Taxa: An R package implementing data standards and methods for taxonomic data

Foster, Zachary; Chamberlain, Scott; Grünwald, Niklaus J.

doi:10.12688/f1000research.14013.1

Cited by 14 publications

(3 citation statements)

References 8 publications

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“… Heat tree representation ( 83 , 84 ) of absolute species abundance in two highly discordant CF-patients ( CF-20 , top row; CF-25 , bottom row) pre-HEMT (A and D), after 14 weeks (B and E), and after 50 weeks (C and F) of treatment with ELX/TEZ/IVA. The lung function of CF-20 (12 years, F/MF, not pretreated with any CFTR modulator, no colonization with P. aeruginosa ) was highly impacted by ELX/TEZ/IVA (FEV 1 , +29%; MEF 25 , +75%), whereas his airway metagenome diversified only slightly (Species numbers, +19; Pielou’s evenness, +0.19; Shannon diversity, +1.06; Simpson diversity, +0.15) (B and C).…”

Section: Resultsmentioning

confidence: 99%

Impact of Elexacaftor/Tezacaftor/Ivacaftor Therapy on the Cystic Fibrosis Airway Microbial Metagenome

et al. 2022

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Shotgun metagenome sequencing of respiratory secretions with spike-in controls for normalization demonstrated that 1 year of high-efficient CFTR modulation with elexacaftor/tezacaftor/ivacaftor extensively reduced the bacterial load. Longer observation periods will be necessary to resolve whether the partial reversion of the basic defect that is achieved with ELX/TEZ/IVA is sufficient in the long run to render the CF lungs robust against the recolonization with common opportunistic pathogens.

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Section: Resultsmentioning

confidence: 99%

Impact of Elexacaftor/Tezacaftor/Ivacaftor Therapy on the Cystic Fibrosis Airway Microbial Metagenome

et al. 2022

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“…We used the “Taxize” package and expertise of each group to standardize the taxonomic names between the IUCN and traits databases (Foster et al., 2018 ). After this, we removed species with missing information about body size and trophic level in traits databases.…”

Section: Methodsmentioning

confidence: 99%

Body size and trophic structure explain global asymmetric response of tetrapod diversity to climate effects

Gusmão,

Tessarolo,

Dobrovolski

et al. 2024

Ecology and Evolution

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Although climate‐based hypotheses are widely used to explain large‐scale diversity patterns, they fall short of explaining the spatial variation among taxonomic groups. Integrating food web and metabolic theories into macroecology is a promising step forward, as they allow including explicit taxon‐specific traits that can potentially mediate the relationship between climate and diversity. Our investigation focuses on the role of body size and trophic structure in mediating the influence of contemporary climate and historical climate change on global tetrapods species richness. We used piecewise structural equation modeling to assess the direct effects of contemporary climate and climate instability of species richness and the indirect effects of climate on tetrapod richness mediated by community‐wide species traits. We found that birds and mammals are less sensitive to the direct effect of contemporary climate than amphibians and squamates. Contemporary climate and climate instability favored the species richness of mammals and amphibians. However, for birds and squamates, this link is only associated with contemporary climate. Moreover, we showed that community‐wide traits are correlated with species richness gradients. However, we highlight that this relationship is dependent upon the specific traits and taxonomic groups. Specifically, bird communities with smaller bodies and bottom‐heavy structures support higher species richness. Squamates also tend to be more diverse in communities with prevalence of smaller bodies, while mammals are correlated with top‐heavy structures. Moreover, we showed that higher contemporary climate and climate instability reduce the species richness of birds and mammals through community‐wide traits and indirectly increase squamate species richness. We also showed that body size and trophic structure are driving a global asymmetric response of tetrapod diversity to climate effects, which highlights the limitation to use the “typical” climate‐based hypotheses. Furthermore, by combining multiple theories, our research contributes to a more realistic and mechanistic understanding of diversity patterns across taxonomic groups.

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“…Infrastructure taxa [46], taxlist [47], taxview [48] Database Access (Online) algaeClassify [49], AmphiNom [50], dyntaxa [6], finbif [51], flora [52], mammals [53], natserv [54], neotoma2 [55], paleobioDB [56], plantlist [57], rcol [58], rebird [59], rentrez [60], rfishbase [61], rgbif [62], ritis [63], Rocc [64], rotl [65], rredlist [66], rtaxref [67], SP2000 [68], taxize [69,70], taxonomizr [71], taxonomyCleanr [72], Taxonstand [73,74], taxotools [75,76], taxreturn [77], TNRS [78,79], tpl [80], twn [81], wikitaxa [82], worms [83], worrms [84], zbank [85] Database Access (Offline) lcvplants [21], ncbit [86], taxadb [88,89], taxalight [90], taxastand…”

Section: Category Name Packagesmentioning

confidence: 99%

Harmonizing taxon names in biodiversity data: a review of tools, databases, and best practices

Grenié¹,

Berti²,

Winter³

et al. 2021

Preprint

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1. The process of standardizing taxa names, taxonomic name harmonization, is necessary to properly merge data indexed by taxon names. The large variety of taxonomic databases and related tools are often not well described. It is often unclear which databases are actively maintained or what is the original source of taxonomic information. In addition, software to access these databases is developed following non-compatible standards, which creates additional challenges for users. As a result, taxonomic harmonization has become a major obstacle in ecological studies that seek to combine multiple datasets.2. Here, we review and categorize a set of major taxonomic databases publicly available as well as a large collection of R packages to access them and to harmonize lists of taxa names. We categorized available taxonomic databases according to their taxonomic breadth (e.g. taxon-specific vs multi-taxa) and spatial scope (e.g. regional vs global), highlighting strengths and caveats of each type of database. We divided R packages according to their function, (e.g. syntax standardization tools, access to online databases, etc.) and highlighted overlaps among them. We present our findings (e.g. network of linkages, data and tool characteristics) in a ready-to-use Shiny web application (available at: https://mgrenie.shinyapps.io/taxharmonizexplorer/).3. We also provide general guidelines and best practice principles for taxonomic name harmonization. As an illustrative example, we harmonized taxon names of one of the largest databases of community time series currently available. We showed how different workflows can be used for different goals, highlighting their strengths and weaknesses and providing practical solutions to avoid common pitfalls.4. To our knowledge, our opinionated review represents the most exhaustive evaluation of links among and of taxonomic databases and related R tools. Finally, based on our new insights in the field, we make recommendations for users, database managers, and package developers alike.

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Taxa: An R package implementing data standards and methods for taxonomic data

Cited by 14 publications

References 8 publications

Impact of Elexacaftor/Tezacaftor/Ivacaftor Therapy on the Cystic Fibrosis Airway Microbial Metagenome

Impact of Elexacaftor/Tezacaftor/Ivacaftor Therapy on the Cystic Fibrosis Airway Microbial Metagenome

Body size and trophic structure explain global asymmetric response of tetrapod diversity to climate effects

Harmonizing taxon names in biodiversity data: a review of tools, databases, and best practices

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