Tapping the Well – Using PubMed

There is much medical information can do to enhance your practice of law. Whether you are a personal injury attorney, a criminal defense attorney, or practice in the area of products liability you will often have a need to research issues that are discussed in the medical literature.

You do not have to be a professional librarian to find the information you are seeking. This article will give you a brief outline of how to do a simple search on PubMed as well as explain some of this database’s special features.

PubMed was developed by the National Center for Biotechnology Information at the National Library of Medicine, located at the National Institutes of Health. It was developed in conjunction with publishers of biomedical literature as a search tool for accessing literature citations and linking to full-text journals at Web sites of participating publishers.

Publishers participating in PubMed electronically supply the National Library of Medicine with their citations prior to or at the time of publication. If the publisher has a Web site that offers full text of its journals, PubMed provides links to that site. PubMed is updated weekly.

PubMed is free to anyone with Internet access and provides access to two main databases, MEDLINE and PreMEDLINE. MEDLINE is the National Library of Medicine’s bibliographic database covering the fields of medicine, nursing, dentistry, veterinary medicine, the health caresystem, and the preclinical sciences. The file contains approximately nine million records dating back to 1966, and covers bibliographic citations and author abstracts from approximately 3,900 current biomedical journals. PreMEDLINE provides citation and abstracts before the citation is indexed with MeSH headings. These records are added daily to PreMEDLINE and appear in PubMed with the tag: [Medline record in progress].

Basic Search Strategy

Pick a search topic, for example: Is chickenpox vaccination harmful to children? First divide the topic into concepts, then find keywords or subject headings (MeSH) to represent these concepts. Finally combine concepts with the Boolean Operators AND, OR, or NOT. The Boolean Operators must be capitalized in a search. These operators are used when searching for more than one concept or search statement

Example: “vaccination OR vaccine” searches for records containing either term (OR) and will retrieve a greater number of records than using each term separately.

Example: “chickenpox AND vaccination” searches for records containing both terms (AND) and will retrieve a fewer number of records than using each term separately

Example: “vaccination NOT rubella” eliminates terms in one search set from a previous set (NOT) and will retrieve fewer records than using the first term separately.

If you use two or more Boolean Operators (AND, OR, NOT) in one search statement, the one on the left is processed first.

Example: “chickenpox AND vaccine OR vaccination” would retrieve articles that have both chickenpox and vaccine and it would also retrieve all articles on vaccination (pneumonia, measles, etc)

To change the meaning use parentheses.

Example: “chickenpox AND (vaccine OR vaccination)” this would retrieve articles that have both chickenpox and either vaccine or vaccination, which would be fewer records than the example above.

You can use Truncation to find the first 150 variations of the root word. Truncation uses the symbol * as a substitute for zero or more characters.

Example: risk* retrieves risk, risks, risk-taking. However the term infection* would not get infection control because there is a space after the word infection.

Another way to search is by using logical terms. To be sure the phrase is recognized use ” “

Example: “Vaccination complications”

Simple Search Strategy Techniques
Enter your search term(s) in the “Search Box” (see below) The terms are matched against a MeSH translation table, Journals translation table, a phrase list and an author index. Use the “Enter” key or click on “Go” to get a display of your results as brief citations in batches of 20 by default. To change the number of items displayed, select a higher number from the pull down menu “Show”. To change the Display format, select from the pull-down menu next to Display.

To search by an author’s name enter the name in the format of last name plus initials (no punctuation)

Example: smith ja

PubMed automatically truncates on the author’s name to account for varying initials and designations such as Jr. or 2nd. This prevents retrieval by smith a, smith b, etc. A name entered with this format will search in the author field. If only the author’s last name is entered, PubMed will search that name in All Fields, not just the Author field. An exception to this is when the author name is found in the MeSH (National Library of Medicine’s Medical Subject Headings) Translation table (e.g., Yang will search as Yin-Yang [MeSH] or Yang [Text Word].)

Note: Use double quotes around the surname and first initial qualified with the author search field tag [au] to turn off the automatic truncation and retrieve based on only the single first initial.

Example: “smith j” [au]

Journal Titles may be entered in full:

As valid MEDLINE abbreviations:

Or as ISSN numbers (a standard number for journals), e.g., 1059-1524:

After you enter your search, your results will be displayed. The display format may be changed by selecting form the pull down menu by the “display” button.

Your Citations can be displayed in any of the following formats.

Summary – This format may include: Author name(s), Title, Journal Source, Record Status (for in-process or publisher-supplied citations), indication if article is non-English, Publication Type for review or retracted publication, “No abstract available” notation, and PubMed and MEDLINE Unique Identifiers.

Brief – Author name, first 10 characters of the title, and the PMID.

Abstract – This format may include: Journal Source, record status for in-process or publisher-supplied citations, Title, indication if article is non-English, Authors, Author Affiliation, Abstract (if present), Publication Types (except for the Journal Article publication type), Personal Name as Subject, Erratum, Retraction,Comments, and PubMed and MEDLINE Unique Identifiers.

Citation – This format may include: Journal Source, record status for in-process or publisher supplied citations, Title, indication if article is non-English, Authors, Author Affiliation, Abstract (if present), Publication Types (except for the Journal Article publication type), Erratum, Retraction, Comments, MeSH Terms, Personal Name as Subject, Chemical Substances, SI-databank accession numbers, Grant numbers, and PubMed and MEDLINE Unique Identifiers.

Advanced Searching Techniques

Using the “Limits” feature:

Click Limits from the Features bar to limit your search to a specific age group, gender, or human or animal studies. Limits also allows you to restrict to articles published in a specific language, and to specific types of articles such as review articles. You can limit by either Entrez or Publication Date. And lastly, you may limit your retrieval to a specific subset of citations within PubMed, such as AIDS-related citations or in-process citations, i.e., PreMEDLINE.

If you select a limit and either run a search or move to another screen, a check will appear in a box next to Limits on the Features bar to indicate that limits have been selected. If you then run a search, the limits in effect will appear in the yellow bar above the Display button. To turn off the limits before you run your next search, click on the box to remove the check (see below)

You may use this feature to limit your retrieval to only citations that contain an abstract by using the check box next to only items with abstracts. Citations to articles published prior to 1975 do not include abstracts.

All citations in PubMed are for journal articles. However, you may limit your retrieval based on the type of material the article represents (e.g., Clinical Trials or Review articles). The Publication Types pull-down menu contains a list of frequently searched publication types. If you do not make a selection, PubMed will not restrict to any particular publication type.

PubMed indexes journals published in approximately forty languages. The Languages pull-down menu contains a list of frequently searched languages. If you do not select a language, PubMed will not limit your retrieval by language.

PubMed contains citations published back to 1966 and new citations are added daily. The Entrez Date is the date the citation was added to PubMed. The Publication Date is the date the article was published. When PubMed displays your search results, the citations are displayed in descending Entrez Date order i.e., last in, first out. If you do not specify a date range, PubMed searches for citations to articles back to 1966.

Use the Entrez Date pull-down menu to limit your search back in time from 30 days to 10 years. The Publication Date pull-down menu toggles between Publication Date and Entrez Date.

Using the Citation Matcher

The Citation Matcher options allow you to find the citation or the PubMed ID of any article in the PubMed database using bibliographic information Use the Single Citation Matcher to look for a single citation. This feature is a fill-in-the-blank form that lets you enter journal citation information to locate a single citation, or items from a particular volume or issue of a journal.

The Batch Citation Matcher allows you to retrieve the PubMed IDs for many articles all at once. This feature requires that you enter the bibliographic information (journal, volume, page, etc.) in a specific format.

If you wish to match citations in bulk by e-mail, send email to [email protected] For instructions, send an message which is empty except for the word “help” in the subject or body.

A list of all journals that are included in the PubMed database is available by FTP in the GNU Zip, Uncompressed, UNIX Compress, or PKZIP format.

Using the “Preview/Index” Feature

The Preview/Index feature is used to preview the number of search results before displaying the citations, refine search strategies by adding one or more terms one at a time, add terms to a strategy from specific search fields, view and select terms from the Index to develop search strategies.

To preview the number of results before displaying the citations, type your term(s) in the query box and click Preview. Preview displays the number of citations in your search results. To refine your search strategy, add another term to the existing term(s) in the query box and click Preview. The additional terms will be combined with the existing terms, and the new search with the new number of citations will display. Continue adding terms until your strategy is complete. To display your results, click on the result number (hypertext) in the Preview display.

You can also use Index to select from a list of terms within a search field. Select a search field from the All Fields pull-down menu, enter a term in the box, and click Index. PubMed displays an alphabetic list of terms in the Index for the selected search field. The number of citations in PubMed that contain the term appears in parentheses to the right of the term. You can scroll up or down the list, or click Up or Down to move along in the Index.

Highlight a term by clicking on it. Then click the appropriate operator, AND, OR, NOT. The selected term will be added to the query box. To OR together multiple terms from an Index display and then add (or AND) them to your search, click on each term while holding down the Ctrl-key(PC) or the Command-key(Mac). When all the terms you want are highlighted, click the connector AND to add the terms to the query.

You may then continue to add additional terms from other search fields. Once your strategy is complete, click Preview to see the number of results, or click Go to display the citations.

For example, to see the MeSH Terms beginning with “chickenpox,” select MeSH Terms from the All Fields pull-down menu, enter the term, chickenpox, in the text box, and click Index. Scroll down in the Index box, highlight the MeSH Term “chickenpox vaccine,” and click AND. “Chickenpox vaccine” [MeSH Terms] will be added to the query box.

Using the Related PubMed Articles Link Each citation in PubMed has a link that will retrieve a pre-calculated set of PubMed citations that are closely related to the selected article. Click on Related Articles to the right of each citation to display the related set of articles. PubMed creates this set by comparing words from the title, abstract, and MeSH terms using a powerful word-weighted algorithm. Citations are displayed in rank order from most to least relevant with the linked from citation displayed first.

Using the History Feature

PubMed will hold all your search strategies and results in the History. You can see your search History by clicking on History from the Features bar. History is only available after you run your first search. History lists and numbers your searches in the order in which you run them. The History displays the search number, your search query, the time of search, and the number of citations in your results. To view the results from a search, click on the number of results.

You can combine searches (see below) or add additional terms to an existing search by using the pound sign (#) before the search number, e.g., #2 AND #6, or #3 AND (drug therapy OR diet therapy). Once you have entered a revised search strategy in the query box, click Go to view the search results. Click Clear History to remove all searches from the History screen and the Preview/Index screen.

The maximum number of queries held in History is 100. Once the maximum number is reached, PubMed will remove the oldest search from the History to add the most current search. .The Search History will be lost after one hour of inactivity on PubMed or any of the other Entrez databases. The Clear History button in History will also clear the Preview/Index history information.

PubMed will move a search statement number to the top of the History if the new search is the same as a previous search. A separate Search History will be kept for each of the Entrez databases although the search statement numbers will be assigned sequentially for all databases .PubMed uses cookies to keep a history of your searches. In order for you to use this feature your web browser must be set to accept cookies .Citations in the Clipboard are represented by the search number #0 which may be used in Boolean search statements. For example, to limit the citations you have collected in the Clipboard to English language citations use the following search: #0 AND english [la]. This does not affect or replace the Clipboard contents.

Saving your search results

To save the entire set of search results use the pull-down menu to select the desired format and then click Save. To save specific citations, click on the check box to the left of each citation (you may move to other pages in the retrieval), when you have finished making your selections, click Save.

The Save option (from the search results page) will save the entire set of search results even if only the first batch of citations are displayed. The maximum number of items that can be saved is 5000. If you try to save a file with more than 5000 citations, PubMed will display a message that instructs you to refine your search. The default file name is query.fcgi. Consider changing the name to something more meaningful to you, and the .fcgi extension to .txt, if you wish to open the file in a text editor or word processing package.

To save citations in HTML format use the Save as… function of your browser. Change the file extension to html. You will only save the citations displayed on the screen so you may wish to use the Show function and Text button to adjust your display as needed.

Printing your search results

Use the print function of your Web browser to print all the information and citations displayed on your web page. Before printing, consider using Show to increase the number of documents per page so that the total number of documents is displayed on one page (maximum: 500 per page). You can only print the citations from the displayed page. You may also wish to display your citations as Text to strip the sidebar menu and toolbars prior to printing your results.


The Clipboard gives you a place to collect selected citations from one search or several searches. You may then want to use the print, save, or order buttons. The maximum number of items that can be placed in the Clipboard is 500. Once you have added items to the Clipboard, you can click on Clipboard from the Features bar to view your selections. Citations in Clipboard are displayed in the order they were added.

Saving from the Clipboard

Citations are initially displayed in the summary format in descending Entrez date order. You can select all or individual citations to display or save in one of the six display formats. Select the desired format from the pull-down menu, click Save to save your selections to a file, or use the Print feature of your web browser to print the citations. Printing from your web browser will only print the information and citations listed on the web page. You may also display citations as plain text without the sidebar menu and toolbars by clicking on the Text button.

Your results may be on more than once page. PubMed will retain your selections from all pages of your results. To mark specific citations to save, click on the check box to the left of each citation and continue to page through your results. Use Save to save all the selected citations to a file.

Ordering full text copies of journal articles

Order allows you to order the full-text copy of an article from a library in your area using the Order Documents (Loansome Doc) feature of PubMed. Prior to using this program you must establish an agreement with a Loansome Doc participating library. Local fees may apply. For information on the medical libraries in your area (or country) that can provide the Loansome Doc service, click on Order Documents from the PubMed sidebar menu, then “Registration” from the Loansome Doc Ordering System screen. Once you have registered with Loansome Doc, you can order citations, by clicking on the check box to the left of each citation. When you have finished marking your selections (you may move to other pages within your results), click Order. You may also use the Clipboard to collect items from multiple searches before ordering.

For some journals the full-text of articles are available via a PubMed link to the publisher’s Web site. Publisher links for the full-text of the article are displayed on the Abstract or Citation display. You may also click on LinkOut to the right of each citation in the abstract, citation or MEDLINE display. LinkOut is a PubMed service that links to outside sources for the full-text of the article, e.g., a publisher’s web site, as well as other resources such as biological databases, and sequencing centers. User registration, a subscription fee, or some other type of fee may be required to access the full text of articles in some journals.

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