# Presentation: 512446

## Point-Blank

- New England Region
- National Network of Libraries of Medicine
- June 2007

*The NN/LM NER is funded by the National Library of Medicine under a contract (#N01-LM-1-3518) with the University of Massachusetts Medical School  in Worcester.*

## What is PubMed? 

The world’s premiere biomedical bibliographic database

Online access to the MEDLINE database 

Developed & maintained by the National Center for Biotechnology Information (NCBI) at the National Library of Medicine (NLM)

- The world’s premiere biomedical bibliographic database
- Online access to the MEDLINE database
- Developed & maintained by the National Center for Biotechnology Information (NCBI) at the National Library of Medicine (NLM)

## Contains citations to journal articles in these major content areas:

Biomedical Sciences
Nursing
Dentistry
Veterinary Medicine
Pharmacy
Allied Health
Preclinical sciences

- Biomedical Sciences
- Nursing
- Dentistry
- Veterinary Medicine
- Pharmacy
- Allied Health
- Preclinical sciences

**Notes:**
“Preclinical sciences” refers to such topics as: human anatomy, physiology, biochemistry, microbiology, immunology, parasitology, and pathology. 

## PubMed also contains information on:

Health policy
Bioinformatics
Health administration
Standards and practice guidelines
Health-related technology
Patient education materials and consumer health information

- Health policy
- Bioinformatics
- Health administration
- Standards and practice guidelines
- Health-related technology
- Patient education materials and consumer health information

## PubMed contains:

17+ million bibliographic citations
1950 – present
5,000+ journals published worldwide are indexed
70+ languages represented
Some freely available full text documents
Links to the other NCBI databases

- 17+ million bibliographic citations
- 1950 – present
- 5,000+ journals published worldwide are indexed
- 70+ languages represented
- Some freely available full text documents
- Links to the other NCBI databases

**Notes:**
As of 1/24/2006:
Free full text is available for about 11% of PubMed’s 16+ million citations
There are about 70 full text books available in the Books Database. The majority of these have to do with molecular biology
The “other” NCBI databases: Nucleotides, Genome, Protein, Structure, and OMIM (Online Mendelian Inheritance in Man).

## Accessing PubMed on the Internet:

http://pubmed.gov

PubMed is freely available wherever there is internet access. No registration. No subscription. No fees. No kidding.

The next slide shows the homepage of PubMed.

- _[http://pubmed.gov](http://pubmed.gov/)_
- PubMed is freely available wherever there is internet access. No registration. No subscription. No fees. No kidding.
- The next slide shows the homepage of PubMed.

## Slide 7

## Part 1: Basic Information and Navigation

Very basic searching that works 
Results
What do those icons mean?
What’s a citation?
In what order are search results displayed?
How can I display and sort my results?
What can I do with my results?

- Very basic searching that works
- Results
- What do those icons mean?
- What’s a citation?
- In what order are search results displayed?
- How can I display and sort my results?
- What can I do with my results?

## Type ‘n Go searching of PubMed: Simply type a term or terms in the Search Box and click Go.

## Note that “and” is the default connector used in PubMed. If more than one term is entered into the search box, PubMed will AND the terms together. 

- Note that “and” is the default connector used in PubMed. If more than one term is entered into the search box, PubMed will AND the terms together.
- If the term **AND** is typed into the search box, it must be in all **CAPITAL** letters. This is also true with the other connecting words allowed:** ****OR**** **and **NOT**.

**Notes:**
As of May 2007, it appears that lower case Boolean connectors (and, or, not) will also “work” in PubMed. However, there is a CAUTION. The lower case connectors do not work perfectly 100% of the time due to many different factors. Therefore, it is advisable to maintain the position that the Boolean connectors need to be in UPPER CASE letters because that will work properly 100% of the time. If we reach a point where the lower case connectors will work properly all the time, NLM will make an appropriate announcement.

**Notes:**
Search = “smallpox” done on 6/11/2004

## What’s in a citation?

- Author names. Click to access abstract.

- Title of the journal article

- Journal title abbreviation and publication information

- The PMID is like a Social Security number for a citation. It is a unique identifier for the citation.

- This tag indicates the level of processing this citation has received. This particular citation has been fully processed.

- This icon indicates this citation has an abstract. Clicking on the icon will bring up the abstract.

## Icons that appear in the Summary Results:

- No abstract available for this citation.

- This citation has an abstract.

- There is free full-text access to this article.

- There is free full-text access to this article through PubMed Central (PMC), an initiative from the National Library of Medicine to encourage publishers to make their content freely available.

## About abstracts:

Some citations have them, some do not. If an abstract appeared in the print publication, there will be an abstract in PubMed.
Abstract length varies: some are very short; some are quite lengthy

To see the abstract, click on the author name or the icon in the Summary Format.

- Some citations have them, some do not. If an abstract appeared in the print publication, there will be an abstract in PubMed.
- Abstract length varies: some are very short; some are quite lengthy
- To see the abstract, click on the author name or the icon in the Summary Format.

**Notes:**
The National Library of Medicine indexes literature. It does not abstract literature.

## More on results. Here is a search for childhood immunization refusal

**Notes:**
Search done 6/19/2007

## Some article titles are in brackets. Why?
Some articles have no authors listed. Why?

- Some article titles are in brackets. Why?
- Some articles have no authors listed. Why?

- Brackets indicate the article is published in a language other than English

- If no authors are listed in PubMed, it’s because no authors were listed in the print version of the article.

- Summary format: this is the default format for displaying results in PubMed.

- Showing 20 items per page

- Number of results for this search

- Number of pages of results

- The Action Bar

- Number of articles within this set of results that are the publication type = Review

**Notes:**
“Review” is a certain publication type in PubMed. It is not a clinical trial or an editorial or a systematic review. Review articles are those that review the literature on a subject and, as such, may be useful for background information or more introductory information on a topic. To see the Review articles in this set of results, simply click on the Review tab. The Review tab in PubMed is a default which may be changed through a My NCBI account. 

## Other searches may produce many more results, still in Summary format, on many pages.

- Move from one page to the next by clicking on **Next**
- Or, move many pages at a time by putting a number in the box next to **Page** and then clicking on the **Page** button.
- The way information displays on the page may also be altered.

**Notes:**
Search = bioterrorism done on 2/25/2005
NOTE: The “ALL” tab indicates the total number of results for this search. The “Review” tab indicates that 501 of those citations are Review articles. Click on the “Review” tab to see just the citations for the review articles.

## Other Display Formats are available:

- To change from one display option to another, simply **highlight** the desired forma.

- Different formats are useful for different reasons.
- The **Abstract** format will show the abstract (where available).
- The **AbstractPlus** format shows the abstract and the first 5 Related Articles.
- The **Citation** format will show the abstract (if available) as well as the MeSH terms used to index the citation.

## In what order are search results displayed?

**Notes:**
This may sound like a silly question, but it’s not. It’s one of the major misunderstood things about PubMed.

## Slide 21

**Notes:**
Search: “ethics AND reproduction” done on 6/14/2004
Search results: 12,356 citations. This shows the citations that were #1-4 on 6/14/2004

## Results are displayed in Entrez date order

The citation that:
meets the search criteria 			
And
was most recently added to the database 

will be displayed first.

It is possible to sort citations into order by publication date.

- The citation that:
- meets the search criteria
*And*
- was most recently added to the database
- will be displayed first.
- It is possible to sort citations into order by publication date.

## Sorting results

- Sort options:
- the publication date of the article
- the first named author’s last name
- the last named author’s last name
- the title of the journal

- Select the desired sort option by **highlighting **it.

## When searching is complete, what can be done with the results?

Citations may be printed, emailed, or saved in various ways

Use the Send To options:           

- Citations may be printed, emailed, or saved in various ways
- Use the Send To options:

## First, select citations: Click the box next to the citation

- Have several pages of results? That’s OK. PubMed will keep track of your selected citations as you move from page to page.

**Notes:**
Search for bacterial meningitis vaccine done 1/24/2006

## Now, choose the Send to option: 
Simply highlight the desired option

- Simply **highlight** the desired option

## Send to “Printer” opens a new window that allows easy printing of the selected citations

**Notes:**
Note that this is giving a nice, printer-friendly option of the information as it was displayed on the PubMed screen. If you want the abstracts (where available) included, then first display the chosen citations in a format that includes the abstract (Abstract, AbstractPlus, Citation, MEDLINE) and then use the Send To Printer option.

## Send to “Text” strips away graphics:

**Notes:**
Citations are now in a good form for printing using the computer browser’s print feature. NOTE that this is a wysiwyg (what-you-see-is-what-you-get) system. First display the information in the desired format, sorted in the desired way, and then use Send To Text.

## Send to File saves the selected citations as a computer file. Choosing this option will open a dialog box on your computer asking where you’d like to save the file.

Send to Clipboard places the selected citations on PubMed’s Clipboard

Send to Email allows users to email citations 

Send to RSS allows users to set up an RSS feed for this search

Send to Order allows users with Loansome Doc accounts to request copies of selected articles electronically

- Send to _**Clipboard**_ places the selected citations on PubMed’s Clipboard
- Send to _**Email**_ allows users to email citations
- Send to _**RSS**_ allows users to set up an RSS feed for this search
- Send to _**Order**_ allows users with Loansome Doc accounts to request copies of selected articles electronically

## CAUTION: If you do not select specific citations when you choose a Send To option, you are selecting all the citations in a given result set

Up to 500 citations  will be added to the Clipboard
Up to 10,000 citations  will be saved in a computer file
All the citations on a single page will appear in text only format

- Up to 500 citations  will be added to the **Clipboard**
- Up to 10,000 citations  will be saved in a computer **file**
- All the citations on a single page will appear in **text** only format

## Clipboard: Holds selected search results

- Select citations. Highlight Clipboard.

**Notes:**
Clipboard is a designated area within cyberspace that will hold selected citations during a search session.
Items are placed on the clipboard by using the Send to CLIPBOARD option. In the Send to menu, simply highlight “Clipboard.” Access the Clipboard itself by clicking on the “Clipboard” tab under the search box.

## When citations are added to the Clipboard:
A pink banner confirms the addition
The number of each selected citation turns green

- A pink banner confirms the addition
- The number of each selected citation turns green

**Notes:**
When items are added to the clipboard, a message appears onscreen (pink).
Citation numbers change to green. Should this citation come up in a subsequent search, you’ll know at a glance that you’ve already looked at it and saved it to the Clipboard. No duplicate citations are collected.

## Clipboard holds selected search results
Those citations stay on the Clipboard until:
The user manually removes them 
				–or-
There are 8 hours of inactivity on that computer. Close the PubMed browser, shop for airline tickets, read the Globe online, then open PubMed again -- the Clipboard items will still be there, provided there have not been 8 hours of inactivity on that computer.

- Those citations stay on the Clipboard until:
- The user manually removes them
- 				–or-
- There are 8 hours of _inactivity_ on that computer. Close the PubMed browser, shop for airline tickets, read the Globe online, then open PubMed again -- the Clipboard items will still be there, provided there have not been 8 hours of inactivity on that computer.

**Notes:**
CAUTION: When NCBI was working to improve the Entrez system and introducing “Entrez 2.0” there were reports that the Clipboard items (and the History) at times disappeared. So, if you’re putting citations on the Clipboard that you definitely need, it would be a good idea to deal with them as soon as possible rather than waiting for hours. Just a word to the wise....

## Accessing the Clipboard

Click on the Clipboard tab under the search box

- Click on the **Clipboard** tab under the search box

## This is the Clipboard:

**Notes:**
Note that now the Clipboard tab under the search box has come to the fore. Also, note that all the citation numbers here are green.

## Once in the Clipboard, the usual Send to options are there along with two new ones:

Use Clip remove to remove items from the Clipboard. Select item(s), highlight Clip remove.
My NCBI Collections: Allows users who have set up an account to save selected citations for longer periods of time than the Clipboard allows. 

- Use **Clip remove** to remove items from the Clipboard. Select item(s), highlight Clip remove.
**My NCBI Collections: **Allows users who have set up an account to save selected citations for longer periods of time than the Clipboard allows.

**Notes:**
NOTE: To learn more about My NCBI and My NCBI Collections, click on “Tutorial” from the blue sidebar in PubMed. There you will find several Quick Tours to help you learn to use this handy feature of PubMed.

## Send to Email

Select Format and Sorting options

Add a note if desired

Insert email address

Click Mail

- Select Format and Sorting options
- Add a note if desired
- Insert email address
- Click **Mail**

**Notes:**
NOTE: Some email systems do not like HTML formatted emails. If you work in a text email environment, you’re probably well aware of it. If at all possible, send email from PubMed in the HTML format because the email will arrive with additional functionality: click the author names and the AbstractPlus format will appear; the Related Articles link will be active, etc. 

## A word about email and PubMed

The sender for emails sent from PubMed will be “Sent by PubMed.”

RULE OF THUMB: send emails to yourself first and then forward them on to colleagues. That way, your name will appear as the sender.

- The sender for emails sent from PubMed will be “Sent by PubMed.”
**RULE OF THUMB**: send emails to yourself first and then forward them on to colleagues. That way, your name will appear as the sender.

**Notes:**
NOTE: The PubMed email feature allows emailing to only one email address. If you want to email citations to several colleagues, then follow the rule of thumb: email to yourself first and then forward on to however many email addresses (or lists) you wish.

## Review
Searching
Type and Go: the simplest form of searching
Changing the way information displays on the page
The Action Bar: display, show, sort
Selecting citations
Save / print / email citations
Using the Send To options

- Searching
- Type and Go: the simplest form of searching
- Changing the way information displays on the page
- The Action Bar: display, show, sort
- Selecting citations
- Save / print / email citations
- Using the Send To options

## Part 2: The Inside Scoop
More on Type ‘n Go searching
Using Limits to focus a search
The devil’s in the details
MeSH
Citations & Levels of processing
Automatic Term Mapping
History, Related Articles, and the Single Citation Matcher in PubMed
How to learn more

- More on Type ‘n Go searching
- Using Limits to focus a search
- The devil’s in the details
- MeSH
- Citations & Levels of processing
- Automatic Term Mapping
- History, Related Articles, and the Single Citation Matcher in PubMed
- How to learn more

## One way to narrow a broad search is to add additional terms to the search.

For example, searching for citations about smallpox vaccine? Type both words into the search box:

It’s still Type ‘n Go. 

- For example, searching for citations about smallpox vaccine? Type both words into the search box:
- It’s still Type ‘n Go.

**Notes:**
NOTE: Consider the information you’re looking to find in PubMed; choose the most relevant concepts; type them into the search box. PubMed will automatically AND them together. LESS is MORE. Just type and go. Trust me on this. It works. 

## Practice Searching

In Dec. 2002, newspapers reported that indoor hot tubs may be making people sick with a respiratory ailment. What’s in PubMed about this?

Your search?

- In Dec. 2002, newspapers reported that indoor hot tubs may be making people sick with a respiratory ailment. What’s in PubMed about this?
- Your search?

**Notes:**
Minneapolis Star Tribune 12/3/2002 “Indoor hot tubs may release bacteria that make you sick”
This is STILL type ‘n go.

## Slide 43

**Notes:**
Search done 3/28/2005. Would other searches have worked? Sure. The searcher could have typed: hot tub respiratory illness. The point here, though, is that type ‘n go searching is usually a pretty decent way to get good results in PubMed.

## Fall 2002, NPR reported that a physician was claiming that duct tape could get rid of warts. Can you find information in PubMed on this topic?

Your PubMed search? 

- Your PubMed search?

## Slide 45

**Notes:**
Search done 3/28/2005. Again, could other search terms have been used? Sure. But, these work.

## Many people find that the most common problem when using PubMed is that they get too many results

Adding terms to your search can help reduce the number of citations retrieved

Is there another way to reduce retrieval and focus in on the topic of interest?

- Many people find that the most common problem when using PubMed is that they get too many results
- Adding terms to your search can help reduce the number of citations retrieved
- Is there another way to reduce retrieval and focus in on the topic of interest?

**Limits**

**Yes!**

**Yes!**

## Using Limits can significantly reduce the number of items retrieved. Use it to focus a search.
Some of the most popular limiters are:
Language
Publication Type
Date of publication
Free full text
Access the Limits page by clicking on the Limits tab:

- Using **Limits** can significantly reduce the number of items retrieved. Use it to focus a search.
- Some of the most popular limiters are:
- Language
- Publication Type
- Date of publication
- Free full text
- Access the Limits page by clicking on the **Limits** tab:

**Search Builders**

- One or more author names or journal titles may be selected here and added to your search

**Limits**

- Use this to limit to free full text or full text (not free) or to restrict your retrieval to only items with abstracts.

- Pre-specified date ranges may be chosen or you may enter a date range of your own specification

- Select none, one, or several options in any of these categories to focus your search results

- To use this option, chose a field from the drop down menu. Any terms entered into the search box will be tagged with the appropriate field tag and  PubMed will search for the specified term in the specified field **only**.

**Notes:**
While this slide looks confusing, it simply shows how many different options are available to searchers on this page in PubMed. Many choices can be made. Note that it is not strategically a good idea to make choices in each available category on this page. Think carefully about what information you want to retrieve and make choices accordingly.

## Let’s limit our previous search for “smallpox vaccine” to just items written in English

And then, let’s use the Type of Article limit to restrict our retrieval to citations that are Practice Guidelines

- And then, let’s use the Type of Article limit to restrict our retrieval to citations that are Practice Guidelines

- When finished making selections, simply click on Go at the top or bottom of the Limits page to re-run the search with the chosen Limits applied.

**Notes:**
NOTE: On 6/2/2006, the search “smallpox vaccine” (no Limits applied) yielded 3,110 results.

## Search results using Limits: 

- PubMed clearly shows which Limits have been applied.

**Notes:**
Note the box next to the “Limits” tab under the search box is also checked. That’s another indicator that Limits have been applied to this search. Note, too, that retrieval has been dramatically reduced in this case: to 7 items from over 3,000. That big reduction is due primarily to the choice of “practice guideline” as the type of article.

## It’s just as simple as that.

PubMed is deceptively simple to use and yet very sophisticated. 

The devil’s in the details. 

- PubMed is deceptively simple to use and yet very sophisticated.
- The devil’s in the details.

**Notes:**
Looking at some of the details......

## The major details:

What’s the organizational structure of this database?

How does PubMed search?

- What’s the organizational structure of this database?
- How does PubMed search?

## Indexing allows efficient retrieval of relevant information from a database. Indexing describes content.

MeSH is the controlled vocabulary used for indexing citations in PubMed. 

MeSH  Medical Subject Headings

- MeSH is the controlled vocabulary used for indexing citations in PubMed.
- MeSH  _**Me**_dical _**S**_ubject _**H**_eadings

**Notes:**
(2) What is the organizational structure of the database?  Two principles to understand here. 
The first is that citations are arranged in Entrez date order, the date the citations were added to the database. We talked about this when trying to figure out what order search results are displayed.
The second is MeSH – Medical Subject Headings – the indexing vocabulary for this database.
Librarians will talk about the “thesaurus” for a given database or about “controlled vocabulary.” 
Indexing allows all articles on the same subject to be retrieved when a search is done regardless of the specific terminology used by the authors. It’s all about co-location. 
What if, like Dan Quayle, you spell “potato” with an e  POTATOE and I spell potato without the e  POTATO. If my only choice for searching was standard key word searching, I’d have to search using both variations of the spelling in order to locate all the articles about potatoes. 
Or, more closely related to the subject at hand, what if I talk about the variations between British and American spelling? Colour v color; paediatrics v pediatrics
Indexing relieves the searcher from having to know all the spelling variations and terminology variations in order to retrieve all the articles on a given topic. 
And, in PubMed, looking at the MeSH terms assigned to a certain article can give the searcher clues on how to construct a better search.

## The Citation Format displays the MeSH terms associated with a given indexed citation

**Notes:**
Terms with * are the major MeSH terms associated with this article.
Viewing the Citation format may be informative – what MeSH terms would be useful in finding other articles like this one? 

## How can I find out if a given term is a MeSH term?

Use the MeSH Database

Click on the link from the blue sidebar

- Use the MeSH Database
- Click on the link from the blue sidebar

## PubMed’s MeSH Database:

**Notes:**
Type “cancer” into the search box.....

## The MeSH database allows searchers to look up terms and build searches.
These animated tutorials teach searchers how to use the MeSH database. They are available on the MeSH Database page. Each takes only minutes to view.

- These animated tutorials teach searchers how to use the MeSH database. They are available on the MeSH Database page. Each takes only minutes to view.

## Types of citation status tags in PubMed:

[PubMed – as supplied by publisher]

[PubMed – in process]

[PubMed – indexed for MEDLINE]

[PubMed – OLDMEDLINE]

[PubMed]

[PubMed – author manuscript in PMC]

- [PubMed – as supplied by publisher]
- [PubMed – in process]
- [PubMed – indexed for MEDLINE]
- [PubMed – OLDMEDLINE]
- [PubMed]
- [PubMed – author manuscript in PMC]

**Notes:**
(1) What’s in the database?
We talked about general content information before.
We know this is a bibliographic database – it is full of bibliographic citations.
It is important to understand that there is a distinction between citations in PubMed. Understanding this explains why people may appear to be doing the same search but get different results. 

NOTE: In 2007, the [PubMed – OLDMEDLINE] citations are beginning to disappear as those old citations have their indexing terms mapped to current MeSH terminology and their citation tags change, accordingly, to [PubMed – indexed for MEDLINE] 

## Why would searchers want to know the different types of citations in PubMed?

Only [PubMed – indexed for MEDLINE] citations have been indexed with MeSH terms. These citations will be retrieved by doing a MeSH term search.

All the other citation types have no indexing attached to them. These citations will not be found by a MeSH term search.

- Only [PubMed – indexed for MEDLINE] citations have been **indexed **with MeSH terms**. **These citations *will* be retrieved by doing a MeSH term search.
- All the other citation types have no indexing attached to them. These citations will *not* be found by a MeSH term search.

**Notes:**
NOTE: If I build a search from the MeSH database, using only MeSH (indexing) terms, the ONLY citations that will be retrieved are the [PubMed – indexed for MEDLINE] citations. None of the other citations will be retrieved.

## OK, so MeSH is the organizing principle behind PubMed

If I don’t know MeSH, can I still get good results searching PubMed?

Yes! 

Why?

- If I don’t know MeSH, can I still get good results searching PubMed?
- Yes!
- Why?

**Notes:**
The answer is “YES!” and we’ve seen that today. I can search for “smallpox” or “hot tub lung” and get decent results. 
Why is that?
Partially, it is because a lot of the terms we will just naturally choose to use as search terms ARE MeSH terms – we’ll be using MeSH without knowing we’re using it (heart, smallpox, lung, etc).
Mostly, however, it is due to the way PubMed works. 

## Automatic Term Mapping:

The 3 steps PubMed goes through every time a search is executed 

1. MeSH
2. Journal Title
3. Author

- The 3 steps PubMed goes through every time a search is executed
- 1. MeSH
- 2. Journal Title
- 3. Author

**Notes:**
Entrez = the search & retrieval system behind PubMed. It is very sophisticated
Automatic Term Mapping = the process PubMed goes through every time a search is executed

## The Details Tab

- Look at **Details** to see what PubMed did with your search terms

**Notes:**
The DETAILS box reveals how Entrez, the search and retrieval mechanism behind PubMed, has mapped your search. What terms were included and how? What terms were ignored and why? What, EXACTLY, did PubMed search? 

## 

Check the DETAILS tab!

- Check the DETAILS tab!

- PRACTICE SAFE
- SEARCHING

**Notes:**
Checking the Details tab is a good habit to get into. It will clearly show the exact terms used to search the database. It will also help searchers become a bit more familiar with MeSH terminology.

## Search measles and the Details box shows the actual search run by PubMed :

**Notes:**
Measles IS a MeSH term – and we see that in the PubMed Details screen in the Query Translation Box. Notice, also, that PubMed is doing a search for both the MeSH term and the text word. 
Why?
One of the reasons is to catch those newer citations – the “as supplied by publisher” and “in process” citations – and “OLDMEDLINE” citations. There are no MeSH terms associated with those citations. The implication of that? If only MeSH terms are searched, then Entrez is looking for a word in a field of the record named the MeSH field. “As supplied by publisher” citations, “in process citations”, and “OLDMEDLINE” citations have NO INFORMATION in the MeSH FIELDS. They cannot be retrieved by a MeSH term search.

## Automatic Term Mapping has mapped the word to its appropriate MeSH term(s)

Note that text words have also been added to the search. Why? To help retrieve those non-indexed citations mentioned earlier.

If a user types in a non-MeSH term as a search term, what happens?

- Note that text words have also been added to the search. Why? To help retrieve those non-indexed citations mentioned earlier.
- If a user types in a non-MeSH term as a search term, what happens?

## Here’s how “drooling” is mapped:

**Notes:**
PubMed finds the appropriate MeSH term here, too. Note, again, that the text word supplied by the searcher (the term typed into the search box) has also been added to the search. Why? To pick up the non-indexed citations. This may introduce a bit of noise into the search results but, without it, the non-indexed citations would be ignored. *Many of the non-indexed citations are the NEWEST information in the database.

## What’s up with this:

- [TIAB] =Title or Abstract
- Medline[sb] = the subset of all indexed citations
- Remember that there are citations in PubMed that are not indexed with MeSH terms. This is how PubMed works to improve retrieval from all those non-indexed citations. It is looking for the word “sialorrhea” in a title or an abstract in all those citations that do ***not*** have MeSH indexing.

**Notes:**
The “sialorrhea”[TIAB] means that PubMed is looking for this specific word in any article title (TI) or any abstract (AB). Medline[sb] is the subset of PubMed that is indexed with MeSH terms. The NOT indicates that PubMed is looking for the word “sialorrhea” in the article titles and abstracts of all the citations that do NOT have MeSH indexing. The remainder of this search strategy covers the indexed citations. Without the user having to think about it, PubMed automatically improves retrieval.

## Step 1: PubMed looks for a match with a MeSH term. If a match is found, PubMed uses that MeSH term and runs the search. 

If no MeSH match is found, Automatic Term Mapping moves to step 2: looking for a match with a journal title. If a match is found, PubMed uses that title and runs the search.

If no match is found with journal titles, it’s on to step 3: looking for a match with author names.

- If no MeSH match is found, Automatic Term Mapping moves to _step 2_: looking for a match with a **journal** **title**. If a match is found, PubMed uses that title and runs the search.
- If no match is found with journal titles, it’s on to _step 3_: looking for a match with **author** **names**.

**Notes:**
Automatic Term Mapping explained again.....

## Step 2: Searching for a journal title

**Notes:**
Type into the search box the complete (and accurate) journal title, or type in the official MEDLINE abbreviation for a journal and PubMed will map it correctly. All the results will be from the journal specified. 

## 

Check the DETAILS tab!

- Check the DETAILS tab!

- PRACTICE SAFE
- SEARCHING

**Notes:**
Checking the Details tab is a good habit to get into. It will clearly show the exact terms used to search the database. It will also help searchers become a bit more familiar with MeSH terminology.

## Since “New England Journal of Medicine” is not a MeSH term, PubMed finds no match. So, it moves to the 2nd step: journal titles. And there it finds a match!

**Notes:**
Notice that no text words are appended to the journal title search. Why? Because every citation in PubMed HAS a journal title field in the record. There is no need to try to “catch” citations that may not have this information in the record. 

## So, citations from journals may be retrieved by typing in the name of the journal or the MEDLINE abbreviation for the journal in the search box.

Find all the citations from the journal “Brain”

Your search?

- Find all the citations from the journal “Brain”
- Your search?

## Oops. What happened?

**Notes:**
OOPS. What happened?

## 

Check the DETAILS tab!

- Check the DETAILS tab!

- PRACTICE SAFE
- SEARCHING

**Notes:**
Check the Details tab!! See what happened – exactly – in this search.

## Brain maps to the MeSH term, “brain.” PubMed didn’t even get to the 2nd step!

**Notes:**
“Brain” IS a MeSH term. Remember the order of Automatic Term Mapping? Since Brain is a MeSH term, PubMed constructs the search using that MeSH term and stops. It thinks it’s done. So, what do we need to do to find all the citations from the journal “Brain?”

## Tell PubMed what field to search.

This turns off Automatic Term Mapping

- This turns **off** Automatic Term Mapping

**Notes:**
Direct PubMed to the field you want it to search by using square brackets to surround the field name. Here, we use “journal” so PubMed looks only in the journal name field. There are standard two letter abbreviations for the field names, too. Those are available in the PubMed Help document. For journal title, the two letter abbreviation is TA (for title abbreviation). NOTE: this can be a bit tricky. If you use [title], PubMed will look for citations with the word “brain” in the ARTICLE TITLE --- as title refers to the title of an article, not the name of a journal. 

## Now, PubMed is no longer mapping the term. It is simply searching the field it has been directed to search. 

**Notes:**
Using a field tag such as [journal] will turn OFF the automatic term mapping feature in PubMed. *NOTE: There are two other, easy way to retrieve all the citations from a given journal: (1) Use the Limits page or (2) Use the Single Citation Matcher.

## Step 3: Author Searching
Format for author names in PubMed:
			Last Name Initial(s) 

- Format for author names in PubMed:
- 			Last Name Initial(s)

- NOTE: there is no punctuation between last name and initials

**Notes:**
NOTE: No punctuation is used between the last name and the initial
So, a search for all the citations in PubMed written by Berryman D -- ?

## Slide 79

**Notes:**
PubMed recognizes the format and recognizes this as an author name. All the citations in the results set will have Berryman D as an author. (None of these references are me, by the way, nor are they anyone related to me.) 
What would happen if my last name was, say, Treat? Treat actually maps to the MeSH term “therapy” and so, once again, you’d have to direct PubMed to look in the author field by using the square brackets and the word Author. For example, treat [author]. NOTE: As of May 2005, it is possible to search for the first named author or to search the full name of an author (for citations from 2002 to the present). See PubMed’s Help for additional information.

## Now that we know about Automatic Term Mapping in PubMed, let’s see how it works with a multi-term search query

Let’s look at a search for head lice shampoo:

- Now that we know about Automatic Term Mapping in PubMed, let’s see how it works with a multi-term search query
- Let’s look at a search for **head lice shampoo**:

## Head lice shampoo is NOT a Mesh term, it’s not a journal title, and it’s not an author name.

**Head lice shampoo** is NOT a Mesh term, it’s not a journal title, and it’s not an author name.

- So, the term on the furthest right is chopped off and PubMed looks at the remaining words as a group. Here, **head lice**. That maps to a MeSH term, pediculus. We can see the same format we’ve seen in previous MeSH mapping.

- Now, PubMed looks at the term previously cut.

- PubMed handles all multiple word queries like this. It looks at the whole group as a single unit. If it can’t map it, it chops from the right and looks at the remaining words. And so it goes until it can either map or it runs out of words.

**Shampoo** is not a MeSH term, a journal title, or an author name. So, PubMed looks for this term in all fields.

**Notes:**
NOTE: If you’re working in PubMed and you want a record of the search you ran, this is the page to print.

## A note on Phrases:
PubMed does NOT do any proximity searching or adjacency searching
Using quotation marks will force PubMed to check its phrase table, but if the phrase does not appear on that phrase table, Automatic Term Mapping will be applied.
It is recommended that terms be searched with no quotation marks first.

- PubMed does NOT do any proximity searching or adjacency searching
- Using quotation marks will force PubMed to check its phrase table, but if the phrase does not appear on that phrase table, Automatic Term Mapping will be applied.
- It is recommended that terms be searched with _no_ quotation marks first.

**Notes:**
NOTE: If a phrase does not appear on the phrase table in PubMed, then PubMed will ignore the phrase and apply automatic term mapping. If this should happen, it does NOT meant that the phrase does not appear in any title or abstract in the database. It just means that the phrase is not on PubMed’s phrase table.

## Truncation
The asterisk * is the truncation symbol
Only end-of-word truncation is allowed in PubMed
Cardio* is allowed
Col*r is not allowed
*megaly is not allowed
Truncation turns off Automatic Term Mapping

- The asterisk * is the truncation symbol
- Only end-of-word truncation is allowed in PubMed
- Cardio* is allowed
- Col*r is not allowed
- *megaly is not allowed
- Truncation turns off Automatic Term Mapping

## Using truncation, search for all the variations of the term handwash

## 

Check the DETAILS tab!

- Check the DETAILS tab!

- PRACTICE SAFE
- SEARCHING

**Notes:**
Checking the Details tab to see what happens when an * is used in the search.

## Slide 86

**Notes:**
Using the Details tab, it is easy to see the variations of “handwash” that were used in the search. Note that Automatic Term Mapping has been turned OFF.

## Sometimes, a truncated search will prompt a cautionary message in PubMed: 

**Notes:**
The best thing to do in this situation is to follow the instructions in the pink banner and lengthen the root of the word.

## Additional details:

Boolean searching is allowed:
AND, OR, NOT
+ or – signs not allowed

Combining words MUST be in all CAPITAL letters 

Nesting – using parentheses – is allowed. PubMed processes searches from left to right unless ( ) are used.

- Boolean searching is allowed:
- AND, OR, NOT
- + or – signs *not* allowed
- Combining words MUST be in all **CAPITAL** letters
- Nesting – using parentheses – is allowed. PubMed processes searches from left to right *unless* ( ) are used.

**Notes:**
Note 1: Using nesting will change the search order in PubMed. As a rule, PubMed processes searches from left to right. If nesting is used, it’s just like algebra: PubMed will perform the search in parentheses first and then combine that set with the other search terms in a left to right order. This means:
Head injuries AND football OR boxing  is a different search than:
Head injuries AND (football OR boxing). Those two searches will retrieve different result sets. Very different.

Note 2: Remember that the default connector in PubMed is “AND.” People believe that if they type “and” in lower case into their search, PubMed is “reading” it even though it’s not in capital letters. No, PubMed is NOT reading the lower-case “and.” It is simply and automatically assuming that you mean “AND” and uses its default connector.

## So, we’ve talked a bit about the major details:
What’s the organizational structure of this database?
How does PubMed search?

What else is there?

- What’s the organizational structure of this database?
- How does PubMed search?
- What else is there?

## Searches may be constructed using the:

Search box: Type and Go. Highly recommended.

MeSH database: see animated tutorials on the MeSH database page.

History function

- Search box: Type and Go. Highly recommended.
- MeSH database: see animated tutorials on the MeSH database page.
- History function

**Notes:**
We’ve seen how to use the search box on the top of the PubMed screens. And we’ve seen that Automatic Term Mapping is a powerful tool.
The tutorials on the MeSH database page will teach you how to construct MeSH searches. Just remember that a search that consists only of MeSH terms will NOT retrieve the non-indexed citations. That can be OK. Just be aware of the implications of your chosen strategy.
The History function can be useful for constructing searches.

## History 
Keeps a record of searches performed
Rerun searches
Delete searches
View the Details for a selected search
Combine previous searches to make new searches

Access History by clicking on the History tab under the search screen

- Keeps a record of searches performed
- Rerun searches
- Delete searches
- View the Details for a selected search
- Combine previous searches to make new searches
- Access History by clicking on the History tab under the search screen

**Notes:**
Accessing History

## Slide 92

**Notes:**
History is keeping track of the searches I’ve done in this session. Notice that the search numbers may not be in order – or some may be missing. This is because: (a) searches may be deleted by the user; (b) if a search is done early in a session and repeated later in a session, that search will rise to the top of the list, but keep its original search number; or (c) searches done in the MeSH database or the Journals database will be numbered as if they were in this history, but they will reside in their own history tabs and not appear here.

## History remains until there are 8 hours of inactivity or until the searches are manually deleted from History.

The Clear History button will delete everything in History. 

- The **Clear History** button will delete *everything* in History.

**Notes:**
NOTE: 8 hours of inactivity means the same thing here as it does in the Clipboard. The History will remain until there are 8 hours of inactivity on the computer. 

## Each of the query numbers is hyperlinked. Click on the query number and a menu will appear:

## Combine searches using AND, OR, or NOT

Erase this specific search from History using Delete

Return to this search using Go

See the Details tab for this search using Details

This search can be saved in My NCBI

- Combine searches using **AND**, **OR**, or **NOT**
- Erase this specific search from History using **Delete**
- Return to this search using **Go**
- See the Details tab for this search using **Details**
- This search can be **saved** **in** **My NCBI**

## To find information about smallpox and bioterrorism

Click on the search number for smallpox, highlight AND

Click on the search number for bioterrorism, highlight AND

Click Go at the right side of the search box to run the search.

- Click on the search number for smallpox, highlight AND
- Click on the search number for bioterrorism, highlight AND
- Click Go at the right side of the search box to run the search.

**Notes:**
Constructing a search using History: use the option menu that appears when the search number is clicked OR just type the search numbers into the search box yourself. Remember that a # must precede a search number (or else PubMed will just look for all the occurrences of that number in the database). Also remember that connecting words (AND, OR, NOT) must be in caps.

## Some final thoughts on searching PubMed:

Related Articles
Single Citation Matcher
My NCBI

- Some final thoughts on searching PubMed:
- Related Articles
- Single Citation Matcher
- My NCBI

## Related Articles: Articles similar to the one you are viewing are displayed automatically  in AbstractPlus format:

**Related Articles**: Articles similar to the one you are viewing are displayed automatically  in AbstractPlus format:

**Notes:**
NOTE: This is the ONLY time in PubMed that search results are returned in relevancy ranked order.
On 6/19/2007, these related articles were displayed for the article titled “Drinking and flying.” NOTE: The related articles are displayed in Relevancy Ranked order. What does this mean for the average searcher? Well, if the top citation is nothing like you were hoping to find, then you probably don’t need to bother with the 2nd or 3rd or 4th. But, if citation #1 is exactly what you were looking for, then keep on browsing through the rest of the results. When the magic works, it really works. But, when the magic doesn’t work....don’t waste your time.

## Related Articles may also be retrieved via the Related Articles link on the Summary format:

- Related Articles may also be retrieved via the **Related Articles link** on the Summary format:

- Find one article you like, click **Related Articles** and PubMed will do a search for similar articles. Read about the algorithm for this related articles search in PubMed’s Help

## The Single Citation Matcher in PubMed

-      From the blue sidebar, click here

- Fill in one or more boxes and PubMed will search for citations that meet your specifications.

**Notes:**
As of May 2005, it is possible to limit author searches to the first named author. That’s why the checkbox for “Only as first author” appears in the Single Citation Matcher. See the Help in PubMed for additional information on this feature.

## My NCBI

This free service allows users to set up accounts and:
Customize their searching
Save search strategies and have PubMed automatically email them updated results
Save search results indefinitely
Turn on highlighting of search terms
And more...

- My NCBI
- This free service allows users to set up accounts and:
- Customize their searching
- Save search *strategies* and have PubMed automatically email them updated results
- Save search *results* indefinitely
- Turn on highlighting of search terms
- And more...

## Learn more about My NCBI

From the blue side bar in PubMed, click on Tutorials. Several “Quick Tours” are available for My NCBI

From the NER website, see the “Using My NCBI” presentation

- Learn more about My NCBI
- From the blue side bar in PubMed, click on Tutorials. Several “Quick Tours” are available for My NCBI
- From the NER website, see the “Using My NCBI” presentation

## Other capabilities of PubMed

Journals Database
Clinical Queries
Special Queries
LinkOut

- Journals Database
- Clinical Queries
- Special Queries
- LinkOut

## So, you want to learn more?

Overview
Tutorial
Help & FAQ
New/Noteworthy

- Overview
- Tutorial
- Help & FAQ
- New/Noteworthy

## Animated tutorials are on how to use the MeSH database and how to construct author and subject searches are available on this NLM website:
http://www.nlm.nih.gov/bsd/dist_edu.html

There is a PubMed manual available on the web:
http://www.nlm.nih.gov/pubs/web_based.html

Contact your regional medical library for information on free training:
http://nnlm.gov

- _[http://www.nlm.nih.gov/bsd/dist_edu.html](http://www.nlm.nih.gov/bsd/dist_edu.html)_
- There is a PubMed manual available on the web:
- _[http://www.nlm.nih.gov/pubs/web_based.html](http://www.nlm.nih.gov/pubs/web_based.html)_
- Contact your regional medical library for information on free training:
- _[http://](http://nnlm.gov/)__[nnlm.gov](http://nnlm.gov/)_

## Hmmm..... Better write a note to myself to check the Details tab in PubMed