Cook Daniel L, Neal Maxwell L, Hoehndorf Robert, Gkoutos Georgios V, Gennari John H
Biomedical & Health Informatics, Univ, of Washington, USA.
J Biomed Semantics. 2013 Apr 15;4 Suppl 1(Suppl 1):S2. doi: 10.1186/2041-1480-4-S1-S2.
As the number and size of biological knowledge resources for physiology grows, researchers need improved tools for searching and integrating knowledge and physiological models. Unfortunately, current resources-databases, simulation models, and knowledge bases, for example-are only occasionally and idiosyncratically explicit about the semantics of the biological entities and processes that they describe.
We present a formal approach, based on the semantics of biophysics as represented in the Ontology of Physics for Biology, that divides physiological knowledge into three partitions: structural knowledge, process knowledge and biophysical knowledge. We then computationally integrate these partitions across multiple structural and biophysical domains as computable ontologies by which such knowledge can be archived, reused, and displayed. Our key result is the semi-automatic parsing of biosimulation model code into PhysioMaps that can be displayed and interrogated for qualitative responses to hypothetical perturbations.
Strong, explicit semantics of biophysics can provide a formal, computational basis for integrating physiological knowledge in a manner that supports visualization of the physiological content of biosimulation models across spatial scales and biophysical domains.
随着生理学领域生物知识资源的数量和规模不断增加，研究人员需要更完善的工具来搜索、整合知识以及生理模型。遗憾的是，当前的资源——例如数据库、模拟模型和知识库——只是偶尔且独特地明确其描述的生物实体和过程的语义。
我们提出了一种基于《生物学物理学本体论》中所呈现的生物物理语义的形式化方法，该方法将生理知识划分为三个部分：结构知识、过程知识和生物物理知识。然后，我们通过计算将这些部分整合到多个结构和生物物理领域中，形成可计算的本体，通过这些本体可以对知识进行存档、重用和展示。我们的关键成果是将生物模拟模型代码半自动解析为生理图谱，这些图谱可以显示并用于询问对假设扰动的定性响应。
强大、明确的生物物理语义可以为整合生理知识提供一个形式化的计算基础，从而支持跨空间尺度和生物物理领域对生物模拟模型的生理内容进行可视化。
