by Cindy Schmidt
Revised July 2019
Warning: Do NOT work on this tutorial in Internet Explorer. Instead switch to another internet browser, and go to
http://library1.unmc.edu/gots/tutorial/pubmedippe
Instructions:
PubMed contains over 30 million records. Each record provides information about a article.
Unfortunately, there is no single searching method that best fits all the records in PubMed.
Why?
PubMed contains 3 different sets of records.
Every PubMed record in each of the three record sets contains:
Only MEDLINE records are indexed and contain the indexer dependent:
Which of the following searches can retrieve Pubmed records that are not indexed MEDLINE records?
Indexed records:
Unindexed Records (Click here to see a screenshot of an un-indexed record):
Indexed records/MEDLINE records are usually retrieved most easily and effectively with medical subject heading (MeSH) searches.
Unindexed records, in general, do not contain medical subject headings (MeSH) and, thus, cannot be retrieved using medical subject heading (MeSH) searches. The searcher must use keyword searches to retrieve these records.
This tutorial will guide you through a MeSH search for MEDLINE records (indexed records) and then a keyword search for both indexed and unindexed records. Both searches will be focused on a single clinical question.
Clinical Situation: You have a patient who just watched a documentary about the use of capsaicin to treat peripheral neuropathy. Although she just watched the documentary, she knows it was produced several years ago. She wants to know whether results of clinical trials continue to support this treatment and whether she should give it a try.
Open a Word document and type a list of the important concepts in this question. (Some students find this easier if they are asked, instead, to list the words they might type into a quick Google search.)
Does your list include the following two concepts?
capsaicin peripheral neuropathy
If not, add these concepts to your list.
Have you also listed any of the following in your list of search concepts?
If so, type the word "LIMIT" next to these concepts.
When you are working on a MeSH search of MEDLINE, things like publication characteristics (language, publication type) and subject characteristics (human vs. animal, gender, age) are best applied as limits. Don't include these concepts in your initial search. You will apply limits corresponding to these concepts after running your initial, MEDLINE search.
These concepts are often best left out of a keyword search.
It's easiest to construct a MeSH search if you know how PubMed's indexers expect you to search.
Does your search fit into one of the six search types shown below? If so, copy the search template and paste it into your Word document.
1. Drug safety/consumer product safety “Drug A/adverse effects”[mesh] OR “Drug A/poisoning”[mesh] OR “Drug A/toxicity”[mesh] OR (“Drug A”[mesh] AND “drug effects”[sh]) OR (“Drug A”[mesh] AND (“Safety”[mesh] OR “consumer product safety”[mesh]))
2. Drug A (Procedure A) that doesn’t cause harm (organ that could be harmed is not specified) “Drug A”[mesh] AND “drug effects”[sh]
3. Drug A (Procedure A) that doesn’t cause (or is least likely to cause) harm to Organ B “Drug A”[mesh] AND “Organ B/drug effects”[mesh]
4. Drug A (Procedure A) causes Disease B (“Drug A/adverse effects”[mesh] OR “Drug A/poisoning”[mesh] OR “Drug A/toxicity”[mesh]) AND (“Disease B/etiology”[mesh] OR “Disease B/chemically-induced”[mesh])
5. Drug or chemical or supplement A used to treat Disease B (“Drug-chemical-supplement A/therapeutic use”[mesh] OR "Drug-chemical-supplement A/administration and dosage"[mesh]) AND (“Disease B/drug therapy”[mesh] OR "Disease B/therapy")
6. Disease A results in occurrence of Disease B “Disease A/complications”[mesh] AND “Disease B/etiology”[mesh]
Did you say that the search fits template #5 -
Drug or chemical or supplement A used to treat Disease B (“Drug-chemical-supplement A/therapeutic use”[mesh] OR "Drug-chemical-supplement A/administration and dosage"[mesh]) AND (“Disease B/drug therapy”[mesh] OR "Disease B/therapy")
If so, you're correct.
You don't know yet what subject headings or subheadings are available for the capsaicin and peripheral neuropathy concepts, but after looking at the templates, you should be hoping to produce a search similar to the following:
("capsaicin/therapeutic use"[mesh] OR "capsaicin/administration and dosage"[mesh]) AND ("peripheral neuropathy/drug therapy"[mesh] OR "peripheral neuropathy/therapy"[mesh] )
You might wish to copy this planned search into your Word document so that you can refer to it later.
Now that you've outlined your search, it's time to actually look up the needed medical subject headings (MeSH) and construct your search.
Click here to open a PubMed page with UNMC full-text buttons. You may be asked to login with your UNMC e-mail username and password if you are using an off-campus computer or are using the campus wireless network.
In the future when you need to use PubMed without the help of this tutorial, you can reach this same version of PubMed by going to the Library homepage and clicking on the "Literature Databases" button. When the "Literature Databases" page appears, click on the "MEDLINE via PubMed" link.
People who are not affiliated with UNMC occasionally find this tutorial, you can still use most of this tutorial. Click here to open PubMed without the UNMC full-text links.
You should now see the PubMed homepage in your new browser window.
capsaicin
-- in the search box and click on the search button.
A list of about 5 MeSH headings will appear. These five headings appear because the descriptions of all these headings contain the word capsaicin.
In this case, you want to use the first heading in the list -- Capsaicin
Look at your Word document.
What subheading/s do you want to use with the capsaicin heading?
Did you say that you want to use the "therapeutic use" subheading and the "administration and dosage" subheading with capsaicin?
If so, you are correct.
A search that uses a heading without subheadings will retrieve both articles indexed with the heading alone and articles indexed with the heading and any subheading. Use subheadings only when there are just a few aspects of the heading topic (1-3 aspects) that are central to your clinical question.
You now need to search for a peripheral neuropathy heading.
peripheral neuropathy
-- in the MeSH search box (see red box in figure above) and hit the "search" button (red arrow).
Of the options that appear, the first option "peripheral nervous system diseases" is the most likely to include all forms of peripheral neuropathy.
When the detailed "peripheral nervous system diseases" page appears, refer to your notes again. Which subheadings do you plan to use with this heading?
Did you say "drug therapy" and "therapy"?
If so, you are correct!
Before you add these "peripheral nervous system diseases/subheading" combinations to the search builder, think twice.
Scroll to the bottom of the page to see the list of broader and narrower headings. Would a broader or narrower heading be better?
In the figure below, you can see part of the 'tree' for "Peripheral Nervous System Diseases." You can see the whole list in your MeSH database window.
Before you consider switching headings, it's important that you understand that PubMed "explodes" headings by default. What does this mean?
When you search with
"peripheral nervous system diseases/drug therapy"[mesh] OR "peripheral nervous system diseases/therapy"[mesh]
PubMed retrieves records indexed with the terms you've listed but it also retrieves all records indexed with the narrower headings in combination with the subheadings you've chosen. For example,
will retrieve articles indexed with any of the following:
"peripheral nervous system diseases/therapy"[mesh] "peripheral nervous system diseases/drug therapy"[mesh] "acrodynia/therapy"[mesh] "acrodynia/drug therapy"[mesh] "diabetic neuropathies/therapy"[mesh] "diabetic neuropathies/drug therapy"[mesh] "causalgia/therapy"[mesh] "causalgia/drug therapy"[mesh] etc.
Should you switch to a broader or narrower heading or stay with your current choice?
In this case, the --
"Peripheral Nervous System Diseases/drug therapy"[mesh] OR "Peripheral Nervous System Diseases/therapy"[mesh]
-- search that you've already selected is best.
Because you want to retrieve the articles about treatment of peripheral nervous system diseases in general, as well as the articles about treatment of specific peripheral nervous system diseases that the exploded "peripheral nervous system" heading will retrieve. You don't want to retrieve the articles about non-peripheral-nervous-system-related "neuromuscular diseases" that would be included among the results retrieved by the broader "neuromuscular diseases" heading.
Scroll back up to the "PubMed Search Builder."
Which Boolean operator --
AND OR NOT
-- do you want to use to join the "capsaicin/____" and "peripheral nervous system diseases/_____" terms?
If you said --
AND
, you are correct!
You should use AND to join the capsaicin concept to the peripheral neuropathy concept because you want both concepts to be present in every record you retrieve. If you wanted either the capsaicin or the peripheral neuropathy concept to be present in each record retrieved, you would choose OR to join the concepts.
If you added the "peripheral nervous system diseases/administration and dosage"[mesh] and the "peripheral nervous system diseases/therapeutic use"[mesh] one at a time, you will need to fix the parentheses. Remove the ) between the two terms you just added and enclose the two terms in a set of parentheses. If you don't fix the parentheses, your search will retrieve everything indexed with the last OR'd term in your search whether or not the items retrieved have anything to do with capsaicin.
Review the search statement that has been created. Do you need to edit the parentheses or Boolean operators? If so, make the needed changes.
You could remove all the extra parentheses added by the search builder. At a minimum, check the following:
1. Is there a set of parentheses enclosing each set of OR'd terms?
2. Are there any parentheses nested inside the set of parentheses that encloses a set of OR'd terms? If so, is the inner set both opened with a - (- and closed with a - ) - inside the outer parentheses. If not, the inner parenthesis will break the function of the outer set. Fix the problem before proceeding.
You should now be looking at PubMed search results. "PubMed" should appear automatically in the drop-down menu to the left of your search statement (red box in screenshot below).
You should be looking at a list of at least 219 results ( arrow in the figure).
Now it's time to add any desired limits/filters. For the purposes of this tutorial, use the "Randomized-Controlled Trials", "Humans", and "English" limits/filters.
After the application of the filters, at least 35 records should remain. The "Filters Activated" warning will appear (red box).
Look at the full-text buttons that appear under the abstracts. Under some records you will see buttons that say, "Free" or "Open Access."
If you want to see full text and a "Free" or "Open Access" button is available, try it first.
Most records have publishers' buttons that say nothing about free or open access. These buttons usually just give you a chance to pay for the article. If the Library happens to buy access from the publisher and you happen to be on-campus, the publisher's button may provide access without asking for payment. However, using the "GetIt!@UNMC" button first usually saves time as we frequently buy full text from non-publisher, full text vendors.
This record has PubMed ID #(PMID) 30472337
Usually you will be taken directly to the webpage for the specific article and you will just have to look for the .pdf or “full-text” link or icon.
Occasionally (as may occur in this case), you will be taken to a homepage for the journal or a journal vendor. When this happens, try one of the following:
1. Find a journal search box and search for the article's title. The title of the article should be present toward the top of the right-hand side bar.
2. Find and click on a "back issues", "previous issues", "journal contents", or "archives" button or link. Use the publication year, volume, issue and page numbers in the right-hand side bar to located the needed article.
If you see the article's abstract, but can’t find the .pdf/full-text icon or link, it may be hidden behind the right-hand sidebar. Click the arrow at the top of the side-bar (arrow #1 in screenshot above) to expose the portion of the window behind the sidebar.
If you see an error message on the left-hand side of the page instead of the full-text webpage:
(a) Look at the right-hand side bar to see if there’s another source that you can try (arrow #2 in the figure).
(b) If there is no other source licensed by the library, try the “Search Google Scholar By Title” link (arrow #3) . A free version may be available through Google Scholar.
(c) If Google Scholar isn’t helpful call or e-mail the library to request help obtaining the article or use the "Order item through Interlibrary Loan" (arrow #4) to request that we obtain a copy of the article for you. More details on Interlibrary Loan appear later in this tutorial.
The "Sorry, this item is not available through the library's online subscriptions" statement (arrow #1 in figure) means that the McGoogan Library does not have a license or subscription for the electronic form of this article.
Sometimes, you can obtain a free version of the article through Google Scholar by clicking the “Search Google Scholar By Title” link (arrow #2 in figure). Links to freely available items appear on the right-hand side of the Google Scholar page.
Alternately, you can order it through the Library’s Interlibrary Loan service (arrow #3 in figure). There is no charge for this service.
When you click the "Order item through Interlibrary Loan" button, a login form will appear.
If you haven't created an Interlibrary Loan account in the past, you will be asked to enter some information. Add the "Free UNMC" billing method to the Billing Table when asked to do so. If a pre-populated request form doesn't appear, go back to the "360 link" tab and click the blue button again.
90% of requests are filled within 2 weekdays. Very,very few English-language articles are unobtainable.
When the Library receives an article that you've requested, the article is posted in your Interlibrary Loan account. The Library sends you an e-mail to let you know that the article is available. You just have to log into your account within 30-days to download and save or print the article.
The MeSH-based search you've just performed will only retrieve indexed records (MEDLINE records). These are the only records that contain medical subject headings and the only records that have assigned subject characteristics (age, gender, human/animal) and assigned publication types.
It's now time to search for unindexed records. To perform a comprehensive keyword search, the type of search you will need to perform for your third year group project, you have to try to think of every word or phrase an author might use to indicate that he/she is talking about the concept of interest to you. You've already outlined the important concepts in this search. Take a few seconds to try to think of one or two alternate terms an author might use to indicate that he/she is talking about the concepts of capsaicin or peripheral neuropathy. Did you come up with any alternate terms? It's often hard to think of synonyms. That's why it's important to consult sources that can help. The tutorial will guide you through this process.
The MeSH database can actually be quite helpful to the keyword searcher. Why? For each MeSH heading there is a list of entry terms. This list includes some of the other terms authors have used for the heading concept. The MeSH database may also contain narrower terms that should be included in your search.
It's important that you understand that you'll now be using the MeSH database to find new keywords -- you should not add terms with [mesh] tags to this search. (Do not use the "Add to Search builder" button while constructing this search).
-- to the list .
Do you have the following list of terms?
capsaicin Capsaicine 8-Methyl-N-Vanillyl-6-Nonenamide 8 Methyl N Vanillyl 6 Nonenamide Axsain Zacin Capsidol Zostrix Capzasin Gelcen Katrum NGX-4010 NGX 4010 NGX4010 Capsicum Farmaya Capsin
If not, correct your list of terms.
Next:
Did you end up with the following search statement/strategy?
(capsaicin OR Capsaicine OR 8-Methyl-N-Vanillyl-6-Nonenamide OR "8 Methyl N Vanillyl 6 Nonenamide" OR Axsain OR Zacin OR "Capsicum Farmaya" OR Capsidol OR Zostrix OR Capzasin OR Gelcen OR Katrum OR NGX-4010 OR "NGX 4010" OR NGX4010 OR Capsin)
When you work on your PHPR 622 systematic review project, you should also search for alternate drug names in Martindale's: The Complete Drug Reference. Martindale's via LexiComp. Your PHPR 622 search strategy should include the English and foreign-language generic names, alternate hyhpenated, unhyphenated and no-space forms of any investigational names (as shown for “NGX-4010” in the search strategy above); and (if you're not working on an over-the-counter drug/supplement/treatment) all trade/proprietary/brand names.
You do not need to take the time to create a list of all the names of the various kinds of peripheral neuropathies for this tutorial. Instead, just use the alternate terms for neuropathy listed in the MeSH database entry for diabetic neuropathy.
diabetic neuropathy
You should now be looking at the detailed entry for “diabetic neuropathies”.
Neuropathy Neuropathies Polyneuropathy Polyneuropathies Mononeuropathy Mononeuropathies Amyotrophy Amyotrophies Neuralgia Neuralgias
If you were really needed the results of a comprehensive search, I would ask you to construct a much longer and more comprehensive list that included the names of lots of specific, peripheral nervous system diseases.
Now that you have a list of alternate terms for your neuropathy concept, ask yourself whether your search should include any of the term variants listed below (or include truncated terms that would retrieve these variants):
Please note: the examples listed below are not necessarily relevant to the tutorial search!
Add additional terms to your list until you can answer yes or not applicable to each of the above questions.
Add any terms that you missed to your list.
Create a search statement from your terms.
Did you come up with either of the following search strategies for your peripheral neuropathy concept?
(Neuropath* OR Polyneuropath* OR Mononeuropath* OR Amyotroph* OR Neuralgi*) - or - (Neuropathy OR Neuropathies OR neuropathic OR Polyneuropathy OR Polyneuropathies OR polyneuropathic OR Mononeuropathy OR Mononeuropathies OR mononeuropathic OR Amyotrophy OR Amyotrophies OR amyotrophic OR Neuralgia OR Neuralgias OR neuralgic)
If not, correct your search statement.
Now it's time to join the capsaicin keyword search statement to the neuropathy keyword search statement. What Boolean Operator (AND, OR, or NOT) should be used for this operation?
Did you say that --
--- should be used ? If so you are correct.
Did you come up with a search strategy like either of the following:
(Neuropath* OR Polyneuropath* OR Mononeuropath* OR Amyotroph* OR Neuralgi*) AND (capsaicin OR Capsaicine OR 8-Methyl-N-Vanillyl-6-Nonenamide OR "8 Methyl N Vanillyl 6 Nonenamide" OR Axsain OR Zacin OR "Capsicum Farmaya" OR Capsidol OR Zostrix OR Capzasin OR Gelcen OR Katrum OR NGX-4010 OR "NGX 4010" OR NGX4010 OR Capsin)
--or--
(Neuropathy OR Neuropathies OR neuropathic OR Polyneuropathy OR Polyneuropathies OR polyneuropathic OR Mononeuropathy OR Mononeuropathies OR mononeuropathic OR Amyotrophy OR Amyotrophies OR amyotrophic OR Neuralgia OR Neuralgias OR neuralgic) AND (capsaicin OR Capsaicine OR 8-Methyl-N-Vanillyl-6-Nonenamide OR "8 Methyl N Vanillyl 6 Nonenamide" OR Axsain OR Zacin OR "Capsicum Farmaya" OR Capsidol OR Zostrix OR Capzasin OR Gelcen OR Katrum OR NGX-4010 OR "NGX 4010" OR NGX4010 OR Capsin)
If not, make any needed corrections.
Now add an --
[all]
-- tag to the end of your search strategy, as shown below:
(Neuropath* OR Polyneuropath* OR Mononeuropath* OR Amyotroph* OR Neuralgi*) AND (capsaicin OR Capsaicine OR 8-Methyl-N-Vanillyl-6-Nonenamide OR "8 Methyl N Vanillyl 6 Nonenamide" OR Axsain OR Zacin OR "Capsicum Farmaya" OR Capsidol OR Zostrix OR Capzasin OR Gelcen OR Katrum OR NGX-4010 OR NGX 4010 OR NGX4010 OR Capsin)[all]
(Neuropathy OR Neuropathies OR neuropathic OR Polyneuropathy OR Polyneuropathies OR polyneuropathic Mononeuropathy OR Mononeuropathies OR mononeuropathic OR Amyotrophy OR Amyotrophies OR amyotrophic OR Neuralgia OR Neuralgias OR neuralgic) AND (capsaicin OR Capsaicine OR 8-Methyl-N-Vanillyl-6-Nonenamide OR "8 Methyl N Vanillyl 6 Nonenamide" OR Axsain OR Zacin OR "Capsicum Farmaya" OR Capsidol OR Zostrix OR Capzasin OR Gelcen OR Katrum OR NGX-4010 OR NGX 4010 OR NGX4010 OR Capsin)[all]
The [all] will stop PubMed from attempting to autocorrect your search terms.
There are several useful variations of the keyword search that you may want to run.
1. Start by looking at a subset of the results that includes practice guidelines, consensus statements, meta-analyses, and systematic reviews. The subset includes un-indexed and indexed records.
The "Systematic reviews" "Articles Types" filter (available through customization of the left-hand filters) now only locates systematic reviews, not practice guidelines. It still, like our "systematic rev.+ meta-analyses + guidelines" custom filter and unlike other "Articles Types" filters, will find both indexed and unindexed records. The two "Systematic reviews" filter and our "systematic rev.+ meta-analyses + guidelines" custom filter are both little invisible search strategies composed of combinations of journal names, keywords, MeSH, and publication type terms.
Among the useful results of the systematic subset search is a 2017 article in the Cochrane Database of Systematic Reviews that looked at the efficacy of high dose capsaicin.
2. The second way you will use your keyword search is to search for unindexed records. To find unindexed records for randomized controlled tirlas:
random*
-- to the end of your search strategy.
Remember, you should not apply a "Randomized Controlled Trials" or a Humans limit to a search for unindexed records. These filters looks for tags that are added to records by indexers.
3. The third, and final, variation of your keyword search is a version used to check the adequacy of your MeSH search. You limited the MeSH search to randomized controlled trials, about humans, in English.
At this point, your search would look something like:
#15 NOT #8
If, in the future, you work on such a comparison, you should:
"Capsaicin"[Mesh] AND "Peripheral Nervous System Diseases"[Mesh]
Filters: Randomized Controlled Trial; Humans; English
Of course, a few additional irrelevant results were also retrieved by this search (most concerning induction of pain by capsaicin).