OmniSearch: A semantic search tool for discovering microRNAs' critical roles in h

描述（由申请人提供）：MicroRNAs （miRNAs）通过调节各自的靶基因在生物过程中发挥关键作用。因此，mirna与人类癌症密切相关。人工整合mirna及其靶基因的信息是具有挑战性的：劳动密集型，容易出错，并且受制于生物学家的先验知识，因为它涉及到大量的异构数据源。我们的目标是开发OmniSearch，一个语义搜索工具，以帮助癌症生物学家以自动化和高效的方式揭示mirna在人类癌症中的关键作用。目标1：我们将开发microRNA靶点本体（OMIT），这是第一个microRNA域本体。OMIT将正式定义miRNA知识，并将提供一个全球元数据模型（即数据交换标准和公共数据元素）作为自动化知识获取的基础。我们将在既定的标准内工作，并为广泛的生物本体组贡献新的术语。目标2：根据OmniSearch元数据模型，我们将开发OmniSearch，包括自动语义数据注释和集成工具以及用户友好的语义搜索界面。由此产生的知识库将包含完全机器可读的数据，这些数据集成了来自不同来源的数据：miRNA目标预测数据库、基因本体、PubMed和KEGG PATHWAY。OmniSearch将在语义层面呈现统一的知识，这与癌症生物学家正在寻找的最相关。AIM 3：最后，我们将设计用例，然后是一组求值查询。OmniSearch将在知识的准确性、构建方法的效率（减少人力劳动）以及系统的友好性和可用性方面进行彻底和迭代的评估。我们将定期以有组织的方式征求反馈意见

DESCRIPTION (provided by applicant): MicroRNAs (miRNAs) perform critical roles in biological processes by regulating respective target genes. Thus, miRNAs are closely associated with human cancers. The manual integration of information on miRNAs and their target genes is challenging: labor-intensive, error-prone, and subject to biologists' prior knowledge - because it involves an extremely large amount of heterogeneous data sources to be explored. Our objective is to develop OmniSearch, a semantic search tool to assist cancer biologists in unraveling critical roles of miRNAs in human cancers in an automated and highly efficient manner. AIM 1: We will develop ontology for microRNA target (OMIT), the first miRNA domain ontologies. OMIT will formally define miRNA knowledge and will provide a global metadata model (i.e., data exchange standards and common data elements) as the foundation for automated knowledge acquisition. We will work within established standards and contribute new terminology to a wide range of bio-ontology groups. AIM 2: According to the OMIT metadata model, we will develop OmniSearch, including an automated semantic data annotation & integration tool and a user-friendly semantic search interface. The resultant knowledgebase will contain completely machine-readable data integrated from heterogeneous sources: miRNA target prediction databases, Gene Ontology, PubMed, and KEGG PATHWAY. OmniSearch will present unified knowledge, at the semantic level, that is most relevant to what cancer biologists are seeking. AIM 3: Finally, we will design use cases followed by a set of evaluating queries. OmniSearch will be thoroughly and iteratively evaluated in the knowledge accuracy, the efficiency of construction methods (the reduction of human labor), and the system friendliness and usability. On a regular basis and in a structured manner, we will solicit feedback from the community and incorporate domain experts' opinions to further improve the system. Feedback mechanisms will take place throughout the entire project lifetime. This project will handle critical needs recognized by the NCI ITCR Initiative: establishing data exchange standards and common data elements; sustained effort to promote data sharing; enhanced support of community-based, research-driven informatics technology development; improved mechanisms to support software development. Expected deliverables include OMIT ontologies as miRNA data exchange standards and common data elements; OmniSearch for miRNA data sharing and automated knowledge acquisition; a unified miRNA knowledgebase; and use cases and evaluating queries. OmniSearch can be used to obtain unified miRNA knowledge and bring insights into the regulation and control of cancer disease processes. By providing a deeper understanding of miRNAs' functions, OmniSearch will also assist miRNA bio-curation and new biological experiment design. Thus, the project can significantly accelerate cancer biology research. And, OmniSearch is by its nature extensible and can be readily generalized to other biomedical areas.