Using multiple ontologies to integrate complex biological data

Mary Shimoyama; Victoria Petri; Dean Pasko; Susan Bromberg; Wenhua Wu; Jiali Chen; Nataliya Nenasheva; Anne Kwitek; Simon Twigger; Howard Jacob

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Using multiple ontologies to integrate complex biological data

机译：使用多种本体整合复杂的生物数据

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The strength of the rat as a model organism lies in its utility in pharmacology, biochemistry and physiology research. Data resulting from such studies is difficult to represent in databases and the creation of user-friendly data mining tools has proved difficult. The Rat Genome Database has developed a comprehensive ontology-based data structure and annotation system to integrate physiological data along with environmental and experimental factors, as well as genetic and genomic information. RGD uses multiple ontologies to integrate complex biological information from the molecular level to the whole organism, and to develop data mining and presentation tools. This approach allows RGD to indicate not only the phenotypes seen in a strain but also the specific values under each diet and atmospheric condition, as well as gender differences. Harnessing the power of ontologies in this way allows the user to gather and filter data in a customized fashion, so that a researcher can retrieve all phenotype readings for which a high hypoxia is a factor. Utilizing the same data structure for expression data, pathways and biological processes, RGD will provide a comprehensive research platform which allows users to investigate the conditions under which biological processes are altered and to elucidate the mechanisms of disease.

机译：大鼠作为模型生物的优势在于其在药理学，生物化学和生理学研究中的用途。从这些研究中获得的数据很难在数据库中表示出来，事实证明创建用户友好的数据挖掘工具很困难。大鼠基因组数据库已经开发了一个基于本体的综合数据结构和注释系统，可以将生理数据与环境和实验因素以及遗传和基因组信息整合在一起。 RGD使用多种本体将复杂的生物信息从分子水平整合到整个有机体，并开发数据挖掘和表示工具。通过这种方法，RGD不仅可以指示菌株中观察到的表型，还可以指示每种饮食和大气条件下的特定值以及性别差异。通过这种方式利用本体的强大功能，用户可以以自定义的方式收集和过滤数据，以便研究人员可以检索所有缺氧较高的表型读数。通过将相同的数据结构用于表达数据，途径和生物学过程，RGD将提供一个全面的研究平台，使用户能够研究生物学过程发生改变的条件并阐明疾病的机制。

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《Comparative and functional genomics》 |2005年第8期|共6页
作者
Mary Shimoyama; Victoria Petri; Dean Pasko; Susan Bromberg; Wenhua Wu; Jiali Chen; Nataliya Nenasheva; Anne Kwitek; Simon Twigger; Howard Jacob;
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正文语种 eng
中图分类分子生物学;
关键词
RGD; Rat Genome Database; phenotype; ontology; physiology;

机译：RGD;大鼠基因组数据库;表型;本体论;生理学;

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1. Using multiple ontologies to integrate complex biological data [J] . Mary Shimoyama, Victoria Petri, Dean Pasko, Comparative and functional genomics . 2005,第7a8期

机译：使用多种本体整合复杂的生物数据
2. The Semantic Metadatabase (SEMEDA): Ontology Based Integration of Federated Molecular Biological Data Sources [J] . Jacob Kohler, Steffen Schulze-Kremer In silico biology: An international on computational biology . 2002,第3期

机译：语义元数据库（SEMEDA）：基于本体的联合分子生物学数据源集成
3. SEMEDA: ontology based semantic integration of biological databases. [J] . Kohler J, Philippi S, Lange M Bioinformatics . 2003,第18期

机译：SEMEDA：基于本体的生物数据库语义集成。
4. Integrating Biological Process Modelling with Gene Expression Data and Ontologies for Functional Genomics (Position Paper) [C] . Liviu Badea, Doina Tilivea International Workshop on Computational Methods in Systems Biology . 2003

机译：将生物过程与基因表达数据和本体进行整合功能基因组学（位置纸）
5. Ontology based system to integrate phenotype data from multiple studies. [D] . Shimoyama, Mary. 2011

机译：基于本体的系统，用于整合来自多个研究的表型数据。
6. Using Multiple Ontologies to Integrate Complex Biological Data [O] . Mary Shimoyama, Victoria Petri, Dean Pasko, 2005

机译：使用多种本体整合复杂的生物数据
7. Using Multiple Ontologies to Integrate Complex Biological Data [O] . Howard Jacob, Simon Twigger, Anne Kwitek, 2006

机译：使用多种本体整合复杂的生物数据

Using multiple ontologies to integrate complex biological data

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