PMID- 29322929 OWN - NLM STAT- MEDLINE DCOM- 20190225 LR - 20200306 IS - 1752-0509 (Electronic) IS - 1752-0509 (Linking) VI - 11 IP - Suppl 7 DP - 2017 Dec 21 TI - Ontology-based systematic representation and analysis of traditional Chinese drugs against rheumatism. PG - 130 LID - 10.1186/s12918-017-0510-5 [doi] LID - 130 AB - BACKGROUND: 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. RESULTS: 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. CONCLUSIONS: 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. FAU - Liu, Qingping AU - Liu Q AD - Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China. liuqingping@gzucm.edu.cn. AD - 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. liuqingping@gzucm.edu.cn. FAU - Wang, Jiahao AU - Wang J AD - 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. FAU - Zhu, Yan AU - Zhu Y AD - Institute of Information on Traditional Chinese Medicine, China Academy of Chinese Medical Sciences, Beijing, 100700, China. FAU - He, Yongqun AU - He Y AD - 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. yongqunh@umich.edu. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20171221 PL - England TA - BMC Syst Biol JT - BMC systems biology JID - 101301827 SB - IM MH - *Biological Ontologies MH - Humans MH - Knowledge Bases MH - *Medicine, Chinese Traditional MH - Rheumatic Diseases/*drug therapy MH - *Semantics PMC - PMC5763303 OTO - NOTNLM OT - Bioinformatics OT - OCMR OT - Ontology OT - Rheumatism OT - Traditional Chinese medicine COIS- ETHICS APPROVAL AND CONSENT TO PARTICIPATE: Not applicable. CONSENT FOR PUBLICATION: Not applicable. COMPETING INTERESTS: The authors declared that they have no competing interests. PUBLISHER'S NOTE: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. EDAT- 2018/01/13 06:00 MHDA- 2019/02/26 06:00 PMCR- 2017/12/21 CRDT- 2018/01/12 06:00 PHST- 2018/01/12 06:00 [entrez] PHST- 2018/01/13 06:00 [pubmed] PHST- 2019/02/26 06:00 [medline] PHST- 2017/12/21 00:00 [pmc-release] AID - 10.1186/s12918-017-0510-5 [pii] AID - 510 [pii] AID - 10.1186/s12918-017-0510-5 [doi] PST - epublish SO - BMC Syst Biol. 2017 Dec 21;11(Suppl 7):130. doi: 10.1186/s12918-017-0510-5.