Meta-modeling methods for biological processes

生物过程的元建模方法

• 批准号: 8836848
• 负责人: Mark E. Whipple
• 金额: $ 22.39万
• 依托单位: UNIVERSITY OF WASHINGTON
• 依托单位国家: 美国
• 财政年份: 2014
• 资助国家: 美国
• 起止时间: 2014-09-01 至 2016-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8836848
• 关键词: Address; Anatomic Sites; Anatomic structures; Anatomy; Automation; Biological; Biological Models; Biological Process; Biology; Case Study; Categories; Code; Collection; Computational Biology; Computer Simulation; Computers; Data; Data Aggregation; Data Analyses; Data Set; Generations; Genes; Genetic Transcription; Hand; Head and Neck Cancer; Information Resources; Lymphatic System; Malignant Neoplasms; Maps; Markov Chains; Medical; Medicine; Methods; Modeling; Nature; Neoplasm Metastasis; Network-based; Nodal; Ontology; Operative Surgical Procedures; Output; Pathway interactions; Pilot Projects; Primary Neoplasm; Process; Public Health; Publishing; Radiation; Radiation therapy; Reading; Research; Research Personnel; Resources; Site; Staging; Structure; Surgical Pathology; Techniques; Terminology; Testing; Time; Tumor stage; Universities; Washington; Work; Writing; abstracting; base; biomedical informatics; biomedical ontology; cancer radiation therapy; cancer therapy; computer framework; computer program; data modeling; design; experience; health knowledge; high risk; improved; neoplastic cell; novel; programs; theories; tumor

 DESCRIPTION (provided by applicant): Many projects are under way to create or derive computational models of biological processes, using one or more biomedical ontologies or other biomedical knowledge resources as a basis for the model structure. One such project, which we have started, is to model the local/regional spread of tumor cells (metastasis) so that an accurate target for radiation therapy can be defined. This approach uses the structure of the lymphatic system as defined in the UW Foundational Model of Anatomy (FMA) to produce a tumor dissemination model for any specific anatomic site where the primary tumor may be located. Such models are tedious to build manually and are prone to errors in transcription of the structures. We propose to further develop this approach to modeling tumor dissemination as a case study for developing automated methods for generating dynamic models from biomedical ontologies. The project will investigate the use of new mathematical formalism as a way to facilitate the mapping from an ontology to a model, and apply the formalism to the FMA/tumor dissemination problem as a proof of concept. The specific medical problem we are addressing has the potential to significantly increase the accuracy of radiation therapy target volume definition. This is a criticl step in more fully utilizing the power of modern computer controlled radiation therapy treatment machinery and techniques. The general methods may significantly help researchers to generate new models, insure that such models are consistent, and also possibly aid in identifying any inconsistencies in the biomedical ontologies themselves.

 描述（由申请人提供）： 许多项目正在使用一个或多个生物医学本体或其他生物医学知识资源作为模型结构的基础来创建或得出生物过程的计算模型。我们已经开始的一个这样的项目是对肿瘤细胞（转移）的局部/区域扩散进行建模，以便可以定义准确的放射治疗靶标。该方法使用UW解剖学基础模型（FMA）中定义的淋巴系统的结构，为任何可能位于原发性肿瘤的特定解剖部位生成肿瘤传播模型。这样的模型可以手动构建，并且容易出现结构转录的错​​误。我们建议进一步开发这种方法来建模肿瘤传播作为一种案例研究，以开发自动化方法，以从生物医学本体学生成动态模型。该项目将调查使用新的数学格式化作为促进从本体到模型的映射的一种方式，并将格式化应用于FMA/肿瘤传播问题作为概念证明。具体的医疗问题是解决有可能显着提高辐射疗法目标体积定义的准确性。这是更充分利用现代计算机控制的放射治疗治疗机械和技术的力量的关键一步。一般方法可能会大大帮助研究人员生成新的模型，确保此类模型是一致的，并可能有助于确定生物医学本体本身中的任何矛盾。