中医临床治疗学主要是基于整体“证候”诊断的中药复方治疗学。其“证候”病理基础是多样的，复方化学成分是多样的，药物作用途径、环节和靶点也是多样的。实际上这是一个高度的复杂体，故有人称中医为“复杂科学”。很显然，采用单因素分析方法和检测技术，如寻找某些单一病理分子与中医“证候”的关联，分离中药单一化学成分研究中药治病的作用机理等，并不适合中医学整体治疗和复方用药的特点。系统生物学理论与组学技术（如蛋白质组、代谢组、基因组等）的发展与应用，为克服上述矛盾提供了条件，因为组学技术能够动态、高效地测定机体在整体条件和多因素作用下多种蛋白质大分子及多种小分子的谱学特征，以及描述多分子间的相互作用规律。因此，组学技术将是研究中医“复杂科学”的强大工具，为揭示中医“证候”的发生机理、体质学说的科学内涵、中药复方治疗复杂性疾病的作用原理等重大科学问题提供了可能。当然，采用组学技术研究中医药，尤其要注意严谨的科学设计，以及研究对象和干预因素的标准化和一致性，同时采用生物信息学和计算机科学等分析海量数据的相互关联。这样，便能建立一个适合中医学研究特点的、优质高效的组学技术平台，大力推动传统中医药理论和经验与现代科学的合理结合，以及中医药现代化。

Therapeutics of Chinese medicine (CM) mainly uses herbal formulas to treat illnesses, based on holistic differentiation analysis of CM patterns. It is believed that pathological variations of CM patterns in a patient, effective chemical components in herbal formula, and pathways and targets of drug actions are highly diversified. CM has been, therefore, deemed as a "Complex Science" for its sophisticated nature. In this context, determining a single relevant factor using analytical methods and techniques, such as investigating the association between CM patterns and pathological biomarkers in the patient, and isolating a single compound from herbs to understand its therapeutic effects and molecular mechanisms, does not agree with the nature of CM using herbal formula for holistic treatment. The development and application of newly established theories of systems biology and the omics technologies, including proteomics, metabonomics, and genomics, will provide a powerful tool to overcome the discrepancy, as the said technologies can dynamically and effectively define the profiles of multiple large protein molecules, multiple small molecules in the body, as well as interactions between large and small molecules, under a given physical condition. In other words, omics technologies will become an efficient tool for investigating this "Complicated Science". Thus, some major scientific issues in CM, such as underlying pathogenesis and pathological characteristics of CM patterns, scientific foundations of CM constitutional theories and practices, and underlying therapeutic mechanisms of herbal treatment of complicated refractory diseases, can be well addressed. When applying omics technologies in research activities, the protocol design and standardized research subjects/experimental elements shall be emphasized. Meanwhile, one has to study the ties between different omics data using biostatistics analytical method and computing technology. In doing so, an efficient omics technical platform for CM research can be established to promote the reasonable integration of TCM theories and experiences with modern sciences, realizing TCM modernizations.