The use and limits of scientific names in biological informatics.
The use and limits of scientific names in biological informatics.
复制标题
DOI：
10.3897/zookeys.550.9546
复制
发表时间：
2016
期刊：
影响因子：
1.3
通讯作者：
Remsen D
中科院分区：
文献类型：
--
作者：
Remsen D
科学名称用于标记生物多样性信息：与物种有关的信息。然而，名称及其基本的分类定义是不稳定和模糊的。这对名称作为标识符和生物信息学中有效索引工具的效用产生了不利影响，因为在生物信息学中，名称通常用于搜索、检索和整合物种信息。符号学为描述分类单元名称和分类单元概念之间的关系提供了一个通用模型。它区分了句法和语义，句法支配名称之间的关系，语义代表这些标签和它们所指的分类群之间的关系。在符号学语境中，语义的变化（即，分类学界限）并不总是导致句法上相应的和反映性的变化。此外，当句法变化确实发生时，它们可以响应于语义变化或响应于句法规则。名称和分类群之间的基本关系缺乏一致性，限制了在生物信息学中如何在最初锚定以及随后的检索和整合相关生物多样性信息时使用科学名称。精确度和召回率是衡量相关性的两个指标。在生物分类学中，召回率受到句法变化或歧义的负面影响，而精确度则受到语义变化或歧义的负面影响。由于句法的变化与语义的变化无关，因此可以单独使用科学名称或将其合并为同义集合，以提高模式识别或搜索和检索的召回率。但是，不能使用名称来提高精度。这是因为语法的变化并不能唯一地标识限定的变化。这些观察结果限制了在依赖名称作为分类群标识符的生物信息学应用中科学名称的效用。用于组织和整合分类群信息的分类系统和服务必须适应科学名称固有的语义模糊性。对界限差异的捕捉和表达（即，多个分类单元概念）必须伴随有不同的概念标识符，这些概念标识符可以与传统的科学名称相关联地使用，或者替代传统的科学名称。
Scientific names serve to label biodiversity information: information related to species. Names, and their underlying taxonomic definitions, however, are unstable and ambiguous. This negatively impacts the utility of names as identifiers and as effective indexing tools in biological informatics where names are commonly utilized for searching, retrieving and integrating information about species. Semiotics provides a general model for describing the relationship between taxon names and taxon concepts. It distinguishes syntactics, which governs relationships among names, from semantics, which represents the relations between those labels and the taxa to which they refer. In the semiotic context, changes in semantics (i.e., taxonomic circumscription) do not consistently result in a corresponding and reflective change in syntax. Further, when syntactic changes do occur, they may be in response to semantic changes or in response to syntactic rules. This lack of consistency in the cardinal relationship between names and taxa places limits on how scientific names may be used in biological informatics in initially anchoring, and in the subsequent retrieval and integration, of relevant biodiversity information. Precision and recall are two measures of relevance. In biological taxonomy, recall is negatively impacted by changes or ambiguity in syntax while precision is negatively impacted when there are changes or ambiguity in semantics. Because changes in syntax are not correlated with changes in semantics, scientific names may be used, singly or conflated into synonymous sets, to improve recall in pattern recognition or search and retrieval. Names cannot be used, however, to improve precision. This is because changes in syntax do not uniquely identify changes in circumscription. These observations place limits on the utility of scientific names within biological informatics applications that rely on names as identifiers for taxa. Taxonomic systems and services used to organize and integrate information about taxa must accommodate the inherent semantic ambiguity of scientific names. The capture and articulation of circumscription differences (i.e., multiple taxon concepts) within such systems must be accompanied with distinct concept identifiers that can be employed in association with, or in replacement of, traditional scientific names.