Visually Overviewing Biodiversity Open Data Digital Collections

After years of mass digitisation initiatives in Natural History institutions, large biodiversity collections have emerged on the web as open data. Studies on climate change and nature conservation rely heavily on this data to understand the distribution, presence/absence, changes over time, and interaction of species, and community ecology. For the institutions that hold this data, the exploration and verification of the records they produce are critical to support new modes of studying, analysing, and accessing biodiversity information. However, the process of data verification is challenging given the complex relationships between the data. This poses difficulties to the diagnosis of completeness, correctness, and good coverage of the domain. To this day, there is no clear understanding of to what extent existing visualization techniques can systematically support the task of data verification. To support research in this area, this paper reviews the visualisation solutions by focusing on a function-based visual exploration concept that can be integrated into a data verification pipeline for biodiversity datasets. Beyond reviewing the state of the art, we describe a data verification pipeline following such concept for biodiversity collections of the National Museum/Federal University of Rio de Janeiro, Brazil. The pipeline is targeted to domain expert users in supporting strategic decisions on data maintenance, as well as also having the potential to support general users in contextualising the datasets.

Content

Author and article information

Contributors

Asla Medeiros e Sá

Franklin Alves de Oliveira

Bruno Schneider

Karina Rodriguez Echavarria

Cristiana Silveira Serejo

Conference

Publication date (Print): July 2022

Pages: 1-8

Affiliations

[0001]School of Applied Mathematics

Fundação Getúlio Vargas

FGV/EMAp, Rio de Janeiro, Brazil

https://emap.fgv.br/

[0002]Data Analysis and Visualization Group

Universität Konstanz

Konstanz, Germany

https://www.vis.uni-konstanz.de/

[0003]Centre for Secure, Intelligent and Usable Systems,

University of Brighton, UK

https://orcid.org/0000-0002-8679-1602

[0004]Museu Nacional

Universidde Federal do Rio de Janeiro

MN/UFRJ, Rio de Janeiro, Brazil

https://www.museunacional.ufrj.br/

Article

DOI: 10.14236/ewic/ODAK22.4

SO-VID: 0f138128-ef18-46ac-b62b-e0d6125a4a19

License:

This work is licensed under a Creative Commons Attribution 4.0 Unported License. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/

Conference name: Proceedings of the Symposium on Open Data and Knowledge for a Post-Pandemic Era ODAK22, UK

Conference acronym: ODAK 2022

Conference number:

Conference location: Brighton, UK

Conference date: June 30-July 1, 2022

Conference sponsor: Electronic Workshops in Computing (eWiC)

Conference theme: Open Data and Knowledge for a Post-Pandemic Era

History

Product

1477-9358 BCS Learning & Development

Self URI (article page): https://www.scienceopen.com/hosted-document?doi=10.14236/ewic/ODAK22.4

Self URI (journal page): https://ewic.bcs.org/

REFERENCES

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2021b Specify software https://www.specifysoftware.org/
V BarveJ Otegui 2016 06 bdvis: visualizing biodiversity data in R Bioinformatics 32 19 3049 3050
T BentonC Benton, and D Sharp 1975 Form and function: A source book for the history of architecture and design 1890-1939 Crosby Lockwood Staples
J Bertin 1967 Semiology of graphics: diagrams, networks, maps (translated by william j. berg)
M Card 1999 Readings in information visualization: using vision to think Morgan Kaufmann
S CeccarelliA BalsalobreM. E CanoD CanaleP LobbiaR StarioloJ. E RabinovichG. A Marti 2020 Analysis of chagas disease vectors occurrence data: the argentinean triatomine species database Biodiversity data journal 8
Z FosterS ChamberlainN Grünwald 2018 Taxa: An r package implementing data standards and methods for taxonomic data [version 2; peer review: 4 approved] F1000Research 7 272
Z FosterT Sharpton, and N Grünwald 2017 02 Metacoder: An r package for visualization and manipulation of community taxonomic diversity data PLOS Computational Biology 13 2 1 15
M GrahamJ Kennedy 2014 Vesper: Visualising species archives Ecological Informatics 24 132 147
J JanickiN NarulaM ZieglerB GuénardE Economo 2016 Visualizing and interacting with large-volume biodiversity data using client-server webmapping applications: The design and implementation of antmaps.org Ecological Informatics 32 185 193
W JetzJ. M McPhersonR. P Guralnick 2012 Integrating biodiversity distribution knowledge: toward a global map of life Trends in Ecology & Evolution 27 3 151 159
Y MabroukiA TaybiG ChavanonA BerrahouA Millán 2018 Distribution of aquatic beetles from the east of morocco (coleoptera, polyphaga) Arxius de Miscel. lània Zoològica 185 211
B OndovN Bergman, and A Phillippy 2011 09 Krona: Interactive metagenomic visualization in a web browser BMC bioinformatics 12 385
J OteguiA. H Ariño 2012 06 BIDDSAT: visualizing the content of biodiversity data publishers in the Global Biodiversity Information Facility network Bioinformatics 28 16 2207 2208
A. J Pérez-LuqueJ. M Barea-AzcónL Álvarez-RuizF. J Bonet-GarcíaR Zamora 2016 Dataset of passerine bird communities in a mediterranean high mountain (sierra nevada, spain) ZooKeys 552 137
A. J Pérez-LuqueF. J BonetR Pérez-PérezR AspizuaJ LoriteR Zamora 2014 Sinfonevada: Dataset of floristic diversity in sierra nevada forests (se spain) PhytoKeys 35 1
Z QuJ Hullman 2016 Evaluating visualization sets: Trade-offs between local effectiveness and global consistency Proceedings of the Sixth Workshop on Beyond Time and Errors on Novel Evaluation Methods for Visualization 44 52
B Shneiderman 2003 The eyes have it: A task by data type taxonomy for information visualizations The craft of information visualization 364 371 Elsevier
J StaskoR CatramboneM Guzdial, and K McDonald 2000 An evaluation of space-filling information visualizations for depicting hierarchical structures International journal of human-computer studies 53 5 663 694
M WardGrinsteinD Keim 2015 Interactive Data Visualization: Foundations, Techniques, and Applications, Second Edition (2nd ed.) A K Peters/CRC Press
H Wickham 2010 A layered grammar of graphics Journal of Computational and Graphical Statistics 19 1 3 28
L Wilkinson 1999 The grammar of graphics Statistics and Computing Springer
F WindhagerP FedericoG SchrederK GlinkaM DörkS MikschE Mayr 2018 Visualization of cultural heritage collection data: State of the art and future challenges IEEE Transactions on Visualization and Computer Graphics 25 20 Online browser: http://collectionvis.org

Comments

Comment on this article

[1] 2020 Gbif: The global biodiversity information facility (year) what is gbif? https://www.gbif.org/what-is-gbif .

[2] 2021a Specify insight app https://www.specifysoftware.org/products/insight/

[3] 2021b Specify software https://www.specifysoftware.org/

[4] V BarveJ Otegui 2016 06 bdvis: visualizing biodiversity data in R Bioinformatics 32 19 3049 3050

[5] T BentonC Benton, and D Sharp 1975 Form and function: A source book for the history of architecture and design 1890-1939 Crosby Lockwood Staples

[6] J Bertin 1967 Semiology of graphics: diagrams, networks, maps (translated by william j. berg)

[7] M Card 1999 Readings in information visualization: using vision to think Morgan Kaufmann

[8] S CeccarelliA BalsalobreM. E CanoD CanaleP LobbiaR StarioloJ. E RabinovichG. A Marti 2020 Analysis of chagas disease vectors occurrence data: the argentinean triatomine species database Biodiversity data journal 8

[9] Z FosterS ChamberlainN Grünwald 2018 Taxa: An r package implementing data standards and methods for taxonomic data [version 2; peer review: 4 approved] F1000Research 7 272

[10] Z FosterT Sharpton, and N Grünwald 2017 02 Metacoder: An r package for visualization and manipulation of community taxonomic diversity data PLOS Computational Biology 13 2 1 15

[11] M GrahamJ Kennedy 2014 Vesper: Visualising species archives Ecological Informatics 24 132 147

[12] J JanickiN NarulaM ZieglerB GuénardE Economo 2016 Visualizing and interacting with large-volume biodiversity data using client-server webmapping applications: The design and implementation of antmaps.org Ecological Informatics 32 185 193

[13] W JetzJ. M McPhersonR. P Guralnick 2012 Integrating biodiversity distribution knowledge: toward a global map of life Trends in Ecology & Evolution 27 3 151 159

[14] Y MabroukiA TaybiG ChavanonA BerrahouA Millán 2018 Distribution of aquatic beetles from the east of morocco (coleoptera, polyphaga) Arxius de Miscel. lània Zoològica 185 211

[15] B OndovN Bergman, and A Phillippy 2011 09 Krona: Interactive metagenomic visualization in a web browser BMC bioinformatics 12 385

[16] J OteguiA. H Ariño 2012 06 BIDDSAT: visualizing the content of biodiversity data publishers in the Global Biodiversity Information Facility network Bioinformatics 28 16 2207 2208

[17] A. J Pérez-LuqueJ. M Barea-AzcónL Álvarez-RuizF. J Bonet-GarcíaR Zamora 2016 Dataset of passerine bird communities in a mediterranean high mountain (sierra nevada, spain) ZooKeys 552 137

[18] A. J Pérez-LuqueF. J BonetR Pérez-PérezR AspizuaJ LoriteR Zamora 2014 Sinfonevada: Dataset of floristic diversity in sierra nevada forests (se spain) PhytoKeys 35 1

[19] Z QuJ Hullman 2016 Evaluating visualization sets: Trade-offs between local effectiveness and global consistency Proceedings of the Sixth Workshop on Beyond Time and Errors on Novel Evaluation Methods for Visualization 44 52

[20] B Shneiderman 2003 The eyes have it: A task by data type taxonomy for information visualizations The craft of information visualization 364 371 Elsevier

[21] J StaskoR CatramboneM Guzdial, and K McDonald 2000 An evaluation of space-filling information visualizations for depicting hierarchical structures International journal of human-computer studies 53 5 663 694

[22] M WardGrinsteinD Keim 2015 Interactive Data Visualization: Foundations, Techniques, and Applications, Second Edition (2nd ed.) A K Peters/CRC Press

[23] H Wickham 2010 A layered grammar of graphics Journal of Computational and Graphical Statistics 19 1 3 28

[24] L Wilkinson 1999 The grammar of graphics Statistics and Computing Springer

[25] F WindhagerP FedericoG SchrederK GlinkaM DörkS MikschE Mayr 2018 Visualization of cultural heritage collection data: State of the art and future challenges IEEE Transactions on Visualization and Computer Graphics 25 20 Online browser: http://collectionvis.org

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