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PubMed tutorial : IGM help

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Scope Note MeSH Medline Updated : September 22, 1999. This document is a training support; it is summary and need to be comment.

A new Beta Version of PubMed is on line.
See NLM Technical Bulletin
, 1999,  September-October.

Free Medline accesses
PubMed access
PubMed site
Why use MeSH terms
See the MeSH tree, find the MeSH terms
Internet Grateful Med (IGM)
Search PubMed
Save the search strategies
What you must know
To know more
Search examples (in French)

Free Medline accesses

This is a very rapidly moving field and it is very difficult to have a precise appreciation. Some sites have begun comparative studies of these different accesses :

  1. Dr Felix's Free MEDLINE Page by the Gloucestershire Royal Hospital Library (UK). The US mirror site is preferred. See especially the National Library of Medicine Supplement which lists the NLM’free Medline accesses and PubMed Free MEDLINE® Lowdown! which summarizes good and bad points of PuBMed. They are reported in the Lis-medical.

  2. Medline Resource Center by Organising Medical Networked Information (UK). See especially Evaluating Medline : PubMed. See also Evaluation criteria for different versions of the same database - a comparison of Medline services available via the World Wide Web by Betsy Anagnostelis, Royal Free Hospital School of Medicine, UK and Alison Cooke, University of Wales, Aberystwyth, UK. Originally presented at Online Information 97: the 21st International Online Information Meeting, London, 9-11 December 1997.

  3. For more precise information about PubMed, the NNLM (National Network of Libraries or Medicine - US) lists tutorials, comparative studies, and so on : PubMed and Grateful Med Information.

  4. Tutorial PubMed / Internet Grateful Med by the The New Hampshire NLM Project

See also :

PubMed access

Between the all free Medline accesses, PubMed seems to be the most interesting. Its experimental version has been launched for a few months. The official announcement of PubMed was June, 26 1997, by Vice President Al Gore. PubMed is a project of the National Center for Biotechnology Information (NCBI) at the NLM. Three particular topics : PreMedline, Related articles and PubMed Journals Full Text.

For PreMedline see this page.

When relevant references appear, the link Related articles, which are used with an algorithm, make it possible to retrieve similar citations using a mouse click. It can also be used for detection of "sciencific misconduct". See : Medline Searches Turn Up Cases of Suspected Plagiarism and The Internet: A Powerful Tool for Plagiarism Sleuths by E. Marshall. - In Science, 1998, 279, pp 473-4.

PubMed Journals Full Text propose a link to a full text of many journals. Most them are available only for subscribers.

PubMed site

The home page gives access to a basic search mode and links to several documents. It is recommended to read Overview and Help : last updated January 1999 for a better understanding of how to use PubMed. Other links go to sites which work in the area of PubMed ie. Internet Grateful Med, NLM, NIH, NCBI and information about Clinical Alerts, Clinical Queries and Citation Matcher.

The use of Advanced Search is better than the basic mode, because it proposes more possibilities for searching.

Why use MeSH terms

a significant example : search regarding "neoplasm recurrence".

recurrence [All Fields] --> 133 446 documents
Neoplasm Recurrence, Local --> 33 425 documents

Search with MeSH terms give comparatively better results. A more elaborate analysis of these results (not displayed) shows that the references which are not indexed with MeSH terms are the least relevant. Therefore it is necessary to use MeSH terms. Also it is necessary to consult MeSH thesaurus, except when we are certain that the searched term has no synonym, but that is very rare.
See also MeSH terms must be used in Medline searches by M. Clarke in BMJ 1997 Apr 19; 314(7088): 1203.

See the MeSH tree, find the MeSH terms

The latest "PubMed System Update - January 26, 1998" allows users to browse the MeSH tree and find the subheadings that are associated with MeSH terms. The "mapping" feature of PubMed will map synonyms of terms to the appropriate MeSH terms. But we persist to recommend the use of IGM to find MeSH terms because we believe that IMG's "mapping" is more powerful.
For example, the search term "recurrence" maps only to the MeSH term "Recurrence" in PubMed, whereas the term maps to "Recurrence", "Neoplasm Recurrence", "Local Pathologic Processes", "Disease", "Neoplastic Processes Neoplasm, Residual" in IGM. The same with anorexia.

PubMed does not provide any information about subheadings, e.g., for therapy = "Used with diseases for therapeutic interventions except drug therapy, diet therapy, radiotherapy, and surgery, for which specific subheadings exist. The concept is also used for articles and books dealing with multiple therapies ". This information is available by IGM (see also MeSH 2000 browser from the National Library of Medicine. Access to MeSH Tree Structures, Scope Note, synonyms, annotations, subheadings, ...)

On the other hand, PubMed's MeSH tree is clearer than the IGM's tree.

Internet Grateful Med

Here we do not describe the different capabilities of searching with IGM. They are complex enough. We will therefore focus on the possibility of consulting the thesaurus.

From the home page, click directly on Proceed. Enter a search term, e.g. "bladder cancer", and click on Find MeSH/Meta Terms button located at the top of the page. IGM then displays the Metathesaurus Browser Screen. The IGM algorithm displays the MeSH terms that are the nearest to the search terms (the Ovid "mapping" function provides quite similar results). Click on the best MeSH term, "bladder neoplasms" for this search. The Metathesaurus Information Screen gives :

Concept permits the use of Focus and Qualifiers with explanations and advise. The Focus (MeSH Major Topic in PubMed) will be explained further. The qualifiers permit to limit a search with particular topics, ie. surgery or etiology for a disease, physiology or anatomy of an organ, ...
MeSH Tree Context(s) allows us to navigate into the MeSH tree. When a term is present in many trees which have immediate access. This function permits to know more about the thesaurus structure and to expand or on the contrary to restrict a search..
Additional MeSH Information contains both an historical note and advice on how to use MeSH terms.
Some "bugs" can appear during a consultation of the tree ; they are know by the IGM staff and will be removed. When the response time seems too long, connect again.

Search PubMed

We recommend the use of simultaneous MeSH Browser and IGM as they are complementary functions. The New User's Survival Guide (Rev. November 26, 1997) specifies that "It [IGM] helps the user create and refine a search, then submits the search to Elhill or PubMed, NLM's retrieval engines".
Search MeSH terms with IGM like previously described, "copy and paste " on PubMed MeSH Browser to consult the tree or Advanced Search after choice MeSH Terms in Search Field (automatic) and search. Then follow instructions.

To save the strategies, two possibilities:

  1. It is possible to save the strategy in a URL format but "this procedure works only in Basic Mode and in Boolean Search Mode. It does not work in when in the Advanced Mode or from the query box on the Document Summary page" (source "PubMed Training Workbook for End-Users: The Basics of Searching PubMed",  National Library of Medicine, July 1998).

  2. Linda Milgrom and Michael Boer from the National Network of Libraries or Medicine suggest to save the URL: see PubMed : Initial Impressions in Supplement, Summer 1997, vol 28, n 3 (paragraph "linking to PubMed"). For example, to search references about Sudden Infant Death with MeSH terms and textwords for 1998, see URL for short format (author, title, source) or with abstracts

"PubMed's future plans include a feature where you be able to view a picture of the strategy--similar to Internet Grateful Med's "Details of search" button... In addition, the plans also call for this feature to include an edit function so that a search strategy can be easily revised and submitted". NLM Technical Bulletin, 1997, Nov-Dec.

See also  J.A.D.E Journal Abstracts Delivered Electronically,  National Center for Emergency Medicine Informatics (Us).

What you must know

1. Explosion
When MeSH term is, e.g. "Colitis", the explode command is a default command. So PubMed operates an addition of all terms listed under colitis :

  Colitis, Ischemic
  Colitis, Ulcerative
    Megacolon, Toxic
    Enterocolitis, Pseudomembranous

2. Focus = MeSH Major Topic
Focus is a limitation of a search to retrieve only relevant references. But be careful ; for a disease, the focus excludes about 40% of the references, and 70% for a technique :

sciatica [MeSH Terms] --> 244 documents
sciatica [MeSH Major Topic] --> 146 documents

cholecystectomy [MeSH Terms] -->1308 documents
cholecystectomy [MeSH Major Topic] --> 572 documents

The focus must be used with caution.

3. All Fields
Search with All Fields is necessary in three cases :

Click on Advanced Search and choose All Fields in Search Field. Search is now operating in all fields : title, abstracts, exploded MeSH terms (of course, only when MeSH terms are used), etc... Don't forget to use the right truncation, e.g. "evalua*", to get all title and abstract words like evaluate, evaluation, evaluable, ... (but do not use truncation with MeSH terms).

Each PubMed search field is available by automatic mode or by List Terms. List Terms allows displaying and consultation of the alphabetic index (institution, author, journal name, language, title words, abstract words, publication type, ...) or the numerical index (page number, part of issue, publication date, ...).
It is possible, at all times, to limit a search with Pub. Date Limit. This command works with the field Entrez Date, daily updated. To limit annually, use the field Publication Date (syntax : 1996:1998) in Search Field.

4. Limit by age

It is possible to limit searches by age groups, with these "Check Tags":

Infant, Newborn first month after birth
Infant between 1 and 23 months
Child, Preschool 2 to 5 of age
Child 6 to 12 of age
Adolescence 13 to 18 of age
Adult 19 to 44 of age
Middle Age 45 to 64 of age
Aged (65 and over)

To use limit, do not explode these terms and do not restrict search to major topic headings only ; use the syntax "Child" [MESH:NOEXP] from Detailed Display command. See also French-English complete list of Check Tags, published by Dic Doc INSERM.

5. Limit by journals from PubMed new July 27, 1999

The following journal subsets are now available to search :
Abridged Index Medicus     jsubseta  (AIM journal titles)
Dental                                 jsubsetd
Nursing                               jsubsetn

For example: 
neoplasms AND jsubseta

6. Related Articles

This link, which appears in the front of each reference, allows the user to find similar references with an algorithm which compares MeSH terms, title and abstract words. This command allows the user to complete or expand a search without supplementary procedure to find MeSH terms. But Related Articles don't read Scope Note and previous indexing for recent MeSH terms !

7. Strange results

Be careful, "Heart attack", with "MeSH browser", is not mapped to "myocardial infarction". But "heart attack" in "all fields" = ("myocardial infarction"[MeSH Terms] OR heart attack[Text Word]) ...

To know more

Some interactive exercises (in French). See also, for candidates : Advanced Boolean search especially Syntax of Complex Boolean Expressions.

See also Medline Ovid/Web mode d'emploi (in French).

Benoit Thirion
The author is grateful to Marie-Lise Shams (webmaster of Acronyms for health information resources
) and Richard Medeiros for their editorial assistance.

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