Enhanced XAO: the ontology of Xenopus anatomy and development underpins more accurate annotation of gene expression and queries on Xenbase
Enhanced XAO: the ontology of Xenopus anatomy and development underpins more accurate annotation of gene expression and queries on Xenbase
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DOI：
10.1186/2041-1480-4-31
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发表时间：
2013-10-01
影响因子：
1.9
通讯作者：
Zorn, Aaron M.
中科院分区：
文献类型：
--
作者：
Segerdell, Erik;Ponferrada, Virgilio G.;Zorn, Aaron M.
背景：非洲爪蛙爪蟾（Xenopus laevis）和热带爪蟾（Xenopus tropicalis）是著名的动物模式生物。对非洲爪蟾的研究有助于了解人类疾病的遗传、发育和分子机制。爪蟾解剖学本体论（Xenopus Anatomy Ontology， XAO）反映了爪蟾的解剖学和胚胎学发育。XAO提供了一致的术语，可以应用于解剖特征描述，以及一组关系，表明每个解剖实体如何与胚胎，蝌蚪或成年青蛙中的其他实体相关。XAO是Xenbase （http://www.xenbase.org）功能的组成部分，Xenbase是爪蟾模型生物数据库。结果：在过去的五年中，我们显著地扩展了XAO，增加了612个解剖学术语，2934个它们之间的关系，640个同义词和547个本体交叉引用。现在每个术语都有一个定义，因此数据库用户和管理员可以确定他们在指定解剖实体时选择了正确的术语。现在每个解剖术语都断言了发育时间信息，本体提供了内部检查，确保高质量的基因表达和表型数据注释。XAO现在有1313个已定义的解剖学和发育阶段术语，已经与Xenbase表达和解剖学术语搜索集成在一起，它可以在各种数据类型（包括图像、克隆和出版物）之间建立链接。对XAO结构和解剖定义的改进也增强了对其他模式生物和人类解剖本体的交叉参考，为爪蟾数据和其他脊椎动物之间提供了一座桥梁。本体论是免费向所有用户开放的。结论：扩展和改进的XAO可以增强爪蟾研究数据的捕获，并有助于通过文本匹配和手动管理执行复杂的基因表达、表型和抗体检索和分析机制。它对跨分类群本体的全面参考有助于将这些数据集成到人类疾病建模中。
Background: The African clawed frogs Xenopus laevis and Xenopus tropicalis are prominent animal model organisms. Xenopus research contributes to the understanding of genetic, developmental and molecular mechanisms underlying human disease. The Xenopus Anatomy Ontology (XAO) reflects the anatomy and embryological development of Xenopus. The XAO provides consistent terminology that can be applied to anatomical feature descriptions along with a set of relationships that indicate how each anatomical entity is related to others in the embryo, tadpole, or adult frog. The XAO is integral to the functionality of Xenbase (http://www.xenbase.org), the Xenopus model organism database.Results: We significantly expanded the XAO in the last five years by adding 612 anatomical terms, 2934 relationships between them, 640 synonyms, and 547 ontology cross-references. Each term now has a definition, so database users and curators can be certain they are selecting the correct term when specifying an anatomical entity. With developmental timing information now asserted for every anatomical term, the ontology provides internal checks that ensure high-quality gene expression and phenotype data annotation. The XAO, now with 1313 defined anatomical and developmental stage terms, has been integrated with Xenbase expression and anatomy term searches and it enables links between various data types including images, clones, and publications. Improvements to the XAO structure and anatomical definitions have also enhanced cross-references to anatomy ontologies of other model organisms and humans, providing a bridge between Xenopus data and other vertebrates. The ontology is free and open to all users.Conclusions: The expanded and improved XAO allows enhanced capture of Xenopus research data and aids mechanisms for performing complex retrieval and analysis of gene expression, phenotypes, and antibodies through text-matching and manual curation. Its comprehensive references to ontologies across taxa help integrate these data for human disease modeling.