Document 7163

Agenda
Database Structure
& Information Retrieval
Lisa Traditi, MLS, AHIP
April 2008
Medical data
Database structure
Controlled vocabulary vs. natural
language
Medical Subject Headings (MeSH)
Medical data
“Scientific disciplines generally develop precise
terminology or notation that is standardized
and accepted by all workers in the field.
Medicine is remarkable for its failure to develop
a standardized vocabulary and
nomenclature….”
-Ted Shortliffe, M.D., Ph.D., Stanford
University School of Medicine
Medical Coding Schemes
Which ones are you using?
ICD-10 (World Health Organization)
ICD-10-CM (Health Care Financing
Admin.)
z SNOMED (American College of Pathology)
z CPT (American Medical Association)
z
z
Data-to-Knowledge spectrum
Datum
z
Single observational point described objectively
Information
z
Gained from the formal or informal
analysis/interpretation of data
Knowledge
z
Organized data + information that has been
synthesized
Database structure
Records
Definition of a Database?
…Collection of data organized
especially for rapid searching
and retrieval
Unstructured Record
9236556 NLM Schwartz, L M. Fisher, E S. Tosteson, N A. Woloshin, S. Chang, C H. Virnig, B A. Plohman, J.
Wright, B. Department of Veterans Affairs Medical Center, White River Junction, Vt, USA. Treatment and health
outcomes of women and men in a cohort with coronary artery disease. Archives of Internal Medicine.
157(14):1545-51, 1997 Jul 28. Arch Intern Med. 157(14):1545-51, 1997 Jul 28. Print 0372440, 7fs AIM, IM
UNITED STATES Age Factors. Aged. Cohort Studies. Coronary Disease/di [Diagnosis]. Coronary Disease/px
[Psychology]. *Coronary Disease/th [Therapy]. Female. Health Status. Hospitalization. Humans. Linear
Models. Male. Research Support, Non-U.S. Gov't. *Sex Factors. Socioeconomic Factors. Treatment
Outcome. BACKGROUND: Women with coronary artery disease are treated differently than men. Although
mortality has been studied, functional outcomes for women and men have not been prospectively compared.
METHODS: The Manitoba Health Reform Impact Study used hospital databases to identify all residents aged 45
years and older in Manitoba who were hospitalized for a myocardial infarction between October 1, 1991, and
September 30, 1992. Cohort members were interviewed twice, an average of 16 and 25 months after
hospitalization. Baseline and follow-up measures included treatments (eg, physician visits, diagnostic testing,
revascularization, and cardiac medications), physical health status (physical component summary [PCS] score
derived from the Medical Outcomes Study Short Form 36), reinfarction, and mortality. RESULTS: Of the 820
patients who completed the initial survey, 31 died during the follow-up period, and 734 completed the follow-up
survey. Data were complete for the primary outcome (PCS score) and all relevant covariates for the 677 patients
who were included in this study Women constituted 34% of this cohort. Although women had more physician
visits during follow-up, they were less likely to have undergone treadmill testing or angiography (odds ratio, 0.68;
95% confidence interval, 0.46-0.99). Women were equally likely to report taking beta-adrenergic blocking agents,
but were less likely than men to report the use of aspirin (odds ratio, 0.69; 95% confidence interval, 0.48-0.98).
After adjusting for baseline differences in PCS scores, age, income, social supports, and the levels of angina
and dyspnea, the PCS score for women declined by 1.4 points, while the score for men improved by 0.2 points
(P = .03). During the follow-up period, reinfarction and mortality rates were low overall, but were not different in
men and women. CONCLUSIONS: In this cohort of patients with known coronary artery disease, we found less
aggressive treatment of coronary artery disease and less use of aspirin among women than among men during 1
year of observation. After controlling for baseline differences, women with coronary artery disease experienced a
more rapid decline in physical health status than did men during 1 year of follow-up. 0003-9926 Journal Article.
English 19970814 20041117 1997 20041220
Structured Record
Unique Identifier
9236556
Record Owner
NLM
Authors
Schwartz LM. Fisher ES. Tosteson NA. Woloshin S. Chang
CH. Virnig BA. Plohman J. Wright B.
Institution
Department of Veterans Affairs Medical Center, White River
Junction, Vt, USA.
Title
Treatment and health outcomes of women and men in a
cohort with coronary artery disease.
Source
Archives of Internal Medicine. 157(14):1545-51, 1997 Jul 28.
Abbreviated Source
Arch Intern Med. 157(14):1545-51, 1997 Jul 28.
Publishing Model
Print
NLM Journal Code
0372440, 7fs
Journal Subset
AIM, IM
Country of Publication
UNITED STATES
MeSH Subject Headings
Age Factors
Aged
Cohort Studies
Coronary Disease / di [Diagnosis]
Coronary Disease / px [Psychology]
*Coronary Disease / th [Therapy]
Female
Health Status
Hospitalization
Humans
Linear Models
Male
Research Support, Non-U.S. Gov't
*Sex Factors
Socioeconomic Factors
Treatment Outcome
Abstract
BACKGROUND: Women with coronary artery disease are treated
differently than men. Although mortality has been studied,
functional outcomes for women and men have not been
prospectively compared. ….
ISSN
0003-9926
Publication Type
Journal Article.
Language
English
Entry Date
19970814
Revision Date
20041117
Year of Publication
1997
Update Date
20041220
Database structure
Records
Fields
z Indexes
z
Exercise: What MeSH terms would you assign?
Differential response to antidepressants in women with premenstrual
syndrome/premenstrual dysphoric disorder – A randomized controlled trial
BACKGROUND: Studies show that selective serotonin reuptake inhibitors are effective for
severe premenstrual syndrome and premenstrual dysphoric disorder. This study compares
the efficacy of a selective serotonin reuptake inhibitor with that of a tricyclic antidepressant to
determine whether efficacy for premenstrual syndrome/premenstrual dysphoric disorder is a
general or more serotonergic effect of antidepressants.
METHODS: After 3 screening months, 189 subjects were randomized to sertraline hydrochloride,
desipramine hydrochloride, or placebo for 3 months of double-blind treatment. The flexible
dosage range was 50 to 150 mg/d. The outcome measures included the Penn Daily
Symptom Report (DSR), the Hamilton Depression Rating Scale, the Clinical Global
Impressions-Severity Scale, the Quality of Life Scale, and Patient Global Ratings of
Functioning and Improvement. Analyses included all subjects with treatment data, with the
last observation carried forward. RESULTS: Sertraline was significantly more effective than
placebo or desipramine; desipramine was not better than placebo (F2,163 = 12.47, P<.001).
All DSR factors were more improved with sertraline compared with desipramine and placebo;
the factors for mood (P<.001) and pain (P = .05) were significant, and the results of all
outcome measures were consistent. A history of depression, postmenstrual symptom levels,
and other diagnostic variables added individually as covariates did not alter the treatment
results. At end point analysis, DSR symptoms had decreased by more than 50% in 40
subjects (65%) in the sertraline group, 18 subjects (36%) in the desipramine group, and 16
subjects (29%) in the placebo group (P<.001).
CONCLUSIONS: The comparison of 2 classes of antidepressants strongly favored the
serotonergic drug, which effectively reduced symptoms and improved functioning and was
well tolerated by women with severe premenstrual syndrome. A history of depression did not
alter the treatment results.
MeSH (Medical Subject Headings)
Overview of Vocabulary Development & Changes for 2008 MeSH
http://www.nlm.nih.gov/pubs/techbull/nd07/nd07_mesh.html
z
z
z
MeSH – for notes
456 Descriptors were added for 2008 MeSH
288 Descriptor terms were replaced with more up-to-date terminology
46 Descriptors were deleted
Totals by Type of Terminology
z
z
z
z
24,767 Descriptors
83 Subheadings/Qualifiers
172,451 Supplementary Concept Records (SCRs)
ftp://nlmpubs.nlm.nih.gov/online/mesh/.newterms/mshnew2008.txt
Previous Years Comparison:
24,357 Descriptors in 2007
494 Descriptors added for 2007 MeSH
z
z
z
z
933 new terms added in ’06
487 new terms added in ’05
666 new terms added in ‘04
1250 new terms added in ‘03
There was a major reclassification and
retreeing of the Leukemia and
Lymphoma terms … The following new
headings were added:
Leukemia, Prolymphocytic, B-Cell
Leukemia, Large Granular Lymphocytic
Precursor Cell Lymphoblastic LeukemiaLymphoma
Precursor B-Cell Lymphoblastic LeukemiaLymphoma
Leukemia, Myeloid, Chronic, Atypical, BCRABL Negative
Leukemia, Myelomonocytic, Juvenile
Lymphoma, Extranodal NK-T-Cell
Lymphoma, Primary Cutaneous Anaplastic
Large Cell
Examples:
Heart Failure (with entry term of Heart
Failure, Congestive)
Heart Failure, Diastolic
Heart Failure, Systolic
Extensively Drug-Resistant Tuberculosis
(not to be confused with Tuberculosis,
Multidrug-Resistant)
Four new specific strains of E. coli
added
Enterohemorrhagic Escherichia coli
Enteropathogenic Escherichia coli
Enterotoxigenic Escherichia coli
Shiga-Toxigenic Escherichia coli
There were also significant changes
related to the Coronary Disease tree.
… The following new terms were added
New Disaster-Related Headings
to the Coronary Disease tree:
Coronary Artery Disease (with entry terms of
Coronary Arteriosclerosis and Coronary
Atherosclerosis)
Coronary Occlusion (do not confuse with
Coronary Stenosis)
Acute Coronary Syndrome
Disaster Medicine
Mass Casualty Incidents
Weapons of Mass Destruction
A new entry term of note for the MeSH
term Civil Defense is Emergency
Preparedness.
MeSH Tools
Annotated, alphabetic
Trees, hierarchical
Permuted, rotated
MeSH
Major principle = specificity
indexers assign the most specific terms
z indexers do not routinely assign more
general terms as well
z
MeSH
Publication types
Check tags
Geographics
Subheadings
Reasons to Use MeSH
Allows for more precise MEDLINE
queries
Takes advantage of high quality
indexing
Takes advantage of Ovid’s mapping
Can combine with textword searching to
approach (but never achieve)
comprehensive retrieval
Vocabulary Issues:
Controlled vs. Natural Language
Controlled Vocabulary
Advantages:
consistent and
dependable
z documented
z arranged
alphabetically,
hierarchically, etc.
z
Disadvantages:
out of date
expensive
z human error
z
z
Vocabulary Issues:
Vocabulary Issues
Controlled vs. Natural Language
Natural Language
Advantages:
z
must use lots of
synonyms
z must know vocabulary
of discipline
z simplifies searching
z
z
cheap
up to date
z simplifies
searching
z
z
Solutions -- real and potential:
Disadvantages:
Educate searchers
Improve database design
z Systems/software to assist
z
z
http://www.nlm.nih.gov/research/umls/umlsmain.html
MeSH
Recall = sensitivity
# of relevant citations retrieved by a search
# of relevant citations in the database
z
ability of the search to retrieve relevant
citations from the database
Ovid mapping
UMLS
MeSH
Precision = specificity
# of relevant citations retrieved
total # of citations retrieved
z
ability of the search to discriminate
between relevant and irrelevant
citations
Major searching goal
Unambiguous retrieval = sensitive,
specific, reliable
Sensitive = all the data I want
z Specific = only the data I want
z Reliable = same data for every query
Questions? Comments?
z
Database Structure & Information Retrieval
Lisa Traditi, MLS, AHIP