Quick Guide to SearchingPubMed®

February 2009

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What’s in PubMed PubMed

Table of Contents

What’s in PubMed..........................................................................................................................................................3

Access to PubMed...........................................................................................................................................................3

PubMed’s Home Page.....................................................................................................................................................4

Building the Search.........................................................................................................................................................4Automatic Term Mapping (ATM)..............................................................................................................................5Details screen..............................................................................................................................................................5Searching with MeSH and the MeSH Database.........................................................................................................7Search by Field...........................................................................................................................................................9Limits .......................................................................................................................................................................12Truncation (finding all terms that begin with a given text string)............................................................................14Stopword List............................................................................................................................................................14Boolean Logical Operators.......................................................................................................................................14Nesting......................................................................................................................................................................14

Managing the Results....................................................................................................................................................15Display Options........................................................................................................................................................15Show….....................................................................................................................................................................15Sort by…...................................................................................................................................................................15Related Articles.........................................................................................................................................................16

Keeping the Results......................................................................................................................................................17Send to Menu............................................................................................................................................................17History.......................................................................................................................................................................18

PubMed Services..........................................................................................................................................................19Finding a specific ciation..........................................................................................................................................19Journals Database......................................................................................................................................................20Clinical Queries........................................................................................................................................................21

Getting the Articles.......................................................................................................................................................22LinkOut.....................................................................................................................................................................22Ordering Articles / Interlibrary Loan........................................................................................................................24

Additional Tools...........................................................................................................................................................24MyNCBI...................................................................................................................................................................24Tutorials....................................................................................................................................................................25

PubMed currently includes over 18 million bibliographic citations, of which about 17 million are Medline records.

While there are no full-text articles in the PubMed database itself, there are links to the full-text of articles at participating publishers’ Web sites.

PubMed includes such diverse topics as microbiology, delivery of health care, nutrition, pharmacology and environmental health.

Coverage is worldwide, but most records (about 90%) are from English-language sources or have English abstracts.

Approximately 79% of the citations are included with the published abstract.

Access PubMed

PubMed can be searched from its URL “alias” pubmed.gov, but to take advantage of the LinkOut feature (described later), you must access from

http://www.ncbi.nlm.nih.gov/sites/entrez?holding=pauwkalib_fftThis link is available on the PIC channel and the Farley Library channel.

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PubMed’s Home Page

DatabaseSelection box

PubMed Home Page sidebar, with links to help, documentation, tools and related resources

Links to search help

Building the SearchThere are 3 general ways of searching PubMed:

Searching with keywords / or text words Searching through the subject headings (MeSH) Searching in field(s)

Basic/Default Searching (Keywords / Text Words)

Search: Find citations to articles about having a rash and a fever.

Entering Search Terms Enter significant terms in the query box (e.g., rash fever). Click on the Go button. View Details to check PubMed’s translation (more about this later in the workbook) Use the Clear button to erase the contents of the query box.

Automatic Term Mapping (ATM)

Details screenYou can see how PubMed processes your search by clicking on the Details tab located below the search box.

Translations are shown in the grey box towards the bottom of the screen.

“Unqualified” or “untagged” terms (terms that are entered without telling PubMed what kind of term they are) that are entered in the query box are matched against:

Subjects, using theo MeSH (Medical Subject Headings) Translation Table (headings, subheadings,

synonyms) Journals, using the

o Journals Translation Table Authors and Investigators, using the

You can insert your cursor in the translation box and edit it if you wish.

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If no match is found?

PubMed breaks apart the phrase and repeats the automatic term mapping process until a match is found.

Terms that don’t make a match will be searched in “All Fields.” Individual terms will be combined (ANDed) together.

PubMed breaks apart a long phrase from right to left.

PubMed has a “citation sensor” that enables it to “sense” when you are looking for a specific article instead of many articles on a topic. For example, if the terms you enter appear to be a name and a journal title and a date, it will try to match this with citations in PubMed. If your search invokes the Citation Sensor, you will see a yellow area above the default retrieval with links to one or more citations for your consideration.

Medical Subject Headings (MeSH® Vocabulary) Searching

Another, efficient method of searching is to use the controlled vocabulary MeSH.

Click on MeSH Database on the blue sidebar on the PubMed home page or select MeSH from the database selection box on the home page and click Go.

Type in your term and the results are displayed in the Summary format for MeSH. If there is an exact match for the term searched, this term will display first in the retrieval. Additional terms are listed in relevance-ranked order based on the search term entered.

To search using the term, put a check in the box in front of it and change the Sent to drop down menu to “Search box with AND.”

You may want to search using a specific aspect of a term; e.g., effects of drugs on the knee. Click on the hyperlinked text for the term and you will see the full record and the subheadings that can be applied to it, including drug effects. If more than one aspect of a term is needed, check additional subheadings.

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Put a check in the box in front of “effects” and change the drop down box to Send to Search Box with AND.

Continue searching for appropriate terms/subheadings in the MeSH database and adding them to the search box. When all terms have been entered hit the Search PubMed button. This will take you out of the MeSH database back into the PubMed search mode.

Another advantage to searching via he MeSH database is the ability to Restrict to Major Topic headings. Under the subheadings, you will see a box that you can check to limit your search to citations where the heading (and/or subheadings) is the major focus of the article. When you Send the term to the Search Box with AND, it will now appear with [MAJR] instead of the normal [Mesh].

When you enter a MeSH heading as a search term, PubMed automatically Explodes it. This means that you retrieve citations for the more specific terms that are indented below your term in the MeSH tree structure. PubMed automatically explodes subheadings as well. There are various groups or families of subheadings that are related. For example, if you search using the subheading adverse effects, you will also retrieve articles indexed with poisoning and toxicity. If you search with therapy, you will automatically get all kinds of therapies such as diet therapy, drug therapy, nursing, prevention & control, radiotherapy, rehabilitation, surgery, etc. Usually you will want to explode MeSH terms and their subheadings, but searching in the MeSH database gives you the option to turn off the explosion by checking the Do Not Explode This Term box below the subheadings.

Field Searching

One final way to search is to do Field Searching. The default in PubMed is to look for your search terms in all fields of an article’s record (key-word or free-text searching). But it is possible to perform a more directed search by telling the database where to search for your terms. This is done by qualifying the term with the Field Tag or abbreviation. You can specify these fields in two ways:

1. Specify fields in the Search Box by entering the field qualifiers or “tags” in square brackets [ ] immediately following the terms to which they apply.

Some commonly searched fields are title word [ti], author [au], journal title [ta], language [la], publication type [pt]. You can find a full list of the search fields and their tags in the PubMed Help:

http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=helppubmed.section.pubmedhelp.Search_Field_Descrip

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2. Use the Advanced Search screen, and select a field from the dropdown menu.

IndexThe Index provides an alternative way to limit your search to specific fields. To use, click onPreview/Index found below the Search Box or go to the Advanced search screen and scroll down the page to Index of Fields and Field Values. Change the value in the All Fields drop down menu to the field you want and enter your term in the box. Click on Index. You will see an alphabetical list of terms used in the database along with a number indicating how many citations contain that word/phrase. Scroll down the list and select the term(s) you are interested in by clicking on the term(s). If you want more than one, hold down the CTRL key; they will be ORed together.) Click on the button for the Boolean operator to tell PubMed how to add the word(s) to your search. Continue viewing, selecting and adding search terms until your strategy is complete. Then click the Search button either at the top of the screen of in the search area.

In this example, click on the AND button which adds your terms to the Advanced Search top query box. Then click the Search button to run the search:

*Best Practice*Searching with MeSH rather than keywords offers some advantages: 1. You will retrieve articles that are more relevant. Indexers weigh the relative importance of a

term to the whole article.2. You are more likely to retrieve all instances of a subject, no matter what terms are used. 3. If an articles does not have your term(s) in the title, and it does not have an abstract, you will

still retrieve it because it is assigned the MeSH term after an indexer has read the entire article and determined that the article is about your topic.

4. You can make your search very specific by adding relevant subheadings to the MeSH term and/or making the heading a Major Topic of the article.

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MeSH headings, however, are not without limitations. 1. If a topic is new, there may not yet be an established MeSH term for it. 2. Although not new, some topic may not have been assigned a MeSH heading (e.g., nicotine

replacement, Heimlich maneuver, acute chest syndrome).3. Indexers are human; they may be inconsistent, miss a concept, or not index a concept correctly.4. Not every concept in an article can get a thesaurus term (e.g. increased, compared)5. There may be a time lag of up to three months before an article is indexed for Medline (i.e., you

may miss the most recent research).6. Very old items still lack MeSH.

Searching with keywords (text words) also has some advantages:1. You can retrieve terms that are new, novel or have not been assigned a MeSH heading.2. You can use them if you can’t find the right term(s) in MeSH.3. In PubMed, keywords automatically map to the MeSH terms.4. You can be more precise that with some MeSH headings. (e.g., MeSH has terms for some

population groups such as Asian Americans, but if you want to look for information on the Hmong, you will need to search this as a keyword.)

Keyword searching also has disadvantages:1. You may get too many hits, lots of which may barely mention your term(s). All words are

“weighted” the same.2. Too many hits to read through is an inefficient use of your time.3. You may get “false drops” (e.g., you search for AIDS and get articles on hearing aids, nursing

aids and the disease AIDS).4. Some words do not map successfully (e.g., EBM should lead to the MeSH term “evidence-

based medicine,” but it does not).

So, which should you use? You need to develop skills in searching MeSH as this often is the best, most efficient way to locate relevant information. This can work perfectly if you know you will get an acceptable amount of retrieval and/or are not looking for very specific or very new information. However, sometimes, for completeness, both MeSH terms and keywords should be used in your search strategy. Using both offers a safety net so you won’t miss good or important articles.

Refining your search strategy

Limits Click on the Limits Tab under the search box

PubMed allows you to apply a number of filters to your search. This gives you results that are more specific and relevant.

Click on the Limits tab under the Search box.

You can limit your search by age group, sex, human/animal studies, language, publication type, dates and other parameters. It is NOT a good practice to “Limit to Full text” at the top. This function does NOT recognize our local library holdings, so using it will eliminate some full-text articles that are available to Wilkes users.

Click he appropriate box(es) in one or more of the limits. You may check multiple boxes in one type of limit. Click on search to perform limit the results you already have for a search or to “set” the limits for a search you are about to perform.

Once you have set limits, the ones in effect will appear in a yellow bar above the Display button on all screens.

Limits are in effect until you remove them. To turn off all limits before you run another search, click the Clear All button at the bottom of the Limits page or click in the box next to the Limits tab on a Search screen.

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PubMed Search Tips

TruncationThe truncation feature provides the ability to for all terms that begin with a given string of letters. For example, if you are interested in subjects expressed by words such as economics, economical, economy, etc., you would enter econom*. PubMed will search all fields for words beginning with that string. Note that PubMed will search only the first 150 variations.

StopwordsPubMed has a list of commonly found words that, if entered will be ignored during the search. These stopwords are omitted because they could potentially return every document in the database! Some examples are a, and, the, was, made, km, etc.

Boolean OperatorsIf you do not include Boolean operators in your search, PubMed will automatically use AND between terms. E.g, “vitamin c common cold” is translated as “vitamin c AND common cold.” Enter Boolean operators in UPPERCASE characters to combine or exclude search terms:

AND retrieves results that include all the search terms. OR retrieves results that include at least one of the search terms. NOT excludes the retrieval of terms from your search.

NestingWhen using multiple Boolean operators in PubMed, they are processed left to right.

Example: salmonella AND hamburger OR eggsThis will retrieve records that include both terms salmonella AND hamburger as well as all records with the term eggs, whether or not they contain the other two terms.

To change the order in which terms are processed, enclose the terms(s) in parentheses. The terms inside the set of parentheses will be processed as a unit and then incorporated into the overall strategy. This is called nesting.

Example: salmonella AND (hamburger OR eggs)This will retrieve records that contain the term salmonella, as well as one or both of the terms hamburger OR eggs.

Working with Search Results

Search Results Screen and Display OptionsPubMed displays your search results in Summary format with 20 citations on a page. The drop-down menus that appear above your search results allow you to change the type of display, the number of citations shown and what to “do” with your results. Use the Page button (or Next or Previous) to move to a different page of the results.

The default is to show All search results, with the number of citations retrieved. PubMed also automatically gathers, under a different tab, the number of Review articles found for your search.

Search results initially display in a summary format (basic citation with no abstracts or links).

o The Abstract view will show icons for Linking out to full-text articles.o To display the abstract for a journal article, click the title link for each citation.

Some citations do not have abstracts and will include the note “No abstract available.”

o To see the Abstract view of all citations, change the Display to Abstract. o If you do not select any citations by clicking in the checkboxes to the left of the

authors’ names, all the citations will be displayed in the selected format. The default is to Show 20 citations per page. If there are more than 20 citations, they will be

displayed on subsequent pages. Other options are 5, 10, 50, 100, 200, 500. Sort is by “last relevant article into the database is first displayed.” Other options are by

author, publication date, journal title or article title.

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Related Articles

Under each citation there will be a hyperlink to Related Articles which PubMed finds by comparing words from the Title and Abstract as well as MeSH headings. Related Articles are displayed on a new screen in rank order from most to least relevant, with the citation you link from displayed first.

Notice of Full TextSome citations will also indicate that the full-text of the article is available at the journal’s home site or in PubMed Central, a digital archive. Click on the link to access the free article.

“Keeping” Your Search ResultsOnce you review your results and find “good” articles, you’ll need to “do” something to keep them. The Clipboard provides a temporary place to store the citations you have selected from one or more searches. PubMed gives you a number of options in the Send to drop down menu. The most logical one to begin with is the Clipboard option. At the end of your search session,click on the Clipboard tab and use the Send to options from that page to move your citations to a more permanent place.

Send to MenuThe Send to pull-down menu allows you to manage your search results in various ways.

Use Clipboard to collect selected citations from one search or several searches that you may want to print, save, or order. o The maximum number of items that can be placed in the Clipboard is 500.o To place an item in the Clipboard, click on the box to the left of the citation and select

Clipboard from the Send to menu. o Once you have added a citation to the Clipboard, the item number color will change and the

Clipboard link displays to the right of the search box.o To see the contents of the Clipboard, click on the Clipboard Tab.o Remove citations by putting a check in the box and clicking on Clip Remove.

Clipboard Tips: If you send items to the Clipboard without selecting citations using the check-box,

PubMed will add up to 500 citations from your retrieval to the clipboard. The maximum number of items that can be added to the clipboard is 500. The clipboard will be lost after 8 hours of inactivity.

Use Text to redisplay citations omitting the graphics components. o Text will display either selected citations, or if no citations are selected, all the citations on

the page (that is the displayed screen only, not necessarily all the citations retrieved by the search).

o Before using the Text option, consider changing the display format and the number of items displayed on each page.

Use File to save and send your entire set of search results to a file. o Use the Display pull-down menu to select the desired format, then select File to save the

results in the format selected.

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o To mark selected citations to save and send to a file, click on the check-box to the left of the item number as you go through each page of your retrieval. After you have finished selecting citations, choose a display format. Then select File from the Send to menu.

o Send to File displays the citations with Author names on top followed by title.

Use Printer to print search results. o Choose the items you want to print and the display format before using the Send to Printer

option. If you do not make any selections, the "print page" that is created will include the items in the display format currently shown on the search results screen.

o The Send to Printer option creates a printer-friendly page. Click the Print this page button.

Use Email to send your search results to yourself or anyone else you desire. o Choose the format type you would like (ie. summary, abstract, etc.) and select how you want the

citations sorted. Choose the file type you would like the list to be save as (Text or HTML).o Choose how many of the citations you would like to have sent.o Enter the email address to which you are sending the list. o Enter a message along with the E-mail, if desired.

E-mail Tips: You may E-mail up to 500 items. The HTML option allows the PubMed e-mail messages to display as a results page with

hyperlinks to Related Articles, etc. The recipient's e-mail service must be set for HTML view to allow for proper display.

Ordering Articles

PubMed has a feature for professionals who are affiliated with a health sciences library to order articles from their searches. This is not a feature that you should use. If you need articles, send them to Text, copy and paste the citations into a e-mail and send them to barbara.nanstiel@wilkes.edu. You may also use the e-mail function to send them, but MAKE SURE YOU ENTER YOUR NAME IN THE MESSAGE BOX; if you do not, they are sent from nobody @ncbi.nlm.nih.gov (No kidding!) and there is no way to find out who the requester is.

Search HistoryAs you perform each search in PubMed your search history builds up. To view your search history click on the History link below the search box. The history page shows all the searches that have been run along with any restrictions or limits that have been applied. Each search will be given a number along with the number of items found in each search. To view the results from any search click on the number.

The search history can be useful feature for building your search strategy and can be used to combine searches or add additional terms to existing searches. Combine searches by entering the search number (using the number sign #) and making sure to capitalize the Boolean operators (e.g., #17 AND #21).

OR you can click on the search number, choose the Boolean operator that appears in the Options drop down box, and continue adding appropriate search numbers. When you are done, click Go to perform the search.

History Tips: The search history displays the searches in the order of searching; however the numbering

may not be continuous as numbers are applied to other processes such as displaying results in different formats.

Up to 100 searches can be held in the history; once this limit is reached the oldest search is deleted and the most current added to the list.

A search history will be lost after 8 hours of inactivity in the database. To use the search history feature in PubMed your web browser must be enabled to accept

cookies. Clearing the search history will remove all the searches.

PubMed ServicesIn addition to the link for the MeSH database, you will find additional tools and services on the blue Sidebar.

Single Citation MatcherIn addition to the Citation Sensor that helps you find a specific article, you can use the Single Citation Matcher which is a fill-in-the blank kind of form that allows you to enter all or part of the information about an article. This is especially useful if you need to verify a citation. Enter as much information as you have (e.g., journal name, volume and first page). If your information is not enough to identify a unique article (e.g., you have the journal name, author and some words from the title), you may be presented with a number of possible citations.

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Journals Database

The PubMed Journals database allows you to look up information about a PubMed journal and/or to search for articles in that title. You can search for a journal using the journal’s full title, the PubMed abbreviation, or its International Standard Serial Number (ISSN).

Enter your search term(s) and hit enter or click on Go. If you search with only one or a few words, you will see a list of all possible titles. If you search with the full title or PubMed abbreviation, you will usually see one or a few (e.g., J Cardiol will retrieve Journal of Cardiology, which you may have meant, as well as American Journal of Cardiology, Journal of the American College of Cardiology, etc.). To see the full record, click on the title.

Retrieval display order is alphabetical, except if the term has an exact match which will display first.

Note that the Title Abbreviation is the information you should use for citing an article in the Vancouver format.

Click on the Links and then on PubMed to search for all citation in the journal in the PubMed database.

Clinical Queries PubMed has specialized search queries that are intended for clinicians. These built-in search filters limit retrieval to articles that report research done with specific methodologies.

If you choose to search by Clinical Study category, type your search term(s) in the box provided, and then choose the filter category: etiology, diagnosis, therapy or prognosis. You may also select the emphasis: Sensitivity (most relevant articles but probably some less relevant ones) or Specificity (mostly relevant articles but possibly missing a few).

If you choose to search for Systematic Reviews, you will retrieve systematic reviews and meta-analyses for your search topic. Enter your subject and hit Enter or Go.

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Medical Genetics SearchesChoose Medical Genetics Searches for various topics in medical genetics. Enter your search term(s) and topic of interest and hit Enter or Go.

Getting the ArticlesGetting the Articles PubMed does not include copies of journal articles. However, PubMed does offer links to the full text of journal articles when links are available. Access to some articles will be free. Access to others will require that you register, subscribe to the journal, or pay a fee in order to view the full-text of an article. .

LinkOut Links to full text resources from PubMed are available through a service called LinkOut. When you click on LinkOut icons or links in PubMed, you leave PubMed and are directed to

the full text at an external site.

Look for icon links to full text resources on the Abstract, AbstractPlus or Citation display formats.

The icon links to full-text from the AbstractPlusformat.

Links to Publiserh and to PubMed Central.

Only FREE if this word appears on the icon.

Below the abstract, you may see an icon that is only visible to members of the Wilkes community. There are two such icons and one or both may be shown:

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?holding=pauwkalib

If Wilkes owns a title in paper format, the abstract display will include a yellow icon with the Wilkes logo and the words “Print Journal.” Some of these may be housed in the PIC; others in the Farley Library and you can visit either library to get the journal. If we have electronic access to a journal, there will be a blue icon with the logo and the words “Fulltext Journal.” You will simply click on this icon to gain access to the journal article. Remember that PubMed itself is not full text, so you will be taken “out” of the database, perhaps to the publisher’s Web site or perhaps to another database like EbscoHost. If you are taken to EbscoHost, there is a possibility that you may not access the article. Some publishers impose what is called an “embargo” on the latest issues of a journal; e.g., Headache, Full Text: 01/01/2000 to present (with a 12 Month delay).

Remember, in order for the LinkOut function to display Wilkes-owned materials, you must search PubMed through the PIC or Library links on the Wilkes Portal (i.e., at the the following address):

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?holding=pauwkalib

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Ordering Articles Wilkes Doesn’t HaveIf you need an article and there is no LinkOut icon, you can still get access to it through interlibrary loan. You may notice that, in the Send to drop-down menu, there is an option to “Order” articles.

DO NOT use this feature. (This is meant for health care professionals who are not affiliated with a medical library, but who have set up formal arrangements to order documents through a system called Loansome Doc. You do not need to set up a Loansome Doc account.)

You can either fill out an interlibrary loan request form from the library’s Web site (Farley or PIC) or copy and paste the citation (in text form and including the PMIC) into an e-mail and mail it to barbara.nanstiel@wilkes.edu.

Do It Yourself!This document is meant as a handy guide to searching PubMed and, as such, does not cover all its many features. Some you may want to investigate on your own.

My NCBIMy NCBI is your personal space on the National Library of Medicine computer system. It allows you to

Save search strategies that are run automatically on a regular basis. PubMed search results are then e-mailed to you.

Save search strategies to run at a later date to retrieve information added to PubMEd after you last ran the search.

Select filtering options to customize and group search results Apply User Preferences including highlights search terms and changing the single citation

display format.

Tutorials

If you have any questions or need more in-depth information about PubMed, MeSH, or any other features, click on the Help / FAQs or Tutorial links on the bluesidebar of the PubMed home page or go to

http://www.nlm.nih.gov/bsd/disted/pubmed.html

Tutorials

Finally, the last tip. This is the place to go if you have any questions or need more in depth information about PubMed, MeSH, or any of the features I’ve mentioned here. There’s lots to discover, so happy searching—and get back to the bench!

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