Regenbase: A Searchable Database to Organize Regeneration Knowledge via Ontologie

Regenbase：通过 Ontologie 组织再生知识的可搜索数据库

• 批准号: 8653627
• 负责人: John L Bixby
• 金额: $ 56.44万
• 依托单位: UNIVERSITY OF MIAMI SCHOOL OF MEDICINE
• 依托单位国家: 美国
• 财政年份: 2012
• 资助国家: 美国
• 起止时间: 2012-05-15 至 2016-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8653627
• 关键词: Afferent Neurons; Area; Axon; Back; Biological; Biological Assay; Brain; Brain Diseases; Brain Injuries; Budgets; Cancer Immunology Science; Cell Death; Cells; Cellular biology; Chemical Structure; Cicatrix; Complementary DNA; Computer software; Corticospinal Tracts; Data; Data Analyses; Data Set; Databases; Dendrites; Development; Disease; Drug Compounding; Evaluation; Family; Funding; Future; Gene Expression; Gene Expression Profile; Genes; Genomics; Goals; Growth; Healthcare Systems; Human Genome Project; Individual; Informatics; Information Systems; Injury; Investigation; Knowledge; Link; Literature; Maps; Methodology; Molecular Bank; Molecular Target; Natural regeneration; Nerve; Nerve Regeneration; Nervous System Trauma; Nervous system structure; Neurons; Neurosciences; Online Systems; Ontology; Outcome; Paper; Pattern; Peripheral Nerves; PubChem; Resources; Scientist; Semantics; Societies; Solutions; Source; Speed; Spinal cord damage; Spinal cord injury; Stroke; Structure of rubrospinal tract; System; Technology; Terminology; Text; Translational Research; Traumatic Brain Injury; United States National Institutes of Health; Work; axon growth; axon regeneration; base; biomedical ontology; cell motility; computer based Semantic Analysis; data integration; data mining; drug discovery; graphical user interface; information display; information framework; injured; knockout gene; knowledge base; novel; novel therapeutics; overexpression; painful neuropathy; repaired; research study; screening; small molecule; success; text searching; therapy development; tool; vector

DESCRIPTION (provided by applicant): This application seeks funds to develop RegenBase - a novel information system to seamlessly integrate diverse data that are produced by neuroscientists and cell biologists studying nervous system injury, disease and cell motility with other resources, such as the Neuroscience Information Framework and the BioAssay Ontology. Over the past decade the NIH has funded the development of informatics tools and ontologies to allow the integration and interrogation of the massive and diverse data sets that have been produced by the human genome project. In the area of neuroscience the most advancement have been made in the creation and annotation of large anatomical data sets that reveal patterns of gene expression and connectivity. Genesat and the BrainMaps are excellent examples and are easily searched using the Neuroscience Information Framework (NIF) portal. But it is still surprisingly difficult to search for information related to repairing the injured nrvous system. To overcome this road block it is critical to build the essential tools that allow semantic web approaches to link diverse data repositories with ontologies that allow them to be interpreted and analyzed. The success of this initiative critically relies on an effective informatcs solution to integrate the various (current and future) data types generated by neuroscientists working on nervous system injury, as well as large-scale screening efforts (such as the Molecular Libraries Probe Center Network, MLPCN) into coherent data sets and to make them accessible, interpretable, and actionable for scientists of different backgrounds and with different objectives. We propose to develop a novel knowledge-based, extensible information system of interconnected components that leverages semantic-web technologies and domain level ontologies. This system is tentatively called RegenBase (Regeneration dataBase). Tremendous progress has been made during the last decade developing semantic web technologies with the goals of formalizing knowledge, linking information across different domains, and integrating large heterogeneous data sets from diverse sources. To develop RegenBase on a fast-track with limited resources, we will leverage technologies and tools from the National Center for Biological Onotology and the recently launched BioAssay Ontology. The long-term goal of the RegenBase system is seamless "on-the fly" data integration and analysis via a semantic "Linked Data" approach that is scalable with respect to information volume and complexity. RegenBase will incorporate biomedical domain-level ontologies, including our recently developed BioAssay Ontology (BAO), to semantically associate related data types and to provide a knowledge context of the underlying experiments and screening outcomes. The overarching goal of this proposed RegenBase system is to allow bench scientists to link data and results from studies on nervous system injury and disease to data and knowledge from other domains with an emphasis on molecular targets and the small molecules that perturb their function to speed the development of novel therapeutics.

描述（由申请人提供）：本申请寻求资金用于开发RegenBase——一个新颖的信息系统，可以将神经科学家和细胞生物学家研究神经系统损伤、疾病和细胞运动的各种数据与其他资源（如神经科学信息框架和生物测定本体）无缝集成。在过去的十年里，美国国立卫生研究院资助了信息学工具和本体的开发，以便对人类基因组计划产生的大量不同的数据集进行整合和查询。在神经科学领域，最大的进步是创建和注释揭示基因表达和连接模式的大型解剖数据集。Genesat和BrainMaps是很好的例子，可以很容易地使用神经科学信息框架（NIF）门户进行搜索。但是，搜索与修复受损神经系统有关的信息仍然非常困难。要克服这个障碍，关键是要构建允许语义化的基本工具