In the previous lecture we went over the process of building a search. We identified the major concepts of a topic. We used Boolean to define the

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Arabella Greer
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In the previous lecture we went over the process of building a search. We identified the major concepts of a topic. We used Boolean to define the relationships between concepts.

1 In the previous lecture we went over the process of building a search. We identified the major concepts of a topic. We used Boolean to define the relationships between concepts. And we discussed common database search techniques. In this lecture, we ll focus on a specific resource PubMed, which is probably the resource you should become most familiar with (for now and for post DDS). 1

2 In this lecture, I will give you a formal introduction to PubMed and discuss some of its specialized features that help clinicians target and find good evidence. A good portion of the talk will centre on Medical Subject Headings the controlled vocabulary PubMed uses to describe articles. 2

3 First, to access PubMed use one of the proxied links on the Taubman Library and School of Dentistry sites. When you use these proxied links, you will be prompted to authenticate through with your Unique Name and Kerberos password. It s important that you use these proxied links so that when you search PubMed you can access the library s complete collection of full text articles. 3

4 PubMed is a tremendously important biomedical health sciences database. It is compiled and maintained by the National Library of Medicine (NLM), which is a division of the National Institutes of Health (NIH). Its primary function is to serve as an entry point to the MEDLINE database, which represents the largest portion of PubMed s 21+ million citations. We ll discuss MEDLINE again in a few slides, but to sum up the relationship here: PubMed is the government s interface to freely access the MEDLINE database. You ll hear of other MEDLINE databases, like Ovid MEDLINE, which are access points to the same database, and are able to exist because the NLM makes MEDLINE data available to anyone who wants it. In addition to PubMed, there is PMC, which is a database of freely available full text articles. All 2+ million PMC citations are findable in PubMed, so you do not have to use a separate interface to access this content. I mention this so that you re aware of the growing body of freely available full text literature thanks in part to PMC and Open Access initiatives which you ll be able to take advantage of now and, more importantly, in your post DDS career. [CLICK] As an aside: The Clinical Queries, which I ll mention a few times through these 3 lectures is accessible on this page. In the middle column, near the bottom. 4

When you run asearch in PubMed and we ll use the same example we used in the previous lecture (is oral hygiene effective for preventing caries in children) this is how the results are displayed.

5 When you run asearch in PubMed and we ll use the same example we used in the previous lecture (is oral hygiene effective for preventing caries in children) this is how the results are displayed. [CLICK] The main results are in the center. Note that there is no relevancy ranking here. The citations that appear at the top are those that have been most recently added to the database. [CLICK] Below the search box is the Save Search option. Saving a search will allow you set up alerts so that you re notified when new citations enter the database that meet your search criteria. Setting up such alerts is a great way to keep current on clinical topics of interest and on ongoing research projects. [CLICK] Use the Filters to limit your search to publication types, age groups, languages, etc. In this case, I limited our oral hygiene and dental caries search to English, children, and review articles. Note that I did not include the word children in my search, b/c it is preferable to target age groups with the Ages filter. [CLICK] The Search Details provides PubMed s translation of your search. The search details can help diagnosis and fix poor searches and provide insight into how PubMed interprets and understands your search query. PubMed generally does a fine job interpreting searches and returning relevant results, but there are times when that s not the case. If you see poor results or think there is more out there than you re seeing, take a look at the Details to make sure the translation is appropriate. I will discuss this again in a few slides. 5

Click on a citation title to view the abstract. Most citations will have abstracts and they will always be in English, even if the paper is non English.

6 Click on a citation title to view the abstract. Most citations will have abstracts and they will always be in English, even if the paper is non English. MGet it links appear to the right of the abstract if you access PubMed through one of the methods I described earlier. The MGet It link will connect you to the full text if available. Below the MGet It link, but not displayed on this slide, is a Related Articles field, which will directly connect you to citations similar to the one you re currently looking at. 6

7 With that we are done with the general PubMed orientation part of this talk. You can search PubMed well enough without knowing anything more than that. Break your topic into searchable concepts. Take those searchable concepts to PubMed. Use Boolean to describe the relationships between those concepts. Click search. Look at the results. Use MGet It to get the full text. Done. But, lying beneath PubMed s surface is a powerful language that, if used properly, can drastically improve the quality of searches and retrieval sets. Effective use of this language can save you time (which is important to clinicians) and provide you with extremely targeted sets of results. The language I m talking about is MeSH or Medical Subject Headings and it s the language that describes and connects the majority of citations in PubMed. And it s what I ll focus on in the next few slides. 7

Back to the fluoride supplement abstract. Below most abstracts you will see an expandable menu of MeSH Terms. If you expand the menu, you will see a list of the controlled (i.e., MeSH) terms associated with that citation.

8 Back to the fluoride supplement abstract. Below most abstracts you will see an expandable menu of MeSH Terms. If you expand the menu, you will see a list of the controlled (i.e., MeSH) terms associated with that citation. [CLICK] This is a real life example of a controlled vocabulary that we talked about in the previous lecture. Each one of the terms listed in the menu (child, dental caries, fluorides, etc) represents a piece of the article s content. The vocabulary is very large, with more than terms, but each term represents a specific concept and is applied consistently to most PubMed citations. This means that all citations dealing with Dental Caries are described with the MeSH term Dental Caries. From a practical searching point of view, this means that every article on dental caries regardless of whether authors refer to the concept as dental caries or cavities will be described with that one controlled term dental caries. 8

An example: If a run a search on bad breath, you would expect to see results that have those two words bad and breath somewhere in the abstract, title, author, journal fields, etc.

9 An example: If a run a search on bad breath, you would expect to see results that have those two words bad and breath somewhere in the abstract, title, author, journal fields, etc. But, if we look at the Search Details, which I pointed out earlier in the lecture, we will see that PubMed, without us necessarily knowing, runs two types of searches a keyword and controlled vocabulary search. Let s look at the Details a little more closely. 9

10 As you can see right away, focusing on the red text, PubMed has taken my bad breath search and run a keyword (All Field) search for halitosis, bad AND breath, and bad breath as a phrase. I searched for bad breath and PubMed connected bad breath to the CONCEPT of halitosis, plus included a couple variations on bad breath. That s impressive. Not only is it looking for occurrences of the two words I typed into the search box, it s also looking for words I didn t include (halitosis). [CLICK] 10

11 It s also taking my bad breath concept and associating it with the MeSH concept HALITOSIS. Again, the MeSH Term is a controlled term that is used throughout the database to capture all articles on that concept. In this example, PubMed connects bad breath to the MeSH Term Halitosis, which means we will get articles in our results that use one or both of halitosis and bad breath. As we see in this example, PubMed does both a keyword and MeSH search automatically, which is one of the reasons why you can search PubMed effectively without knowing much more than what I went over at the beginning of this talk. However, there are ways to manipulate the MeSH vocabulary to enhance the effectiveness of your searches. Before I demonstrate this, though we first need to understand its limitations. 11

PubMed is made up of several different collections of citations, the largest of which is called MEDLINE. Take a look at the two images on this slide.

12 PubMed is made up of several different collections of citations, the largest of which is called MEDLINE. Take a look at the two images on this slide. The top image is a set of everything in PubMed as of the day I took the image. PubMed interprets the search all[sb] as 1) all, meaning all, everything, and 2) [sb], meaning subset. Put together, that means the subset ALL, which comes out to almost 22 million citations. This means that every search you run in PubMed is run against a collection of nearly 22 million citations. If I run a medline[sb] search, PubMed will give me every MEDLINE citation in the database, which, as you can see in the bottom image, comes out to nearly 20 million. Therefore, roughly 20 million of the ~22 million citations you find in PubMed are from the MEDLINE database. This is important for 2 reasons: 1) All citations in MEDLINE have MeSH terms, so that means nearly ~20 million citations have MeSH terms. Take it one step further it means that ~20 million citations are indexed & described with a consistent vocabulary, which in practice means that if PubMed is interpreting your search terms correctly, you can feel confident you re getting the majority of citations on your topic. The caveat is that and this leads to our second point 2) There are ~2 million citations that are in PubMed that don t have MeSH terms (~22m ~20m). These are, for the most part, really old citations (i.e, pre 1950s) and very new citations that are in the process of being assigned MeSH terms. Within the context of EBD, we don t care about really old citations (those pre 1950s ones) b/c their findings are more than likely outdated and inappropriate to apply to a patient in But missing out on new literature is problematic. 12

13 Therefore, if you search with MeSH terms alone which is what I m going to do next you will miss out on new, unindexed items. To capture those unindexed items, you need to include keywords basically, you need to do what you saw PubMed do automatically in the Search Details. 12

Now, let me show you through a series of searches how understanding and manipulating the MeSH vocabulary can enhance your searches: [CLICK] This first search is simple.

14 Now, let me show you through a series of searches how understanding and manipulating the MeSH vocabulary can enhance your searches: [CLICK] This first search is simple. If you look at the search details, you ll see that PubMed is searching for both keywords and MeSH terms, which is good, but the result set is very large. Of course, you can use filters (like reviews, English language, published in the last 5 years) to effectively narrow this search to a more manageable result set. but for the purposes of this demonstration, let s put the filters aside and use MeSH alone to narrow our results. [CLICK] In this search I have forced PubMed to just retrieve citations that have been indexed with both DENTAL CARIES and ORAL HYGIENE MeSH terms. This [mesh] search works only because both DENTAL CARIES and ORAL HYGIENE are MeSH terms. You can t add [mesh] to everything you search for, only those terms that are MeSH terms. I ll discuss ways find MeSH terms at the end of the talk. By focusing our search on MeSH, our result set is 1500 citations lighter than the previous. [CLICK] That s still a hefty set, though. To narrow it down further, you can do what they call MAJOR the MeSH terms. Simply replace [mesh] with [majr]. Majoring a MeSH term means that you will retrieve only those citations that are truly focused on in this case Dental Caries and Oral Hygiene. The 545 results we see in this set were in the previous set of 3058, but by majoring the 13

15 MeSH terms, we ve eliminated all citations that are not primarily about dental caries and oral hygiene. Each search is in essence getting rid of more and more noise. Again, the caveat is that by running a very focused search with MeSH vocabulary, we are missing out articles that haven t yet been indexed with MeSH terms. 13

We can overcome this limitation by adjusting how PubMed does its keyword searching. To perform this adjustment, we ll use the Boolean operator OR and qualifiers [title/abstract] and [title].

16 We can overcome this limitation by adjusting how PubMed does its keyword searching. To perform this adjustment, we ll use the Boolean operator OR and qualifiers [title/abstract] and [title]. [CLICK] In this first search, I ve continued to major the MeSH terms, but I have used OR to add in the keyword CARIES and then qualified it with [title/abstract]. This tells PubMed to bring back citations that have the word CARIES in the title and/or abstract. The second half of the search is cut off, but I did the same thing for ORAL HYGIENE (i.e., I added a few oral hygiene techniques, like mouthwash, flossing, etc. as [title/abstract] keywords). Since we ve added in keywords, our results balloons to [CLICK] To narrow further, we can force PubMed to just look for the word CARIES in the title of citations and nowhere else. This is done by replacing [title/abstract] with [title]. [CLICK] We re now down to 691 citations that are really focused on the topic of Dental Caries and Oral Hygiene, which is a much more targeted and narrower result set than our first search that returned [CLICK] And if we apply filters, we can narrow it down further. In this case we re down to 20 when apply the Review filter. 14

17 There is absolutely nothing wrong with that first search that retrieved 4551 results, but using the MeSH vocabulary well can help you eliminate much of the noise you ll otherwise see frequently in your results and hopefully help you practice evidence based dentistry a little more efficiently. 14

18 If you would like more information about PubMed and PubMed features, feel free to contact me or visit the PubMed Tutorials and Help page. For more information about MeSH, visit the NLM s MeSH website. You may also wonder where you can find MeSH terms. The MeSH menu located under citation abstracts (as I showed earlier) is a great way to identify MeSH terms, particularly if you re pulling them from a citation that s relevant to your search topic. Knowing how one good citation is indexed can help you build a more effective search to capture similar citations. The most complete list of MeSH terms is accessible in the MeSH database, which not only lists out the MeSH terms, but also offers MeSH term definitions, subheadings (which I didn t go into), and visuals of MeSH s hierarchical structure (which I showed in the first lecture). The Search Details also includes MeSH terms related to your PubMed searches. The Advanced Search page, which is linked to from underneath the main PubMed search box, has a Search Builder section, which lets you select fields to isolate your searches to, such [title], [title/abstract], [journal], etc. 15

19 To summarize: Learn how to search PubMed effectively. It s probably what you ll be using most frequently now and in the future. Don t feel obligated to explicitly use MeSH all the time. Know it exists and how to use it so when you need to, you can. Use both MeSH and keywords in your searches to get at both indexed and non indexed citations Use filters to narrow your results Major MeSH terms, but recognize it s limitations. 16

20 To review: What is the name of the largest subset of PubMed citations? MEDLINE What is the name of the database of freely available NIH funded articles? PubMed Central What does MeSH stand for? Medical Subject Headings You should use MeSH alone in your searches? (T/F) False (use keywords too) 17

21 Thank you. 18

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