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PubMed Basics

PubMed (created by the National Library of Medicine in Bethesda, MD) pubmed logois the most important source for scholarly, peer-reviewed articles in molecular biology, cell biology, and all aspects of medicine. Over 5000 scholarly journals from around the world are indexed in PubMed, and new articles are added every day. PubMed also provides links to relevant information in other NCBI databases, such as BLAST (a tool to help you find similarities between proteins), Nucleotide (genome, gene, and transcript sequence data), and PubChem (a database of information about biologically active small molecules).

A few things to remember about PubMed:

  • PubMed is really helpful, but it is only an index. This means that you can find descriptions of scholarly articles, usually including abstracts (summaries) of the articles - but you have to follow external links to find the full text of the articles. Most of the articles are behind a paywall, not accessible to the general public. When you search PubMed, you're searching the titles, authors, publication information, abstracts, and indexing terms attached to each article - but you're not searching the entire contents of the articles themselves.
  • PubMed is freely available on the Internet at pubmed.gov. You don't need to be affiliated with UC Berkeley, or any university, to use PubMed. HOWEVER, if you want to see links to full-text articles that are not available to the general public, you should use the UC-customized version of PubMed. Instead of just typing in "pubmed.gov", enter this URL:
  • When you click on an article title in PubMed, you will usually see an abstract of the article and a link to a publisher's website. Usually, if you click on that link, you will find that the article is behind a paywall; you'll be asked to pay for it. Don't do this! UC Berkeley has probably already subscribed to the journal. Instead, click on the orange UC-eLinks button (uc-elinks button). This will give you a link to the full article, if UC Berkeley has access to it, AND you won't have to pay for anything.

pubmed screenshot

  • Just because you find an article in PubMed, it doesn't necessarily mean that UC Berkeley has access to it - we may not have subscribed to the journal that the article was published in. However, we do have access to most journals, so if it seems like we don't have something you're looking for, ask a librarian before you give up. Also, we can get the article from another library for you, for free (although you'll have to wait for it).

Searching PubMed

Searching PubMed is easy. You can just enter your search words in the search box and press the Search button; PubMed will automatically cross-reference your search words to the appropriate scientific or medical terms. For example, if you enter "heart attack causes," PubMed will search for "heart attack causes" but it will also search for "myocardial infarction etiology." You can use the basic search box to combine your terms - you can enter the author's name and the subject terms all in the same box - or you can go to Advanced Search to search specifically by author name, institution, article title, date range, etc.

Searching by topic: just enter your search words (e.g., neanderthal genome, pancreatic cancer genetics). You can then use the filters on the left sidebar to narrow down your results by article type (clinical trial, review article, etc.), date, species (humans or other animals), age group, language, and so on.

Searching by author: enter the last name first, followed by initials with no space between them (e.g., full rj). If you don't enter the author names in this format, PubMed won't know that you're looking for an author name and will return irrelevant results. If you enter the author's full name (no initials) PubMed usually won't understand that form of the name, either.

You can also enter the word "author" in square brackets after the name: full rj [author]. This is especially useful when your author has a last name that's likely to appear in other contexts, like "Cell" or "Heart" (these are actual author names in PubMed)!

Searching by institution: This is useful if you want to see what research is going on in labs at various universities that you might want to transfer to. Because of the way that university names can vary when entered into PubMed (UC Berkeley, Univ of Calif Berkeley, University of California Berkeley, etc.) it's best to search with a ZIP code instead. You can find ZIP codes in Google Maps. UC Berkeley's ZIP code is 94720; so to do a search for all articles in PubMed that have a UC Berkeley-affiliated first author, enter 94720 [affiliation].

  • Be aware that when you do an author search, the articles in your search results will include the author you're looking for even if they're not the first author listed. But when you do an affiliation/institution search, your search results will ONLY include articles where the FIRST author is affiliated with the institution you're looking for. Only one affiliation is listed per article, even when the authors are from different universities and are collaborating on the article.
  • You can combine these search types: if you want to find articles from UC Berkeley that mention retroviruses, enter 94720 [affiliation] and retroviruses. Or go to Advanced Search and use the Search Builder to enter "94720" as an affiliation, and "retroviruses" as All Fields (this will find the word in any part of the article's description).

More Help with PubMed

PubMed has a lot of help on its website, including links to YouTube tutorials.question mark photo

The Bioscience Library has a brief, printable PubMed guide [pdf].

For more sophisticated PubMed searching, you can search with MeSH (Medical Subject Headings), which is the system of specialized terms that are used to organize and classify articles in PubMed. Here's a YouTube tutorial.

Last Update: September 05, 2013 17:36