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Transcript of Document databases in medicine. Alpe Adria Master Course :: Medical Informatics :: Dr. J. Dimec:...
Alpe Adria Master Course :: Medical Informatics :: Dr. J. Dimec: Document databases in medicine. 2
Bibliographic databases: Medline
The biggest and the most developed bibliographic database in biomedicine.
Built in National Library of Medicine (NLM), Bethesda, USA.
Available in e-form for a period 1966 – today. Includes bibliographic data about journal papers
from 4.600+ journals in biomedicine. 76% of records with English abstract. Still the most important information tool in
biomedical sciences.
Alpe Adria Master Course :: Medical Informatics :: Dr. J. Dimec: Document databases in medicine. 3
Bibliographic databases: Medline
Size: 12.000.000+ bibliographic records. Growth: 2000+ / day. Each record contains subject description, made of
MeSH descriptors. The database is free of charge, because it is built
in governmental agency. Numerous installations by secondary providers
could be very expensive. Installation on NLM (PubMed) is free of charge,
pretty clumsy, but improving all the time.
Alpe Adria Master Course :: Medical Informatics :: Dr. J. Dimec: Document databases in medicine. 4
MeSH
Subject description in Medline records is composed of MeSH (Medical Subject Headings) descriptors and qualifiers.diabetes mellitus / drug therapy
Qualifiers define the extent of concept represented by descriptor.
Medline records contain additional concepts which are chemical and pharmacological terms.
descriptor qualifier
Alpe Adria Master Course :: Medical Informatics :: Dr. J. Dimec: Document databases in medicine. 5
MeSH
Thesaurus MeSH is built hierarchically. Descriptors are very often placed on a different
places inside the same hierarchical tree – an example of a descriptor Nose in a hierarchy Anatomy.
Face [A01] Cheek Chin Eye Forehead Mouth Nose
Respiratory System [A04] Larynx Lung Nose
Nasal BoneNasal CavityNasal MucosaNasal Septum
Sense Organs [A09] Ear Eye Nose
Olfactory MucosaVomeronasal Organ
Taste Buds
Alpe Adria Master Course :: Medical Informatics :: Dr. J. Dimec: Document databases in medicine. 6
MeSH
There are 15 hierarchies.
Each descriptor could be placed in more than one hierarchy, e.g.
Creutzfeldt-Jakob syndromecould be C10 - Nervous System Diseases or F3 - Mental Disorders
Alpe Adria Master Course :: Medical Informatics :: Dr. J. Dimec: Document databases in medicine. 7
MeSH: example of the position of descriptorNorepinephrine
Alpe Adria Master Course :: Medical Informatics :: Dr. J. Dimec: Document databases in medicine. 8
MeSH
Thesaurus MeSH is used for indexing and searching in Medline.
It is accessible onhttp://www.nlm.nih.gov/mesh/2003/MBrowser.html
Its hierarchical nature helps with navigation while selecting the most appropriate
descriptor, broadening and narrowing the query.
Alpe Adria Master Course :: Medical Informatics :: Dr. J. Dimec: Document databases in medicine. 9
Bibliographic databases – trends
The gap between the worlds of bibliographic databases and full document databases is narrowing.
Bibliographic record is often the pointer to the real document.
Full document is usually accessible only if user’s institution has a commercial contract with the publisher.
Alpe Adria Master Course :: Medical Informatics :: Dr. J. Dimec: Document databases in medicine. 10
e-journal databases
Most big publishers of scientific literature offer their journals also in the e-form on the web.
The most precious source of information, but expensive.
For the academic user the access is usually organised by the consortia of libraries which negotiate with the publishers.
An example of a big e-journal database is Science Direct by Elsevier Science Publishers.
Alpe Adria Master Course :: Medical Informatics :: Dr. J. Dimec: Document databases in medicine. 11
e-journal databases
A growing number of scientific e-journals which is accessible free of charge.
Some of them are “born digital”, some are published by minor publishers which are still searching their niche.
Some renowned publishers are putting their journals on the web free of charge after some time elapse since publishing.
Reason: pressure of the scientific public.
Alpe Adria Master Course :: Medical Informatics :: Dr. J. Dimec: Document databases in medicine. 12
e-journal databases
Alpe Adria Master Course :: Medical Informatics :: Dr. J. Dimec: Document databases in medicine. 13
e-journal databases
Alpe Adria Master Course :: Medical Informatics :: Dr. J. Dimec: Document databases in medicine. 14
e-journal databases
Alpe Adria Master Course :: Medical Informatics :: Dr. J. Dimec: Document databases in medicine. 15
e-journal databases
Alpe Adria Master Course :: Medical Informatics :: Dr. J. Dimec: Document databases in medicine. 16
e-journal databases
Alpe Adria Master Course :: Medical Informatics :: Dr. J. Dimec: Document databases in medicine. 17
e-journal databases
Alpe Adria Master Course :: Medical Informatics :: Dr. J. Dimec: Document databases in medicine. 18
Health portals
Type of an web information tool that is especially well developed in medicine.
Portals are web pages with pointers to documents or other information tools.
Developers are trying to cover some field of medicine or inform some user group with as diverse and quality documents as possible.
The greatest number of health portals is meant for lay public; some are built for practicing professional.
Alpe Adria Master Course :: Medical Informatics :: Dr. J. Dimec: Document databases in medicine. 19
Health portals
Health portals for non-professionals are trying to educate an informed patient.
The best are owned by the (mostly US) governmental health agencies and big clinics – institutions that gain most with the informed patient.
Such portals bring descriptions of diseases or conditions, aetiologies, prognoses and descriptions of treatments, usually on a very high quality level.
Alpe Adria Master Course :: Medical Informatics :: Dr. J. Dimec: Document databases in medicine. 20
Health portals
1st type: Contents collected from various payable sources,
linked together and commented. Mostly reliable information, lots of work used to build, commercial owners.
2nd type: Collection of pointers to web sources.
Sometimes less reliable information, less work used to build, non-commercial owners.
Alpe Adria Master Course :: Medical Informatics :: Dr. J. Dimec: Document databases in medicine. 21
Health portals
3rd type: Built by governmental health agencies and
clinics. Only reliable information, information written at the agency or clinic, lots of referential literature (health encyclopaedia,
pharmacopoeia…).
Alpe Adria Master Course :: Medical Informatics :: Dr. J. Dimec: Document databases in medicine. 22
Health portals: 1st type
MD Consult Built by an association of medical publishers. Offer information from 50+ peer-reviewed
sources: publishers, medical associations, US government agencies.
Web access:http://www.mdconsult.com/
Alpe Adria Master Course :: Medical Informatics :: Dr. J. Dimec: Document databases in medicine. 23
Health portals: MD Consult
Examples of searchingthrough referentialliterature, practicaladvice and data ondrugs are following.
Alpe Adria Master Course :: Medical Informatics :: Dr. J. Dimec: Document databases in medicine. 24
Health portals: MD Consult
Part of a list of textbooks. Result of a search with query “myocardial infarction AND aspirin”.
Alpe Adria Master Course :: Medical Informatics :: Dr. J. Dimec: Document databases in medicine. 25
Health portals: MD Consult
Part of a textbook index with pointers to pages and part of a pagewhere the subject corresponds to the query from the previous slide.
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Health portals: MD Consult
Part of an index of topics an institutions that gave practical adviceto perform medical practice.
Alpe Adria Master Course :: Medical Informatics :: Dr. J. Dimec: Document databases in medicine. 27
Health portals: MD Consult
Part of an index ofdatabase on drugs,their pharmacologicalactions and usage.
Alpe Adria Master Course :: Medical Informatics :: Dr. J. Dimec: Document databases in medicine. 28
Health portals: MD Consult
Alpe Adria Master Course :: Medical Informatics :: Dr. J. Dimec: Document databases in medicine. 29
Health portals: 2nd type
CliniWeb Built by Oregon Health & Science University. Pointers to public web medical sources, indexed
with the descriptors from MeSH. While navigating the hierarchy of descriptors we
find the pointers to the web sources, and trigger the search in Medline (PubMed).
Web access:http://www.ohsu.edu/cliniweb/index.html
Alpe Adria Master Course :: Medical Informatics :: Dr. J. Dimec: Document databases in medicine. 30
Health portals: CliniWeb
Alpe Adria Master Course :: Medical Informatics :: Dr. J. Dimec: Document databases in medicine. 31
Health portals: CliniWeb
Alpe Adria Master Course :: Medical Informatics :: Dr. J. Dimec: Document databases in medicine. 32
Health portals: 3rd type
National Institutes of Health, Health Information Information from NIH and other US government
health agencies. Information meant for laypeople and medical
doctors; high quality. Effective linkage to MedlinePlus, a portal with
similar characteristics.
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National Institutes of Health, Health Information
Alpe Adria Master Course :: Medical Informatics :: Dr. J. Dimec: Document databases in medicine. 34
National Institutes of Health, Health Information
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National Institutes of Health, Health Information