Document databases in medicine. Alpe Adria Master Course :: Medical Informatics :: Dr. J. Dimec:...

Document databases in medicine

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.


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.


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


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


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


MeSH: example of the position of descriptorNorepinephrine


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.

http://www.nlm.nih.gov/mesh/2003/MBrowser.html


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.


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.


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.


e-journal databases


e-journal databases


e-journal databases


e-journal databases


e-journal databases


e-journal databases


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.


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.


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.


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…).


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/


Health portals: MD Consult

Examples of searchingthrough referentialliterature, practicaladvice and data ondrugs are following.



Part of a list of textbooks. Result of a search with query “myocardial infarction AND aspirin”.



Part of a textbook index with pointers to pages and part of a pagewhere the subject corresponds to the query from the previous slide.



Part of an index of topics an institutions that gave practical adviceto perform medical practice.



Part of an index ofdatabase on drugs,their pharmacologicalactions and usage.




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

http://www.ohsu.edu/cliniweb/index.html


Health portals: CliniWeb


Health portals: CliniWeb


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.


National Institutes of Health, Health Information







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Document databases in medicine. Alpe Adria Master Course :: Medical Informatics :: Dr. J. Dimec:...

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