Research Resources
From CrnaBIZ-Wiki
- Searching PubMed- Lesson 1*
Good Morning, Class!
Welcome to a course on how to search PubMed® via your home computer. Here are the objectives for today's lecture. After reading this material and performing the actions called for in today's text, you should be able to:
1. Describe what PubMed® is and how it is maintained and updated
2. Use your Internet Browser to access the National Library of Medicine's FREE PubMed® website
3. Conduct an initial search using two search terms
4. Select several citations
5. Send the selected citations in an e-mail message to me
- Introduction:*
This class is an experiment. I hope that you will be patient with my efforts, and additionally that you will all comment freely on how I could improve these "Lessons". I will be giving you step-by-step instructions, but owing to the many ways in which people might be accessing the Internet, the steps might be out of line with what you are experiencing on your own computer. If so, please e-mail me to let me know.
For that same reason, you will note that I am using the most bare-bones of e-mail messages. I will not use any formatting (bold, italics, colors, etc.), and only occasionally add pictures or other multi-media goodies, because I cannot be sure that you all will be able to read such things. Let me know if you find the formatting troublesome- I have added a lot of "white space" to make it easier to read, but if it is too much, let me know.
When you e-mail me with problems, make sure that you tell me how you are accessing the Internet-
1. What type of computer/system do you have (Macintosh or Windows, XP or Vista, etc.)
2. What Browser software are you using (Internet Explorer, FireFox, Safari, etc.)
3. What type of e-mail program are you using (MS Outlook, Outlook Express, Macintosh Mail, Eudora)
Also, I suggest that you figure out a couple of things about your e-mail program so that you can save these materials for reference later:
1. Your e-mail program should allow you to create a new folder to store your mail.
2. Name the folder "PubMed Course"
3. Each time you receive one of these messages, transfer the message into the PubMed Course folder. I would also keep any correspondence between you and I in there as well. I know that there are various computer skill levels represented by the people reading these course materials. I ask those of you who are very experienced to have patience with my attempts to make this course understandable to even the newest "newbie" of the bunch. And those of you who _are_ newbies, please feel free to e-mail me if you don't understand what is going on. Or in the worst case scenario, give me a call-
Work: (509) 456-8150
Home: (509) 747-0819
No calls after 10pm Pacific, please! And it is ok to call me at work, although I may be busy. And again, as a final note, please give me feedback on the course and how you think it could be improved. Just send your comments to my e-mail address, <dsimonson@mac.com>.
- PubMed- What it is*
To get started, click on the URL (Uniform Resource Locator) below. After it takes you to the PubMed website, come back to this message so that we can talk about what you are seeing. You may want to print this message out so that you can read along while you are clicking through the various parts of the website.
This will take you to the PubMed portal, which actually turns (after you click on it) into a different URL than what you just clicked on (you may note this if you look at the highlighted URL in your toolbar). Here it is:
http://www.ncbi.nlm.nih.gov/sites/entrez/
Don’t worry, they are both the same. You could have instead have typed in
(note the “.com” instead of “.gov”) and it would take you to the same place. The PubMed folks wanted to make it as easy as possible for you, so they bought up all of the pubmed URL variations and made them all take you to the same place.
So where is www.ncbi.nlm.nih.gov/sites/entrez/? Let me decode some of the acronyms. “ncbi” is the National Center for Biotechnology Information. “nlm” is the National Library of Medicine. “nih” is the National Institute of Health. All three of these government programs join together to offer access to the gamut of scientific literature and data through one portal- “Entrez”. This French word for entry or portal is the name of “the integrated, text-based search and retrieval system used at NCBI for the major databases, including PubMed, Nucleotide and Protein Sequences, Protein Structures, Complete Genomes, Taxonomy, and others.” (1)
We obviously are only interested in the PubMed portion of the Entrez databases, which contain the references to articles in the Medical and Nursing literature, most of them found in the MEDLINE database maintained by the National Library of Medicine. If all of these acronyms are confusing to you, you are not alone. However, it is not necessary to be aware of all the details going on behind the scenes to become adept at searching the MEDLINE database through PubMed. The important point to remember is that PubMed is just a “front end” that allows you to search many different databases of medical literature easily and with a single interface.
- Looking Around the PubMed Page*
After clicking on
You should be looking at the PubMed homepage. The NCBI logo should appear in the upper left-hand corner, then the PubMed logo to the right of that.
There are several things for you to note on this page before we get started searching. First of all, you should immediately "bookmark" the PubMed homepage so you can return easily. To do this, go up to your Bookmarks (Safari and FireFox) or Favorites (Windows Internet Explorer) menu, and choose Add. Now you will be able to return anytime by going to your Bookmarks or Favorites menu and selecting the PubMed Home choice.
On the left side of the page are several hypertext links (highlighted text which when clicked takes you to other pages) which will take you to pages explaining all about Entrez and PubMed. You could avoid any more of these classes if you simply read the help and example files listed here. I am hoping to provide you with a more CRNA-friendly explanation, however, so it may help to read the help files _and_ the lessons I am going to be sending you. The “Tutorials” link is particularly helpful, as they have video-based tutorials that explain in very user-friendly manner all of the subtleties of searching using NCBI and PubMed.
- This is an important place to stop if you are having problems. If you are not able to get to the PubMed web page, you need to stop here and e-mail me to let me know what problems you are having. You will not be able to complete the rest of this lesson until you are able to get to the PubMed homepage. List your phone number in the message, so that if it is apparent that you are too messed up for me to fix via e-mail I can call you.**
- Performing Your First PubMed Search*
Now, after all of this discussion, we will get on to performing our first search. Once at the PubMed homepage, click your cursor on the text-entry box just after the “Search PubMed for” statement – it’s there toward the top of the page.
When you see your cursor blinking in the box, type in the following search terms:
myasthenia anesthesia
Now click on the “Go” button.
You should be taken to a web page listing the first 20 references that PubMed found with both “myasthenia” AND “anesthesia” located in them. If you look at the top of the list, you should see in small text, “Items 1 – 20 of 384”. This points out that of the 384 articles found (there may be more by the time you read this), and only the first 20 are on this page. You can move to the next 20 articles by clicking on the “Next” button you see to the far right of that statement.
For many of you, I offer congratulations! You have just completed your first PubMed search!
- Selecting an Article to Review*
Once you have found an article amongst these that you are interested in, click on the little checkbox to the left of the number of the article. For this lesson, I would like you to click (at a minimum) the checkbox next to “Bogaert F, Verhaeghen D, Herregods L.; Myasthenia gravis and thymectomy: an anaesthetic approach.” Go down the list and check off any other the ones you are interested in. If you wish, you can go to the next page and do the same. Once you have clicked on all of the interesting articles, go to the top of the page and click on the drop-down menu just after “Display” and chose [AbstractPlus] (the brackets indicate that this is a menu choice).
You should see the page reload, and now the page should contain only those articles you checked off. This is one way to shrink the number of citations to a manageable few, although I will show you how to limit citations in other ways in the upcoming lesson.
This will give us a few citations to work with for the next step.
- Sending the Citations via e-mail*
Now we will begin to see the power of PubMed. Let’s imagine that you have found 3 or 4 reference citations that support your position in a clinical discussion on myasthenia gravis and anesthesia. One of them is the Bogaert article you checked above. You would like to send these references to your colleague to inform your discussion.
The display line towards the top of the page should say “Display [AbstractPlus] Show [20] [Sort By] [Send to]”. Click on the [Send to] drop-down menu and choose “E-mail”. This will load a new page where you can specify sending the citations to your colleague. You can accept the default formats and sorting, and in the box titled “Your name or additional text” you can type in your name and “PubMed Homework”. Then, in the box labeled E-mail, type my email address: dsimonson@mac.com
Click on the “Mail” button. You may want to repeat this process and put down your own email address instead of mine. Then the results will be sent to your inbox as well.
Your homework is done!! When I get the message, I will respond and let you know how you did. In the meantime, try out a few more searches just to give yourself some practice. Have fun- you can’t screw up!
- This is the End of Lesson 1*
References
(1) http://www.ncbi.nlm.nih.gov/Database/index.html
============================================================
Dan Simonson CRNA, MHPA e-mail: dsimonson@mac.com Nurse Anesthetist Phone: (509) 456-8150 Fax: (707) 897-1486 Cell: (509) 981-6274 The Spokane Eye Surgery Center, W. 208 Fifth, Spokane, WA 99204
