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 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: bibliographic records.  Growth: / 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. descriptorqualifier

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 Bone Nasal Cavity Nasal Mucosa Nasal Septum Sense Organs [A09] Ear Eye Nose Olfactory Mucosa Vomeronasal 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 syndrome could 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 descriptor Norepinephrine

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 on  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 1 st type:  Contents collected from various payable sources, linked together and commented.  Mostly reliable information,  lots of work used to build,  commercial owners. 2 nd 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 3 rd 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: 1 st 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:

Alpe Adria Master Course :: Medical Informatics :: Dr. J. Dimec: Document databases in medicine.23 Health portals: MD Consult Examples of searching through referential literature, practical advice and data on drugs 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 page where the subject corresponds to the query from the previous slide.

Alpe Adria Master Course :: Medical Informatics :: Dr. J. Dimec: Document databases in medicine.26 Health portals: MD Consult Part of an index of topics an institutions that gave practical advice to 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 of database on drugs, their pharmacological actions 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: 2 nd 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:

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: 3 rd 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.

Alpe Adria Master Course :: Medical Informatics :: Dr. J. Dimec: Document databases in medicine.33 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

Alpe Adria Master Course :: Medical Informatics :: Dr. J. Dimec: Document databases in medicine.35 National Institutes of Health, Health Information

Alpe Adria Master Course :: Medical Informatics :: Dr. J. Dimec: Document databases in medicine.36 National Institutes of Health, Health Information