Structural Cell Biology III
2010
Last update August 2010 by Mick Draper
Table of Contents
Introduction to the PubMed Database
PubMed is a database of citations to more than 19 million journal articles from over 4,600 of the world's most significant health sciences and life sciences journals. These PubMed citations to articles come from journals in the fields of medicine, nursing, dentistry, veterinary medicine, health care systems, and life sciences. Most of the articles date from 1960 to the present.
Access to PubMed
The University of Adelaide Library has a customized version of PubMed that provides direct links to Uni of Adelaide electronic journals. You can use this version of PubMed by finding it on
The Library web site, in the right hand side bar.
You can also use The Catalogue to find PubMed.
The Library's Databases site for Anatomical Sciences
Right click here to open PubMed in a new window or a new tab
MeSH Database
PubMed has a subject index called the MeSH Database.
Using MeSH you can find citations to articles on a huge range of topics in PubMed.
Click on MeSH Database under the More Resources heading to open the MeSH search box.
Notice that there are some online tutorials for using the MeSH Database.
You can use these for revision.
PubMed operates efficiently using Medical Subject Headings or MeSH.
These subject headings are used to index articles so that you can find citations on a particular topic no matter what words and phrases are used by the authors in their article titles, and abstracts to describe the contents.
Using the MeSH cell membrane structures will find citations to all indexed articles on this topic.
This subject heading will also retrieve citations to articles on cell-matrix junctions, intercellular junctions, and myelin sheaths etc. without you having to type all of these terms into the Search box.
Using MeSH
Type a single search term into the MeSH database
e.g.cell membrane structures
Click on Go.
MeSH database offers a definition of the term.
Scroll down the screen.
Notice that there are subheadings for this MeSH. More on subheadings later.
Continue to scroll down the screen to Entry Terms.
We'll come back to these later too.
Scroll down further to see the where cell membrane structures
fits in the hierarchy of MeSH.
Notice that there are other terms above, and importantly, more MeSH indented below Cell Membrane Structures.
The indented terms in the list of MeSH are used for particular cell membrane structures, so they are subsets of the general term.
Unless you tell PubMed otherwise all the indented subjects listed will be included in your search for the MeSH Cell Membrane Structures.
This process is called EXPLOSION. It saves a lot of typing and finds all sorts of cell membrane structures even if you don't know what they were or what they are called.
The exploded search is equivalent to typing
cell membrane structures OR cell-derived microparticles OR cell-matrix junctions OR castameres OR focal adhesions OR hemidesmosomes OR coated pits, cell-membrane ...
The + sign next to Synapses (and other terms) means that there are other, more specific MeSH included with this term.
These more specific MeSH will also be included in an exploded PubMed search of Cell Membrane Structures.
You should look at the more specific and broader terms to make sure you are using the best term for your search.
A diversion about OR Logic
OR logic is used to combine terms when you want citations to articles containing either one or both terms joined by OR to be included in the search results.
Try another MeSH search.
Clear the previous search if necessary.
Type in cytoplasmic filaments and click on Go.
This time the term typed in isn't a MeSH, but the program recognizes the term and finds the appropriate MeSH.
If you scroll down the screen you'll notice that again there are other more specific MeSH indented under Cytoskeleton
When you can't find a MeSH
Some terms you enter may not be found by the MeSH Database.
In such cases PubMed offers a few suggestions, mainly based on alphabetical similarities.
If the MeSH database doesn't help find a MeSH try typing in another term that describes your topic.
We'll return to this later.
Using MeSH to Search for Articles
Try a search on your cell structure or cell type .
Type the term into the MeSH Database. I'll be using Cell Membrane Structures.
If you find a MeSH click on Links over on the right of the screen.
A box will appear. Click on PubMed.
PubMed runs the search for, and displays all citations with this MeSH or any of the indented more specific MeSH. There was a mere 111,126 citations on this topic when I searched in July 2010.
Combining MeSH Database Searches
For this assignment you have to search for a topic in cell biology AND a particular method for investigating the topic.
To search for citations on this we can combine two MeSH using AND logic.
Here is a search for citations to articles that include the topic cell membrane structures and the technique fluorescence spectroscopy.
Combine MeSH for these two concepts using AND logic to find citations to articles that include both concepts.
Open the MeSH database and type in cell membrane structures.
Click on the Go button.
Click in the box to the left of the MeSH.
Click on Send to, then on Search Box with AND
The MeSH appears in the PubMed Search box.
Next we want to search for fluorescence spectroscopy.
Clear cell membrane structures from the MeSH search box (but not the PubMed Search box)
Type fluorescence spectroscopy into the MeSH database search box.
Click on the Go button.
If the search finds more than one MeSH, click on the link to the most appropriate one.
Click in the box to the left of Spectrometry, Fluorescence.
Again click on Send to then Search Box with AND
Now both concepts appear in the PubMed Search box.
Click on the PubMed Search button.
The search result appears in PubMed.
The search found 499 citations to articles in July 2010.
MeSH Subheadings
Clear the PubMed search box.
Use the pull down menu to change PubMed to MeSH.
Type in your cell search term again (cell membrane structures)
Click on the Search button.
This will return you to the MeSH screen for the term.
Scroll down the screen to view the subheadings.
Click in the box to the left of any of the subheadings to be included in the search.
Subheadings make your search more specific. If you don't click in the boxes for any of the subheadings then all of the subheadings will be included in the search.
I selected both metabolism and physiology.
Will PubMed use OR logic or AND logic to combine these?
The subheadings in this search will also be added to all the more specific MeSH indented below Cell Membrane Structures in the MeSH hierarchy, and citations with these MeSH and subheadings will be included in the results.
Click on the Send to button and then click on Search Box with AND.
This will put your search terms into the PubMed Search box.
Notice that PubMed has used OR logic to combine the subheadings so that the search will find citations that could include either or both of the metabolism or the physiology of cell membrane structures.
Spectrometry, Fluorescence.
Click on the link and then view the subheadings.
Click in the box to the left of the subheading methods.
Click on Send to.
Click on Search Box with AND.
Now the combined search appears in the PubMed Search box.
Click on the Search PubMed button to search for articles on
Fluorescence spectrometry methods for examining metabolism or physiology of cell membrane structures.
Remember that all the more specific MeSH will also be searched with these subheadings.
This search found 60 citations in July 2010.
Citations appear in summary format, but you can change this to show abstracts and sometimes link to the full text.
Major MeSH
Medical Subject Headings are divided into two groups, Major MeSH and Minor MeSH
Major MeSH are assigned to articles where a topic is a major aspect of an article.
You can restrict your searches to Major MeSH to focus your search.
You can also combine Major MeSH and MeSH Subheadings.
Search for Cells as a MeSH.
Click in the box to restrict your search to Major MeSH
Select Subheadings if you like.
Send to the Search box.
In this example I've chosen to AND this with Western Blot as the method
Displaying Results
Summary Display
This is the default display after each search that finds more than one citation.
Summary shows you the article title, author(s), publication details, and unique PubMed ID.
To change the display click on Display Setting or the down pointing arrow.
Click in the radio button to the left of Abstract [not Abstract (text)]
Click on the Apply button.
Abstract Display
This will include an abstract of each article where one is available.
The Abstract display may also include an icon where the full text of the article may be available.
You will actually be able to get full text only if the Library has a subscription, or if the journal is freely available on the internet.
If you don't find an icon it doesn't necessarily mean that the full text isn't available.
This is particularly true for older articles which the Library may have in print rather than electronic format.
You can use the abbreviated journal title shown in PubMed to check the library holdings in the catalogue, but it's safer to use the full title of the journal.
To see the full journal title, point your mouse cursor over the abbreviated journal title in the PubMed citation but don't click.
The full journal title will appear for a few seconds.
To find more citations to articles that are similar to any one you have found click on Related citations in the PubMed result.
PubMed runs an algorithm that searches on title words, abstract words, and MeSH to find similar articles.
Reference Values
PubMed contains a large proportion of citations on clinical and pathological topics.
Sometimes it's important to be able to find citations to articles on healthy
cells.
This can be difficult in PubMed, but one way is to add the
MeSH
Reference Values
to your search using AND logic.
Note that this will significantly reduce the number of references found.
Now even though the articles may still be about some disease or disorder, they probably contain some information about healthy cells.
You might also like to include the MeSH Humans in some of your searches.
For most of you this will be all you'll need to find articles for your assignment
Title and abstract term searches
As well as using the MeSH Database you can search for words and phrases from the titles and abstracts of citations.
This method of searching is useful when you can't find a MeSH, or to find citations of articles that aren't (yet) indexed.
Citations not indexed include very recent articles.
If you want comprehensive searches it's important that you
Use at least one MeSH for each of your search concepts.
Include other terms that authors are likely to use.
Logic Grids
It's always useful to decide on the main concepts.
It's usually best to write this as an 'answerable question'.
What studies are there that use electron microscopes to investigate erythrocytes?
There are two concepts to this search; the method electron microscopes, and the cells erythrocytes.
We need to find terms that describe these concepts and combine them appropriately in PubMed to find citations to articles.
Begin your logic grid by writing down these two concepts
| electron microscopes |
erythrocytes |
We need to add a MeSH to each column and perhaps other terms that to make the search more comprehensive and possibly find more recent articles.
Let's go back to the MeSH Database and look for electron microscopes.
A search for Electron Microscopes in the MeSH database finds the term Spectroscopy, Electron Energy-Loss but this doesn't look appropriate.
Under the MeSH search box is a list of suggestions. The first of these, Electron microscopy looks best.
Click on this link.
The MeSH is Microscopy, Electron.
Electron Microscopy is listed as an Entry Term.
We can add these to the left hand column of the logic grid.
| microscopy, electron[mh] |
erythrocytes |
| electron microscopy[tiab] |
|
microscopy, electron[mh], tells PubMed to search the phrase as a Medical Subject Heading.
To search a phrase electron microscopy in the titles and abstracts of citations in the PubMed database add [tiab] to the phrase
e.g. electron microscopy[tiab]
Adding [tiab] makes PubMed search this as a phrase.
Now look at the more specific MeSH listed under Microscopy, Electron
These MeSH will be searched as part of the explosion, but if you want these terms searched in the titles and abstracts of citations to articles that don't yet have MeSH added, you should include them in the logic grid.
You can also look at their entry terms to see other terms to add to your grid.
Don't include inverted terms such as Microscopy, Electron Scanning.
You don't need to include scanning electron microscopy or transmission electron microscopy because these are covered by electron microscopy[tiab].
Remember to include [tiab]
| microscopy, electron[mh] |
erythrocytes |
| electron microscopy[tiab] |
|
| electron microscope[tiab] |
|
| immunoelectron microscopy[tiab] |
|
Next add a MeSH and synonyms or alternative terms for erythrocytes to the second column of the logic grid.
To find these you can also look at the MeSH Database.
Erythrocytes turns out to be the MeSH.
The Entry Terms listed under Erythrocytes include erythrocyte, red blood corpuscle, red blood corpuscles, red blood cell, and red blood cells.
These can be added to the logic grid.
Notice also the more specific MeSH Reticulocytes.
You could click on the link to reassure yourself that this is an appropriate term.
You might want to include the terms reticulocytes, reticulocyte, erythroid cells and erythroid cell in your logic grid.
Truncation
Use the truncation symbol * to reduce typing.
Adding * after a word stem will allow PubMed to search for any word or phrase that includes the stem.
electron microscop*[tiab] will find
electron microscopy[tiab] OR electron microscope[tiab] OR
electron microscopes[tiab] etc
Don't truncate MeSH
You should check that any phrase truncations you are thinking of making by entering the term in the PubMed database (not the MeSH Database),
and then checking on the Search details area (right hand side of the screen and down a bit) to see how PubMed is searching for the phrase
Don't truncate within a phrase such as electron* microscopy[tiab]
Now the logic grid could look like this.
| microscopy, electron[mh] |
erythrocytes[mh] |
| electron microscop*[tiab] |
erythrocyte*[tiab] |
| immunoelectron microscop*[tiab] |
red blood cell*[tiab] |
| cryoelectron microscop*[tiab] |
red blood corpuscle*[tiab] |
| |
reticulocyte*[tiab] |
| |
erythroid cell*[tiab] |
Logic Rules
Combine the terms in each column using OR logic.
Enclose the terms from each column in round brackets.
Joint the two column searches using AND logic.
(microscopy, electron[mh] OR electron microscop*[tiab] OR immunoelectron microscop*[tiab] OR cryoelectron microscop*[tiab]) AND (erythrocytes[mh] OR erythrocyte*[tiab] OR red blood cell*[tiab] OR red blood corpuscle*[tiab] OR reticulocyte*[tiab] OR erythroid cell*[tiab] )
Enter this in the PubMed database (not the MeSH database) and click on the Go button to get the result.
This found 8278 citation in late July 2010.
PubMed is a large database so you can often find lots of citations.
Another way of restricting results, and to find citations that are about healthy subjects is to add the MeSH Reference Values.
The MeSH humans will restrict your citations to articles that include human subjects.
Output
To see details of how to mark references, save, print or email them use the main PubMed Tutorial at
http://www.adelaide.edu.au/library/guide/med/dent/dentpm.html#26
Limits
PubMed has several ways of reducing to manageable levels, the number of citations found. You should always be aware with this that you may lose important articles.
Click on the Limits link.
The Limits options appear.
Language
For this exercise it might be useful to select English in the Languages limit. This will ensure that the articles you find are written in English.
Dates
You can limit your search to the publication dates.
Use Limits Published in the Last...
To set a publication date of 1995 to 2008 select Specify date range.
When you have selected your limits click on Search at the bottom of the Limits screen or at the search box.
Limits remain in place until you cancel them by clicking on Remove in the yellow bar below the search box.
For more detail on limits see the main PubMed tutorial at
http://www.adelaide.edu.au/library/guide/med/dent/dentpm.html#15
Review Articles
Click on the Review tab to limit your search to articles that review the literature in a field. Note that review articles do not normally report the results of experiments but comment on the more significant experiments.
Remember you can click on Related citations to get a list of all articles 'similar' to the parent article.
When you really can't find a MeSH
Sometimes it might be quite hard going finding a MeSH that covers the topic you want. Here's a method that usually gets results.
Enter the topic you want as a title search search in the PubMed database
If your topic is in the title of an article then it's probably an important part of the article.
Now display the citations found in Abstract format.
Click on the link to display the MeSH.
From looking through some of citations found, you might decide that the best way to search MeSH for Actin Cables would be to combine
actins[mh] AND cytoskeleton[mh]
Using PubMed Summary
1 Think of an answerable question relevant to this assignment.
2 What are the main concepts in this question? Write them down.
3 Are there synonyms of, or alternative terms for each of these concepts?
Write these below the main concepts to form columns of search terms.
4 Use the MeSH Database to find at least one MeSH for each of the main
concepts and add these to the appropriate column. Add the field tag [mh].
5 Other terms should include the field tag [tiab].
Entry Terms in the MeSH Database can often supply useful synonyms.
6 Type the terms from the first column into the PubMed database search box making sure you
use OR logic between each of the terms and enclose all the terms from the column in round brackets.
7 Type a space then AND then another space.
8 Type in the terms from the second column again using OR logic between
the terms and enclosing all the terms in round brackets.
9 Repeat for each column of terms.
10 Click on Go.
11 Use Limits if necessary.
12 Try again using different terms if you can't find appropriate articles.
13 Use Related Articles if you can't find enough citations.
14 If you are still struggling, ask Mick Draper for help.
Other Resources
Biosis Previews
Informit Health Databases
Click on Health in the list of subjects (later you could try clicking on Sciences)
Click in the box to the left of Health
How to read an article
A short set of notes by Mick Draper on the main aspects of critically reading journal articles
How to read a paper
A set of articles by Trisha Greenhalgh published in BMJ. The emphasis in these articles is on evidence based medical practice.
|
