Tanja Bekhuis, PhD, MS, MLIS, AHIP, leads the Evidence in Documents, Discovery, and Analysis (EDDA) Group, Department of Biomedical Informatics (DBMI), University of Pittsburgh School of Medicine.
Past members of the EDDA Group
(NIH/NLM 5R00LM010943). Dr. Tanja Bekhuis (Principal Investigator) is the recipient of a career development award from the US National Library of Medicine (NLM), National Institutes of Health (NIH). To carry out this research, she often collaborates with Dr. Dina Demner-Fushman, Staff Scientist at the Lister Hill National Center for Biomedical Communications, NLM.
Translation of biomedical research into practice depends in part on the production of quality systematic reviews that synthesize available evidence. Unfortunately, about 20% of reviews are never completed. Of those that reach fruition, the average time to completion may be 2.4 years, with a reported maximum of 9 years. A major bottleneck occurs when teammates screen studies. In the first step, they independently identify provisionally eligible studies by reading the same set of perhaps thousands of titles and abstracts. To date, researchers have used supervised machine learning (ML) methods in an attempt to automate identification of eligible randomized controlled trials (RCTs). However, finding nonrandomized (NR) studies for inclusion in systematic reviews has yet to be addressed. This is an important problem because RCTs may be unlikely or even unethical for some research questions. The proposed research is significant because it will help support translation of biomedical research to improve human health. Moreover, developing procedures to identify NR studies is essential for the expeditious translation of a very large body of research.
This terminology is available in the NCBO BioPortal http://bioportal.bioontology.org/ontologies/EDDA. Tanja Bekhuis (PI); Eugene Tseytlin and Kevin Mitchell (developers), Ashleigh Faith (taxonomist). For details regarding the rationale for its development, see Bekhuis, Demner‑Fushman, Crowley, JMLA, 2013. To optimize its usefulness for other researchers, we are updating the terminology and will release a new version in the BioPortal.
This is a continuation of research reported in Bekhuis et al., PloS One, 2014. Currently, we are focusing on extracting information from excerpts of full-text scientific articles to improve automatic classification. Additionally, we are working on methods to visualize and label clustered studies.
The EDDA Group is building a prototype to view latent themes in a set of documents for various kinds of users. We envision a Web-based, interactive Lens to assist expert searchers, such as librarians and informationists, clinical researchers, and methodologists.
We are designing filters (search strategies) to improve retrieval of studies about potential prognostic biomarkers for oral squamous cell carcinoma—the most common form of cancer affecting the oral cavity.
Dr. Bekhuis often collaborates with Dr. Heiko Spallek and a group of researchers at the University of Pittsburgh School of Dental Medicine and the American Dental Association. We are interested in promoting implementation and adherence to recommendations in clinical practice guidelines to improve patient care. Currently, we are focused on methods to persuade dentists to adopt a simple, noninvasive procedure to prevent or treat incipient caries (tooth decay), a common and chronic disease. If left untreated, it is the source of significant pain and loss of teeth. Treating tooth decay in the US—excluding costs for impaired quality of life and impact on morbidity—costs about $60 billion annually. Moreover, poor oral health is a risk factor for serious systemic problems, such as diabetes and cardiovascular disease. In 2013, we published a “highly accessed” article in BMC Oral Health titled “Are dentists interested in the oral systemic disease connection? A qualitative study of an online community of 450 practitioners.” This article was also featured in the British Dental Journal, 2013. Natural language processing and pattern matching enabled this research.
Dr. Heiko Spallek, Executive Director, Dr. Bernard Costello, Director of Translational Research, and Dr. Tanja Bekhuis, Director of Translational Research Methods, are leading development of a new Center for Informatics in Oral Health Translational Research, in the School of Dental Medicine. The overarching mission of the new Center is to support research and education aimed at improving delivery of dental care and patient outcomes, as well as treatment of oral and maxillofacial conditions, particularly those related to systemic health. This Center significantly expands the mission of the former Center for Dental Informatics.
Bekhuis T, Tseytlin E, Mitchell KJ. A Prototype for a Hybrid System to Support Systematic Review Teams: A Case Study of Organ Transplantation. International Workshop on Biomedical and Health Informatics, IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Bethesda, MD, US, November 9, 2015, 8 pp. Available via ResearchGate: http://tinyurl.com/nncd6pj.
Bekhuis T. Keywords, discoverability, and impact [invited commentary]. JMLA: J Med Lib Assoc. 2015 Jul;103(3):119-20. doi: 10.3163/1536-5050.103.3.002. PMCID: PMC4511049.
Faith A, Bekhuis T. HTA Database Canadian Repository [review of a repository for health technology assessments]. JMLA: J Med Lib Assoc. 2015 Oct;103(4):239-40. doi: 10.3163/1536-5050.103.4.021. PMCID: PMC4613395.
Frazier JJ, Stein CD, Tseytlin E, Bekhuis T. Building a gold standard to construct search filters: a case study with biomarkers for oral cancer. JMLA: J Med Libr Assoc. 2015 Jan;103(1):346-354.
Bekhuis T, Tseytlin E, Mitchell K, Demner-Fushman D. Feature engineering and a proposed decision-support system for systematic reviewers of medical evidence. PLoS One. Epub2014 Jan 27; 9(1):e86277. doi:10.1371/journal.pone.0086277. PMCID: PMC3903545.
Bekhuis T, Kim K, Valappil B, Spallek H. Adapting the Scottish PRIME Fissure Sealant Questionnaire for implementation research in the United States: lessons learned [report in APA PsycEXTRA database]. American Psychological Association (APA). 2014. doi: 10.1037/e502572014-001.
Bekhuis T, Kim K, Valappil B, Spallek H. PRIME Fissure Sealant Questionnaire—US Version [questionnaire in APA PsycTESTS database]. American Psychological Association (APA). 2014. doi: 10.1037/t27847-000.
Song M, O'Donnell JA, Bekhuis T, Spallek H. Are dentists interested in the oral-systemic disease connection? A qualitative study of an online community of 450 practitioners. BMC Oral Health. 2013 Nov 21;13(1):65. PMCID: PMC3924341 (highly accessed article).Featured in British Dental Journal. 2013;215(11): 545: 6 December 2013. doi:10.1038/sj.bdj.2013.1152.
Bekhuis T, Demner-Fushman D, Crowley RS. Comparative effectiveness research designs: an analysis of terms and coverage in MeSH and Emtree. J Med Lib Assoc. 2013;101(2):92-100. PMCID: PMC3634392
Bekhuis T, Demner-Fushman D. Screening nonrandomized studies for medical systematic reviews: A comparative study of classifiers. Artif Intell Med. 2012 Jul;55(3):197-207. Epub 2012 Jun 5. PMCID: PMC3393813
Bekhuis T, Kreinacke M, Spallek H, Song M, O'Donnell AJ. Using natural language processing to enable in-depth analysis of clinical messages posted to an Internet mailing list: A feasibility study. J Med Internet Res. 2011, 13(4):e98. PMCID: PMC3236668
Bekhuis T. Chlorhexidine varnish may prevent dental caries in children and adolescents [invited evaluation of a systematic review]. Journal of Evidence-based Dental Practice, 2011, 11(2):84-6 PMID: 21605831.
Bekhuis T, Demner-Fushman D. Towards automating the initial screening phase of a systematic review. Stud Health Technol Inform. 2010, 160(Pt 1):146-50. PMID: 20841667.
Spallek H, Song M, Polk DE, Bekhuis T, Frantsve-Hawley J, Aravamudhan K. Barriers to implementing evidence-based clinical guidelines: A survey of early adopters. J Evid Based Dent Pract. 2010, (10)4, 195-206. PMCID: PMC3011934.
Bekhuis T. Music therapy may reduce pain and anxiety in children undergoing medical and dental procedures [invited evaluation of a systematic review]. Journal of Evidence-based Dental Practice, 2009, 9(4), 213-14. DOI:10.1016/j.jebdp.2009.03.002. PMCID: PMC2778574.
Bekhuis T, Thyvalikakath T, Oliver R. Interventions for treating ameloblastomas of the jaws [protocol]. Cochrane Database of Systematic Reviews, 2009, Issue 4. Art. No.: CD003975. DOI: 10.1002/14651858.CD003975.pub2.
Bekhuis T. Conceptual biology, hypothesis discovery, and text mining: Swanson's legacy [in top ten of most accessed articles]. Biomedical Digital Libraries, 2006, 3:2. PMCID: PMC1459187.