Topics and Trends in Dental and

levelsordData Management

Nov 20, 2013 (3 years and 6 months ago)

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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


University of Pittsburgh School of Dental Medicine

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Overview


Goals of project


Steps involved in the project


Present status of the project


Summary

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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

1.
Develop a search strategy:


retrieve all references to dental and craniofacial
journal articles indexed in MEDLINE

2.
Determine the characteristics of a dental or
craniofacial “research” article.

3.
Use computer programs to “learn” these
characteristics in order to facilitate retrieval.

4.
Use computerized methods to identify trends in
dental and craniofacial research.

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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


~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?


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


Acceptable reliability in each group (


> 0.70)


0.70, 0.75, 0.85, 0.77, 0.76



Majority rating determined abstract category
.






Dental research

591

60%

Dental non
-
research

115

12%

Non
-
dental

129

13%

Not sure

3


0%

No majority

152

15%

TOTAL

990

100%

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Title and MeSH findings

Rating

N

Unique
journal
titles

Unique
major
MeSH

% in
“Dental”
Journals

Dental Research

591

250

1027

(2092 total)

62%

Dental Non
-

Research

115

78

224

(321 total)

68%

Non
-
dental

129

120

411

(478 total)

5%

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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)


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)


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

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%

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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%


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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%

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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

Document i

Word 3

p
3

Word n

p
n

Word 1

p
1

Word 2

p
2

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IPS results

Title and abstract only

Titles&Abstracts

Recall or
Sensitivity

Specificity

Precision or
PPV

Training set

(n = 693)

0.63

0.79

0.82

Test set

(n = 297)

0.64

0.62

0.71

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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


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


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:

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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