Liu Qingping, Wang Jiahao, Zhu Yan, He Yongqun
Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China.
Unit for Laboratory Animal Medicine, Department of Microbiology and Immunology, Center for Computational Medicine and Bioinformatics, and Comprehensive Cancer Center, University of Michigan Medical School, 1301 MSRB III, 1150 W. Medical Dr, Ann Arbor, MI, 48109, USA.
BMC Syst Biol. 2017 Dec 21;11(Suppl 7):130. doi: 10.1186/s12918-017-0510-5.
Rheumatism represents any disease condition marked with inflammation and pain in the joints, muscles, or connective tissues. Many traditional Chinese drugs have been used for a long time to treat rheumatism. However, a comprehensive information source for these drugs is still missing, and their anti-rheumatism mechanisms remain unclear. An ontology for anti-rheumatism traditional Chinese drugs would strongly support the representation, analysis, and understanding of these drugs.
In this study, we first systematically collected reported information about 26 traditional Chinese decoction pieces drugs, including their chemical ingredients and adverse events (AEs). By mostly reusing terms from existing ontologies (e.g., TCMDPO for traditional Chinese medicines, NCBITaxon for taxonomy, ChEBI for chemical elements, and OAE for adverse events) and making semantic axioms linking different entities, we developed the Ontology of Chinese Medicine for Rheumatism (OCMR) that includes over 3000 class terms. Our OCMR analysis found that these 26 traditional Chinese decoction pieces are made from anatomic entities (e.g., root and stem) from 3 Bilateria animals and 23 Mesangiospermae plants. Anti-inflammatory and antineoplastic roles are important for anti-rheumatism drugs. Using the total of 555 unique ChEBI chemical entities identified from these drugs, our ChEBI-based classification analysis identified 18 anti-inflammatory, 33 antineoplastic chemicals, and 9 chemicals (including 3 diterpenoids and 3 triterpenoids) having both anti-inflammatory and antineoplastic roles. Furthermore, our study detected 22 diterpenoids and 23 triterpenoids, including 16 pentacyclic triterpenoids that are likely bioactive against rheumatism. Six drugs were found to be associated with 184 unique AEs, including three AEs (i.e., dizziness, nausea and vomiting, and anorexia) each associated with 5 drugs. Several chemical entities are classified as neurotoxins (e.g., diethyl phthalate) and allergens (e.g., eugenol), which may explain the formation of some TCD AEs. The OCMR could be efficiently queried for useful information using SPARQL scripts.
The OCMR ontology was developed to systematically represent 26 traditional anti-rheumatism Chinese drugs and their related information. The OCMR analysis identified possible anti-rheumatism and AE mechanisms of these drugs. Our novel ontology-based approach can also be applied to systematic representation and analysis of other traditional Chinese drugs.
风湿病是指关节、肌肉或结缔组织出现炎症和疼痛的任何疾病状态。许多传统中药长期以来一直用于治疗风湿病。然而，这些药物的综合信息来源仍然缺失，其抗风湿机制也尚不清楚。抗风湿传统中药本体将有力地支持对这些药物的表示、分析和理解。
在本研究中，我们首先系统收集了26种中药饮片的报告信息，包括其化学成分和不良事件（AE）。通过大量复用现有本体中的术语（例如，用于中药的中医药物本体（TCMDPO）、用于分类学的NCBI分类法、用于化学元素的ChEBI以及用于不良事件的OAE）并建立连接不同实体的语义公理，我们开发了风湿病中医本体（OCMR），其中包括3000多个类术语。我们的OCMR分析发现，这26种中药饮片由3种两侧对称动物和23种被子植物的解剖实体（例如，根和茎）制成。抗炎和抗肿瘤作用对于抗风湿药物很重要。利用从这些药物中鉴定出的总共555个独特的ChEBI化学实体，我们基于ChEBI的分类分析确定了18种抗炎化学物质、33种抗肿瘤化学物质以及9种具有抗炎和抗肿瘤双重作用的化学物质（包括3种二萜类化合物和3种三萜类化合物）。此外，我们的研究检测到22种二萜类化合物和23种三萜类化合物，其中包括16种可能对风湿病具有生物活性的五环三萜类化合物。发现6种药物与184种独特的AE相关，其中三种AE（即头晕、恶心呕吐和食欲不振）每种都与5种药物相关。几种化学实体被归类为神经毒素（例如邻苯二甲酸二乙酯）和过敏原（例如丁香酚），这可能解释了一些中药不良事件的形成。使用SPARQL脚本可以有效地查询OCMR以获取有用信息。
开发OCMR本体是为了系统地表示26种传统抗风湿中药及其相关信息。OCMR分析确定了这些药物可能的抗风湿和AE机制。我们基于本体的新方法也可应用于其他传统中药的系统表示和分析。
