巨大的:一个R包整合分类信息跨脊柱
Felix Specker1,2, Andrea Paz1, Thomas W Crowther1
1Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland.
PeerJ
|March 4, 2024
概括
Treemendous是一个新的R包,它在多个分类学数据库中标准化树种名称. 该软件解决了相互矛盾的数据,通过确保一致的物种识别来改善生物多样性研究.
科学领域:
- 生物多样性研究的研究.
- 计算生物学是一种计算生物学.
- 生态生态学 生态生态学
背景情况:
- 整合生物多样性数据需要在各种数据库中标准化物种名称.
- 现有的名称解析工具很难调和来自多个来源的相互矛盾的分类学信息.
- 需要一种原则性的方法来结合来自不同骨干的分类学数据.
研究的目的:
- 推出Treemendous,一个开源的R包,用于解决和翻译树种名称.
- 为了能够整合具有不一致的分类学起源的物种列表.
- 提高生物多样性数据集中物种识别的准确性和一致性.
主要方法:
- 开发了一个R包,整合了来自四个公共数据库的分类学关系.
- 实现基于图形的代匹配,使用跨骨干的同义词接受关系.
- 使用户能够在不同的分类学骨干之间翻译物种列表.
主要成果:
- 非常有效地解决冲突和不一致的分类学数据.
- 该包增加了物种名称匹配率,并最大限度地减少了数据丢失.
- 为独立使用或与现有工具集成提供灵活的工作流.
结论:
- 在生物多样性研究中,Treemendous为树种名称的标准化提供了一个强大的解决方案.
- 该方案促进了数据的同化和合并,增强了森林生物多样性和树生态研究.
- 该工具可以提高数据的一致性,并减少生态研究中的数据丢失.
相关概念视频
Phylogeny
44.1K
Phylogeny is concerned with the evolutionary diversification of organisms or groups of organisms. A group of organisms with a name is called a taxon (singular). Taxa (plural) can span different levels of the evolutionary hierarchy. For instance, the group containing all birds is a taxon (comprising the class Aves), and the group of all species of daisies (the genus Bellis) is a taxon. Phylogenies can likewise include just one genus (i.e., depict species relationships) or span an entire kingdom.
44.1K
Phylogenetic Trees
45.3K
Phylogenetic trees come in many forms. It matters in which sequence the organisms are arranged from the bottom to the top of the tree, but the branches can rotate at their nodes without altering the information. The lines connecting individual nodes can be straight, angled, or even curved.
45.3K
Evolutionary Relationships through Genome Comparisons
5.7K
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
5.7K
Introduction to R
267
R is a powerful software environment for statistical computing and graphics. Originating as an implementation of the S language, developed at Bell Laboratories, R has evolved into a robust, open-source statistical software favored by statisticians and data scientists worldwide. Its comprehensive suite includes data manipulation, calculation, and graphical display capabilities, making it versatile for data analysis and visualization. Its programming language is at the core of R's...
267
Pedigree Analysis
84.2K
Overview
84.2K
The Tree of Life - Bacteria, Archaea, Eukaryotes
32.4K
The “tree of life” describes the evolution of life and the evolutionary relationships between organisms. The root of the tree is the common ancestor to all life on Earth. All other species radiate from this point, much like the branches of a tree. The numerous tips of these branches on the tree of life represent every living, or extant, species. Extinct species, which are species that no longer exist, can be found towards the center of the tree. Currently, these organisms, both...
32.4K


