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MEDLINE Interfaces & Related Resources

 

MEDLINE-Related Resources


MEDLINE from the National Library of Medicine (NLM)

Other Interfaces to MEDLINE

Medical Subject Headings (MeSH)

MEDLINE Tutorials

In-Process Citations in PubMed

Journals on the Web

NLM Resources

Health Information on the Web


This page is based on Appendix A from Brian Katcher's MEDLINE: a guide to effective searching in PubMed and other interfaces. 2nd ed. San Francisco: Ashbury Press; 2006


 

 

MEDLINE-Related Resources

These pages are based on an appendix from Katcher BS. MEDLINE: a guide to effective searching in PubMed and other interfaces. 2nd ed. San Francisco: Ashbury Press; 2006. They contain links (not possible from the printed pages -- see sample book pages) and are continually updated.

MEDLINE is a bibliographic database that is produced by the National Library of Medicine. Because MEDLINE is so large (more than 13 million records) and so exquisitely organized, it is generally considered to be the premiere index to the world's medical literature of biomedical journal articles. PubMed is the most frequently used version of MEDLINE.

These pages describe a number of MEDLINE-related resources on the Web. Some of these are within the National Library of Medicine’s Web site, which is among the most important health sites on the Web.

The text below has also been chunked into smaller pages, with navigation on the left.

MEDLINE from the National Library of Medicine (NLM)

The National Library of Medicine, which produces MEDLINE and licenses it to other vendors, provides free access on its Web site:

PubMed. If you are not already using MEDLINE, PubMed is the best place to start (unless you are starting out at an academic institution that uses Ovid). PubMed is very fast, easy to use, and has excellent on-line MeSH help. PubMed provides context-specific links to other Entrez databases and to resources beyond the National Library of Medicine. Among experienced searchers not using a particular university-based MEDLINE interface such as Ovid, PubMed has become the de facto standard.

PubMed is MEDLINE with additional citations that have not yet been indexed for MEDLINE or are beyond its scope, as well as citations from OLDMEDLINE (pre-1966 citations). An NLM Fact Sheet explains the difference between MEDLINE and PubMed.

For serious searches in any MEDLINE interface, you will want to give some thought to the MeSH that best describe the concepts you are researching, and PubMed's MeSH Database is particularly helpful in this regard. In fact, you can even construct your search strategy from within this well-designed MeSH Database, which can be reached from a link on the PubMed home page.

Late in 2009, a new PubMed interface was rolled out. This new interface allows easier access to the features described in my book. In particular, the page that displays your search results includes a box (search details) that shows how your query was processed. For more information about each element, see PubMed Help or NLM's more detailed MEDLINE/PubMed Data Element Descriptions information page. (And, yes, I'm glad the interface-specific text in my book was limited to Appendix A.)

PubMed's Clinical Queries and Topic-Specific Queries filters (linked from PubMed's home page) provide a handy means for starting a search. After an initial search, you will probably want to construct additional search strategies based on what you have learned.

To get the most out of this interface, take a look at PubMed’s Tutorials (linked from the PubMed home page).

Gateway. NLM Gateway is intended for users who come to the National Library of Medicine without knowing what is there or how best to search for it. NLM Gateway provides a single interface for searching in a number of the Library’s resources, including PubMed, MedlinePlus (described below, under “Health Information on the Web”), the NLM Catalog, ClinicalTrials.gov, DIRLINE (Directory of Health Organizations), and others. NLM Gateway's most remarkable feature is that it searches simultaneously within multiple retrieval systems. Its Find Terms button leads you to information about the Medical Subject Headings (MeSH) that might encompass the terms you enter.

If you know that what you are looking for is in MEDLINE, then PubMed is a more appropriate interface, because its limits feature is specific to MEDLINE. (The limits button in the NLM Gateway is for categories, such as journal articles, consumer health, books/serials/AV, or databanks.) However, NLM Gateway provides access to much more information than can be found in MEDLINE. A full description of what's available from NLM Gateway can be found on its "About" page.

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Other Interfaces to MEDLINE

PubMed (public site) and Ovid (many institutions) are the most widely used, but there are other interfaces to MEDLINE on the Web. Some are free, some are free with registration, and some are fee-based. A sampling: Medscape (a Web site for clinicians), BioMedSearch.com (combines PubMed with other sources), Infotrieve (specializes in document delivery), and PaperChase.

If you are affiliated with a major teaching institution, you can probably apply for a remote access account that will make your home or office computer screen look like the one in the library. Such libraries generally use either the Ovid interface to MEDLINE or a customized version of PubMed that has been tailored to best serve the library's patrons. In addition, many university libraries offer full-text access to a growing number of on-line journals for which they have paid subscriptions. (See Journals on the Web.) For copyright reasons, remote access is limited to those with library privileges.

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Medical Subject Headings (MeSH)

Deliberate and careful use of Medical Subject Headings (MeSH)--the National Library of Medicine's controlled vocabulary for health-related concepts--is a major contributor to complete and precise MEDLINE searches.

An excellent publicly available resource for using MeSH is the Entrez MeSH Database. A link to this MeSH Database can be found on the PubMed search screen. The MeSH Database home page includes links to three excellent tutorials. (And there's more MeSH information on the NLM Distance Education Web site.)

Use the MeSH Database to determine what concepts from this controlled vocabulary best describe your search topic. PubMed search strategies can be constructed from within this database.

When you find an interesting article in PubMed, use the Citation display to see the MeSH terms that were used to index it. Each of these MeSH terms (some of them with subheadings, some of them as Major MeSH) will appear as a hyperlink. You can use these links to learn more about these MeSH. You can also use them as the basis for a new search (selected MeSH terms will be searched exactly as they were applied to the citation, with subheadings, etc). You may see additional Entrez database search links options for some terms. If there are substances in the Citation display, they may include links to PubChem databases.

Other MeSH resources from the National Library of Medicine include what might be called a “Medical Subject Headings Home Page,” with links to a number of other MeSH-related resources, including a Fact Sheet with detailed information about MeSH and a MeSH Browser. (For most users, the MeSH Database will be more useful.)

The National Library of Medicine's Unified Medical Language System (UMLS) links other controlled vocabularies to MeSH. Among these are RxNorm (standard names for clinical drugs, which can be searched with a downloadable browser called RxNav), SNOMED CT (the College of American Pathologists' Systematized Nomenclature of Medicine--Clinical Terms), and more than 100 other source vocabularies. PubMed and the Entrez MeSH Database use the Unified Medical Language System to link entry terms to MeSH.

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MEDLINE Tutorials

The National Library of Medicine's PubMed Tutorial (a page with links to animated tutorials) will provide you with an excellent overview of PubMed and the MeSH vocabulary. This frequently updated page now includes more than a dozen animated quick tours. Check out this wonderful resource.

Whether you normally use PubMed or another source of MEDLINE, the MeSH Vocabulary portion is worth reviewing. The three MeSH tutorials can also be accessed from PubMed's MeSH Database.

Many institutional libraries use Ovid MEDLINE and have created their own web-based tutorials (also of value for users of PubMed and other interfaces to MEDLINE).

If your institutional library offers MEDLINE classes, take one.

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In-Process Citations in PubMed

It takes some time for articles to be indexed for MEDLINE. High-profile journals like JAMA or the New England Journal of Medicine are indexed within days, but other journals take weeks to months. As citations are received from publishers, before they are indexed for MEDLINE, they are placed in PubMed and are available from the default query box. These citations are based on the electronic files received from the publisher and are marked with one of two tags: "PubMed - as supplied by publisher" (as they are added) or, more commonly, "PubMed - in process" (accuracy of bibliographic data being reviewed and MeSH vocabulary being assigned, if the article is within the scope of MEDLINE).

If you search by author, journal, or unqualified words, these in-process citations will appear at the top of your search results. Further down you will see citations whose Medical Subject Headings (MeSH), Publication Types, Substance Names, and other indexing elements have been added. These are tagged as "PubMed - indexed for MEDLINE."

While it is generally preferable to use all of the indexing features that are built into MEDLINE, you may wish to augment your searches with in-process citations.

There are several ways to keep track of in-process citations. If you are interested in a particular journal, you can see its articles as they are added to PubMed. Just enter the full name or its official abbreviation (for help see the Journals Database). If you subscribe to a journal, you may be able to have the table of contents e-mailed to you upon publication. Most journals publish the table of contents of the most recent issue on their Web site (see Journals on the Web). You can also store a pre-constructed search strategy in "My NCBI" (a PubMed service) and have the results sent to you by e-mail.

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Journals on the Web

Many journals are available on the Web in full text, but free access is often limited to subscribers. Most academic medical center libraries maintain online subscriptions for students and faculty (Links to full-text journal articles can be found within Ovid or PubMed searches, depending on the institution).

When you see the icon (green banner) in the Summary display of your PubMed search results, it means you can see the full text article for free. An increasing number of journals provide free full text access to all or some of their articles, sometimes within six months or a year after initial publication. Here are some additional sources of free full text articles:

PubMed Central

The National Library of Medicine's PubMed Central is an archive of free full-text articles. Articles in PubMed Central are sometimes also available from the publishers' Web sites, but those in PubMed Central are published in a standard format to insure their permanence on the Web.

When you see the icon (orange and green banner) in the Summary display of your PubMed results, it means that the article can be found in PubMed Central. If you like, you can use the "limits" tab in PubMed and, under "subsets," limit your searches to PubMed Central.

Open Access Journals

An increasing number of journals are developing publishing models that facilitate free access to full text articles. Some institutions, such as the University of California at San Francisco, encourage researchers to consider publishing their work in open access or reasonably priced journals as means of protecting scholarly communication. Here are some resources:

Directory of Open Access Journals (DOAJ)

BioMed Central

Public Library of Science (PLoS)

A recent essay in the New England Journal of Medicine (April 13, 2006), discusses the issue of open access journals.

Finding Journal Names

If you need help in finding the name of a journal, try the Entrez Journals Database. The opening page also provides the means to find information about Entrez journals that have links to full-text web sites.

Articles Not Available on the Web

Much of what you find in MEDLINE will not be available on the Web as a full-text document, but you can still obtain a copy if you do not have convenient access to a medical library. The National Library of Medicine's Loansome Doc allows you to order documents after first establishing an agreement with a nearby medical library. Detailed information about Loansome Doc is available on the National Library of Medicine’s Web Site, in the Fact Sheets section. Links to Loansome Doc are built into PubMed and NLM Gateway. Documents are available in a variety of forms (mail, fax, pickup, or internet), depending on the capacity of the local library. Charges vary, also depending on the local library.

If you have an My NCBI account (a free PubMed service), you can configure it for other document delivery services (Loansome Doc is the default).

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NLM Resources

The National Library of Medicine offers a wide array of web-based resources in addition to PubMed/MEDLINE, as can be seen from their home page and from their list of NLM Databases & Electronic Resources. At this writing, there are 70 such resources -- everything from accurate and clearly written health information for consumers (MedlinePlus, which is also available for mobile devices) to the NLM Catalog (books, audiovisuals, journals, and electronic resources, all indexed with MeSH) to the Visible Human Project to a collection of online books (Bookshelf) to the original Index Catalog of the Library of the Surgeon General's Office to Images from the History of Medicine to the National Center for Biotechnology Information (NCBI)'s Entrez databases.

You can save your PubMed search strategies by creating a free "My NCBI" account (a PubMed service). You can even schedule regular repeat searches and receive the results via e-mail.

The NLM Technical Bulletin publishes information about changes as they occur, and back issues are well indexed. For example, a recent issue announced the release of RxNav, a downloadable browser for RxNorm, the NLM repository of standard names for clinical drugs.

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Health Information on the Web

There's a tremendous amount of health information on the Web, but most of it suffers from two basic problems:

1. It varies widely in quality. When you find a new site, look to see who sponsors it, and determine its intended audience. Is it current? What is its evidence base? The Medical Library Association has a similar list of questions on its site. MedlinePlus has a useful page of links, entitled Evaluating Health Information.

2. Unlike MEDLINE and other structured databases, most of the Web is completely unorganized. Search engines look at all the words on a Web page, as well as the links to and from the Web page (and, in some cases, additional criteria) for determining its ranking in response to a query. The ranking of "hits" from a search may or may not be suitable to your needs. Sometimes it's helpful to start elsewhere than Google.

Here is a sampling of useful places to go:

Interesting Search Tools

Google Scholar. In addition to its well-known main search page, Google offers a variety of specialized search pages. Google Scholar uses Google's search algorithm, but its results are limited to articles and books of scholarly interest. According to Google, you can use it "to find articles from a wide variety of academic publishers, professional societies, preprint repositories and universities, as well as scholarly articles available across the web." You can set Scholar's Preferences to show links within your affiliated medical library.

Searches for health information in Scholar will often point to PubMed abstracts. When you find useful articles in Scholar, determine how they were indexed for PubMed (MeSH terms), and do another search in PubMed using these terms. Why? Because of the way that Scholar ranks hits, it is likely to miss the latest papers, and -- more importantly -- it lacks PubMed's ability to conduct Boolean searches based on the concepts that are represented by MeSH terms. You can see the MeSH terms for an article by displaying it in the "citation" format.

Google Scholar, still in beta at this writing, is attracting a lot of attention from medical librarians (see Banks 2005 and Henderson 2005).

Scirus. Scirus limits its results to scientific information. Its default mode searches both journals and the web, and its results page provides a link to each search. Less well known than Google Scholar, this is a powerful tool. Highly recommended.

OAIster (find the pearls...). OAIster is the University of Michigan Digital Library's attempt at creating a collection of freely available, previously difficult-to-access, academically-oriented digital resources.

Practice Guidelines

Of course you can search for specific practice guidelines within MEDLINE/PubMed by limiting your search to Publication Type "Practice Guideline" and following the links, but there are other resources for practice guidelines:

The National Guideline Clearing House is the Agency for Healthcare Research and Quality's (AHRQ) public archive for evidence-based clinical practice guidelines. AHRQ guidelines can also be accessed from HSTAT (Health Services/Technology Assessment Text), which is an electronic book on the National Center for Biotechnology Information's Bookshelf. These are all free full text resources.

Evidence Based Medicine

Some evidence based medicine resources require a subscription, but here is a sampling of free resources:

Consumer Sites

These sites are also useful for health professionals. The Medical Library Association (MLA) has produced a User's Guide to Finding and Evaluating Health Information on the Web, which includes a list of their "top ten" most useful consumer web sites. My own favorite is MedlinePlus, which has links to carefully vetted health topic pages, a serviceable medical dictionary, links to patient drug information sheets, and links to all the current health news, in reverse chronological order (organized by day). Health-related stories are a staple of the media, and we often are questioned about them. This is a good way to find enough information to locate the study itself.

Libraries

Librarians are experts in the organization of intellectual resources (historically, this has been books), so it is not surprising that medical librarians have made significant attempts at organizing medical information on the Web. Here is a sampling:

  • HealthWeb, a collaborative project of health science libraries in the Greater Midwest Region of the US and the National Library of Medicine
  • The Recommended Core Collection of Web Sites for Hospital Libraries, created by the Camden Campus Library of the University of Medicine & Dentistry of New Jersey, is another useful list of links.
  • Hardin MD is a directory of directories, organized by topic areas. Links to more links. Compiled by Eric Rumsey at the Hardin Library for the Health Sciences at the University of Iowa -- a very rich site.
  • The National Library of Medicine (NLM) - see NLM Resources on this Web site.
  • There are many such directories, but a different approach to using the Web is Jan's Search Tips, which takes the form of a well-written blog. Quite a few MEDLINE-related tips can be found in its archives.

Academic medical center libraries subscribe to a variety of Web-based resources that can be accessed from the library (or remotely by affiliates of the library). A sampling:

  • EMBASE - a bibliographic database with a somewhat different scope than MEDLINE. Offers extensive coverage of the drug and biomedical literature.
  • Web of Science - A bibliographic database with excellent search capabilities for cited reference searching.
  • Cochrane Database of Systematic Reviews - Evidence-based reviews of the clinical literature. (Abstracts of the Cochrane Reviews are free-of-charge).
  • Drug Information Fulltext - Full text access to American Hospital Formulary Service Drug Information.
  • Harrison's Online - Full text access to Harrison's Principles of Internal Medicine.

Librarians themselves are the best resource; visit your library.

U.S. Government

The National Institutes of Health (NIH) is the premier institution for biomedical research. As you might expect, its Web site is huge. Each of its many institutes and centers has its own Web site. (The National Library of Medicine (NLM), which produces MEDLINE/PubMed, is part of NIH.)

The Department of Health and Human Services is the overall government agency for health. Its Web site is designed for the general public. However, it also contains links to the various NIH institutes and centers, the Food and Drug Administration (FDA), the Centers for Disease Control and Prevention (CDC), the Agency for Healthcare Research and Quality (AHRQ), and other U.S. Government health agency Web sites.

The U.S. Government's role in biomedical research, public health, and health care delivery has been the subject of a great deal of literature, and it is all well indexed in MEDLINE. There are MeSH for each of the above-named agencies. To use these in your MEDLINE searches, go to the Entrez MeSH Database and take a look. Here is a link to United States Dept. of Health and Human Services within the MeSH Database.

Public Health Sites

If you are working in public health, take advantage of Partners in Information Access for the Public Health workforce.

Other useful public health sites:

Professional Associations

A great deal of highly specialized health-related information on the Web is managed by specific professional associations. Become a member of the organizations that represent what you do.

Images

Google's wonderfully spare search page provides a link to Google Image Search, where you can find images to spruce up your presentations. Less well known but more powerful for serious educational purposes is HEAL (Health Education Assets Library). HEAL describes itself as "a digital library that provides freely accessible digital teaching resources of the highest quality that meet the needs of today's health sciences educators and learners." HEAL is peer reviewed, and its images are organized by MeSH. The CDC maintains a Public Health Image Library. The National Library of Medicine maintains Images from the History of Medicine.

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Updated January 24, 2010

This is an updated version of Appendix A, from Brian Katcher's MEDLINE: a guide to effective searching in PubMed and other interfaces (see navigation bar). Please send comments to brian[at-sign]healthysf.org

The URL for this page is:

http://www.ashburypress.com/resources.html