| The method of omics is used in the multi-scale quantitative simulaton for anatomical structure and physiological function of organisms in the physiome research. The Physiome Project constructs anatomical structure and physiological function databases, and designs specialized markup language to achieve the collaboration and sharing of digital life models. It affords physiological simulation of main organs and computing services for medical care. The anatomical structures of human and small animal are always compatible with the physiological function. However, an obstacle for multi-scale modeling in Physiome research is lacking of complete high resolution anatomical structure of multi species, and physiological function databases. Current markup languages could not describe mass anatomical structure and the data derived from it. As a consequence, the connection between structure and function could not be established. What's more, the collaboration mechanism of Physiome Project depends on the estimates from peer-reviewed journals, which is hysteretic, easy to neglect typographical errors, and inconvenient to record the updates of models.Based on structure and function databases of human and small animals, the China Physiome Project (CPP) is dedicated to optimization of the connection between biological structure and function, as well as between mathematical models and experimental data. The collaboration research for multi-scale modeling of human and small animals has been implemented in CPP. The main research contents and results are listed below:(1) Several structure and function information databases have been developed. The anatomical data are obtained from the datasets of the Visible Chinese Human and digital rat and the physiological function information is obtained by literature mining. The mass segmentation image data and identification information is managed and stored in the 2-D segmentation databases. The 3D anatomical structure databases describe structure information of 50 human organs using Visual Reality Markup Language (VRML), which can be browsed online with interactive operation in 3-D form; the physiological function databases contain the information of not only physiological function entities but also connections between various functions. They strengthen data support for Physiome research.(2) The hierarchy of data is defined according to Medical Subject Heading (MeSH) which could standardize naming of model and structure to make a tree-structured system in CPP; Multiscale Modeling Markup Language (M3L) has been designed to standardize the descripton of hierarchy, structure, data and mathematical algorithms of models with the specialized DTD file. The M3L introduces relational data model in hierarchical data model to increase the flexibility and versatility of the model and data description. The standardization of models and data avoids mistakes and ambiguous from literatures, and hence enhance efficiency of models and data integration.(3) Collaboration and sharing mechanism has been established based on Wiki in CPP. Open-ended mode could assure the validity of the data and models. With Wiki system, an encyclopedia website will be introduced to describe the model. Version control would record the development history of models, helping to compare the differences between different versions, which the peer-review journals have not taken into account.The CPP is based on high resolution datasets of human and small animals, and will help operate interdisciplinary multi-scale modeling in aeronautics, astronautics, clinical measurements and treatments, drug discovery and medical teaching. It has improved the medical information databases of our nation and would help researchers and doctors to carry out more extensive research and experiments. |
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