J Periodont Res. 2018;1–11. wileyonlinelibrary.com/journal/jre | 1 © 2018 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd 1 | INTRODUCTION Rheumatoid arthritis (RA) and periodontal disease (PD) are both complex disorders. Both involve gene-environment interaction, aberrant immune activation, and long-standing chronic inflamma- tion. A positive association of RA and PD is reported by a few ep- idemiologic studies. 1-3 Shared risk factors such as smoking, older age, and HLA-DRB1 genotype may explain this association in part. Received: 2 October 2018 | Revised: 1 November 2018 | Accepted: 18 November 2018 DOI: 10.1111/jre.12632 ORIGINAL ARTICLE Biological links in periodontitis and rheumatoid arthritis: Discovery via text-mining PubMed abstracts Aneesha Acharya 1,2 | Simin Li 3 | Xiangqiong Liu 4,5 | George Pelekos 1 | Dirk Ziebolz 3 | Nikos Mattheos 1 1 Faculty of Dentistry, The University of Hong Kong, Sai Yin Pun, Hong Kong 2 Department of Periodontology, Dr. D.Y. Patil Vidyapeeth, Pune, India 3 Department of Cariology, Endodontology, and Periodontology, University Leipzig, Liebigstr, Germany 4 Shanghai Genomap Technologies, Shanghai, China 5 College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China Correspondence Nikos Mattheos, Prosthodontics, Faculty of Dentistry HKU, 3 F, Prince Philip Dental Hospital, Sai Yin Pun, Hong Kong. Emails: nikos@mattheos.net; mattheos@hku.hk Funding information The University of Hong Kong Background and Objective: Primary research concerning molecular pathways that link rheumatoid arthritis with periodontitis is limited. Biomedical literature data min- ing can offer insights into putative linkage mechanisms toward hypothesis develop- ment, based on information discovery. The aim of this study was to explore potential Periodontitis-Rheumatoid Arthritis biological links by analysing “overlapping” genes reported in biomedical abstracts. Material and Methods: PubMed abstracts for terms: (a) “Periodontitis” or “Periodontal Diseases” (PD), (b) “Rheumatoid arthritis” (RA), and (c) their combination with “AND” (RA+PD), were each text-mined to extract genes using “Human Genome Nomenclature Committee” (HGNC) symbols. A gene-set common to RA and PD abstracts was determined (RA∩PD). Gene ontology (GO) profiles of RA∩PD and RA+PD were compared using “GoProfiler.” Minimum order protein-protein interaction (PPI) and gene-miRNA networks of “differential genes” between RA∩PD and RA+PD were constructed with “networkAnalyst.” Results: Among 1676 genes documented in RA (10 5241 abstracts), and 893 genes in PD (80 982 abstracts), 535 genes were common (RA∩PD), from which 35 genes were also documented in RA+PD (415 abstracts). 41 GO-terms significantly different be- tween RA∩PD and RA+PD GO profiles represented 38 biological processes includ- ing; nitric oxide metabolism, immunoglobulin production, hormonal regulation, catabolic process down-regulation, and leukocyte proliferation. The 500 differential genes’ PPI and gene-miRNA networks showed REL, TRAF2, AQP1 genes, and miR- NAs 335-5p, 17-5p, 93-5p with genes HMOX1 and SP1 as hub nodes. Conclusions: Text-mining biomedical abstracts revealed potentially shared but un- investigated links between PD and RA, meriting further research. KEYWORDS bioinformatics, biomedical text mining, information extraction, periodontal diseases, periodontal medicine, periodontitis, rheumatoid arthritis