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Datamining MEDLINE for Topics and Trends in Dental and Craniofacial Research

Datamining MEDLINE for Topics and Trends in Dental and Craniofacial Research . William C. Bartling, D.D.S. NIDCR/NLM Fellow in Dental Informatics Center for Biomedical Informatics University of Pittsburgh Titus K. L. Schleyer, D.M.D., Ph.D. Director, Center for Dental Informatics

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Datamining MEDLINE for Topics and Trends in Dental and Craniofacial Research

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  1. Datamining MEDLINE for Topics and Trends in Dental and Craniofacial Research William C. Bartling, D.D.S. NIDCR/NLM Fellow in Dental Informatics Center for Biomedical Informatics University of Pittsburgh Titus K. L. Schleyer, D.M.D., Ph.D. Director, Center for Dental Informatics University of Pittsburgh School of Dental Medicine 1 of 25

  2. Overview • Goals of project • Steps involved in the project • Present status of the project • Summary 2 of 25

  3. Goal of the project • To perform an accurate and thorough content analysis of the published dental and craniofacial research literature indexed in MEDLINE 3 of 25

  4. Outline of project • Develop a search strategy: • retrieve all references to dental and craniofacial journal articles indexed in MEDLINE • Determine the characteristics of a dental or craniofacial “research” article. • Use computer programs to “learn” these characteristics in order to facilitate retrieval. • Use computerized methods to identify trends in dental and craniofacial research. 4 of 25

  5. 1. Search strategy • MEDLINE was chosen as the database. • MeSH was searched manually for dental and craniofacial descriptors. • Decision to keep or discard term • Text word searches to determine completeness • Search limited to : • English language • Publication type • Abstract present • 1966-October, 2002 5 of 25

  6. Results of search • ~450,000 English language articles in: • DENTISTRY • STOMATOGNATHIC SYSTEM (not PHARYNX) • STOMATOGNATHIC DISEASES (not PHARYNGEAL DISEASES) • ~61,000 articles indexed with dental MeSH terms not in above set • ~134,000 articles remaining after limiting to journal articles containing abstracts 6 of 25

  7. 2. What is a dental research article? • 1000 abstracts randomly chosen • 5 groups of 200 abstracts each • 16 expert judges • 3 judges assigned to each group (1 group: n = 4) • Judges categorize each article as: • Dental or craniofacial research • Dental or craniofacial, non-research • Non-dental • Not sure • Web interface for judging- PHP with mySQL 7 of 25

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  10. Expert judging results • Acceptable reliability in each group ( > 0.70) • 0.70, 0.75, 0.85, 0.77, 0.76 • Majority rating determined abstract category. 10 of 25

  11. Title and MeSH findings 11 of 25

  12. Dental research top 10 journal titles(n = 591) • J Periodontol 25 4.2% • J Dent Res 20 3.4% • Arch Oral Biol 18 3.0% • J Prosthetic Dent 13 2.2% • J Clin Periodontol 13 2.2% • Community Dent Oral Epidemiology 11 1.9% • Oral Surg Oral Med Oral Pathol 10 1.7% • J Oral Rehabil 10 1.7% • Tie: Scand J Dent Res, J Oral Maxillofac Surg, J Endod, Am J Ortho Dentofacial Orthoped 9 1.5% 12 of 25

  13. Dental non-research top 10 journal titles(n = 115) • J Prosthet Dent 11 9.6% • Br Dent J 5 4.3% • J Dent Educ 4 3.5% • J Dent Child 4 3.5% • J Am Coll Dent 3 2.6% • Arch Otolaryngol 3 2.6% • Tie: 13 journals 2 1.7% 13 of 25

  14. Non-dental top 10 journal titles(n = 129) • J Biol Chem 4 3.1% • J Comp Neurol 2 1.6% • J Cell Biol 2 1.6% • Biochim Biophys Acta 2 1.6% • Biochemistry 2 1.6% • Anat Rec 2 1.6% • Acta Otolaryngol(Stockh) 2 1.6% • 113 other titles 1 0.8% • 26 of these titles also occur in “dental research” set. 14 of 25

  15. J Biol Chem Biochim Biophys Acta Anat Rec Physiol Behav Oral Surg Oral Med Oral Pathol Laryngoscope J Oral Pathol Med J Oral Maxillofac Surg J Invest Dermatol J Infect Dis J Dent Educ J Bone Miner Res J Bacteriol Int J Biochem Infect Immun FEBS Lett Eur J Pharmacol Eur J Cell Biol Carbohydr Res Cancer Res Arzneimittelforschung Arch Dis Child Anat Anz Am J Epidemiol Am J Anat Acta Pathol Microbiol Immunol Scand Journals containing both “dental research” AND “non-dental” Can we limit our search by journal type? 15 of 25

  16. Dental Caries Mouth Neoplasms Mouth Mucosa Gingiva Periodontal Diseases Periodontitis Mandible Dental Implants Carcinoma, Squamous Cell Submandibular Gland 27 4.6% 22 3.7% 19 3.2% 19 3.2% 18 3.0% 17 2.9% 17 2.9% 17 2.9% 15 2.5% 14 2.4% Top dental research major MeSH (n = 591) 16 of 25

  17. Dental Education Denture Design Mandible Maxilla Dentistry Surgical Flaps Osteotomy Denture, Complete Dentists Dental Restoration, Permanent 7 6.1% 7 6.1% 6 5.2% 5 4.3% 5 4.3% 4 3.5% 4 3.5% 4 3.5% 4 3.5% 4 3.5% Dental non-research major MeSHn = 115 17 of 25

  18. Submandibular Gland Skin Epidermal Growth Factor Adenylate Cyclase Salivary Glands Hip Prosthesis Fluorides Chromosomes Chlorides Cementation 4 3.1% 4 3.1% 4 3.1% 4 3.1% 3 2.3% 3 2.3% 3 2.3% 3 2.3% 3 2.3% 3 2.3% Non-dental major MeSHn = 129 18 of 25

  19. 3. Use computers to extract dental research articles • IPS-Identify Patient Sets (Dr. Greg Cooper et al, University of Pittsburgh) • Uses naïve Bayes method of “text classification.” • Training set (n = 693) to train system • Test set (n = 297) to test system • Calculate success of retrieval in test set using model created from training set. 19 of 25

  20. IPS creates a document vector for each document or set of documents Document i Word 1 p1 Word 2 p2 Word 3 p3 Word n pn 20 of 25

  21. IPS results Title and abstract only 21 of 25

  22. Additional retrieval methods • JDI-Journal Descriptor Indexing(NLM) • Takes free text of title and abstract and assigns journal “type” • MTI-Medical Text Indexer(NLM) • Assigns MeSH descriptors based on free text • Will compare performance of these methods with IPS 22 of 25

  23. 4. Identify trends in dental research • Use the appropriate method to successfully retrieve all dental research articles from MEDLINE. • Using information visualization and/or representation techniques to • Analyze content of dental research literature • Identify trends in dental research • Identify opportunities in dental research 23 of 25

  24. Summary • A comprehensive content analysis of the dental and craniofacial research literature has not been done. • Computerized methods may help to retrieve and categorize this literature. • Study of the published dental research can help researchers to identify trends and to possibly reveal future research opportunities. 24 of 25

  25. Many thanks to the following: • Amy Gregg, MLIS-Dental Reference Librarian • Falk Library for the Health Sciences • University of Pittsburgh • Shyam Visweswaran, MD- NLM Fellow in Intelligent Systems • Center for Biomedical Informatics • University of Pittsburgh • All of my expert raters! • This research is supported with a training grant from the National Institute of Dental and Craniofacial Research and the National Library of Medicine 25 of 25

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