Skip Navigation Bar
NLM Technical Bulletin Header
Article Navigation Bar Table of Contents NLM Technical Bulletin Home Page Back Issues Index
  June 6, 2003 [posted]
 
 
  PubMed CentralTM in Entrez
 
 

drop cap letter for p ubMed Central (PMC), NLM's digital archive of life sciences journal articles, is now accessible as an Entrez database at http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PMC. This means you can search the full text of articles in PMC in much the same way as you now search PubMed, with History, Limits, Preview/Index, and Clipboard features.

The articles in PMC can be divided into two groups: regular PMC articles for which the full text is viewable directly in PMC, and PubLink articles for which full text is viewable only at the journal's own site. Regular PMC articles are always free. Most PubLink articles require a subscription for some time - usually a year or less - after they are published, and then are free to everyone. For a complete list of PMC journals, click on 'Journal List' in the sidebar of the PMC Entrez search page or go directly to http://www.pubmedcentral.gov/.

The default PMC search is limited to articles that are free (including PubLink free). To include all PMC articles in your search, simply uncheck the Free full-text only box at the right of the search form (see Figure 1). Note that PMC indexes and searches the full text of all articles, even the PubLink articles which can be viewed only at the journal site. Articles in the early issues of some journals, for which the full text is available only as a PDF file, are the one exception. In these cases, PMC searches only the citation and abstract, just as PubMed does.

  PubMed Central Search Form

The standard PMC search technique is labeled SmartSearch, reflecting the fact that it is based on an automated analysis of the title, abstract and full text of each article. SmartSearch is intended to increase the relevance of your search results. It does not search every word in the article as a simple full text search would do. To do that (search every word), uncheck the SmartSearch box on the search form (see Figure 1).

In other respects, a standard PMC search works much like a PubMed search, automatically identifying, where practical, author names, journal titles, or known phrases in the input search string, and mapping search terms to MeSH terms. Although most PMC items have a corresponding PubMed citation (the exceptions are material such as book reviews, which are out of scope for PubMed), some of these citations may not be indexed for MEDLINE and therefore will not have MeSH terms attached in either PubMed or PMC.

PMC also uses automated analysis to identify terms in an article that most likely are organism names. These names are then used to provide bi-directional links between the article and related records in the Entrez Taxonomy database. A search using a common name for an organism is translated to its scientific name whenever possible. For example, yeast Saccharomyces cerevisiae, and mouse Mus musculus. Organism names may also be searched directly via the [organism] field. To avoid a lot of false hits, the text analysis algorithm generally does not tag as an organism those terms that are commonly used in other contexts, e.g., Erica, or Paris.

Search Results
PMC search results are displayed in order of relevance, by default. (The relevance algorithms are still being refined and the PMC team welcomes any observations you may have that are based on a systematic analysis of PMC search results. Send your comments to: pubmedcentral@nih.gov). Results may be re-sorted (see Figure 3) by journal title, issue date, date of online publication (Epub Date), or date the article was added to PMC (PMC Live Date).

For an article with full text viewable directly in PMC, the citation on the search result page (see Figure 2) will include links to an [Abstract] if one exists, to the [Full Text], and in most cases to a [PDF] copy of the article. PubLink articles have only [PubLink] which takes you to a PMC 'abstract view' of the article where you can find a direct link to the full text at the journal site, as well as the details of when access restrictions on the full text will be lifted if it is not already free.

  PMC Search Result Excerpt Showing Links Popup Menu

The Links popup menu (see Figure 2) associated with each article in a PMC search result page is similar to the PubMed Links menu. Special to PMC are a link to the Taxonomy database, which was mentioned earlier, and a Referenced articles link which produces a PubMed list of the articles in the References section of the PMC article. (Of course, the PubMed list will only include referenced articles that are cited in PubMed.) A Referenced articles link is not available from PMC articles in the early issues of some journals, for which the full text is available only in the form of a PDF file. As in PubMed, you can display a combined set of links for a group of articles by using the checkbox alongside each article to select the articles and then using the 'Display' option at the top of the result page (see Figure 3).

  Display Options For PMC Search Results

Search Limits
Use the Limits page to restrict your search to one or more of the following:

  1. Only articles that are viewable directly in PMC.
  2. A specific journal or author.
  3. An issue/article publication date range.
  4. Articles added to PMC in a specific period.
  5. Search only in a specific database field, or in specific parts of an article, such as the methods section, figure and table captions, or section headings.

Preview/Index
You can browse the indexes for any PMC search field from the Preview/Index page. These search fields are the same as those available on the Limits page. Fields of special interest are:

  • Body - All Words (same as ArticleBody): all words and meaningful phrases (multi-word terms) found in the body of an article, i.e., all sections following the abstract and preceding the references section. Stopwords and phrase recognition are handled in exactly the same way as for PubMed.
  • Body - Key Terms: relevant words and phrases from the title, abstract and full text of each article. This is the index behind SmartSearch, mentioned earlier.
  • Methods - Key Terms: similar to 'Body - Key Terms' except limited to words and phrases found in the Methods section of an article.
  • Figure/Table Caption: limited to words and phrases found in the captions/legends of figures and tables in an article.
  • Filter: to look at specific subsets of the database, such as everything that has a corresponding record in PubMed (searched as "pmc pubmed"[Filter]), or all PubLink articles (searched as "publink"[Filter]), or all articles that have associated corrections (searched as "is corrected"[Filter]). Advanced searchers, note that the 'pubmed pmc' filter in PubMed is the same as the 'pmc pubmed' filter in PMC - both define the set of articles that are common to PubMed and PMC.

Citation Searching
The PMC Citation Search screen (see Figure 4), accessible from the sidebar of any search page, is similar to the PubMed citation matcher. The citation search runs with the Free full-text only option. To find all matching articles, including PubLink subscription articles, run your search, uncheck the 'Free full-text only' box on the search result page and then rerun the search (press Go) from there.

  PMC Citation Search

Should I Search PubMed or PMC?
If you know to begin with that you want to limit your search results to articles in PMC, we recommend searching PMC directly rather than searching PubMed with the PubMed Central subset limit. The PMC search includes the fields that are searchable in PubMed, plus the full-text SmartSearch and the other new features mentioned here, such as taxonomic names.

In PubMed, setting the PubMed Central subset limit is the same as adding 'AND pubmed pmc local[sb]' to your search. Either way will give you only articles whose full text is viewable directly in PMC. Another way of extracting the PMC articles from a PubMed search result set is to display 'PMC Links' for the complete result set, using the Display button at the top of the results page. This will show the relevant citations on a PMC search results page, from which you can go directly to the full text. Be aware, though, that Entrez will truncate your secondary result set (in this case, the PMC citations) at 500 items. Displaying 'PMC Links' is equivalent to adding 'AND pubmed pmc[sb]' to your PubMed search. It selects all PMC articles, including PubLink articles that may still be available only to subscribers.

Want to Know More?
If you have questions about Entrez-PubMed Central that are not answered by this article, see the online help at http://www.ncbi.nlm.nih.gov/entrez/query/Pmc/pmchelp.html, or write to: pubmedcentral@nih.gov.



By Ed Sequeira
National Center for Biotechnology Information

black line separting article from citation

Sequeira E. PubMed CentralTM in Entrez. NLM Tech Bull. 2003 May-Jun;(332):e3.

 


Article Navigation Bar NLM Technical Bulletin Home Page Back Issues Index Previous Page Next Article
U.S. National Library of Medicine, 8600 Rockville Pike, Bethesda, MD 20894
National Institutes of Health, Department of Health & Human Services
Copyright, Privacy, Accessibility, Viewers and Players
Freedom of Information Act (FOIA)
Last updated: 13 April 2012