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Medical Sciences HonoursLast updated Jan 2012 by Mick Draper Logic GridsBefore beginning a search it's a good idea to use a logic grid to formulate your search. Write out the main concepts and underneath each add any synonyms or alternative terms. What effect do single nucleotide polymorphisms have on Codeine
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.
Access to PubMed
PubMed is available from quick links on the Library Home
Right click on the link to the Customised version of PubMed |
| polymorphism, single nucleotide[mh] |
| single nucleotide polymorphism*[tiab] |
Notice that I've added a * to the end of the search of titles and abstracts for single nucleotide polymorphism.
The asterisk is the truncation symbol in PubMed.
It
will search all the words that begin with the root letters.
organ* will find organ OR organelle OR organelles OR organic OR organisation
and many other terms
It's safest not to truncate MeSH.
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 snps[tiab] to the logic grid.
| polymorphism, single nucleotide[mh] |
| single nucleotide polymorphism*[tiab] |
| snps[tiab] |
Search for Codeine in the MeSH database.
In the logic grid add the MeSH for codeine and also look in the Entry Terms for other terms that might turn up in titles or abstracts.
| polymorphism, single nucleotide[mh] | codeine[mh] |
| single nucleotide polymorphism*[tiab] | codeine[tiab] |
| snps[tiab] | n methtylmorphine[tiab] |
| isocodeine[tiab] |
Check the more specific MeSH to see if these are relevant.
Remember they will be automatically searched as subject headings in the search for codeine[mh], but you might want to include a search of these terms in titles and abstracts or [tw].
| polymorphism, single nucleotide[mh] | codeine[mh] |
| single nucleotide polymorphism*[tiab] | codeine[tiab] |
| snps[tiab] | n methtylmorphine[tiab] |
| isocodeine[tiab] | |
| hydrocodon*[tiab] | |
| oxycod*[tiab] |
Logic Rules
This grid will help sort out 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.
(polymorphism, single nucleotide[mh] OR single nucleotide polymorphism*[tiab] OR snps[tiab])
(codeine[mh] OR codeine[tiab] OR n methtylmorphine[tiab] OR isocodeine[tiab] OR hydrocodon*[tiab] OR oxycod*[tiab])
Join the bracketed terms by AND logic.
The search from this logic grid becomes
(polymorphism, single nucleotide[mh] OR single nucleotide polymorphism*[tiab] OR snps[tiab]) AND (codeine[mh] OR codeine[tiab] OR n methylmorphine[tiab] OR isocodeine[tiab] OR hydrocodon*[tiab] OR oxycod*[tiab])
This can be entered into the PubMed search box.
Click on the Search button.
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.
Enter the second concept that you want to find as a MeSH.
Click on the link for codeine.
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 in the boxes to the left of of the two subheadings.
Click on the Add to search builder button.
Notice that the terms are combined using OR logic.
Click on the Search PubMed button to complete the search.
You can also type MeSH plus subheading searches straight into logic grids and PubMed.
If you do this it's best to enclose the MeSH and subheading in double quotes that way PubMed will know that you are looking for subheadings.
("morphine/pharmacokinetics"[mh] OR "morphine/pharmacology"[mh]) AND (infant[mh] OR infant*[tiab] OR newborn*[tiab] OR neonat*[tiab])
Citations found by searches are initially displayed in Summary form. This includes
article title
author(s)
abbreviated journal title and publication details
a PubMed Identification number and stage of indexing
a link to similar citations
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.
Click on the Apply button.
The results will display in the new format.
Clicking on a Uni of Adelaide Online icon should take you (fairly) directly to the full text of the article.
If you can't find a Uni of Adelaide icon then we may still have the full text.
You can try looking for the title of the article in Summon.
A higher percentage option is to search for the title of the journal in the Catalogue or Summon.
In PubMed point your cursor at the abbreviated journal title.
PubMed will briefly display the full title of the journal.
Go to the Library Catalogue or Summon and enter the title of the journal to see whether we have access to the full text in electronic or print format.
Click on Advanced Search in PubMed.
In Search Builder, change the search field to Journal.
Type in the title, abbreviated title or ISSN (International Standard Serial Number) of the journal you want to search.
If you see the title of the journal you want come up below as you type you can click on this.
If your title doesn't automatically come up, click on Show Index and click on the title you want.
Click on Add to Search Box.
Click on Search.
All the citations from this journal in PubMed 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 Medicus and Excerpta Medica prior to 1960.
The search
(drug interactions[mh] OR drug interaction*[tiab]) AND (morphine[mh] OR morphi*[tiab])
finds many citations so you may want to limit the search.
Date and language limits are often useful.
Click on Limits.
You can limit by author, journal title, date and several other parameters.
Limiting by Language is probably a good idea for honours students.
It often takes time to find foreign language articles, and translation may be expensive.
Other limits may cut out citations that don't have MeSH because some limits such as Human, Animals, Male, Female, and the age groups are MeSH.
Click on one of the PubMed Search buttons at the top and bottom of the screen to limit your search.
Once you have set limits they will remain in place for later searches.
See the limits in activated listed in the top left of the screen.
Review Articles
PubMed will provide a link to review articles included in the results of your searches.
Reviews are useful if you are just beginning your work in a particular area, they will point to the significant articles.
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.
Use the drop down menus to decide on a category, and then choose either a narrow or broad search.
PubMed searches the Clinical Study Categories, Systematic Reviews, and Medical Genetics.
You can change the Medical Genetics topics independently.
Click on the link below to find PubMed searches on these study types
Add your search terms using AND.
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.
Click on the Related citations link at the bottom of a PubMed reference.
PubMed will produce a list of all citations to articles 'related' to the parent article.
The parent article is always listed first.
Selecting Citations, Clipboard and EndNote
To select individual citations click in the box to the left of the article title.
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.
You can also add Related citations to the Clipboard.
When you are finished collecting citations click on the Clipboard link.
To send to EndNote click on File, because PubMed doesn't have direct export to EndNote.
An extension to the drop down box will appear.
Change the format to MEDLINE.
Click on Create File.
You'll get a dialogue box that you can use to save the file.
Make sure the button to the left of Save File has a dot inside it then click OK.
In the next dialogue box you can change the name of the file and decide where you want to save it.
Retain the file extension .txt.
Open EndNote.
Open a new library.
Click on File
Click on Import
If PubMed (NLM) isn't showing in the Import Option box then click on the down arrow and select it.
Click on the Choose File box and locate the file saved from PubMed.
Click on the Import button and watch your references appear.
EndNote Help
You can get access to the EndNote program from Library A to Z
This has a link to request the software
The Library has a good basic tutorial on how to use EndNote
Movie on how to use PubMed's Clipboard and Import citations into EndNote
Register a username and password.
Once you have a username and password you can enter your searches and save them.
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.
For more information on My NCBI look at the Saving Searches online tutorial
Official PubMed Tutorial
Link to Mick's tutorial on Embase
Scopus is a huge database of journal article citations including all of PubMed from 1996 onwards.
Also included are all the citations from the Embase database from 1996.
Access to the Scopus database is available from the Quick Links on the Library Home, from the Catalogue and from the Anatomical Sciences, Pathology and Pharmacology Databases and Resource Guides sites.
I always use the MeSH database to find appropriate terms, even if I'm going to search Scopus.
Scopus will search for MeSH but don't include any field tags.
Scopus will find the MeSH arthritis, rheumatoid or the natural language phrase rheumatoid arthritis.
Phrases in Scopus have to be enclosed in double quotes without truncation.
Use the singular form of the phrase and Scopus will find most plurals as well.
Here's a logic grid for a Scopus search on bone loss in juvenile rheumatoid arthritis
| "bone resorption" | "arthritis, juvenile rheumatoid" |
| "bone loss" | "juvenile rheumatoid arthritis" |
| osteolysis | "juvenile chronic arthritis" |
| acroosteolys* | "juvenile idiopathic arthritis" |
| "juvenile arthritis" |
("bone resorption" OR "bone loss" OR osteolys* OR acroosteolys*) AND ("arthritis, juvenile rheumatoid" OR "juvenile rheumatoid arthritis" OR "juvenile idiopathic arthritis" OR "juvenile chronic arthritis" OR "juvenile arthritis")
I mostly use Advanced Search because Basic Search has limited space for entering terms.
Scroll down the list of codes and select TITLE-ABS-KEY.
Enter your search between the brackets produced by Scopus.
Select the citations you want to save.
To store them temporarily click on Add to My list.
You can select all of the citations found, or all the citations showing on the screen showing by clicking in the box to the left of All or Page.
Click on the links to the right to check for other articles that cite those found in your search.
Select any of these you want to save and then Add to My List.
When you have finished collecting citations, scroll to the top of the screen and click on My List at the top of the screen.
Click on Select: All.
Click on the Export button.
Use the drop down menu to select EndNote in the Export format box.
Select the format you want,
I suggest abstract.
Click on the Export button.
This will open up your EndNote software and automatically import the Scopus citations.
You can use Scopus to find citations that you know about already, and then view the articles that cite these articles.
You can search by title or do an Author Search.
Alerts in Scopus
Save your search and/or set up an alert or RSS feed for your Scopus searches from the results screen.
Registration is required to set up alerts or save searches, but it's free.
Use this database to search for citations, and to find citations to articles that you know about already.
You have the article
Moore H, Dvorakova K, Jenkins N, Breed W 2002 Exceptional sperm cooperation in the wood mouse Nature 418(6894) 174-177
Find the articles that cite this.
Select the topical coverage in Web of Science and date range.
It's usually best to search for the author with the least common name.
Because we know Bill Breed we'll search for him even though he isn't the first author here.
Click on Cited Reference Search.
Just enter surname, first initial and asterisk.
Click on Search.
Scroll through the resulting citations to find the right one.
If there's an option to View Record click on the link.
Click on Times Cited to view the citing articles.
If there is no option to view record click in the box or boxes next to the citations of interest and then click on Finish Search.
This will produce a list of citations that make reference to one or more of the Breed articles selected.
Select the citations you want to keep.
Scroll to the bottom of the screen to send citations to EndNote.
If you want all the citations click in the Records radio button and type 1 to #.
Abstract format is probably the better option.
Alternatively click on Add to Marked List.
Click on Marked List at the top of the screen.
Select the parts of the citations that you want to save.
Scroll down and click on EndNote (not EndNote Web)
Topic Searches
You can use Web of Science and other databases in the Web of Knowledge to search for topics.
Web of Knowledge searches are similar to Scopus except that truncation has to be included inside the double quotes in phrase searches.
Web of Knowledge won't find inverted MeSH.
("bone resorption" OR "bone loss*" OR osteolys* OR acroosteolys*) AND ("juvenile rheumatoid arthritis" OR "juvenile idiopathic arthritis" OR "juvenile chronic arthritis" OR "juvenile arthritis")
You can select individual citations for saving etc, or your can select all on a screen, or ranges.
I recommend saving citations to the Marked List.
Saving Searches and Alerts
After you have searched, click on Search History.
Click on Save History/Create Alert.
Click on Register.
Register an email address and password.
Once signed in you can name your search and click in the E-mail Alerts box.
I suggest that you change the Alert type to Biblio + Abstract.
Change the email format to field tagged if you want to put these citations into EndNote.
Click on Save.
Other Web of Knowledge Databases
As well as Web of Science it's likely that you'll find some useful citations using Current Contents Connect and Biosis Previews. For some of you CABI might also be useful.
Medline on Web of Knowledge is a pale version of PubMed.
Document Delivery
The Library will provide you with up to 50 interlibrary loans in 2011.
Use the document delivery system to get hold of journal articles not held by the Library.
Click on Library A to Z on the Library home.
Scroll to find Document Delivery, and click on the Request form.
This is a free service as long as you don't ask for fast delivery or for books from overseas.
