Page Roderic D M
Division of Environmental and Evolutionary Biology, Institute of Biomedical and Life Sciences, Graham Kerr Building, University of Glasgow, Glasgow, UK.
BMC Bioinformatics. 2007 May 18;8:158. doi: 10.1186/1471-2105-8-158.
TreeBASE is currently the only available large-scale database of published organismal phylogenies. Its utility is hampered by a lack of taxonomic consistency, both within the database, and with names of organisms in external genomic, specimen, and taxonomic databases. The extent to which the phylogenetic knowledge in TreeBASE becomes integrated with these other sources is limited by this lack of consistency.
Taxonomic names in TreeBASE were mapped onto names in the external taxonomic databases IPNI, ITIS, NCBI, and uBio, and graph G of these mappings was constructed. Additional edges representing taxonomic synonymies were added to G, then all components of G were extracted. These components correspond to "name clusters", and group together names in TreeBASE that are inferred to refer to the same taxon. The mapping to NCBI enables hierarchical queries to be performed, which can improve TreeBASE information retrieval by an order of magnitude.
TBMap database provides a mapping of the bulk of the names in TreeBASE to names in external taxonomic databases, and a clustering of those mappings into sets of names that can be regarded as equivalent. This mapping enables queries and visualisations that cannot otherwise be constructed. A simple query interface to the mapping and names clusters is available at http://linnaeus.zoology.gla.ac.uk/~rpage/tbmap.
TreeBASE是目前唯一可用的已发表生物系统发育的大规模数据库。由于在数据库内部以及与外部基因组、标本和分类数据库中的生物名称缺乏分类一致性，其效用受到阻碍。由于缺乏这种一致性，TreeBASE中的系统发育知识与其他这些来源整合的程度受到限制。
将TreeBASE中的分类名称映射到外部分类数据库IPNI、ITIS、NCBI和uBio中的名称，并构建这些映射的图G。将表示分类同义词的附加边添加到G中，然后提取G的所有组件。这些组件对应于“名称簇”，并将TreeBASE中推断指同一分类单元的名称组合在一起。与NCBI的映射使得能够执行分层查询，这可以将TreeBASE信息检索提高一个数量级。
TBMap数据库提供了TreeBASE中大部分名称到外部分类数据库中名称的映射，并将这些映射聚类为可视为等效的名称集。这种映射使得能够进行否则无法构建的查询和可视化。可在http://linnaeus.zoology.gla.ac.uk/~rpage/tbmap获得一个到该映射和名称簇的简单查询界面。
