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PubMed.be Project Linking databases together Koen Thomeer, MD Promotor: Jan Degryse, MD, PhD.

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Presentation on theme: "PubMed.be Project Linking databases together Koen Thomeer, MD Promotor: Jan Degryse, MD, PhD."— Presentation transcript:

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 1.Preface: before PubMed.be  MedLine database  MeSH database  Filters

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

5 Preface: MedLine MedLine (=Journal Database) –contains > 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 acces to a community paid database?

6 Preface: MedLine Pubmed.com –web interface to have easy acces to MedLine for everbody –but people don’t get the maximum out of the interface => bad results

7 PMID OWN - NLM STAT- MEDLINE DA DCOM LR PUBM- Print IS VI - 20 IP - 2 DP Apr TI - GPs working in solo practice: obstacles and motivations for working in a group? A qualitative study. PG 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. 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 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 04:00 MHDA- 2003/08/09 05:00 PST - ppublish SO - Fam Pract 2003 Apr;20(2):

8 Preface: MeSH MeSH (Medical Subject Headings) –database > medical terms –each with his own definition –each definition has a list with his possible synonyms ex: stroke is a synonym of ‘Cerebrovascular Accident’ –situated in a tree (or multiple trees)

9 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]

10 Nervous System Diseases [C10] Central Nervous System Diseases [C10.228] Brain Diseases [C ] Cerebrovascular Disorders [C ] Basal Ganglia Cerebrovascular Disease [C ] + Brain Ischemia [C ] + Carotid Artery Diseases [C ] + Cerebrovascular Accident [C ] Brain Infarction [C ] + Cerebrovascular Trauma [C ] + Dementia, Vascular [C ] + Hypoxia-Ischemia, Brain [C ] + Intracranial Arterial Diseases [C ] + Intracranial Arteriovenous Malformations [C ] Intracranial Embolism and Thrombosis [C ] + Intracranial Hemorrhages [C ] + Leukomalacia, Periventricular [C ] Sneddon Syndrome [C ] Vascular Headaches [C ] + Vasculitis, Central Nervous System [C ] + Vasospasm, Intracranial [C ] Vertebral Artery Dissection [C ] Preface: MeSH

11 Cardiovascular Diseases [C14] Vascular Diseases [C14.907] Cerebrovascular Disorders [C ] Basal Ganglia Cerebrovascular Disease [C ] + Carotid Artery Diseases [C ] + Intracranial Arteriovenous Malformations [C ] Cerebral Arterial Diseases [C ] + Intracranial Embolism and Thrombosis [C ] + Cerebral Hemorrhage [C ] + Brain Ischemia [C ] Cerebrovascular Accident [C ] Brain Infarction [C ] + Cerebrovascular Trauma [C ] + Hypoxia-Ischemia, Brain [C ] + Intracranial Arterial Diseases [C ] + Intracranial Hemorrhages [C ] + Leukomalacia, Periventricular [C ] Sneddon Syndrome [C ] Vascular Headaches [C ] + Vasculitis, Central Nervous System [C ] + Vasospasm, Intracranial [C ] Vertebral Artery Dissection [C ] Vertebrobasilar Insufficiency [C ] + Preface: MeSH

12 PMID OWN - NLM STAT- MEDLINE DA DCOM LR PUBM- Print IS VI - 20 IP - 2 DP Apr TI - GPs working in solo practice: obstacles and motivations for working in a group? A qualitative study. PG 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. 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 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 04:00 MHDA- 2003/08/09 05:00 PST - ppublish SO - Fam Pract 2003 Apr;20(2):

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 Jul-Aug;4(4): developed this filter: → 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 guideline[pt] 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]))

14 Preface: filters → tested the sensitivity systematic reviews in DARE* “review” articles commented on in ACP* Journal CLUB number of target articles number of target articles retrieved with this filter sensitivity 93% (86%-97%) 97% (91%-99%) *DARE: Database of Abstracts of Reviews of Effects *ACP: American College of Physicians

15 Preface: filters → tested the predictive value Clinical Topic number of articles retrieved true-positive results implied positive predictive value Screening for colorectal cancer % (30%-75%) Thrombolytic theray for venous thromboembolism % (24%-82%) Treatment of dementia (filter) % (41%-60%) Treatment of dementia (review[pt]) % (4%-13%)

16 Preface: filters searchcombinationsensitivityspecificity therapy broad searching 99 % 70 % narrow searching 93 % 97 % diagnose broad searching 98 % 74 % narrow searching 64 % 98 % etiology broad searching 93 % 63 % narrow searching 51 % 95 % prognosis broad searching 90 % 80 % narrow searching 52 % 94 % → Filter clinical queries (Haynes et al): sensitivity and specificity

17 Preface Medline Pubmed.com MeSH Filters? ? one doctor 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

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

21 PubMed.be: MeSH

22 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)

23 PubMed.be: MeSH

24 PubMed.be: Filter Filters: one click => 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 guideline[pt] 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]))

25 PubMed.be: own filter

26 PubMed.be: ready to send!

27 PubMed.be: help files 1 st layer: How to use it? 2 nd layer: Educational part MedLine MeSH Filters Not complete!

28 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 PubMed.be: general

29 Advantages –combination of MeSH and Clinical Queries gives a third dimension! Precision Recall Clinical Queries (clinicals) MeSH (librarians) Clinical articles

30 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 €)

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

32 Overview 1.Preface: before PubMed.be 2.Connecting them: PubMed.be 3.The future: wish list DevelopmentResearch 4.TEST DRIVE!

33 The future: wish list Development –2nd layer help files (educational part) has to be reviewed has to be reviewed need also information about ‘how to evaluate an article?’ (EBM) 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?

34 The future: wish list Research –Evaluation of the project based on: a online users survey a online users survey the web logs (how do people use the site?) the web logs (how do people use the site?) a study: comparison of doing a literature search with or without PubMed.be project a study: comparison of doing a literature search with or without PubMed.be project –Making new filters (with the use of users ‘own filters’)

35 The future: wish list Interested to join? Mail me! >>>

36 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!

37 TEST DRIVE! >> <


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