The teleost anatomy ontology: anatomical representation for the genomics age.
The teleost anatomy ontology: anatomical representation for the genomics age.
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DOI：
10.1093/sysbio/syq013
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发表时间：
2010-07
影响因子：
6.5
通讯作者：
Mabee PM
中科院分区：
文献类型：
--
作者：
Dahdul WM;Lundberg JG;Midford PE;Balhoff JP;Lapp H;Vision TJ;Haendel MA;Westerfield M;Mabee PM
在系统文献中报道的生物体中形态变异的丰富知识一直保持自由文本格式，不切实际地用于大规模合成系统发育工作。这种不合格的格式还排除了与模型有机体数据库中基因组，遗传，发育和表型数据的大知识基础的联系。我们已经努力制作基于策划的，基于本体的进化形态数据库，该数据库映射到这些遗传数据库（http://kb.phenoscape.org），以促进对表型多样性的机械基础和进化的研究。建立此数据库的第一个要求之一是开发多种解剖本体，其目的是以系统和可计算的方式捕获解剖学数据。本体论是对这些概念之间有明确关系的一组概念的形式表示。尤其是多种种解剖学本体论是一种有效的方法，可以代表生物体进化枝中形态结构的多样性，但它们相对于单物种解剖学本体论提出了挑战。在这里，我们描述了Tebost解剖本体论（TAO），这是一种源自斑马鱼解剖本体论（ZFA）的硬骨鱼的多种解剖学本体，目的是注释各种物种的不同形态特征。为了促进与其他解剖学本体论的互操作性，TAO使用常见的解剖学参考本体论作为其上层节点的模板，而Tao和Tao和ZFA则同步，并用斑马鱼术语指定为标本术语的亚型。我们发现，本体架构的细节在查询方面有很大的影响，并且在开发多种特征解剖本体论方面提出了一般挑战，包括对定义的完善，术语之间的特定于分类群的关系以及分类可变的发展途径的代表。
The rich knowledge of morphological variation among organisms reported in the systematic literature has remained in free-text format, impractical for use in large-scale synthetic phylogenetic work. This noncomputable format has also precluded linkage to the large knowledgebase of genomic, genetic, developmental, and phenotype data in model organism databases. We have undertaken an effort to prototype a curated, ontology-based evolutionary morphology database that maps to these genetic databases (http://kb.phenoscape.org) to facilitate investigation into the mechanistic basis and evolution of phenotypic diversity. Among the first requirements in establishing this database was the development of a multispecies anatomy ontology with the goal of capturing anatomical data in a systematic and computable manner. An ontology is a formal representation of a set of concepts with defined relationships between those concepts. Multispecies anatomy ontologies in particular are an efficient way to represent the diversity of morphological structures in a clade of organisms, but they present challenges in their development relative to single-species anatomy ontologies. Here, we describe the Teleost Anatomy Ontology (TAO), a multispecies anatomy ontology for teleost fishes derived from the Zebrafish Anatomical Ontology (ZFA) for the purpose of annotating varying morphological features across species. To facilitate interoperability with other anatomy ontologies, TAO uses the Common Anatomy Reference Ontology as a template for its upper level nodes, and TAO and ZFA are synchronized, with zebrafish terms specified as subtypes of teleost terms. We found that the details of ontology architecture have ramifications for querying, and we present general challenges in developing a multispecies anatomy ontology, including refinement of definitions, taxon-specific relationships among terms, and representation of taxonomically variable developmental pathways.
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影响因子：
7
作者：
Ashburner, M;Ball, CA;Yoon, J
通讯作者：
Yoon, J
影响因子：
14.9
作者：
Avraham, Shulamit;Tung, Chih-Wei;Ilic, Katica;Jaiswal, Pankaj;Kellogg, Elizabeth A.;McCouch, Susan;Pujar, Anuradha;Reiser, Leonore;Rhee, Seung Y.;Sachs, Martin M.;Schaeffer, Mary;Stein, Lincoln;Stevens, Peter;Vincent, Leszek;Zapata, Felipe;Ware, Doreen
通讯作者：
Ware, Doreen
影响因子：
12.3
作者：
Gkoutos GV;Green EC;Mallon AM;Hancock JM;Davidson D
通讯作者：
Davidson D
影响因子：
14.9
作者：
Bult CJ;Eppig JT;Kadin JA;Richardson JE;Blake JA;Mouse Genome Database Group
通讯作者：
Mouse Genome Database Group
影响因子：
7.4
作者：
Ilic, Katica;Kellogg, Elizabeth A.;Rhee, Seung Y.
通讯作者：
Rhee, Seung Y.