PubMed for Orthopaedic Surgeons

Myles Clough, M.D., FRCSC
Kamloops, BC

The US National Library of Medicine codifies the subject matter of thousands of medical journals including over 100 orthopaedic ones. This information, the abstracts and the references are all stored in the Medline Database. PubMed is an Internet site giving access to this database. By using PubMed effectively, one can search the literature efficiently and accurately from ones home computer.

Most orthopaedic surgeons are already aware of this and are familiar with the PubMed system. However, it is easy to be discouraged by the huge volume of citations which some simple queries produce and it is not easy to be sure that you have performed a comprehensive search.

This article aims to review the basics of using PubMed as well as describing some of the useful features of the site. Finally, we will design strategies for coping with common types of orthopaedic searches.

This article is designed to guide you through a series of searches chosen with teaching points in mind. You are encouraged to use it as a practice guide at home. Learning to search is not a spectator sport. 

PubMed Basics
The address of the site is http://pubmed.gov although this address forwards you on to http://www.ncbi.nih.gov/entrez/query.fcgi. You should bookmark the site so you can return to it easily.

The words you want use to find the articles of interest form the search string. Enter the search string into the box at the top of the page and click on Go

The citations found by your search will be displayed on a new page. However, the current search string will still be visible in the search box at the top of the page. You can edit the phrase in this box.

Each citation gives the names of the authors, the title of the paper, and the reference. The authors names form a link to an abstract of the paper. Other links include one to Related Articles which can form a useful extension of the original search.
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Clicking on the Link to the abstract will bring up a page with information about just that one article. cloughfig2.jpg

You can change the nature of the display of the article abstract by choosing something else in the Display box (top left). If you choose Citation it will display everything in the Medline Database that relates to that article. This is useful if you want to know how the librarians classified the subject matter of the article.

When you are looking at a list, another useful thing to do is select the Review tab instead of All (top left). Only those articles classified as Reviews are then displayed.

If you have found an article on the subject that interests you, the easiest way to find more is to click on the Related Articles link. This will display articles which have been classified similarly by the librarians. Because the seed article was about traction and hip fractures you will see that most of the early articles in this list are also on this subject.

The strategy of entering a search string, finding an article on the subject and using the Related Articles link to get a more focused list is the fastest way to get a reasonable reading list.

PubMed Functions
Details - to use this function click on the Details link below the search box. The Details function reveals how PubMed has translated your search string into the search string the engine actually uses.

To make the point, enter the search string intertrochanteric fractures of the hip into the search box. You might think that defining the subject more tightly would refine the search significantly. However, the resulting collection is very similar to the one obtained searching for hip fracture. (see above)
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Looking at Details is always the right thing to do if your search has not turned out as expected. Click on the Details link to discover how the search string was analysed and translated.
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The robot takes the user query intertrochanteric fractures of the hip and breaks it up into components for interpretation. We find that hip fracture and even ischium suddenly appear in the translation. This is the reason the resultant search is very like the hip fracture search.

This is a long way from the intention of the search but you would never have found out why this search failed if you hadnt looked it up in details. It is probably helpful that PubMed translates your query; but it can produce unexpected and undesirable results!

Note that the automatic translation tried to relate the query to the special set of terms used by NLM to classify medical subjects. This is the set of Medical Subject Headings (MeSH for short). In effect, the robot looked up the term intertrochanteric fracture and found it to be a synonym of hip fracture. It therefore expanded the search to include all hip fracture subjects. Because the robot is likely to mistranslate your query into its MeSH term, it is safer to look up the MeSH term and use it directly.

MeSH Database - to use this function click on the MeSH Database link in the blue sidebar.

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The MeSH database contains a vocabulary of terms used by NLM to define medical subjects. If you click on this link you will find a site that allows you to search for the MeSH term specific to your subject. You can find it either by using a search engine or by following a root subject like Wounds and Injuries down a tree to the subject of interest. If you use the database you can select the term and send it to the PubMed search system.

It is important to understand the concept of MeSH terms a specific language used to describe medical topics, even if you dont think you will use them.

MeSH terms associated with the subject of interest can also be found by looking up details of a search or by looking at the full citation of an article which is on the subject.

 

You can define a term in a search string as a MeSH term by using the format subject[MeSH] or by subject[MAJR]. The [MAJR] designation means that the subject is major, a central part of the article. The librarians may say that articles on osteoporosis that only mention hip fractures in passing, have hip fracture as a subject. But in this case it would not be defined as a major subject. If you define a search string term as a MeSH term you must enclose it in quotes.

History - to use this function click on the History link below the search box. The history function keeps track of all the searches you have done during this session and refers to them by number. If your searches get complicated you can link them together using the numbers eg #4 AND #5 NOT #9.

Limits - to use this function click on the Limits link below the search box. You will see a dialog box which allows you to specify the fields (title/author/journal etc) to which the search should apply, the publication type, language, ages, gender and species. The date of publication can also be specified.

Once the limits are defined, run the search again. The limit definitions will be noted in a yellow line near the top of the page and the limited search will be displayed.

MyNCBI - to use this service click on the MyNCBI link in the blue sidebar. This is a way to store searches. The service is free but you must register and permit cookies to be placed on your computer. After you have run a search you can save it by clicking on the Save Search link.
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The dialogue to name the search and store it is self-explanatory. But you will get nonsense if you store a search that uses history numbers. In your next session the history number will refer to some completely different search or be non-existent. You must re-create the whole search string in words before you go to MyNCBI.

If you want to revisit a search, open MyNCBI and click on the name of the search you wish to revisit. If you only want to see papers published since you last looked, then select the search by clicking on the checkbox and then click on Whats New for Selected.

The number of items since the last time you checked will be offered as a link to that list of new citations.

Clinical Queries - to use this service click on the Clinical Queries link in the blue sidebar. This is a filter which selects papers which might be expected to offer a higher level of evidence. The basic idea is that papers with good evidence will allude to clinical trials. This page can be reached by clicking on the link in the sidebar. It offers choices for the category of information and emphasis.

For most orthopaedic surgery searches the sensitive search is more useful. The specific search looks for words requiring the study is a randomized one and these are rare in orthopaedics. If you select the specific search almost all the studies will be about medical treatments because of the difficulty of running randomized trials in orthopaedic surgery.

The search subject is entered in the box and Go is clicked. If you have chosen the sensitive search, all the papers will have some reference to randomization in the title or text. However, a paper containing the words the cases were not randomized would also be selected by this filter.

Common Orthopaedic Search Strategies

  • Quick and dirty find something useful with the fewest possible steps.
    • Formulate a search string describing your subject using medical terminology (jargon). Avoid using words like the, and, of. The longer your search string the shorter the list of citations you will get but the more specific it will be.
    • Review the articles found. If they are sufficient the search has succeeded.
    • If you would like more, select from the list of citations, the article closest to your subject of interest. Click on the Related Articles link to obtain a list of similar papers.
    • If you would like less but higher quality consider using the Reviews tab to obtain reviews and meta-analyses.
    • Advantages
      • Quick.
      • Reasonably comprehensive.
    • Disadvantages
      • List can be quite long with relevant papers throughout.
      • Not comprehensive. Depends on librarians classification being correct.
  • Full to feel sure you have found most of the papers on the subject without too much labour.
    • Open the MeSH database and find the MeSH term closest to the subject of interest.
    • Use subheading if appropriate.
    • Define the MeSH term (or term with subheading) as the Major Subject.
    • Run the search.
    • Review the collection.
    • Too big narrow using:
      • AND terms
      • NOT terms
      • Limits
    • Too small broaden using OR terms.
  • Comprehensive to be sure you havent missed any relevant papers. The overall strategy is to design an inclusive search string that is very broad to capture all the subject papers, and then add more terms to narrow down the collection to include a higher proportion of relevant papers.
    • Find the MeSH term for your subject; define it as the major subject.
    • Add all the synonyms you can think of, linked with the MeSH term with OR (eg colles fracture[majr] OR (fracture AND ("distal radius" OR Smith's OR Barton OR die-punch OR "radial styloid").
    • Consider adding acronyms to the search string (AVN, NOF etc). However, be aware that acronyms may stand for many other non-orthopaedic subjects.
    • Once you find that adding terms does not increase the size of the collection, start narrowing it by adding terms with AND. Since by now this may be a long complicated search string consider using the History function. If your final inclusive string was #10 use the string #10 AND volar plate to obtain a collection narrowed down to the subject of interest. Be aware that the narrowing term (e.g. volar plate) may also need to be tested to make sure it is itself comprehensive so that you find all the distal radius fractures with one part and all the volar plate fixation papers in the other.
  • Update to see only the most recent papers on a particular subject.
    • Design a comprehensive search string that describes your subject (see above). Make sure that you do NOT refer to history numbers in the search string.
    • Run the search again and then open Limits.
    • Select Publication Date and enter a date in the From dialog box. Leave the To box blank. Run the search. PubMed will show only the papers published after the specified date.
    • Open MyNCBI. In the box available give a name for the search. Click on OK to store the search.
    • If, after an interval, you want to see if there are any new papers on this subject, go to the PubMed site and open MyNCBI. If you want to see all the citations, including the ones you have already seen, click on the name of the search. If you only want to see new papers select the subject by clicking on the checkbox then click on Whats New for Selected.
  • Clinical Trials to make sure the studies are RCTs.
    • Formulate an appropriate search string. Copy it to the clipboard.
    • Go to the Clinical Queries page.
    • Select the Sensitive Filter for surgery subjects.
    • Paste your search string into the box and click on Go.

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