The Human Disease Ontology: An integrated, mechanistic knowledge resource for biomedical research.

2020年NHGRI战略计划强调了促进数据和资源互操作性的必要性， 推进基因组研究和促进数据再利用。人类疾病本体（DO）知识库 将提供一种可持续的方法，将与核心数据集有关的越来越多的信息联系起来， 基因组和蛋白质组资源，因为可互操作的基因组资源使精准医学成为可能， 知识传播。DO在疾病知识组织、表示和 标准化，作为多尺度生物医学数据集成和分析的参考框架， 数以千计的临床，生物医学和计算研究人员和世界各地的基因组资源。 扩大DO的疾病数据和复杂疾病模型将提供一个全面的网络， 疾病到疾病关系（DO的疾病体），其表示用于临床诊断的疾病特征相似性网络。 鉴别诊断探讨我们将加深对相互关系的认识和理解， 基因组学与影响人类健康的社会和环境因素之间的联系。我们将提供一个 对基因组变异，生物分子， 环境驱动因素和生物过程的监管要素，并解决基因组学的需要 临床劳动力的培训。我们将在现有协调基因组资源的基础上， 以可扩展和具有成本效益的方式， 方式DO知识库将扩大内容和能力，以支持基因组数据的开发 科学和机器学习/人工智能（ML/AI）方法。本提案的总体目标是 通过DO的疾病组促进疾病数据在广泛有用的生物医学，临床基因组， 蛋白质组学和表观基因组学资源，以推动创新的机器学习研究，并提供资源 优化临床护理。DO是生物医学数据中疾病病因学的事实标准 储存库。保守地说，根据现有的资源统计数据，对指定官员的术语作了注释， 超过150万个生物医学数据元素和引用，在过去5年中增长了10倍。我们提出的 目标定位我们很好地为基因组社区提供全面的疾病资源。我们有 为了实现我们的目标，我在DO知识库中确定了三个主要的改进领域：（1）聚合 跨基因组资源的疾病信息，对复杂疾病进行建模并定义疾病 环境问题;（2）使DO的生产工作流程自动化，实现联合资源查询， 制作多语言DO并传播ML/AI就绪数据集;（3）维护和扩展 DO的合作，建立临床培训疾病分类学计划和召集专题焦点小组。

The 2020 NHGRI Strategic plan highlights the need for facilitating data and resource interoperability for advancing genomic research and promoting data reuse. The Human Disease Ontology (DO) Knowledgebase will provide a sustainable approach for linking the growing bodies of information related to core datasets across genomic and proteomic resources, as interoperable genomic resources enable precision medicine and knowledge dissemination. The DO plays a key role in disease knowledge organization, representation, and standardization, serving as a reference framework for multiscale biomedical data integration and analysis across thousands of clinical, biomedical and computational researchers and genomic resources around the world. Expanding the DO’s disease data and models for complex diseases will provide a comprehensive network of disease to disease relationships (DO’s diseasome) that represents a disease feature similarity network for clinical differential diagnosis exploration. We will deepen our knowledge and understanding of the interrelationships between genomics and the social and environmental factors that influence human health. We will deliver an increasingly comprehensive view of the roles and relationships of genomic variation, biomolecules, environmental drivers and regulatory elements on biological processes, and address the need for genomics training in the clinical workforce. We will build beyond the current set of coordinating genomic resources, offering increasingly automated approaches for aggregating and linking disease metadata in a scalable and cost-effective manner. The DO Knowledgebase will expand content, capacity to support the development of genomic data science and machine learning/artificial intelligence (ML/AI) methods. The overall goal of this proposal is to facilitate the linking of disease data via the DO’s diseaseome across broadly useful biomedical, clinical genomic, proteomic and epigenomic resources, to drive innovative machine learning research and to provide a resource for optimizing clinical care. The DO serves as the de facto standard for disease etiology across biomedical data repositories. Conservatively, based on available resource statistics, terms from the DO have been annotated to over 1.5 million biomedical data elements and citations, a 10x increase in the past 5 years. Our proposed aims position us well for providing a comprehensive disease resource for the genomic community. We have identified three main areas of improvement in the DO Knowledgebase to achieve our goals: (1) aggregating disease information across genomic resources, modeling complex disease and defining the disease environmental exposome; (2) automating the DO’s production workflow, enabling federated resource querying, producing a multi-lingual DO and dissemination of ML/AI ready datasets; (3) maintaining and expanding the DO’s collaborations, establishing a clinical training nosology program and convening topical focus groups.