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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

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

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overview
Overview
  • Goals of project
  • Steps involved in the project
  • Present status of the project
  • Summary

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

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outline of project
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.

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1 search strategy
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

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results of search
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

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2 what is a dental research article
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

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expert judging results
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.

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dental research top 10 journal titles n 591
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%

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dental non research top 10 journal titles n 115
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%

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non dental top 10 journal titles n 129
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.

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journals containing both dental research and non dental
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?

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top dental research major mesh n 591
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)

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dental non research major mesh n 115
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

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non dental major mesh n 129
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

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3 use computers to extract dental research articles
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.

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ips creates a document vector for each document or set of documents
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

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additional retrieval methods
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

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4 identify trends in dental research
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

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summary
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.

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many thanks to the following
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

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