Evolving BioAssay Ontology (BAO): modularization, integration and applications.
Evolving BioAssay Ontology (BAO): modularization, integration and applications.
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DOI：
10.1186/2041-1480-5-s1-s5
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发表时间：
2014
影响因子：
1.9
通讯作者：
Schürer SC
中科院分区：
文献类型：
--
作者：
Abeyruwan S;Vempati UD;Küçük-McGinty H;Visser U;Koleti A;Mir A;Sakurai K;Chung C;Bittker JA;Clemons PA;Brudz S;Siripala A;Morales AJ;Romacker M;Twomey D;Bureeva S;Lemmon V;Schürer SC
在药物和化学探针发现领域中，缺乏描述和注释生物测定和筛选结果的既定标准严重限制了利用公共和专有药物筛选数据以最大限度地发挥其潜力。我们已经创建了BioAssay Ontology（BAO）项目（http：bioassayontology.org），以开发描述低通量和高通量药物和探针筛选测定和结果的相关信息所需的通用参考元数据术语和定义。BAO的主要目标是实现药物筛选数据的有效整合、聚合、检索和分析。自2010年我们首次在BioPortal上发布BAO以来，我们已经大大扩展和增强了BAO，并且我们已经在几个内部和外部合作项目中应用了本体，例如BioAssay Research Database（BARD）。我们描述了BAO的演变，其设计能够模拟复杂的测定，包括配置文件和面板测定，例如基于集成网络的细胞特征库（LINCS）中的测定。在不断发展的BAO的关键问题之一是：我们如何能够提供一种方法来有效地重用和共享我们的本体的各个研究项目之间的特定部分，而不违反本体的完整性和不创建冗余。本文提供了一个全面的回答这个问题，描述了本体模块化的方法，使用分层架构。我们的模块化方法定义了几个不同的BAO组件，并将内部模块与外部模块以及域级组件与结构组件分开。这种方法有助于生成/提取可以适合特定用例或软件应用的派生本体（或视角）。我们描述了BAO的演变与其正式结构，工程方法和内容，使复杂的分析和集成与其他本体和数据集的建模。
The lack of established standards to describe and annotate biological assays and screening outcomes in the domain of drug and chemical probe discovery is a severe limitation to utilize public and proprietary drug screening data to their maximum potential. We have created the BioAssay Ontology (BAO) project (http://bioassayontology.org) to develop common reference metadata terms and definitions required for describing relevant information of low-and high-throughput drug and probe screening assays and results. The main objectives of BAO are to enable effective integration, aggregation, retrieval, and analyses of drug screening data. Since we first released BAO on the BioPortal in 2010 we have considerably expanded and enhanced BAO and we have applied the ontology in several internal and external collaborative projects, for example the BioAssay Research Database (BARD). We describe the evolution of BAO with a design that enables modeling complex assays including profile and panel assays such as those in the Library of Integrated Network-based Cellular Signatures (LINCS). One of the critical questions in evolving BAO is the following: how can we provide a way to efficiently reuse and share among various research projects specific parts of our ontologies without violating the integrity of the ontology and without creating redundancies. This paper provides a comprehensive answer to this question with a description of a methodology for ontology modularization using a layered architecture. Our modularization approach defines several distinct BAO components and separates internal from external modules and domain-level from structural components. This approach facilitates the generation/extraction of derived ontologies (or perspectives) that can suit particular use cases or software applications. We describe the evolution of BAO related to its formal structures, engineering approaches, and content to enable modeling of complex assays and integration with other ontologies and datasets.