Advanced search in Pubmed.
We describe the methodology of advanced search and selecion of search terms in Pubmed, much more specific than the simple search from the text box.
We already know what Pubmed MeSH terms are and how an advanced search can be done with them. We saw that the search method by selecting the descriptors can be a bit laborious, but allowed us to select very well, not only the descriptor, but also some of its subheadings, including or not the terms that depended on it in the hierarchy, etc.
Today we are going to see another method of advanced search a little faster when it comes to building the search string, and that allows us to combine several different searches. We will use the Pubmed advanced search form.
Advanced search in Pubmed
To get started, click on the “Advanced” link under the search box on the Pubmed home page. This brings us to the advanced search page, which you can see in the first figure. Let’s take a look.
First there is a box with the text “Use the builder below to create your search” and on which, initially, we cannot write. Here is going to be created the search string that Pubmed will use when we press the “Search” button. This string can be edited by clicking on the link below to the left of the box, “Edit”, which will allow us to remove or put text to the search string that has been elaborated until then, with natural or controlled text, so we can click the “Search” button and repeat the search with the new string. There is also a link below and to the right of the box that says “Clear”, with which we can erase its contents.
Below this text box we have the search string constructor (“Builder”), with several rows of fields. In each row we will introduce a different descriptor, so we can add or remove the rows we need with the “+” and “-” buttons to the right of each row.
Within each row there are several boxes. The first, which is not shown in the first row, is a dropdown with the boolean search operator. By default it marks the AND operator, but we can change it if we want. The following is a drop-down where we can select where we want the descriptor to be searched. By default it marks “All Fields”, all the fields, but we can select only the title, only the author, only last author and many other possibilities. In the center is the text box where we will enter the descriptor. On its right, the “+” and “-” buttons of which we have already spoken. And finally, in the far right there is a link that says “Show index list”. This is a help from Pubmed, because if we click on it, it will give us a list of possible descriptors that fit with what we have written in the text box.
As we are entering terms in the boxes, creating the rows we need and selecting the boolean operators of each row, the search string will be formed, When we are finished we have to options we can take.
The most common will be to press the “Search” button and do the search. But there is another possibility, which is to click on the link “Add to history”, whereupon the search is stored at the bottom of the screen, where it says “History”. This will be very useful since the saved searches can be entered in block in the field of the descriptors when making a new search and combined with other searches or with series of descriptors. Do you think this is a little messy? Let’s be clear with an example.
Suppose I treat my infants with otitis media with amoxicillin, but I want to know if other drugs, specifically cefaclor and cefuroxime, could improve the prognosis. Here are two structured clinical questions. The first one would say “Does cefaclor treatment improve the prognosis of otitis media in infants?” The second one would say the same but changing cefaclor to cefuroxime. So there would be two different searches, one with the terms infants, otitis media, amoxicillin, cefaclor and prognosis, and another with the terms infants, otitis media, amoxicillin, cefuroxime and prognosis.
What we are going to do is to plan three searches. A first one about article about the prognosis of otitis media in infants; a second one about cefaclor; and a third one about cefuroxime. Finally, we will combine the first with the second and the first with the third in two different searches, using the boolean AND.
Selecting search terms
Let us begin. We write otitis in the text box of the first search row and click on the link “Show index”. A huge drop-down appears with the list of related descriptors (when we see a word followed by the slash and another word it will mean that it is a subheader of the descriptor). If we look down in the list, there is a possibility that says “otitis / media infants” that fits well to what we are interested in, so we select it. We can now close the list of descriptors by clicking the “Hide index list” link. Now in the second box we write prognosis (we must follow the same method: write part in the box and select the term from the index list). We have a third row of boxes (if not, press the “+” button). In this third row we write amoxicillin. Finally, we will exclude from the search those articles dealing with the combination of amoxicillin and clavulanic acid. We write clavulanic and click on “Show index list”, which shows us the descriptor “clavulanic acid”, which we select. Since we want to exclude these articles from the search, we change the boolean operator of that row to NOT.
In the second screen capture you can see what we have done so far. You see that the terms are in quotes. That’s because we’ve chosen the MeSHs from the index list. If we write the text directly in the box it will appear without quotes, which will mean that the search has been done with natural language (so the accuracy of the controlled language of MeSH terms will have been lost). Note also that in the first text box of the form the search string that we have built so far has been written, which says (((“otitis/media infants”) AND prognosis) AND amoxicillin) NOT “clavulanic acid”. If we wanted, we have already said that we could modify it, but we will leave it as it is.
Now we could click “Search” and make the search or directly click on the “Add to history” link. To see how the number of articles found can be reduced, click on “Search”. I get a list with 98 results (the number may depend on when you do the search). Very well, click on the link “Advanced” (at the top of the screen) to return to the advanced search form.
What remains to be done is simpler. We write cefaclor in the text box and give the link “Add to history”. We repeat the process with the term cefuroxime. You can see the result of these actions in the fourth screen capture. You see how Pubmed has saved all the three searches in the search history. If we now want to combine them, we just have to click on the number of each one (a window will open for us to choose the boolean we want, in this case all will be AND).
First we click on # 1 and # 2, selecting AND. You see the product in the fith capture. Notice that the search string has been somewhat complicated: (((((otitis/media infants) AND prognosis) AND amoxicillin) NOT clavulanic acid)) AND cefaclor. As a curiosity I will tell you that, if we write this string directly in the simple search box, the result would be the same. It is the method used by those who totally dominate the jargon of this search engine. But we have to do it with the help of the advanced search form. We click on “Search” and we obtain seven results that will (or so we expect and hope) compare amoxicillin with cefaclor for the treatment of otitis media in infants.
We click again on the link “Advanced” and in the form we see that there is a further search, the # 4, which is the combination of # 1 and # 2. You can already have an idea of how complicated the searching could become combining searches with each other, adding or subtracting according to the boolean operator that we choose. Well, we click on # 1 and # 3 and press “Search”, finding five articles that should deal with the problem we are looking for.
We are coming to the end of my comments for today. I think that the fact that the use of MeSH terms and advanced search yields more specific results than simple search has been fully demonstrated. The usual thing with the simple search with natural language is to obtain endless lists of articles, most of them without interest for our clinical question. But we have to keep one thing in mind. We have already mentioned that a number of people are dedicated to assigning the MeSH descriptors to articles that enter the Medline database. Of course, since the article enters the database until it is indexed (the MeSH is assigned), some time passes and during that time we cannot find them using MeSH terms. For this reason, it could not be a bad idea to do a natural language search after the advanced one and see if there are any articles in the top of the list that might interest us and are not indexed yet.
Finally, commenting that searches can be stored by downloading them to your disk (by clicking the link “download history”) or, much better, creating an account in PubMed by clicking on the link on the top right of the screen that says “Sign in to NCBI. ” This is free and allows us to save the search from one time to another, which can be very useful to use other tools such as Clinical Queries or search filters. But that is another story…