecol Notes 7:365–373. (PMID: 10.1111/j.1471-8286.2007.01698.x187847891890918)
Ewing B, Green P (n.d.) Base-calling of automated sequencer traces using Phred. II Error Probabilities.
Eddy SR (1998) Profile hidden Markov models. Bioinformatics 14:755–763. (PMID: 10.1093/bioinformatics/14.9.7559918945)
Somervuo P, Koskela S, Pennanen J, Henrik Nilsson R, Ovaskainen O (2016) Unbiased probabilistic taxonomic classification for DNA barcoding. Bioinformatics 32:2920–2927. (PMID: 10.1093/bioinformatics/btw34627296980)
Austerlitz F, David O, Schaeffer B, Bleakley K, Olteanu M, Leblois R, Veuille M, Laredo C (2009) DNA barcode analysis: a comparison of phylogenetic and statistical classification methods. BMC Bioinformatics 10(Suppl 14):14. https://doi.org/10.1186/1471-2105-10-S14-S10. (PMID: 10.1186/1471-2105-10-S14-S10)
Boratyn GM, Camacho C, Cooper PS et al (2013) BLAST: a more efficient report with usability improvements. Nucleic Acids Res 41:W29. https://doi.org/10.1093/nar/gkt282. (PMID: 10.1093/nar/gkt282236095423692093)
Eddy SR (1998) Profile hidden Markov models. Bioinformatic Rev 14:755–763. (PMID: 10.1093/bioinformatics/14.9.755)
Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL (2009) BLAST+: architecture and applications. BMC Bioinformatics 10:421. (PMID: 10.1186/1471-2105-10-421200035002803857)
Page RDM (2016) DNA barcoding and taxonomy: dark taxa and dark texts. Philos Trans R Soc Lond B Biol Sci 371:20150334. https://doi.org/10.1098/rstb.2015.0334. (PMID: 10.1098/rstb.2015.0334274817864971186)
Hausmann A, Godfray HCJ, Huemer P, Mutanen M, Rougerie R, van Nieukerken EJ, Ratnasingham S, Hebert PDN (2013) Genetic patterns in European geometrid moths revealed by the barcode index number (BIN) system. PLoS One 8:e84518. (PMID: 10.1371/journal.pone.0084518243583633866169)
Pentinsaari M, Hebert PDN, Mutanen M (2014) Barcoding beetles: a regional survey of 1872 species reveals high identification success and unusually deep interspecific divergences. PLoS One 9:e108651. (PMID: 10.1371/journal.pone.0108651252553194177932)
Blagoev GA, deWaard JR, Ratnasingham S, deWaard SL, Lu L, Robertson J, Telfer AC, Hebert PDN (2016) Untangling taxonomy: DNA barcode reference library for Canadian spiders. Mol Ecol Resour 16:325–341. (PMID: 10.1111/1755-0998.1244426175299)
Layton KKS, Martel AL, Hebert PDN (2014) Patterns of DNA barcode variation in Canadian marine Molluscs. PLoS One 9:e95003. (PMID: 10.1371/journal.pone.0095003247433203990619)
Sharkey MJ, Janzen DH, Hallwachs W et al (2021) Minimalist revision and description of 403 new species in 11 subfamilies of costa Rican braconid parasitoid wasps, including host records for 219 species. Zookeys 1013:1–665. (PMID: 10.3897/zookeys.1013.55600345120878390796)
Fernandez-Triana JL (2022) Turbo taxonomy approaches: lessons from the past and recommendations for the future based on the experience with Braconidae (hymenoptera) parasitoid wasps. Zookeys 1087:199–220. (PMID: 10.3897/zookeys.1087.76720355859428897373)
Cock PJA, Fields CJ, Goto N, Heuer ML, Rice PM (2010) The sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Res 38:1767–1771. (PMID: 10.1093/nar/gkp113720015970)
Salvi D, Berrilli E, D’Alessandro P, Biondi M (2020) Sharpening the DNA barcoding tool through a posteriori taxonomic validation: the case of Longitarsus flea beetles (Coleoptera: Chrysomelidae). PLoS One 15:e0233573. (PMID: 10.1371/journal.pone.0233573324374697241800)
Riedel A, Sagata K, Suhardjono YR, Tänzler R, Balke M (2013) Integrative taxonomy on the fast track - towards more sustainability in biodiversity research. Front Zool 10:15. (PMID: 10.1186/1742-9994-10-15235371823626550)
La SJ, Wheeler Q, Jackway P, Winterton S, Hobern D, Lovell D (2009) Zootaxa, accelerating taxonomic discovery through automated character extraction. Zootaxa 2217:43–55.
Martineau M, Conte D, Raveaux R, Arnault I, Munier D, Venturini G (2017) A survey on image-based insect classification. Pattern Recogn 65:273–284. (PMID: 10.1016/j.patcog.2016.12.020)
Howe K, Bateman A, Durbin R (2002) QuickTree: building huge neighbour-joining trees of protein sequences. Bioinformatics 18:1546–1547. (PMID: 10.1093/bioinformatics/18.11.154612424131)
Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. https://doi.org/10.1093/oxfordjournals.molbev.a040454.
Hebert PDN, Ratnasingham S, de Waard JR (2003) Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proc R Soc Lond B Biol Sci 270:S96. https://doi.org/10.1098/rsbl.2003.0025. (PMID: 10.1098/rsbl.2003.0025)
van Velzen R, Weitschek E, Felici G, Bakker FT (2012) DNA barcoding of recently diverged species: relative performance of matching methods. PLoS One 7:e30490. (PMID: 10.1371/journal.pone.0030490222723563260286)
Paradis E, Claude J, Strimmer K (2004) APE: analyses of Phylogenetics and evolution in R language. Bioinformatics 20:289–290. (PMID: 10.1093/bioinformatics/btg41214734327)
Mantel N (1967) The detection of disease clustering and a generalized regression approach. Cancer Res 27(2):209–220. (PMID: 6018555)
Dixon P (2003) VEGAN, a package of R functions for community ecology. J Veg Sci 14:927–930. (PMID: 10.1111/j.1654-1103.2003.tb02228.x)
Fowler D, Barratt J, Walsh P (2018) Frictionless data: making research data quality visible. Int J Digit Curation 12:274–285. (PMID: 10.2218/ijdc.v12i2.577)
Boettiger C, Chamberlain S, Hart E, Ram K (2015) Building software, building community: lessons from the rOpenSci project. J Open Res Softw 3:8. (PMID: 10.5334/jors.bu)
فهرسة مساهمة: Keywords: Biodiversity; Bioinformatics; DNA barcoding; Research collaboration
المشرفين على المادة: 9007-49-2 (DNA)
تواريخ الأحداث: Date Created: 20240429 Date Completed: 20240429 Latest Revision: 20240429
رمز التحديث: 20240430
DOI: 10.1007/978-1-0716-3581-0_26
PMID: 38683334
قاعدة البيانات: MEDLINE
الوصف
تدمد:1940-6029
DOI:10.1007/978-1-0716-3581-0_26