PhyloSophos: a high-throughput scientific name mapping algorithm augmented with explicit consideration of taxonomic science, and its application on natural product (NP) occurrence database processing DOI Creative Commons
Minhyung Cho, Kwang‐Hwi Cho, Kyoung Tai No

et al.

BMC Bioinformatics, Journal Year: 2023, Volume and Issue: 24(1)

Published: Dec. 14, 2023

Abstract Background The standardization of biological data using unique identifiers is vital for seamless integration, comprehensive interpretation, and reproducibility research findings, contributing to advancements in bioinformatics systems biology. Despite being widely accepted as a universal identifier, scientific names species have inherent limitations, including lack stability, uniqueness, convertibility, hindering their effective use databases, particularly natural product (NP) occurrence posing substantial obstacle utilizing this valuable large-scale applications. Result To address these challenges facilitate high-throughput analysis involving names, we developed PhyloSophos, Python package that considers the properties taxonomic accurately map name inputs entries within chosen reference database. We illustrate importance assessing multiple databases considering syntax-based pre-processing NP an example, with ultimate goal integrating heterogeneous information into single, unified dataset. Conclusions anticipate PhyloSophos significantly aid systematic processing poorly digitized curated data, such biodiversity ethnopharmacological resources, enabling full-scale resources.

Language: Английский

The importance of appropriate taxonomy in Australian mammalogy DOI Creative Commons
Stephen Jackson, Andrew M. Baker, Mark D. B. Eldridge

et al.

Australian Mammalogy, Journal Year: 2022, Volume and Issue: 45(1), P. 13 - 23

Published: Oct. 12, 2022

The use of correct taxonomy to describe and name the earth’s biodiversity is fundamental conservation management. However, there are issues that need be overcome ensure described taxa their scientific names both appropriate widely adopted. Obstacles this include different species definitions, taxonomic instability due accumulation additional specimens in analyses progression science allows better resolution boundaries, inappropriate description naming new without adequate basis self-published journals (known as ‘taxonomic vandalism’). In an effort manage instability, Australasian Mammal Taxonomy Consortium (AMTC), affiliated body Australian Society, has developed several tools include: (1) a standardised list mammal common names; (2) recommendations for information should included published descriptions; (3) support publication aspidonyms (i.e. scientifically acceptable proposed overwrite pre-existing unscientific name). This review discusses these issues, reaffirms foundations research, provides guidelines those publishing research on mammals.

Language: Английский

Citations

8

Collating biodiversity occurrence data for conservation DOI Creative Commons
Dian Spear, Nicola J. van Wilgen,

Anthony G. Rebelo

et al.

Frontiers in Ecology and Evolution, Journal Year: 2023, Volume and Issue: 11

Published: March 16, 2023

Plant and animal checklists, with conservation status information, are fundamental for management. Historical field data, more recent data of digital origin data-sharing platforms provide useful sources collating species locality data. However, different biodiversity datasets have formats inconsistent naming systems. Additionally, most do not an easy option download by protected area. Further, data-entry-ready software is readily available organization staff limited technical skills to collate these heterogeneous create distribution maps checklists areas. The insights presented here the outcome conceptualizing a information system South African National Parks. We recognize that requirement achieving better standardization, sharing use capacity building, internet connectivity, national institutional management support collaboration. focus on some issues need be considered standardization support. outline using taxonomic backbones standardizing utility from Global Biodiversity Information Facility other in this process. we make recommendations fields needed relational databases can used inform decisions steps taken enable easier collation Africa as case study.

Language: Английский

Citations

4

Widespread support for a global species list with a formal governance system DOI Creative Commons
Aaron Lien, Olaf Bánki, Saroj Kanta Barik

et al.

Proceedings of the National Academy of Sciences, Journal Year: 2023, Volume and Issue: 120(45)

Published: Oct. 30, 2023

Taxonomic data are a scientific common. Unlike nomenclature, which has strong governance institutions, there currently no generally accepted institutions for the compilation of taxonomic into an global list. This gap results in challenges conservation, ecological research, policymaking, international trade, and other areas societal importance. Consensus on list its management requires effective standards, including agreed mechanisms choosing among competing taxonomies partial lists. However, frameworks lacking, call 2017 generated critical responses. Any system to compliance is voluntary high level legitimacy credibility those by whom it created. Legitimacy credibility, turn, require adequate credible consultation. Here, we report survey taxonomists, scientists from disciplines, users taxonomy designed assess views test ideas new governance. We found surprisingly degree agreement need species their names, consistent what such should provide how be governed. The suggests that consensus mechanism create, manage, govern single widely all world’s achievable. finding was unexpected given past controversies about merits

Language: Английский

Citations

4

Trends in botanical exploration in Nigeria forecast over 1000 yet undescribed vascular plant species DOI Creative Commons
Abubakar Bello, Stewart M. Edie, Kowiyou Yessoufou

et al.

Annals of Botany, Journal Year: 2023, Volume and Issue: 133(5-6), P. 789 - 800

Published: July 28, 2023

Taxonomists are primary actors of biodiversity assessment. At the same time, there is awareness by taxonomic community at large that field going through a crisis, sometimes referred to as 'taxonomic impediment'. Coupled with ongoing or 6th mass extinction, this impedance puts risk target set in Convention on Biological Diversity's (CBD) Global Biodiversity Framework vision 2050, which calls for urgent action '… put path recovery 2030 benefit planet and people'. This particularly pronounced tropical African countries where studies done an ad hoc basis. In study, our aim investigate historical trends botanical exploration vascular plants Nigeria forecast near-term (50-year) description presently unknown species, we use discuss scenarios effort may be necessary comprehensive assessment country.

Language: Английский

Citations

3

Report of the Special‐purpose Committee on DNA Sequences as Types, established at the XIX International Botanical Congress in Shenzhen, China DOI Open Access
Samuli Lehtonen, Kevin R. Thiele

Taxon, Journal Year: 2023, Volume and Issue: 72(5), P. 1137 - 1142

Published: Oct. 1, 2023

Abstract A Special‐purpose Committee on DNA Sequences as Types was established at the XIX International Botanical Congress (IBC) in Shenzhen, China 2017, with a mandate to report XX IBC recommendations preferred course of action respect sequences potential types under Code Nomenclature for algae, fungi, and plants . This provides synthesis deliberations from this issue. We discuss two options dealing problem that many species, especially microfungi microalgae, can be discovered delimited using eDNA sequencing but cannot currently formally named due requirement either specimen or illustration nominated holotype. One option is expand definition “type” include sequences, while second would allow some taxa without types, application their names instead being determined sequence. should read concert formal proposals amendments effect these options, published issue Taxon

Language: Английский

Citations

3

Quantifying Bias in Hierarchical Category Systems DOI Creative Commons

Katie Warburton,

Charles Kemp, Yang Xu

et al.

Open Mind, Journal Year: 2024, Volume and Issue: 8, P. 102 - 130

Published: Jan. 1, 2024

Abstract Categorization is ubiquitous in human cognition and society, shapes how we perceive understand the world. Because categories reflect needs perspectives of their creators, no category system entirely objective, inbuilt biases can have harmful social consequences. Here propose methods for measuring hierarchical systems categories, a common form organization with multiple levels abstraction. We illustrate these by quantifying extent to which library classification are biased favour western concepts male authors. analyze large data set including more than 3 million books organized into thousands find that related religion show greater bias do literature or history, written men distributed broadly across women. also Dewey Decimal Classification shows level does Library Congress Classification. Although focus on as case study, our general, be used measure both natural institutional range domains.1

Language: Английский

Citations

0

Measuring and explaining disagreement in bird taxonomy DOI Creative Commons
Stijn Conix, Vincent Cuypers, Charles H. Pence

et al.

European Journal of Taxonomy, Journal Year: 2024, Volume and Issue: 943

Published: July 17, 2024

Species lists play an important role in biology and practical domains like conservation, legislation, biosecurity trade regulation. However, their effective use by non-specialist scientific societal users is sometimes hindered disagreements between competing lists. While it well-known that such exist, remains unclear how prevalent they are, what nature is, causes them. In this study, we argue these questions should be investigated using methods based on taxon concept rather than Linnaean names, a concept-based method to quantify disagreement about bird classification investigate its relation research effort. We found there was 38% of all groups birds recognized as species, more three times much indicated previous measures. Disagreement the delimitation most common kind conflict, outnumbering nomenclature rank. high levels conflict rank were associated with lower effort, not case for groups. This suggests taxonomic cannot resolved simply increasing

Language: Английский

Citations

0

Correlates of avian extinction timing around the world since 1500 CE DOI Creative Commons
Kyle D. Kittelberger,

Colby J. Tanner,

Amy N. Buxton

et al.

Avian Research, Journal Year: 2024, Volume and Issue: 15, P. 100213 - 100213

Published: Jan. 1, 2024

Language: Английский

Citations

0

Linear listing order and hierarchical classification: history, conflict, and use DOI Creative Commons
Alessandro Minelli

European Journal of Taxonomy, Journal Year: 2023, Volume and Issue: 908

Published: Nov. 15, 2023

Taxonomic criteria alone are not sufficient to determine a linear sequence for the arrangement of collection specimens according preferred classification or which taxa best discussed in articles books. The choice methodology obtain agreement with hierarchical has been little studied and remains controversial. In this article, I offer an historical background, before examining properties, use limits possible listing criteria. result linearization effort depends on arbitrary choices respect two aspects we intend linearize. One is order be followed immediately subordinate members given taxon, other sets linearized tradition, alphabetic criterion. example presented here, related “orders” Hexapoda, demonstrates need specify very clearly extent composition uncollapsed backbone retained procedure.

Language: Английский

Citations

1

Recommendations for connecting molecular sequence and biodiversity research infrastructures through ELIXIR DOI Creative Commons
Robert M. Waterhouse, Anne‐Françoise Adam‐Blondon,

Donat Agosti

et al.

F1000Research, Journal Year: 2022, Volume and Issue: 10, P. 1238 - 1238

Published: Aug. 1, 2022

Threats to global biodiversity are increasingly recognised by scientists and the public as a critical challenge. Molecular sequencing technologies offer means catalogue, explore, monitor richness biogeography of life on Earth. However, exploiting their full potential requires tools that connect infrastructures resources. As research infrastructure developing services technical solutions help integrate coordinate science resources across Europe, ELIXIR is key player. To identify opportunities, highlight priorities, aid strategic thinking, here we survey approaches which molecular inform understanding biodiversity. We detail example use cases how DNA is: resolving taxonomic issues; Increasing knowledge marine biodiversity; helping understand agriculture critically linked; playing an essential role in ecological studies. Together with examples national programmes, show where progress being made but also common challenges opportunities for future enhancement underlying wider domains. Based emerging themes, propose recommendations guide funding research: bioinformatic need collaborate closely strategically; efforts be aligned harmonised domains; metadata needs standardised data management widely adopted; current scaled up dramatically address anticipated explosion data; bioinformatics support enabled sustained; training end users prioritised; community initiatives proactive focused enabling solutions. For deliver they must connected knowledge: together, sequence collection can advance prevent further decline Earth’s biodiversity.

Language: Английский

Citations

2