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Using PubMed
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| Population | Population` | Intervention | Outcome |
|---|---|---|---|
| osteoporosis | bisphosphonates | oral surgery | jaw osteonecrosis |
For the purposes of this search we can probably ignore the oral surgery part of the search and just look at osteoporosis and bisphosphonates and jaw osteonecrosis
The next step is to add synonyms or alternative terms to each of the columns of the grid
Check in the MeSH database to make sure that you have at least one MeSH in each column.
Osteoporosis is a MeSH.
You should enter this in your PICO Logic Grid as osteoporosis[mh]
This will ensure that PubMed searches for your term as a MeSH.
Scroll down the MeSH database site to look at the Entry Terms.
Entry Terms are useful for suggesting to you synonyms or alternative terms that might be used in the abstracts and titles of articles that don't yet have osteoporosis as a Medical Subject Heading.
From these terms you might like to add osteoporoses, bone loss, and bone losses to your PICO grid.
If you add [tiab] after a search term your search will be restricted to the titles and abstracts of article citations.
Remember you could use [tw] to search all the text words.
Notice that I've added OR to all the terms in the first column except the last term.
This is because we want to search for
osteoporosis[mh] OR osteoporosis[tw] OR ...
In fact I've added a space OR and another space then pressed the Enter key.
If you do this in a Word document you can copy the terms in each logic grid cell and paste them straight into PubMed (if you are using Firefox).
PubMed will read the terms in the column as
osteoporosis[mh] OR osteoporosis[tw] OR osteoporoses[tw] OR bone loss[tw] OR bone losses[tw]
Continue to check on MeSH and alternative terms for bisphosphonates and jaw necrosis
Remember to check more specific MeSH and their Entry Terms for synonyms.
We'll need to divide outcomes into two columns.
One column to cover the concept of jaws, and another for the concept of osteonecrosis.
Check the MeSH for each of these and look at any Entry Terms that might be used by authors in the titles or abstracts of their articles and add these to the PICO grid.
I haven't included all the possible terms in this grid.
What other terms could be added under jaw?
Truncation
You can save a bit of typing by using truncation of terms.
Instead of searching osteoporosis[tw] OR osteoporoses[tiab]
you can type osteoporos*[tw]
This will find all the terms in the titles or abstracts of citations that begin with the letters o-s-t-e-o-p-o-r-o-s
It's best not to truncate MeSH.
Logic
There are two ways to put your search into PubMed.
You can search each of the concepts separately then AND them together.
Method 1
Paste the terms from the first column into PubMed
(Not into the MeSH Database but into the PubMed database)
To get to the PubMed part of the database from the MeSH database click on the drop down menu that is showing MeSH
Scroll up the screen to find PubMed near the top.
Paste in the search terms from the first column of your logic grid.
Click on Search or press the Enter key.
The result for this part of your search appears.
Now click on the X in the PubMed search box to clear this first column search.
Don't panic! PubMed has remembered the result.
Now paste in the terms from the second column of your logic grid.
Continue to add the searches from each of your columns until all of the searches are done.
Now click on the Advanced link.
Click on Add (under the heading Add to search builder) for each of your searches.
Don't worry if the search numbers are sometimes a bit strange.
Click on Search to combine your searches using AND logic.
Method 2
Use the three logic rules
Rule 1
All the terms in a single column (synonyms and alternative terms) must be linked by OR logic.
Rule
2
All terms joined with OR logic must be enclosed in round brackets.
Rule 3
Combine the lists of terms from the different columns (concepts) using AND logic.
Your search becomes
(osteoporosis[mh] OR osteoporos*[tw] OR bone loss*[tw]) AND (bisphosphonates[tw] OR diphosphonates[mh] OR diphosphonates[tw] OR alendronate[tw] OR fosamax[tw]) AND (jaw[mh] OR jaw*[tw] OR maxilla*[tw] OR mandibl*[tw]) AND (osteonecrosis[mh] OR osteonecros*[tw])
Enter your search in the PubMed Search box , not in the MeSH database.
Citations found by searches are initially displayed in the Summary format. This includes
article title
author(s)
abbreviated journal title and publication details
a PubMed Identification number and stage of indexing
a link to Related citations (similar articles)
To change the display format,
click on the link or the down arrow next to Display Settings.
Click in the radio button to the left of Abstract, not Abstract (text).
Click on the Apply button.
The results will display in the new format.
The Abstract display includes bibliographic details and an abstract if one is available.
Abstract displays may include Uni of Adelaide Online icons for online full text article retrieval.
To view the MeSH added to a citation click on the MeSH.
You won't find links to MeSH for As supplied by publisher, or In process citations.
To find full text of articles that don't have online icons, search for the title of the journal in eResources A-Z or in Summon (this will change in 2013).
To search, you'll need to find the full title of the journal in which the article is published.
To do this, point at the abbreviated journal title in PubMed with your cursor.
Don't click.
The full title will soon appear.
You can find some free journals at
BioMed Central
FreeMedicalJournals.com
Highwire Press Free Online Full-text Articles
PubMed Central
PubMed is set up to recognize authors names and you can type in surname a space and up to two initials in the Search box.
Click on Search.
PubMed usually recognizes the form of an author's name, and searches the Author index automatically.
If you know more than one author's name you can combine them using AND logic
Townsend G AND Goss A.
Click on Advanced.
Click on More Resources.
Click on Journals in NCBI Databases.
Type in the title, abbreviated title of the journal you want to search.
If you see the title of the journal you want come up as you type you can click on this.
Click on Search.
Click on Add to search builder.
Click on Search PubMed.
The PubMed citations appear.
PubMed has several ways of reducing the number of citations found to manageable levels. You should always be aware with this that you may lose important articles.
There are cases of patient damage resulting from inadequate searching where vital articles were lost because limits were imposed.
In some instances searches should be made more comprehensive by including pre electronic sources such as older printed Index to Dental Literature, and Index Medicus prior to 1960.
PubMed's Filters appear in the left hand side bar of the results screen in both Summary and Abstract displays.
Limit by availability
You can limit to citations that have abstracts, or free full text. Note that the limit to Full text available doesn't mean freely available through Uni of Adelaide Library and will certainly result in finding fewer articles than we actually can supply.
Limit by publication date
Click on 5 years, or 10 years, or set your own date limits by clicking on Custom range ...
Limit by species
You can limit your search results to Humans or Other Animals, but you should be aware that both of these limits are MeSH. If you choose one of these you will lose all your As supplied by publisher and In process citations.
Limit by article type
You can select a single article type from the list displayed, or you can view all the article types available by clicking on more ... just below Randomized Controlled Trial.
Click in the boxes to the left of any article type that you'd like to have appear on the PubMed sidebar.
You can click in as many boxes as you want.
This won't initially limit your search to these articles types, but when you click on Show these article types will display on the sidebar.
To limit your search results using these filters, just click on one of the Article types.
This will limit your search to that article type.
While this works, annoyingly it removes the other article types you requested so that if you want to select more article types to be included in your search you'll have to click on more again and add them one by one.
Once you have set a limit using a filter, that limit will remain until you clear it.
Adding Multiple Article Types Simultaneously
A more efficient way to add several article types to a search is to OR them together, bracket them and then AND them to your search terms.
To limit our diphosphonate search to articles that are metaanalyses or randomised controlled trials we can add
AND (meta analysis[pt] OR randomized controlled trial[pt])
(osteoporosis[mh] OR osteoporos*[tw] OR bone loss*[tw]) AND (bisphosphonates[tw] OR diphosphonates[mh] OR diphosphonates[tw] OR alendronate[tw] OR fosamax[tw]) AND (jaw[mh] OR jaw*[tw] OR maxilla*[tw] OR mandibl*[tw]) AND (osteonecrosis[mh] OR osteonecros*[tw]) AND (meta analysis[pt] OR randomized controlled trial[pt])
Search for Types of Study
If you are looking for particular study types you might like to look at my study types web site that includes searches on particular study types for PubMed, Embase, and Dentistry and Oral Sciences Source.
Click on the link below to find PubMed, Embase, and Dentistry and Oral Sciences Source searches on various study types including Randomised Controlled Trials, Cross Sectional Studies, Cohort Studies, Practice Guidelines, Evaluation Studies and more.
Add your search terms to the study types searches using AND.
Additional Filters
Click on the additional filters link to view other ways of limiting searches.
Click in the boxes to the left of the additional filter(s) you want, e.g. Journal categories.
Click on Show.
Now you can choose to limit your search to the journal types listed.
You should note that with a topic of such broad interest limiting to Dental journals will mean that you will filter out many of the articles.
The filters for Sex, and Ages use MeSH so that using either of these will remove all As supplied by publisher and In process citations.
You can limit by language to English, but foreign language articles usually have abstracts and it might be worth reading these.
You can restrict your citations to those that are likely to be useful for EBP by using Clinical Queries.
PubMed has developed several strategies for finding EBP info using filters called Clinical Queries.
On the PubMed Home screen click on Clinical Queries under PubMed Tools
.
You can also click on the Advanced link.
At the top of the screen click on More Resources.
Click on Clinical Queries.
Your searches will now be limited to clinical research areas.
Enter your search terms and click on the Search button.
Let's try the search
You have 5 categories to choose from, with two levels of emphasis.
Use the drop down menus to decide on a category.
Choose either a narrow or broad search.
The results for Clinical Study Categories, Systematic Reviews and Medical Genetics citations appear. You can alter the Medical Genetics results by choosing other categories from its own drop down menu.
An alternative way of searching for systematic reviews is to add AND systematic [sb] to your searches in PubMed's Search for box.
The [sb] means that the search is restricted to the subset of PubMed that in this case includes systematic review literature.
There are links to Topic-Specific Queries on the PubMed home screen and at the bottom left of the Advanced Search screen.
NCBI is the place where you can hold saved searches and easily check on new citations added to the database since you last ran your search.
Register a password.
You'll have to wait until you follow the instructions in an email sent to you by PubMed to complete registration.
Run your search.
Click on Save Search.
Give your search a name and click on the Save button.
You can request email alerts for your search.
PubMed uses a weighted algorithm based on title words, abstract words, and MeSH to find other articles in PubMed that are similar to those you have already found by your search.
Click on the Related citations link at the bottom of a PubMed reference.
PubMed will produce a list of all articles 'related' to the parent article.
The parent article is always listed first.
The Related citations have related citations of their own, etc so even if you find just a few relevant citations you can sometimes expand on these by using these links.
A few very recent citations may not have related citations added. If this happens, wait a few days and check on these citations again.
Click in the box to the left of a citation to select it for display, saving, printing, email, or RSS feed.
A tick will appear in the box.
To save all the citations you found select none of them.
PubMed Clipboard
You can add up to 500 citations to the Clipboard of PubMed from several different searches.
Select citations from a search to add to Clipboard.
Click on Clipboard from the Send to pull down menu.
You can now do another search or look at Related citations and save the citations to the Clipboard in the same way.
To view all your citations held in the Clipboard click on the Clipboard link near the top of the right hand side bar.
The saved citations from all your searches will appear in a single set with any duplicates removed.
To clear the Clipboard use the Remove all items or use the Remove from clipboard links to remove individual citations.
Clipboard items are automatically removed after 8 hours of inactivity.
Exporting to EndNote
EndNote is a bibliographic database management system that will organise your citations and make writing your thesis, assignments or articles easier.
To save citations from PubMed to EndNote first open your EndNote Library.
Return to PubMed.
Select those citations you want to keep on all the screens or from the Clipboard.
Click on the Send to drop down menu.
Click on File.
The drop down menu now includes an area for selecting the format.
Always choose MEDLINE.
Click on the Create File button.
What happens now depends on the browser you're using.
Using Firefox is easiest.
Using Firefox
Click on OK to open with EndNote.
If EndNote doesn't appear as the default, use the drop down menu to find it.
You'll get a dialogue box that you can use to open the file to export your selected citations directly to EndNote.
For most recent versions of EndNote this should work well.
When asked to Choose an Import Filter, select PubMed (NLM) and click on Choose.
Your citations should then export into EndNote.
If this doesn't work (usually because your version of EndNote is too old) watch this video.
For more information on using EndNote, the Library has a web site that includes a very useful tutorial, and an import filters site.
Using Internet Explorer
Click on the Save button.
This will produce a dialogue box where you decide where you want to save the file on your computer, and what you want to call the file.
Once you've decided,
Click on Save.
Remember/record where you put this file and what you called it.
In the example below I've saved the file on the desktop and left the file with the default name pubmed_result.txt
When the file has saved click on Close.
In the EndNote program,
Click on File.
Click on Import and then File...
Now you have to find the file you saved.
Click on Choose.
Now if PubMed (NLM) isn't showing in the Import Option box you have to go looking for it.
Click on the drop down menu.
Scroll through the options to find PubMed (NLM).
If it isn't in the list then click on Other Filters.
Scroll through to find PubMed (NLM) in alphabetical order.
Click on the Import button and watch your citations appear in EndNote.
Here is a video on how to import from PubMed using Internet Explorer.
Using Safari
Use the Save File option in PubMed.
Your citations are sent to your Downloads folder.
Open your EndNote library
Click on File
Click on Import
This should wake up your Downloads folder.
Find your file, it should be called pubmed_result.
Find PubMed (NLM) in the Import Options box, (not PubMed Central), use the drop down menu if necessary
Click on the Import button.
Select the items you want to email.
Use the pull down Send to menu and select E-mail.
The Evidents Search Engine uses a modified PICO procedure and a search algorithm to find PubMed citations for those who have trouble remembering all the ins and outs of the PubMed database.
Evidents Search Engine for use in PubMed
BrowZine
BrowZine is an app for iPads (Android support not yet available) that will allow you to access (most of) the Library's online journals without logins.
You can view their promotional video.
The app will let you search for journals by subjects or titles and to put favourite journals on a "book shelf".
You can save particular articles.
Download the free app to your device.
Select the University of Adelaide from the list of institutions.
Login with your University ID (axxxxxx) and network password.
BrowZine will save to Zotero, Dropbox and other services but not yet in EndNote>
BrowZine
is working on sending you notification of new issues of the journals on your bookshelf.
Maureen Bell's Evidence Based Practice site A Barr Smith Library compilation of evidence based practice sites including databases, articles, and sites about evidence based practice
Maureen Bell's PubMed Help Guide
Most of the above and more in half the space
Library's Evidence Based Dentistry Part 1 Introduction to Evidence Based Denntistry
Library's Evidence Based Dentistry Part 3 Using Embase
Library's Evidence Based Dentistry Part 4 Using Dentistry and Oral Sciences Source
Library's Cochrane Library Tutorial
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