HIGH THROUGHPUT LITERATURE CURATION OF GENETIC REGULATION IN BACTERIAL MODELS

细菌模型中遗传调控的高通量文献整理

• 批准号: 9193091
• 负责人: Julio Collado-Vides
• 金额: $ 39.62万
• 依托单位: CENTER FOR GENOMIC SCIENCES
• 依托单位国家: 美国
• 财政年份: 2015
• 资助国家: 美国
• 起止时间: 2015-01-01 至 2018-12-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9193091
• 关键词: Area; Bacteria; Bacterial Model; Binding Sites; Biological; Biological Process; Biology; Biomedical Research; Cells; Classification; Collection; Communities; Complex; Data Set; Databases; Effectiveness; Elements; Escherichia coli; Evolution; Foundations; Future; Gene Expression Regulation; Genes; Genetic; Genetic Programming; Genetic Transcription; Genome; Genomics; Growth; Human; International; Joints; Knowledge; Letters; Linguistics; Literature; Manuals; Methodology; Methods; Modeling; Molecular; Natural Language Processing; Nature; Ontology; Operon; Organism; Paper; Physiological; Physiological Processes; Planet Earth; Process; Property; Publications; Publishing; Reaction; Reading; Regulation; Regulon; Reporting; Research Infrastructure; Series; Signal Transduction; Site; Solid; Source; System; Technology; Text; Training; Transcription Initiation; Transcriptional Regulation; base; cell behavior; digital; electronic book; experience; feeding; functional genomics; improved; innovation; member; microbial community; model organisms databases; novel; novel strategies; promoter; prototype; public health relevance; response; software development; text searching; tool; transcription factor; usability

DESCRIPTION (provided by applicant): The aim of this proposal is to implement a novel way of processing and accessing the vast detailed knowledge contained within collections of scientific publications on the regulation of transcription initiation in bacterial models. In princple, this model for processing and reading information and new knowledge is applicable to other biological domains, potentially benefiting any area of biomedical knowledge. It is certainly criticl to generate new strategies to cope with the ever-increasing amount of knowledge generated in genomics and in biomedical research at large. Improving the efficiency of the traditional high-quality manual curation of scientific publications will enable us also to expand the type of biological knowledge, beyond mechanisms and their elements in the genome, to start including their connections with larger regulated processes and eventually physiological properties of the cell. We will first implement the necessary technology to improve our curation by means of a computational system that has text mining capabilities for preprocessing the papers before a human expert curator identifies which sentences contain the information that is to be added to the database. Premarked options selected by the curators will accelerate their decisions. The accumulative precise mapping between sentences and curated knowledge will provide training sets for text mining technologies to improve their automatic extraction. The curator practices will become more efficient, enabling us to curate selected high-impact published reviews to place mechanisms into a rich context of their physiological processes and general biology. Another relevant component of our proposal is the improved modeling of regulated processes by means of new concepts in biology that capture larger collections of coregulated genes and their concatenated reactions. Starting from all interactions of a local regulator, coregulated regulators and their domain of action will be incorporated to construct the biobricks of complex decisions, as they are encoded in the genome. These are conceptual containers that capture the organization of knowledge to describe the genetic programming of cellular capabilities. These proposals will be formalized and proposed within an international consortium focused in enriching standard models or ontologies of gene regulation for use by the scientific community. Finally, a portal to navigate across all the sentences of a given corpus of a large number (more than 5,000) of related papers will be implemented. The different avenues of navigation will essentially use two technologies, one dealing with automatically generating simpler sentences from original sentences as input, and the other one with the classification of papers based on their theme or ontology. Their combination will enable a novel navigation reading system. If we achieve our aims, this project will give a proof-of-principle prototype with clearly innovative higher levels of large amounts of integrated knowledge. Future directions may adapt these concepts and methods to the biology of higher organisms, including humans.

描述（由申请人提供）：该提案的目的是实施一种新颖的方式处理和访问科学出版物收集中有关细菌模型转录启动的庞大详细知识的方法。在Princple中，这种用于处理和阅读信息和新知识的模型适用于其他生物领域，有可能使任何生物医学知识领域受益。肯定是批评的，生成新的策略来应对基因组学和整个生物医学研究中产生的知识不断增加的知识。提高传统高质量手动策划的科学出版物的效率将使我们能够扩大基因组中机制及其元素的生物学知识类型，从而开始将其与更大的调节过程以及细胞的生理特性进行连接。我们将首先通过具有文本挖掘功能的计算系统来实施必要的技术，以改善我们的策展，以便在人类专家策展人识别的句子中识别包含要添加到数据库的信息之前进行预处理论文。策展人选择的预定选项将加速他们的决定。句子和策划知识之间的累积精确映射将为文本挖掘技术提供培训集，以改善其自动提取。策展人实践将 变得更加有效，使我们能够策划选定的高影响力发表的评论，以将机制置于其生理过程和一般生物学的丰富背景下。我们提案的另一个相关组成部分是通过生物学的新概念改进了受调节过程的建模，这些概念捕获了更大的核心基因及其串联反应的收集。从本地监管机构的所有相互作用开始，调节器调节器 他们的作用领域将被纳入以构建复杂决策的生物怪物，因为它们在基因组中编码。这些是捕获知识的组织来描述细胞能力的遗传编程的概念容器。这些建议将在一个国际联盟内进行形式化和提议，该联盟重点是丰富基因调节的标准模型或科学界使用的基因调节本体。最后，将实施一个门户网站，可以在给定的大量语料库（超过5,000）的所有句子中进行导航。导航的不同途径基本上将使用两种技术，一种用于自动从原始句子中生成更简单的句子作为输入，而另一个则根据其主题或本体学对论文进行分类。他们的组合将使新型的导航阅读系统能够实现。如果我们实现目标，该项目将提供原始原型，并具有明显更高水平的大量综合知识。未来的方向可能使这些概念和方法适应包括人类在内的高等生物的生物学。