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Medical Sciences HonoursLast update February 2009 by Mick Draper Databases for finding journal articlesPubMedPubMed is available from the Library Home
From the Pathology databases site
From the Pharmacology Resource Guide
PubMed is also available from the Catalogue
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bone resorption |
rheumatoid arthritis |
Use the MeSH database to find the subject headings PubMed uses to describe these concepts.
Click on MeSH Database in the side bar on the left
Enter the first term only in the Search for box and click on the Go button.
The MeSH database looks for appropriate Medical Subject Headings.
Click on any appropriate heading to see more detail.
This subject heading was introduced in 1965 but PubMed citations have been retrospectively indexed with this heading back to 1964.
You can include subheadings to make your searches more specific.
If you are interested in this, look at the tutorials about using MeSH on the MeSH Database site
Scroll down to view Bone Resorption in its 'MeSH trees'.
If you search PubMed using Bone Resorption as a Medical Subject Heading, then every citation that has this heading added will be found, and also every citation that has one or more of the more specific MeSH.
This is called explosion and is an extremely powerful search option often finding many subject headings from a single term.
When you enter a MeSH in your logic grid you should add a tag that will tell PubMed you want to search for the term as a subject heading.
bone resorption[mh]
You can add bone resorption[tiab] to you logic grid to include searching this phrase in titles or abstracts.
As long as you have a tag in square brackets after the term it will be searched as a phrase.
Now scroll up to look at the Entry Terms.
Entry Terms are useful in suggesting terms that authors might have used in the titles or abstracts of their articles to describe the content.
Because it takes a while for MeSH to be added to citations, you can find recent articles by including terms from the title or abstract in your search.
The bone resorption part of your logic grid will start to look something like this
| bone resorption[mh] |
| bone resorption[tiab] |
| bone resorptions[tiab] |
| bone loss[tiab] |
| bone losses[tiab] |
Look at the Entry Terms of the more specific MeSH such Osteolysis to continue filling out the logic grid with useful terms that might be used in titles and abstracts of very recent articles.
| bone resorption[mh] |
| bone resorption[tiab] |
| bone resorptions[tiab] |
| bone loss[tiab] |
| bone losses[tiab] |
| osteolysis[tiab] |
| osteolyses[tiab] |
| acroosteolysis[tiab] |
You can use * to truncate terms to reduce typing.
bone loss*[tiab] will search for bone loss[tiab] OR bone losses[tiab]
Don't use truncation with MeSH because it can stop the MeSH being searched, and stops explosion.
| bone resorption[mh] |
| bone resorption*[tiab] |
| bone loss*[tiab] |
| osteolys*[tiab] |
| acroosteolys*[tiab] |
Now look for MeSH and title and abstract terms for the second concept in your logic grid.
Add terms for this concept to your logic grid.
| bone resorption[mh] | arthritis, rheumatoid[mh] |
| bone resorption*[tiab] | rheumatoid arthritis[tiab] |
| bone loss*[tiab] | juvenile idiopathic arthritis[tiab] |
| osteolys*[tiab] | juvenile chronic arthritis[tiab] |
| acroosteolys*[tiab] | still* disease[tiab] |
| caplan* syndrome*[tiab] |
This grid will sort out (most of) the logic for your search.
Join the terms in individual columns using OR logic.
In PubMed the logic terms must be in capitals, OR AND NOT.
Enclose the terms joined by OR logic in a set of round brackets.
Join the bracketed terms by AND logic.
The search from this logic grid becomes
(bone resorption[mh] OR bone resorption*[tiab] OR bone loss*[tiab] OR osteolys*[tiab] OR acroosteolys*[tiab]) AND (arthritis, rheumatoid[mh] OR rheumatoid arthritis[tiab] OR juvenile idiopathic arthritis[tiab] OR juvenile chronic arthritis[tiab] OR still* disease[tiab] OR caplan* syndrome*[tiab])
This can be entered into the PubMed search box.
PubMed shows the result using a Summary display format.
Other Display Formats
Abstract format will let you read the summary of the article, and may present you with a Uni of Adelaide Online icon to link directly to the full text of the article.
Clicking on Uni of Adelaide Online should take you to the full text of the article.
You will see these icons only if you have linked to PubMed through the Uni of Adelaide network.
Not all items held by the Library generate these icons.
If you want full text and there is no icon, use the Library Catalogue to search for the title of the journal that published the article.
If you find too many citations, or you want to limit citations to particular languages, dates, or study types such as randomised controlled trials you can use PubMed limits.
Click on the Limits tab
You can limit by date
You can limit to English
Click on Go at the top or bottom of the screen to enforce the Limits.
Click on the tick in the Limits tab to remove the Limits or they will continue for the next search.
There is a more detailed but still basic PubMed tutorial
and a detailed PubMed Tutorial
and the very detailed Official PubMed Tutorial from the National Library of Medicine (USA)
Saving PubMed citations to EndNote
There is no direct export from PubMed to EndNote, but importing from EndNote isn't too tricky.
First select the PubMed citations you want in your EndNote Library.
Click in the boxes to the left of each citation you want to keep.
Don't select any of the citations if you want to keep all of them.
Change the display format to MEDLINE.
Click on the Send to drop down menu and click on File
This should produce a dialogue box.
If your browser doesn't produce a dialogue box you may have to ask it to let you download.
If this doesn't work you should try another browser, or ask ITS to help.
Save the file somewhere where you can find it later and give it a useful name.
Open your EndNote software and create a library.
The first time you use EndNote for PubMed
Click on Edit.
Point at Import Filters.
Click on Open Filter Manager.
Scroll to find the PubMed (NLM) filter
Click in the box to the left of the filter.
This will put a tick mark in the box.
Close the Filter Manager by clicking on the X in the top right corner of the Filter Manager dialogue.
You won't have to do this again.
Click on File.
Click on Import.
Click on the drop down menu for the Import Option (filter)
Scroll to find PubMed if it doesn't already appear in the box.
Click on PubMed.
Click on the Choose File button.
Find the file you saved from PubMed earlier
Click on the Import button.
The citations you saved will be imported.
Saving Searches and Setting Up Alerts on PubMed
Use My NCBI to save your searches and set up an alert service.
Begin by registering a username and password
For more information on My NCBI look at the online tutorials
Getting Started with My NCBI (5 min., April 2006)
Saving Searches with My NCBI (approx. 4 min., Oct 2008)
and the PDF MyNCBI
Scopus
There is a link to Scopus under Quick Search on the Library home.
You can also use the catalogue, or the Databases tab and click on your discipline name.
Use Advanced Search because Basic Search doesn't give you much room for searching.
I use the Scopus search code for Title Abstract and Keywords
You can use MeSH to search in Scopus including inverted MeSH such as anatomy, comparative
However Scopus will not understand PubMed tags such as [mh] or [tiab]
Scopus uses the logic OR, AND, AND NOT
Phrases should be enclosed in double quotes.
Scopus automatically searches for most plurals so that "opioid addiction" will also find citations with the phrase opioid addictions.
A logic grid for a Scopus search on The Effect of Monoamine Oxidase on the Toxicity of Amphetamines will look something like this.
| monoamine oxidase | amphetamine | drug toxicity |
| "tyramine oxidase" | "2,5 dimethoxy 4 methylamphetamine" | adverse effects |
| "mao a" | mdma | "serotonin syndrome" |
| "mao b" | ecstasy | toxic* |
| methamphetamine | ||
| lots of other terms | ||
This translates into the Scopus search
(monoamine oxidase OR "tyramine oxidase" OR "mao a" OR "mao b") AND (amphetamine OR "2,5 dimethoxy 4 methylamphetamine" OR mdma OR ecstasy OR methamphetamine) AND (drug toxicity OR adverse effects OR "serotonin syndromes" OR toxic*)
Select the citations you want to save.
Store them temporarily in a 'list'.
Check for other articles that cite those found in your search
Select any of these you want to save and add to the list.
When you have finished collecting citations, scroll to the top of the screen and click on My List.
Click on Select All.
Click on Output.
Use the drop down menu to select EndNote.
Select the format you want,
I'd suggest abstract.
Click on the Export button.
This should open your EndNote software.
EndNote should prompt you to select a 'library' to receive the citations.
Use this database to find articles that cite other articles that you know about already.
Chen, ZR, Irvine, RJ, Somogyi, AA et al (1991)
Mu receptor-binding of some commonly used opioids and the metabolites
Life Sciences 48(22) 2165-2171
To find articles that cite this article,
Find the Web of Science database
Scroll down to make any adjustments you want to the citation databases and dates to search.
It's unlikely that anyone will refer to an article before it's published, though sometimes 'in press' articles are cited.
Scroll up and click on Cited Reference Search
Type the name of the author surname first, first initial and asterisk.
(I suggest that if there is more than one author, that you use the one with the most unusual name)
Unless the surname is common, don't fill out the other boxes on the search screen.
You should check on the name with just the first initial, and with all the initials.
This is because people cite names in different ways.
Point at View Record to see the article title to confirm you have the right citation.
Click on View Record to see the full details of the citation including information on the (116) articles that cite this work.
If you want to find citing articles from more than one article you know about, click in the boxes to the left of the relevant known articles.
You'll also need to do this when there is no View Record option for your known article.
Click on Finish Search to view the citing article records.
The citations you find will all have at least one of the Breed articles selected included in their bibliographies.
Articles with the author's name in capitals are those where Breed is the first author.
...Breed WG indicates that Bill Breed is not the first author.
More on EndNote
The Library has an EndNote Software site where you can download the EndNote program, and find training aids.
Training aids include videos on how to import citations from PubMed to EndNote
How to use Cite While You Write to insert citations into a Word document
and an EndNote Tutorial that covers all of the basics needed to use EndNote with Word.
