Proto-OKN Theme 1: BioBricks-OKG An Open Knowledge Graph For Cheminformatics And Chemical Safety

这个NSF原型开放知识网络主题1项目旨在增强开源生物砖系统，将其转化为一个有效的知识图谱后端，以促进对关键化学健康和安全数据的访问，使人工智能能够用于开发新的化学测试和监管方法。目前，跨越健康信息学、毒理学和化学信息学的数据生态系统包括许多不连贯的数据库，可用性不一致。访问、处理和集成来自各种来源的数据以构建健壮的模型是一项挑战。BioBricks开放知识图谱（BioBricks- okg）旨在通过将表格数据半自动化地协调成统一的知识图谱来解决这个问题。这将通过本体对齐方法增强数据库之间的数据共享。此外，BioBricks-OKG的目标是将这些技术扩展到60多个公共卫生和化学信息学数据库，显著改善数据协调和可访问性。BioBricks-OKG将通过促进数据科学和机器学习的整合，极大地造福于公共卫生、医学和生命科学领域。一旦投入使用，诊所、制药公司、监管机构和生物信息学合同研究组织（cro）就可以利用BioBricks-OKG知识图谱进行智能数据查询，从而避免了复杂的数据存储库导航或冗余数据提取管道的需要。该项目利用了BioBricks-AI框架和项目团队在构建以毒理学为重点的知识图谱方面的经验。BioBricks-AI框架提供了开源存储库，可将卫生信息学数据库转换为可分发的序列化格式，用于可扩展的数据分析。这项工作包括将BioBricks-AI存储库和公共卫生数据库简化为一个庞大的图形数据库。该数据库将化学品及其遗传、分子和细胞破坏、健康危害、不良后果途径、测试方法以及与化学品安全和监管相关的其他实体联系起来。国家毒理学计划的替代毒理学方法评估机构间中心（NICEATM）将使用由此产生的BioBricks-OKG来设计、收集信息和评估“新方法方法论”（NAM）测试指南。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

This NSF Proto-Open Knowledge Network Theme 1 project aims to enhance the open-source BioBricks system, transforming it into an effective knowledge graph backend to facilitate access to crucial chemical health and safety data, enabling the use of AI in developing new chemical testing and regulation approaches. Currently, the data ecosystem that spans health informatics, toxicology, and cheminformatics comprises numerous disjointed databases with inconsistent availability. It is challenging to access, process, and integrate data from various sources for robust model construction. The BioBricks Open Knowledge Graph (BioBricks-OKG) is designed to address this issue by semi-automating the harmonization of tabular data into a unified knowledge graph. This will enhance data sharing between databases through ontology alignment methodologies. Furthermore, BioBricks-OKG aims to scale these techniques to over 60 public health and cheminformatics databases, significantly improving data harmonization and accessibility. The BioBricks-OKG will greatly benefit the public health, medical, and life science fields by fostering the integration of data science and machine learning. Once operational, clinics, pharmaceutical companies, regulatory agencies, and bioinformatics Contract Research Organizations (CROs) can utilize the BioBricks-OKG knowledge graph for intelligent data queries, obviating the need for complex data repository navigation or redundant data extraction pipelines. The project leverages the BioBricks-AI framework and the project team's experience in building toxicology-focused knowledge graphs. The BioBricks-AI framework offers open-source repositories that transform health informatics databases into a distributable, serialized format for scalable data analysis. The work involves streamlining BioBricks-AI repositories and public health databases into a vast graph database. This database will link chemicals, their genetic, molecular, and cellular disruptions, health hazards, adverse outcome pathways, testing methods, and other entities relevant to chemical safety and regulation. The National Toxicology Program's Interagency Center for the Evaluation of Alternative Toxicological Methods (NICEATM) will use the resulting BioBricks-OKG for designing, collecting information, and evaluating "New Approach Methodology" (NAM) test guidelines.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.