Enhancing phylogeography by improving geographical information from GenBank.
Enhancing phylogeography by improving geographical information from GenBank.
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DOI：
10.1016/j.jbi.2011.06.005
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发表时间：
2011-12-01
影响因子：
4.5
通讯作者：
Gonzalez, Graciela
中科院分区：
文献类型：
--
作者：
Scotch, Matthew;Sarkar, Indra Neil;Gonzalez, Graciela
系统地理学是一个专注于脊椎动物或病毒等物种的地理谱系的领域。在这里，地理数据，如物种或病毒宿主的位置，与从物种中提取的序列信息一样重要。总而言之，这些信息可以帮助说明物种在一个地理区域内随时间的迁徙，地理对进化历史的影响，或该区域内物种的预期种群。来自NCBI，特别是GenBank的分子序列数据为系统地理学提供了丰富的可用序列数据。然而，地理数据的表示不一致，并且在GenBank条目中稀疏。在推断地理信息的情况下，这可能会阻碍分析，并可能导致错误的结果。在本文中，我们描述了GenBank地理数据的现状，并说明了命名实体识别等自动化处理技术如何增强可用于系统地理研究的地理数据。
Phylogeography is a field that focuses on the geographical lineages of species such as vertebrates or viruses. Here, geographical data, such as location of a species or viral host is as important as the sequence information extracted from the species. Together, this information can help illustrate the migration of the species over time within a geographical area, the impact of geography over the evolutionary history, or the expected population of the species within the area. Molecular sequence data from NCBI, specifically GenBank, provide an abundance of available sequence data for phylogeography. However, geographical data is inconsistently represented and sparse across GenBank entries. This can impede analysis and in situations where the geographical information is inferred, and potentially lead to erroneous results. In this paper, we describe the current state of geographical data in GenBank, and illustrate how automated processing techniques such as named entity recognition, can enhance the geographical data available for phylogeographic studies.