Mining NLM databases: PubMed, Medline and more

Information for this tip sheet comes from handouts distributed at the Health Journalism 2009 panel "Mining Pub Med Central and MedlinePlus." Speakers on that panel were:

• Gail Kouame, consumer health coordinator, National Network of Libraries of Medicine, Pacific Northwest Region
• Linda Milgrom, outreach coordinator/librarian, National Network of Libraries of Medicine, Pacific Northwest Region
• Robert Logan, National Library of Medicine

ClinicalTrials.gov – Easy access to information on clinical trials for a wide range of diseases and conditions. Quickly identify where trials are taking place, investigators and their contact information.

Genetics Home Reference – Information about genetic conditions and the genes responsible for those conditions. Includes descriptions of the symptoms, diagnostic process, and treatment options; excellent handbook and educational materials for background.

Household Products Database – Health effects of common household products under your sink, in the garage, in the bathroom and on the laundry room shelf. Includes information about the chemicals found in these products and contact info for manufacturers.

National Library of Medicine – The National Library of Medicine's web site links to much more information about their programs and resources.

National Network of Libraries of Medicine – Access to a network of medical libraries and agencies with health information expertise. Toll-free phone number: 800-338-7657

National Training Center and Clearinghouse – Free in-depth training on the National Library of Medicine's databases.

PubMed Basics

PubMed is the U.S. National Library of Medicine's search system for health information with more than 18 million references from 5,000 biomedical journals. Many of these references link to abstracts and in some cases, the full text of articles. It is current and comprehensive.

• Tip: To do a basic search, type your keywords into the search box-the system will automatically combine the terms with an "AND" without your typing it in. For example, if you want to find articles about measles outbreaks, just type the words "measles" and "outbreak" into the search box (no quotes).
• Tip: There is an excellent tutorial linked from the left-hand navigation bar on the front page of PubMed.
• Get more tips for using PubMed

PubMed Content

• MedLinePlus.gov – NLM's database of millions of references to articles published in biomedical journals. Information on more than 750 health topics and includes current health news, a full-text medical encyclopedia, information on drugs and herbal supplements, and much more. New articles are added every day, and stories are available for up to 90 days. Special features include:
  • Interactive tutorials are slideshows that tell you about a health condition or medical test.
  • Easy-to-read pages use plain language to help you understand diseases and conditions.
  • E-mail announcement lists alert you when new topics are added to the Web site.
  • Medical encyclopedia with pictures and diagrams to help you understand medical words, tests and procedures.
  • Tip: Click on the "Health Topics" link. Then, either click on the first letter of the topic you are searching, or browse by category. For example, to search for Salmonella, click on Health Topics, then either click on the letter "S" in the banner with the alphabet, OR click on Infections under Disorders and Conditions. You can also type your query into the search box in the upper left-hand corner of the site.
• OLDMEDLINE: Journal article citations from 1948 through 1965
• In-process citations that have not yet been analyzed and indexed for MedLine
• Publisher-supplied citations that may not receive full indexing for MedLine because they are not biomedical in nature
• Links to Entrez molecular biology databases.

PubMed Features

• Sophisticated search capabilities, including spell checker and special tools for searching clinical topics
• Use the MeSH Database to find Medical Subject Heading Terms and build a search strategy.
• Ability to store and automatically receive e-mail updates for saved searches using PubMed's My NCBI.
• Links to full-text articles and to information about library holdings
• Links to other NLM search systems, such as ClinicalTrials.gov, MedLinePlus , NIH Clinical Alerts and Advisories, NLM Gateway and PubMed Central.
• Look at the top of the blue NCBI sidebar for links to an overview, help, FAQs, and an online tutorial.

MeSH Database
Articles are indexed using a powerful vocabulary, called Medical Subject Headings (MeSH). The MeSH Database provides the option of identifying appropriate MeSH terms for searches.

Click on the MeSH Database link on the blue sidebar to search for a particular term or concept. After finding a term, click on the link to view and select subheadings and to refine aspects of the MeSH term. Check the terms desired, then click on the Send To Search Box feature. When finished adding terms, click Search PubMed to run the search.

Clinical Queries
PubMed's Clinical Queries section makes it easier to find articles that report applied clinical research. Click on Clinical Queries on the blue sidebar. Select one of the three options. To search by clinical study category, type search terms in the box provided. Then select one of the filter categories: "etiology," "diagnosis," "therapy," "prognosis," or "clinical prediction guides" and either specific or "broad, sensitive search."

Select "Find Systematic Reviews" to locate systematic reviews, meta-analyses, reviews of clinical trials, evidence-based medicine, consensus development conferences, and guidelines.

Select "Medical Genetics Searches" to find citations and abstracts related to various topics in medical genetics. Choose one or more of the filter categories provided.

PubMed Searching
To search PubMed, type a word or phrase into the query box, then click on the Go button or press the Enter key. Combine search terms with connector words: "AND, "OR" or "NOT". Type connector words in upper case letters. Author names should be entered in the form gerberding jl, but initials are optional. Author names are automatically truncated to account for varying initials.

Below the query box are the Features Tabs: Limits, Preview/Index, History, Clipboard, and Details.

Limits
Feature provides a table with checkboxes for Publication types, Languages, Subsets, Ages, Humans or Animals, Gender, and Publication Date. You can also restrict your search to items with abstracts or links to full text, and make multiple choices within a category. Click on Limits below the query box and make selections. After entering the search and choosing limits, click on the Go button to run the search. A checkmark in a box beside the word Limits indicates that limits are active.

Preview/Index
Feature allows viewing and selecting of searchable fields and subject terms. Preview may be used in conjunction with the Index to construct and combine search statements before viewing the search results. Consult Help for more information.

History
Feature keeps track of search statements and numbers them as links. clicking on teh links provides a menu allowing search statements to be deleted, combined into a search with the AND, OR or NOT connectors, or saved in My NCBI.

Clipboard
Feature allows collecting of selected citations from one or more searches for printing, saving, e-mailing, ordering, or storing in My NCBI Collections. Click the check box beside the citations to select them. Then go to the Send To pull-down menu, and select Clipboard. To see the selected citations, click on the Clipboard features tab.

Details
Feature provides information on how PubMed ran a search. PubMed looks first for the search words as MeSH terms, then journal titles, then authors and also searches "All Fields." Details also shows how PubMed maps terms to MeSH headings.

PubMed Search Results
After clicking on the Go button, PubMed displays a list of results in summary format. To retrieve more information about the search results, use the menu next to Display to pick Abstract, citation, or MEDLINE format.

Related Articles
A helpful PubMed feature is the ability to find citations that are similar to those of interest. To retrieve Related Articles, click on the Related Articles link under the PMID of each citation.

Verifying a Citation
To search for a specific article of a journal issue, click on Single Citation Matcher on the blue sidebar. A form screen will appear. You do not need to fill out the entire form.

My NCBI
PubMed's My NCBI feature stores search strategies, provides automatic e-mail updates, and stores search results as collections. You must register for My NCBI by creating a User Name and Password. Click on My NCBI on the blue sidebar to sign on. My NCBI includes additional features for filtering search results. The tool icon to the right of the features tabs links to a page where up to five search filters may be selected.

Printing & E-mailing
After selecting your citations and the display format, select Text, Printer, or E-mail from the Send To pull-down menu. Text will create a plain text version of the results. The Printer option creates a print-friendly version of the results. E-mail will ask for a selection of additional options and an e-mail address.

Saving Search Results
To save search results, select File from the Send To pull-down menu. You can use the Clipboard to collect citations from multiple searches. To save citations for citation management software, change the display format to MEDLINE before downloading or emailing.

Getting Journal Articles

PubMed does not include copies of journal articles. However, PubMed does offer links to the full text of journal articles when those links are available.

Links to Full Text and Library Holdings
Many PubMed citations have links to the full-text of articles through PubMed Central, through your library's electronic and print holdings, or through the publisher (the latter may require a subscription or may make an article available by pay-per-view). Check with your library for details about your full text links or call your Regional Medical Library at 800-338-7657.

More Options
Copies of articles may also be obtained:

• Direct from the Publisher: Journal publishers and related organizations may provide access to articles for a fee or for free, generally following your registration as an individual or guest. When available, icons to these sources can be found on the single citation display.

• Through LinkOut: Additional links to articles, both free and for a fee, may be available on the LinkOut display. Click on Links to the right of the citation in most PubMed displays and access LinkOut from the dropdown menu.When you click on LinkOut links or icons in the LinkOut display, you leave PubMed and are directed to the full text at an external site. Copyright of these materials remains with the publisher. Users should review all copyright restrictions set forth by the full text provider before reproducing, redistributing, or making commercial use of material accessed through PubMed's LinkOut.

Free Articles
Free copies of available articles may be obtained in a number of ways:

• From PubMed Central: When searching PubMed, look for the green "Free article in PMC" at the bottom of the citation on the summary results screen. This indicates the full-text article is available in PubMed Central, a free digital archive of full-text journal articles maintained by the United States National Institutes of Health. To access the article, click the title link to go to the single citation display, and then click on this "Free full text article in PubMed Central" icon.

• Free from the Publisher: Many publishers offer free full text. Check "Links to free full text" under Advanced Search to find citations publishers have made available through NLM. To access the article, click the title link to go to the single citation display, and then click the free full text article icon. You may also visit those publisher's websites without links or icons, as some publishers provides free access to articles, often after you register as a guest.

• Through an affiliation with a hospital, university, or other institution: Your local medical library is your best option. If you see icons for your library on the abstract this indicates that your library provides a link to the article or has the journal in its collection. If you do not see an icon for your library, ask your librarian about how to determine if your library has access to the journal or article of interest. If your library does not have access to the article you need, ask your librarian about ordering the article from other institutions. Your librarian may also recommend you set up a library filter in My NCBI and/or use the Order feature from the Send to menu.

  DO NOT use either "full text" option under the Advanced Search link in PubMed when working with a library – as you may eliminate articles that are available free to you through that library.

• From Your Local Public Library The National Library of Medicine has a special relationship with public libraries. Also, some libraries have copies of medical journals.Your library may have the article or be able to order a copy of it for you using a service called interlibrary loan. Ask your local librarian and/or check your library's Web site to find out about interlibrary loan options and whether or not there will be a charge.

Loansome Doc

Loansome Doc allows users to order copies of articles from a medical library. You must register with a library to use this service. To register, identify a library offering Loansome Doc service or call your regional medical library at 800-338-7657 for a referral. Contact the library to register and learn about fees and policies.Or, in PubMed, in the left navigation menu under Related Resources, click Order Documents then click on Loansome Doc.

During the Loansome Doc registration process, you will have the opportunity to search for a Loansome Doc provider in your area (U.S. and international). Carefully review the displayed information to identify a library that will provide the service you desire as fees and services vary among these libraries. It is recommended you contact the selected library prior to registering.

After registering with a library that offers Loansome Doc service, PubMed can be used to place orders for copies of articles. Select articles of interest, and then select Order from the Send To pull-down menu.

1. Click the check box next to each citation you want to order. You may move to other pages within your results to select additional citations or hold them on the Clipboard before ordering
2. From the Send to pull-down menu, select Order
3. Follow the on-screen directions

Loansome Doc is the default article delivery service. To use a document delivery provider other than Loansome Doc, click on Document Delivery in My NCBI and follow the instructions

For More Information
In the United States, contact the National Network of Libraries of Medicine (NN/LM), an outreach program of the NLM, at 800-338-7657. The librarians will provide information about libraries in your area with which you may establish an account for the Loansome Doc service.

In Canada, contact the Canada Institute for Scientific and Technical Information (CISTI) at 800-668-1222 for information about libraries in your area.