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Medical Sciences Honours
Last updated February 2013
Write out the main concepts and underneath each add any synonyms or alternative terms.
What effect do single nucleotide polymorphisms have on Codeine
Access to Databases for finding journal articles
Click on the Databases tab on the Library Home.
Click on the link to Health Sciences
There is a short essay on which databases are best to use for various searches.
PubMed is available from Resource Guides on the Library Home.
Right click on the link to the Customised version of PubMed
Here is a search on codeine
The results of the search turn up in what PubMed calls summary format.
This includes the article title
Citations as supplied by publisher have a PubMed ID and a link to related citations but otherwise have only the information provided by the publisher of the article.
Citations to articles that have their subject headings added have the status PubMed - indexed for MEDLINE.
You can get access to the MeSH Database from the PubMed home.
You can also get to the MeSH Database by using the drop down menu on PubMed.
Type a single term into the MeSH database.
The display of the MeSH appears
We want to make PubMed search this term as a subject heading.
I usually use a Word document to set up my logic grids.
Notice that I've added OR at the end of each term. This will make it easier to enter your searches into PubMed later, especially if you use PubMed with a Firefox browser.
organ* will find organ OR organelle OR organelles OR organic OR organisation
I usually don't truncate MeSH, but it's possible to do it.
Now look at the Entry Terms in the MeSH Database, to see if there are other terms you might add to the grid.
Also look at the broader MeSH to see if one of these terms is more appropriate for your search.
It's probably worth adding snp[tw] as well as snps[tw] to the logic grid, along with any particular snps that are of interest.
Search for Codeine in the MeSH database.
Check the more specific MeSH to see if these are relevant.
You can add other terms that you think are appropriate.
polymorphism, single nucleotide[mh] OR single nucleotide polymorphism*[tw] OR snp[tw] OR snps[tw] OR oprm1[tw]
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.
Now paste in the terms from the second column of your logic grid.
codeine[mh] OR codeine[tw] OR n methtylmorphine[tw] OR isocodeine[tw] OR hydrocodon*[tw] OR oxycod*[tw]
Continue until you have searched all the columns.
Your searches to date will appear.
Click on Add (under the heading Add to builder) for each of your searches.
When you have added all of the searches from your logic grid columns, click on Search to combine your searches using AND logic.
Your search becomes
(polymorphism, single nucleotide[mh] OR single nucleotide polymorphism*[tw] OR snp[tw] OR snps[tw] OR oprm1[tw]) AND (codeine[mh] OR codeine[tw] OR n methtylmorphine[tw] OR isocodeine[tw] OR hydrocodon*[tw] OR oxycod*[tw])
Enter your search in the PubMed Search box, not in the MeSH database.
Searching from the MeSH Database
You can also search for more than one subject heading from the MeSH Database
Find the first concept in the MeSH Database and click on the Add to search builder button.
See that the program begins setting up a PubMed search on the MeSH.
Click on Add to search builder button, making sure that the AND logic option is showing.
Click on the Search PubMed button to run this search in the PubMed database.
Sometimes MeSH subheadings can be useful, particularly when you are looking for very specific topics.
Click in the boxes to the left of each subheading you want to search.
The resulting search will find citations to the subject heading only if the subheading is also included.
PubMed will also search for more specific subject headings listed below the MeSH selected, but again only if they also have one of the subheadings included.
Search for morphine with the subheadings pharmacokinetics and pharmacology.
Search for morphine in the MeSH database.
Click on the Add to search builder button.
Click on the Search PubMed button to complete the search.
You can also type MeSH plus subheading searches straight into logic grids and PubMed.
("morphine/pharmacokinetics"[mh] OR "morphine/pharmacology"[mh]) AND (infant[mh] OR infant*[tiab] OR newborn*[tiab] OR neonat*[tiab])Displaying Results
Citations found by searches are initially displayed in Summary form. This includes
To change the display format,
Click in the radio button to the left of Abstract.
The results will display in the new format.Abstract Display
Clicking on a Uni of Adelaide Online icon should take you (fairly) directly to the full text of the article.
You can try looking for the title of the article in Library Search.
A higher percentage option is to search for the title of the journal.
In PubMed point your cursor at the abbreviated journal title.
Click on Advanced Search in PubMed.
Type in the title, abbreviated title of the journal you want to search.
All the citations from this journal in PubMed appear.Filters (Limits)
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.
PubMed's Filters appear in the left hand side bar of the results screen in both Summary and Abstract displays.
Limit by availability
Limit by publication date
Limit by species
Limit by article type
Click in the boxes to the left of any article type that you'd like to have appear on the PubMed sidebar.
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 for other searches until you clear it.
You can restrict your citations to those that are likely to be useful for EBP by using Clinical Queries, Systematic Reviews or Medical Genetics.
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 search link and scroll down to find Clinical Queries at the bottom left of the screen.
Enter your search.
When using Clinical Study Categories you have 5 categories to choose from, with two levels of emphasis.
PubMed searches the Clinical Study Categories, Systematic Reviews, and Medical Genetics.
You can change the Medical Genetics topics independently.
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.
Click in the boxes to the left of the additional filter(s) you want, e.g. Journal categories.
Now you can choose to limit your search to the journal types listed.
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.
If you don't click on any of the citations then all of them will be printed, saved, or emailed.
You can also temporarily save up to 500 citations from different searches to PubMed's Clipboard before using an output option.
Click on the Send to link or the arrow to its right.
Click on Add to Clipboard.
Now you can look at Related citations to find similar articles to those found by 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.
PubMed will produce a list of all citations to articles 'related' to the parent article.
You can also add Related citations to the Clipboard.
To send to EndNote click on File, because PubMed doesn't have direct export to EndNote.
Click on Create File.
You'll get a dialogue box that you can use to open the file to export your selected citations directly to EndNote.
When asked to Choose an Import Filter, select PubMed (NLM) and click on Choose.
Your citations should then export into EndNote.
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.
When the file has saved click on Close.
In the EndNote program,
Click on Import and then File...
Now you have to find the file you saved.
Now if PubMed (NLM) isn't showing in the Import Option box you have to go looking for it.
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.
Now you should be looking at a set of citations in EndNote!
For more information on using EndNote, the Library has a LibGuide that includes lots of EndNote information including where to get access.
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.
Once registration is complete you can run your search.
Give your search a name and save it.
PubMed will then ask you if you want to set up an email alert for new articles that fit this search profile.
The app will let you search for journals by subjects or titles and to put favourite journals on a "book shelf".
Download the free app to your device.
BrowZine will save to Zotero, Dropbox and other services but not yet in EndNote.
PubMed Tutorial The official tutorial from the U.S. National Library of Medicine.
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
Mick's Embase tute (with dental examples)
Mick's Cochrane Library Tute (with dental examples)
Maureen Bell's Scopus Help Guide