PubMed.be Project

1
PubMed.be Project

• Linking databases together

Koen Thomeer, MD Promotor Jan Degryse, MD, PhD
2
Overview

1. Preface before PubMed.be
2. Connecting them PubMed.be
3. The future?
4. TEST DRIVE!

3
Overview

• Preface before PubMed.be
• MedLine database
• MeSH database
• Filters

4
Preface
?
Medline
MeSH
Pubmed.com
one doctor
Filters?
Many complicated databases, only one doctor
5
Preface MedLine

• MedLine (Journal Database)
• contains gt 4600 journals (titel, abstract, )
• accesible to everybody, but very complicated
  (computer language)
• expensive software on the market to get easy acces

Why normal people have to pay to get accesto a
community paid database?
6
Preface MedLine

• Pubmed.com
• web interface to have easy acces to MedLine for
  everbody
• but people dont get the maximum out of the
  interface gt bad results

7
PMID- 12651791 OWN - NLM STAT- MEDLINE DA -
20030324 DCOM- 20030807 LR - 20041117 PUBM-
Print IS - 0263-2136 VI - 20 IP - 2 DP - 2003
Apr TI - GPs working in solo practice obstacles
and motivations for working in a group? A
qualitative study. PG - 167-72 AB - OBJECTIVE
Our aim was to analyse the obstacles and eventual
motivations of solo GPs for working in
group practice. METHODS A qualitative study
using 12 focus groups was carried out in primary
care in French-speaking Belgium. The
subjects comprised four samples of GPs 20 GP
trainers, 18 GP trainees, 25 women GPs and
25 other GPs. The focus groups were taped and
transcribed. Two independent researchers
carried out the analysis using the QSR
NUD.IST software. RESULTS The participants (88
GPs) did not share a common definition of
group practice-in particular multidisciplinary
working-the need for a common pool of patients
and shared premises. Their main sources of
motivation for eventually setting up a group
practice were better quality of life,
continuity of care and sharing professional
knowledge. The main obstacles were a required
agreement between colleagues, the loss of a
personal patient-GP relationship, budgetary
constraints, and divergent views on group
practice and GPs' profession (especially
true for the association of GPs from different
age groups). CONCLUSION The current study
shows that GPs working solo have divergent
views of group practice. However, they clearly
perceive advantages to this type of
association (e.g. better quality of life and
continuity of care). This study also
confirms the high level of stress and tiredness
felt by GPs and especially senior
practitioners. AD - Centre Universitaire de
Medecine Generale, Universite Catholique de
Louvain, Avenue Mounier 5360, 1200 Bruxelles,
Belgium. Jean-Marc.Feron_at_cumg.ucl.ac.be FAU
- Feron, Jean-Marc AU - Feron JM FAU - Cerexhe,
Francoise AU - Cerexhe F FAU - Pestiaux,
Dominique AU - Pestiaux D
FAU - Roland, Michel AU - Roland M FAU - Giet,
Didier AU - Giet D FAU - Montrieux, Christian AU
- Montrieux C FAU - Paulus, Dominique AU -
Paulus D LA - eng PT - Journal Article PL -
England TA - Fam Pract JID - 8500875 SB - IM MH
- Adult MH - Belgium MH - Family Practice MH
- Female MH - Focus Groups MH - Group
Practice MH - Humans MH - Male MH - Middle
Aged MH - Motivation MH - Physicians,
Family/psychology MH - Quality of Health
Care MH - Research Support, Non-U.S. Gov't EDAT-
2003/03/26 0400 MHDA- 2003/08/09 0500 PST -
ppublish SO - Fam Pract 2003 Apr20(2)167-72.
8
Preface MeSH

• MeSH (Medical Subject Headings)
• database gt 22.000 medical terms
• each with his own definition
• each definition has a list with his possible
  synonymsex stroke is a synonym of
  Cerebrovascular Accident
• situated in a tree (or multiple trees)

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Preface MeSH

1. Anatomy A
2. Organisms B
3. Diseases C
4. Chemicals and Drugs D
5. Analytical, Diagnostic and Therapeutic Techniques
   and Equipment E
6. Psychiatry and Psychology F
7. Biological Sciences G
8. Physical Sciences H
9. Anthropology, Education, Sociology and Social
   Phenomena I
10. Technology and Food and Beverages J
11. Humanities K
12. Information Science L
13. Persons M
14. Health Care N
15. Geographic Locations Z

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Preface MeSH
Nervous System Diseases C10 Central
Nervous System Diseases C10.228 Brain
Diseases C10.228.140
Cerebrovascular Disorders C10.228.140.300 B
asal Ganglia Cerebrovascular Disease
C10.228.140.300.100 Brain Ischemia
C10.228.140.300.150 Carotid Artery
Diseases C10.228.140.300.200
Cerebrovascular Accident C10.228.140.300.30
1 Brain Infarction C10.228.140.300.301.200
Cerebrovascular Trauma C10.228.140.300.350
Dementia, Vascular C10.228.140.300.400
Hypoxia-Ischemia, Brain C10.228.140.300.45
1 Intracranial Arterial Diseases
C10.228.140.300.510 Intracranial
Arteriovenous Malformations C10.228.140.300.520
Intracranial Embolism and Thrombosis
C10.228.140.300.525 Intracranial
Hemorrhages C10.228.140.300.535
Leukomalacia, Periventricular
C10.228.140.300.700 Sneddon Syndrome
C10.228.140.300.750 Vascular Headaches
C10.228.140.300.800 Vasculitis, Central
Nervous System C10.228.140.300.850
Vasospasm, Intracranial C10.228.140.300.900
Vertebral Artery Dissection
C10.228.140.300.950
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Preface MeSH
Cardiovascular Diseases C14 Vascular
Diseases C14.907 Cerebrovascular
Disorders C14.907.253 Basal Ganglia
Cerebrovascular Disease C14.907.253.061
Carotid Artery Diseases C14.907.253.123
Intracranial Arteriovenous Malformations
C14.907.253.295 Cerebral Arterial Diseases
C14.907.253.337 Intracranial Embolism
and Thrombosis C14.907.253.378 Cerebral
Hemorrhage C14.907.253.420 Brain
Ischemia C14.907.253.459 Cerebrovascular
Accident C14.907.253.480 Brain Infarction
C14.907.253.480.200 Cerebrovascular
Trauma C14.907.253.535 Hypoxia-Ischemia,
Brain C14.907.253.545 Intracranial
Arterial Diseases C14.907.253.560
Intracranial Hemorrhages C14.907.253.573
Leukomalacia, Periventricular
C14.907.253.612 Sneddon Syndrome
C14.907.253.774 Vascular Headaches
C14.907.253.937 Vasculitis, Central
Nervous System C14.907.253.946
Vasospasm, Intracranial C14.907.253.951
Vertebral Artery Dissection C14.907.253.953
Vertebrobasilar Insufficiency C14.907.253.956

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PMID- 12651791 OWN - NLM STAT- MEDLINE DA -
20030324 DCOM- 20030807 LR - 20041117 PUBM-
Print IS - 0263-2136 VI - 20 IP - 2 DP - 2003
Apr TI - GPs working in solo practice obstacles
and motivations for working in a group? A
qualitative study. PG - 167-72 AB - OBJECTIVE
Our aim was to analyse the obstacles and eventual
motivations of solo GPs for working in
group practice. METHODS A qualitative study
using 12 focus groups was carried out in primary
care in French-speaking Belgium. The
subjects comprised four samples of GPs 20 GP
trainers, 18 GP trainees, 25 women GPs and
25 other GPs. The focus groups were taped and
transcribed. Two independent researchers
carried out the analysis using the QSR
NUD.IST software. RESULTS The participants (88
GPs) did not share a common definition of
group practice-in particular multidisciplinary
working-the need for a common pool of patients
and shared premises. Their main sources of
motivation for eventually setting up a group
practice were better quality of life,
continuity of care and sharing professional
knowledge. The main obstacles were a required
agreement between colleagues, the loss of a
personal patient-GP relationship, budgetary
constraints, and divergent views on group
practice and GPs' profession (especially
true for the association of GPs from different
age groups). CONCLUSION The current study
shows that GPs working solo have divergent
views of group practice. However, they clearly
perceive advantages to this type of
association (e.g. better quality of life and
continuity of care). This study also
confirms the high level of stress and tiredness
felt by GPs and especially senior
practitioners. AD - Centre Universitaire de
Medecine Generale, Universite Catholique de
Louvain, Avenue Mounier 5360, 1200 Bruxelles,
Belgium. Jean-Marc.Feron_at_cumg.ucl.ac.be FAU
- Feron, Jean-Marc AU - Feron JM FAU - Cerexhe,
Francoise AU - Cerexhe F FAU - Pestiaux,
Dominique AU - Pestiaux D
FAU - Roland, Michel AU - Roland M FAU - Giet,
Didier AU - Giet D FAU - Montrieux, Christian AU
- Montrieux C FAU - Paulus, Dominique AU -
Paulus D LA - eng PT - Journal Article PL -
England TA - Fam Pract JID - 8500875 SB - IM MH
- Adult MH - Belgium MH - Family Practice MH
- Female MH - Focus Groups MH - Group
Practice MH - Humans MH - Male MH - Middle
Aged MH - Motivation MH - Physicians,
Family/psychology MH - Quality of Health
Care MH - Research Support, Non-U.S. Gov't EDAT-
2003/03/26 0400 MHDA- 2003/08/09 0500 PST -
ppublish SO - Fam Pract 2003 Apr20(2)167-72.
13
Preface filters

• Filters origin
• Filter systematic review developped by Shojania
  et al.
• Taking advantage of the explosion of systematic
  reviews an efficient MEDLINE search strategy.
  Eff Clin Pract. 2001 Jul-Aug4(4)157-62.
• ? developed this filter

(("systematic review" OR "systematic literature
review" OR meta-analysis pt OR meta-analysis
ti OR metaanalysis ti OR meta-analyses ti
OR evidence-based medicine OR (evidence-based AND
(guideline tw OR guidelines tw OR
recommendations)) OR (evidenced-based AND
(guideline tw OR guidelines tw OR
recommendation)) OR consensus development
conference pt OR health planning guidelines OR
guidelinept OR cochrane database syst rev OR
acp journal club OR health technol assess OR evid
rep technol assess summ OR evid based nurs OR
evid based ment health OR clin evid) OR
((systematic tw OR systematically OR critical
tw OR (study tiab AND selection tiab) OR
(predetermined OR inclusion AND criteri tw) OR
exclusion criteri OR "main outcome measures" OR
"standard of care") AND (survey tw OR surveys
tw OR overview OR review tw OR reviews OR
search OR handsearch OR analysis tw OR
critique tw OR appraisal OR (reduction AND risk
AND (death OR recurrence))) AND (literature tw
OR articles OR publications tw OR publication
tw OR bibliography tw OR bibliographies OR
published OR unpublished OR citation OR citations
OR database OR internet tw OR textbooks tw OR
references OR trials OR meta-analysis mh OR
(clinical tw AND studies) OR treatment
outcome)) NOT (case report ti OR editorial ti
OR editorial pt OR letter pt OR newspaper
article pt))
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Preface filters

• ? tested the sensitivity

systematic reviews in DARE review articles commented on in ACP Journal CLUB
number of target articles 100 103
number of target articles retrieved with this filter 93 100
sensitivity 93 (86-97) 97(91-99)
DARE Database of Abstracts of Reviews of
Effects ACP American College of Physicians
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Preface filters

• ? tested the predictive value

Clinical Topic number of articles retrieved true-positive results implied positive predictive value
Screening for colorectal cancer 19 10 53 (30-75)
Thrombolytic theray for venous thromboembolism 11 6 54 (24-82)
Treatment of dementia (filter) 105 53 50 (41-60)
Treatment of dementia (reviewpt) 170 13 8 (4-13)
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Preface filters
? Filter clinical queries (Haynes et al)
sensitivity and specificity
searchcombination searchcombination sensitivity specificity
therapy broad searching 99 70
therapy narrow searching 93 97
diagnose broad searching 98 74
diagnose narrow searching 64 98
etiology broad searching 93 63
etiology narrow searching 51 95
prognosis broad searching 90 80
prognosis narrow searching 52 94
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Preface
?
Medline
MeSH
Pubmed.com
one doctor
Filters?
Many complicated databases, only one doctor
18
Overview

1. Preface before PubMed.be
2. Connecting them PubMed.be
3. The future?
4. TEST DRIVE!

19
Overview

• 2. Connecting them PubMed.be
• MeSH easy selection
• Filters developped and tested
• Filters possibility to make own filters
• sending to pubmed.com
• help-windows
• advantages
• costs

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PubMed.be
MeSH
Medline
Filters
Pubmed.com
PubMed.be
Many databases, one interface PubMed.be!
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PubMed.be MeSH
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PubMed.be MeSH

• after integrating the MeSH translation form
  INSERM, our MeSH accepts
• French and English search words
• French and English synonyms
• INSERM Institut National de la Santé et de la
  Recherche Medicale (France)

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PubMed.be MeSH
24
PubMed.be Filter

• Filters one click gt big filter!

(("systematic review" OR "systematic literature
review" OR meta-analysis pt OR meta-analysis
ti OR metaanalysis ti OR meta-analyses ti
OR evidence-based medicine OR (evidence-based AND
(guideline tw OR guidelines tw OR
recommendations)) OR (evidenced-based AND
(guideline tw OR guidelines tw OR
recommendation)) OR consensus development
conference pt OR health planning guidelines OR
guidelinept OR cochrane database syst rev OR
acp journal club OR health technol assess OR evid
rep technol assess summ OR evid based nurs OR
evid based ment health OR clin evid) OR
((systematic tw OR systematically OR critical
tw OR (study tiab AND selection tiab) OR
(predetermined OR inclusion AND criteri tw) OR
exclusion criteri OR "main outcome measures" OR
"standard of care") AND (survey tw OR surveys
tw OR overview OR review tw OR reviews OR
search OR handsearch OR analysis tw OR
critique tw OR appraisal OR (reduction AND risk
AND (death OR recurrence))) AND (literature tw
OR articles OR publications tw OR publication
tw OR bibliography tw OR bibliographies OR
published OR unpublished OR citation OR citations
OR database OR internet tw OR textbooks tw OR
references OR trials OR meta-analysis mh OR
(clinical tw AND studies) OR treatment
outcome)) NOT (case report ti OR editorial ti
OR editorial pt OR letter pt OR newspaper
article pt))
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PubMed.be own filter
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PubMed.be ready to send!
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PubMed.be help files
1st layer How to use it?

• 2nd layer
• Educational part
• MedLine
• MeSH
• Filters

Not complete!
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PubMed.be general

• Advantages
• own language
• help windows
• easy MeSH-acces
• easy filter acces with explanation
• possibility to create own filters (filters are
  saved on the server password protected)
• one overview window

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PubMed.be general

• Advantages
• combination of MeSH and Clinical Queries gives a
  third dimension!

Precision
MeSH (librarians)
Clinical Queries (clinicals)
Clinical articles
Recall
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PubMed.be project

• software and hardware costs
• server old desktop (PIII) 0
• operating system Linux 0 number of crashes
  0!
• program language PHP 0
• database mySQL 0
• web server apache 0
• manuals mostly online ( 0 ), but some were
  bought ( 50 )

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PubMed.be
MeSH
Medline
Filters
Pubmed.com
PubMed.be
Many databases, one interface PubMed.be!
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Overview

• Preface before PubMed.be
• Connecting them PubMed.be
• The future wish list
• Development
• Research
• TEST DRIVE!

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The future wish list

• Development
• 2nd layer help files (educational part)
• has to be reviewed
• need also information about how to evaluate an
  article? (EBM)
• Independent from pubmed.com (own interface in
  pubmed.be)
• Informational video how to use?
• English part has to be translated and reviewed
  (program structure has already been finished)
• New layout?

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The future wish list

• Research
• Evaluation of the project based on
• a online users survey
• the web logs (how do people use the site?)
• a study comparison of doing a literature search
  with or without PubMed.be project
• Making new filters (with the use of users own
  filters)

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The future wish list
Interested to join? Mail me! gtgtgt
koen_at_thomeer.be ltltlt
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THANKS!

• Inventing ideas Jan Degryse
• Programming help and advice Nathan Van Overloop,
  Linux-community of Leuven.
• Translations Iwan Van Gool, Valérie Dory.
• Financial and hardware support
• Academisch Centrum voor Huisartsgeneeskunde (KUL)
• Centre Universitaire du Médecine Générale (UCL)
• Software support
• Open Source Community (Fedora RedHat Linux,
  Apache, PHP, MySQL, XSLT, )
• Inserm (for the French MeSH-thesaurus)
• Emotional support
• My wife and son!

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TEST DRIVE!
gtgt http//test.pubmed.be ltlt