Ontology-based systematic representation and analysis of traditional Chinese drugs against rheumatism

Abstract

BackgroundRheumatism 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.ResultsIn 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.ConclusionsThe 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.Electronic supplementary materialThe online version of this article (10.1186/s12918-017-0510-5) contains supplementary material, which is available to authorized users.

Computational Advances in Drug Safety: Systematic and Mapping Review of Knowledge Engineering Based Approaches

“…Basis for other ontologies (Tao et al, 2012; Marcos et al, 2013; Lin and He, 2014; Herrero-Zazo et al, 2015; Guo et al, 2016; Liu et al, 2017; Wang et al, 2017)…”

“…Furthermore, ODNAE extends OAE to facilitate the analysis of drugs causing neuropathy adverse events (Guo et al, 2016). Similarly, OCVDAE extends OAE to facilitate the analysis of ADEs caused by cardiovascular drugs (Wang et al, 2017), and OCMR extends OAE to facilitate the comparative analysis of traditional Chinese drugs regarding rheumatism (Liu et al, 2017).…”

A bioinformatics potpourri

“… CroGO2 is an iterative ranking-based method that measures similarities of cross-categories GO terms using GO term level and interaction information in gene co-function networks [ 57 ]. Ontology of Chinese Medicine for Rheumatism represents 26 anti-rheumatism Chinese drugs together with their chemical ingredients, adverse effects and related information [ 58 ]. Post-translational modification sites MDD-Carb is a tool for prediction of carbonylation sites utilizes maximal dependence decomposition and profile hidden Markov models [ 59 ].…”

Ontological modeling and analysis of experimentally or clinically verified drugs against coronavirus infection

“…Coronavirus Infectious Disease Ontology (CIDO) is a community-based open source biomedical ontology that systematically represents entities associated with coronavirus diseases, including their etiological causes, phenotypes, host-coronavirus interactions, diagnosis, drugs, and vaccines 14 . For drug representation, CIDO reuses terms from three existing ontologies, including Chemical Entities of Biological Interest ontology (ChEBI) 15 , National Drug File – Reference Terminology (NDF-RT) 16 , and Drug Ontology (DrON) 17 , which have been frequently used for drug studies 18 , 19 . ChEBI is a database and ontology of over 56,000 molecular entities of biological significance with a focus on small chemical compounds.…”