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The effect of automated taxa identification errors on biological indices

Johanna Ärje, Salme Kärkkäinen, Kristian Meissner, Alexandros Iosifidis, Türker Ince, Moncef Gabbouj, Serkan Kiranyaz
2017 Expert systems with applications  
Taxa identification errors can, however, have strong effects on the indices and thus on the determination of the ecological status.  ...  Highlights • We study the effects of classification errors from 11 different classifiers on 14 biological indices. • We assess the reasons why certain indices are more sensitive to classification errors  ...  for the grant of Ärje.  ... 
doi:10.1016/j.eswa.2016.12.015 fatcat:3codl77cpfghdiaxihwgjx3b6a

No one-size-fits-all solution to clean GBIF

Alexander Zizka, Fernanda Antunes Carvalho, Alice Calvente, Mabel Rocio Baez-Lizarazo, Andressa Cabral, Jessica Fernanda Ramos Coelho, Matheus Colli-Silva, Mariana Ramos Fantinati, Moabe Ferreira Fernandes, Thais Ferreira-Araujo, Fernanda Gondim Lambert Moreira, Nathalia Michelly da Cunha Santos (+10 others)
2020 biorxiv/medrxiv  
Here, we evaluate the effect of 13 recently proposed filters on the inference of species richness patterns and automated conservation assessments for 18 Neotropical taxa including animals, fungi, and plants  ...  Tests for duplicated information, collection year, basis of record as well as urban areas and coordinates for terrestrial taxa in the sea or marine taxa on land have the greatest effect.  ...  Test Type Rationale Table 3 . 3 The impact of automated filtering on occurrence records for 18 Neotropical taxa downloaded from www.gbif.org.  ... 
doi:10.1101/2020.03.12.974543 fatcat:4nckkewlujhp7ifla5dck2zqju

Automated species identification: why not?

K. J. Gaston, M. A. O'Neill
2004 Philosophical Transactions of the Royal Society of London. Biological Sciences  
The routine identification of specimens of previously described species has many of the characteristics of other activities that have been automated, and poses a major constraint on studies in many areas  ...  In this paper, we consider some of the reasons why automated species identification has not become widely employed, and whether it is a realistic option, addressing the notions that it is too difficult  ...  Discussions with several people have helped shape their views on the role and practice of automated identification; in particular they are grateful to I. D. Gauld  ... 
doi:10.1098/rstb.2003.1442 pmid:15253351 pmcid:PMC1693351 fatcat:f6uzqqrrevdd3mbrathpltnkfu

Phyllometric parameters and artificial neural networks for the identification ofBanksiaaccessions

Giuseppe Messina, Camilla Pandolfi, Sergio Mugnai, Elisa Azzarello, Kingsley Dixon, Stefano Mancuso
2009 Australian Systematic Botany  
The results indicate that this kind of network could be effectively and successfully used to discriminate among Banksia accessions, as the BPNN enabled a 93% unequivocal and correct simultaneous identification  ...  Taxonomic identification is traditionally carried out with dichotomous keys, or at least computer-based identification keys, often on the basis of subjective visual assessment and frequently unable to  ...  , travelling expenses) and for assistance with the identification of Banksia; Mr and Mrs Collins, owners of 'The Banksia Farm', for access to their collection of Banksia species from eastern Australia.  ... 
doi:10.1071/sb08003 fatcat:vc5gzytfyrhsjlmrsty75a3dey

Human experts vs. machines in taxa recognition [article]

Johanna Ärje, Jenni Raitoharju, Alexandros Iosifidis, Ville Tirronen, Kristian Meissner, Moncef Gabbouj, Serkan Kiranyaz, Salme Kärkkäinen
2019 arXiv   pre-print
The step of expert taxa recognition currently slows down the response time of many bioassessments.  ...  We also study the prediction accuracy on different ranks of taxonomic hierarchy in detail.  ...  ACKNOWLEDGEMENTS We thank the Academy of Finland for the grants of Ärje (284513, 289076), Tirronen (289076, 289104) Kärkkäinen (289076), Meissner (289104), and Raitoharju (288584).  ... 
arXiv:1708.06899v4 fatcat:q7lg4bbkdvgk7gnk2x4rvx2lbe

Self-organizing and self-correcting classifications of biological data

G. M. Garrity, T. G. Lilburn
2005 Bioinformatics  
Faced with the need to validate the annotation of thousands of sequences and to generate biologically meaningful classifications based on the sequence data, we turned to statistical methods in order to  ...  Motivation: Rapid, automated means of organizing biological data are required if we hope to keep abreast of the flood of data emanating from sequencing, microarray and similar high-throughput analyses.  ...  ACKNOWLEDGEMENTS We would like to express our thanks to the three anonymous reviewers for their helpful criticism of the original draft of this manuscript.  ... 
doi:10.1093/bioinformatics/bti346 pmid:15731209 fatcat:tkcl7cecwvf2nhhtkem2oi23bu

Computational aspects of systematic biology

T. G. Lilburn
2006 Briefings in Bioinformatics  
The availability of data is crucial if systematic biology is to enter the computer age.  ...  Algorithm development is in an early stage, and only a few examples of integrated applications for systematic biology are available.  ...  Acknowledgements Portions of this work were funded and supported by the Office of Science (BER), US Department of Energy, Grants No. DE¼FG02-04ER63933 and DE¼FG02-04ER63933.  ... 
doi:10.1093/bib/bbl005 pmid:16772262 fatcat:uh3jedjctvfhfgv4nmfjsl2uwu

Prospects and challenges of implementing DNA metabarcoding for high-throughput insect surveillance

Alexander M Piper, Jana Batovska, Noel O I Cogan, John Weiss, John Paul Cunningham, Brendan C Rodoni, Mark J Blacket
2019 GigaScience  
Moreover, the high-throughput nature of recent sequencing platforms could enable the multiplexing of hundreds of diverse trap samples on a single flow cell, thereby providing the means to dramatically  ...  Trap-based surveillance strategies are widely used for monitoring of invasive insect species, aiming to detect newly arrived exotic taxa as well as track the population levels of established or endemic  ...  Acknowledgements We thank the reviewers for comments and suggestions that greatly improved this manuscript.  ... 
doi:10.1093/gigascience/giz092 pmid:31363753 pmcid:PMC6667344 fatcat:x424tbh5gbbbhcewctrvay22fm

Semi-supervised machine learning for automated species identification by collagen peptide mass fingerprinting

Muxin Gu, Michael Buckley
2018 BMC Bioinformatics  
Biomolecular methods for species identification are increasingly being utilised in the study of changing environments, both at the microscopic and macroscopic levels.  ...  The aim was to minimise requirements on prior knowledge of known species while yielding satisfactory sensitivity and specificity.  ...  The analysis carried out here can be replicated through use of the data matrix presented in Additional file 3: Table S2 . The raw data is to be made available on the Archaeology Data  ... 
doi:10.1186/s12859-018-2221-3 pmid:29940843 pmcid:PMC6019507 fatcat:uq6kuaczojdaxda2w2spdt7sgy

Automated geoparsing and georeferencing of Malesian collection locality data
English

Reed Beaman, Barry Conn
2003 Telopea  
The fields of biological informatics and geomatics (biogeomatics) provide tools that streamline and automate acquisition, sharing, analysis, and visualisation of biogeographic data.  ...  Some form of geographic reference is almost always present on specimen labels, an essential source of information for mapping species distributions and performing biogeographic analyses.  ...  Paul Goia (Department of Conservation and Land Management, Western Australia) kindly reviewed this paper for us. One of us (R.S.B.  ... 
doi:10.7751/telopea20035604 fatcat:pl4ztnmdhbe6jk6h2swi3tglf4

Thoughts on screening tests in bacteriology

S P Lapage
1971 Journal of Clinical Pathology  
Taylor for reading the manuscript and providing advice and criticism.  ...  the most likely taxa suggested by the prior identification process.  ...  For example, no use seems to have been made, in the identification of bacteria, of the electrical charge on the bacteria of different species; this might prove a particularly suitable test in an automated  ... 
doi:10.1136/jcp.24.5.404 pmid:4937133 pmcid:PMC477017 fatcat:mlfres5osbgopokpnrdh77zzq4

Studying Ecosystems With DNA Metabarcoding: Lessons From Biomonitoring of Aquatic Macroinvertebrates

Alex Bush, Zacchaeus G. Compson, Wendy A. Monk, Teresita M. Porter, Royce Steeves, Erik Emilson, Nellie Gagne, Mehrdad Hajibabaei, Mélanie Roy, Donald J. Baird
2019 Frontiers in Ecology and Evolution  
A major hurdle has been the time-consuming and challenging process of sorting and identification of organisms, but the rapid development of DNA metabarcoding as a biodiversity observation tool provides  ...  As high-throughput sequencing becomes more rapid and cost-effective, a "big data" revolution is anticipated, based on higher and more accurate taxonomic resolution, more efficient detection, and greater  ...  be automated, further reducing the risk of handling errors and the costs of sequencing (Porter and Hajibabaei, 2018a) .  ... 
doi:10.3389/fevo.2019.00434 fatcat:bxvchcxogvb3pdv6uvwe6a5opa

Character Selection During Interactive Taxonomic Identification: "Best Characters"

Nadia Talent, Richard B. Dickinson, Timothy A. Dickinson
2014 Biodiversity Informatics  
most effectively reduce the number of identification steps required.  ...  We describe two improvements to the algorithm used by Delta-Intkey. The first improves transparency as the number of remaining taxa decreases, by normalizing the range of the coefficient to [0,1].  ...  Committee for agreeing to include NT among their number, an experience that produced a couple of serendipitous insights that encouraged submission of this manuscript.  ... 
doi:10.17161/bi.v9i1.4611 fatcat:itfgfcjkqnfuhbqmpxyurxkoli

Assessing strengths and weaknesses of DNA metabarcoding-based macroinvertebrate identification for routine stream monitoring

Vasco Elbrecht, Ecaterina Edith Vamos, Kristian Meissner, Jukka Aroviita, Florian Leese, Douglas Yu
2017 Methods in Ecology and Evolution  
the number of taxa than the morphology-based protocol, and also yielded 26 a higher taxonomic resolution.  ...  However, few 20 large-scale studies have compared the performance of DNA metabarcoding with that of routine morphological identification. 21 2) We performed metabarcoding using four primer sets on macroinvertebrate  ...  Unfortunately, the identification of benthic 48 taxa to species or even genus level is often difficult or impossible, and the accuracy of such identification is highly 49 dependent on the researcher's  ... 
doi:10.1111/2041-210x.12789 fatcat:uziituook5gx3bn6jnm6xckr64

Repeatability and reproducibility assessment in a large-scale population-based microbiota study: case study on human milk microbiota

Shirin Moossavi, Kelsey Fehr, Ehsan Khafipour, Meghan B. Azad
2021 Microbiome  
Batch effects can mask true biological results and/or result in irreproducible conclusions and interpretations.  ...  The framework consists of three independent stages: (1) verification of sequencing accuracy by assessing technical repeatability and reproducibility of the results using mock communities and biological  ...  We thank Padmaja Subbarao (University of Toronto) Director of the CHILD study, Malcolm R. Sears Received: 20 April 2020 Accepted: 29 December 2020  ... 
doi:10.1186/s40168-020-00998-4 pmid:33568231 fatcat:5zeag2oagvhnbjejn2jpwzdf6y
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