<br>Taxallnomy：NCBI 分类法的扩展，可生成层次完整的分类树,BMC Bioinformatics

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Taxallnomy：NCBI 分类法的扩展，可生成层次完整的分类树
BMC Bioinformatics ( IF 2.9 ) Pub Date : 2021-07-29 , DOI: 10.1186/s12859-021-04304-3
Tetsu Sakamoto _{1,

2} , J Miguel Ortega ₂

Affiliation

NCBI 分类法是多种生物信息学工具和数据库的主要分类来源，因为所有具有存储在 INSDC 上的序列登录的生物体都按其层次结构进行组织。尽管该数据源被广泛使用和应用，但以表格形式表示数据的替代方式将有助于使用信息来处理生物信息学数据。为此，由于某些谱系中缺少某些分类等级，算法可能会为所有分类等级提出临时名称。为了解决这个问题，我们开发了一种算法，该算法采用 NCBI 分类法中的树结构并生成层次结构完整的分类表，保持其与原始树的兼容性。该算法执行的过程包括尝试将分类等级分配给现有的进化枝或“无等级”节点（如果可能），使用其名称作为创建的分类等级名称的一部分（例如 Ord_Ornithischia）或在需要时插入父节点（例如 Cla_of_Ornithischia），这两个例子都是针对恐龙短脊龙谱系的。新的层次结构被命名为 Taxallnomy，因为它包含所有分类等级的名称，并且包含 41 个层次级别，对应于当前在 NCBI 分类数据库中找到的 41 个分类等级。从Taxallnomy中，用户可以获得NCBI分类数据库中所有类群的41个节点的完整分类谱系，而不会对原始树信息造成任何危害。在这项工作中，我们通过将指定等级的分类信息嵌入系统发育树并生成宏基因组图谱来证明其适用性。分类学适用于任何依赖于 NCBI 分类学信息的生物信息学分析。 Taxallnomy 会定期更新，但通过分布式 PERL 脚本，用户可以使用 NCBI Taxonomy 作为输入在本地生成它。所有 Taxallnomy 资源均可在 http://bioinfo.icb.ufmg.br/taxallnomy 上获取。

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Taxallnomy: an extension of NCBI Taxonomy that produces a hierarchically complete taxonomic tree

NCBI Taxonomy is the main taxonomic source for several bioinformatics tools and databases since all organisms with sequence accessions deposited on INSDC are organized in its hierarchical structure. Despite the extensive use and application of this data source, an alternative representation of data as a table would facilitate the use of information for processing bioinformatics data. To do so, since some taxonomic-ranks are missing in some lineages, an algorithm might propose provisional names for all taxonomic-ranks. To address this issue, we developed an algorithm that takes the tree structure from NCBI Taxonomy and generates a hierarchically complete taxonomic table, maintaining its compatibility with the original tree. The procedures performed by the algorithm consist of attempting to assign a taxonomic-rank to an existing clade or “no rank” node when possible, using its name as part of the created taxonomic-rank name (e.g. Ord_Ornithischia) or interpolating parent nodes when needed (e.g. Cla_of_Ornithischia), both examples given for the dinosaur Brachylophosaurus lineage. The new hierarchical structure was named Taxallnomy because it contains names for all taxonomic-ranks, and it contains 41 hierarchical levels corresponding to the 41 taxonomic-ranks currently found in the NCBI Taxonomy database. From Taxallnomy, users can obtain the complete taxonomic lineage with 41 nodes of all taxa available in the NCBI Taxonomy database, without any hazard to the original tree information. In this work, we demonstrate its applicability by embedding taxonomic information of a specified rank into a phylogenetic tree and by producing metagenomics profiles. Taxallnomy applies to any bioinformatics analyses that depend on the information from NCBI Taxonomy. Taxallnomy is updated periodically but with a distributed PERL script users can generate it locally using NCBI Taxonomy as input. All Taxallnomy resources are available at http://bioinfo.icb.ufmg.br/taxallnomy .

更新日期：2021-07-29

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