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Chemistry: PubMed Tutorial

Library & research resources for students in the Chemistry program at Caltech.

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PubMed and NCBI

PubMed is the freely-available public interface for searching the MEDLINE database along with selected other life sciences-related journals. PubMed covers articles mainly in the medical and biomedical fields (more information can be found here).

PubMed is part of the National Center for Biotechnology Information (NCBI), which is part of the National Library of Medicine (NLM) under the National Institutes of Health (NIH). Got it?

Searching PubMed

The main PubMed search bar will search for your term anywhere in a PubMed record about an article - the title, author, keywords, etc. You can search for your term in specific fields using the Advanced searching form, which should look similar to the Web of Science search form.

Once you perform your search and have a list of results, if you wish to narrow your results to specific article types, you can do this from the menu on the left (just like in Web of Science), under Article types. To display more types, click more... and choose which types you want visible in the menu. Then, click on the type in the menu to view just those types. To view the PubMed record for an article, which includes the abstract and full-text access links, click on the title of the article.

PubMed classifies Original Research Articles under the heading Journal Article. When viewing the PubMed record for these types of articles, they will clearly have the major components outlined in the abstract:

Most Review articles will be marked as such, but not all. It is a good idea to read the full text of the article and compare the sections to those expected in an experimental research article to determine the type of article.

Magical MeSH

MeSH stands for Medical Subject Headings, and functions just like Web of Science's KeyWords Plus, but better in many ways. The MeSH terms list is carefully maintained and updated regularly by librarians at the National Library of Medicine, and is often used in conjunction with other databases' own controlled vocabulary. So, knowing MeSH terms will help not only with searching PubMed, but other databases as well.

When searching from the main PubMed search box, PubMed will automatically try to map your search term to MeSH terms, and include those preferred terms in your search automatically. For an example of this, try searching for heart attack, and on the results list scroll down the right side to the Search details section:

PubMed is telling you the preferred MeSH term is myocardial infarction, and including that as a search term will probably get you more relevant results than searching just heart attack.

Accessing Full Text

Many articles that you find in PubMed will say Free Article or Free PMC Article. This means that the full text of the article is freely available to the public. Two reasons articles could be freely available are:
(1) because part or all of the funding for that work came from the NIH. There is a mandate that any such work has to be made publicly available, in PubMed Central (an Open-Access repository), within 12 months of its publication in a subscription journal.
(2) the journal is an Open Access journal and all articles in that journal are freely available regardless of funding mandate. Examples of such journals are the PLoS suite of journals, Nucleic Acids Research, and eLife. More Open Access journals can be found at the Directory of Open Access Journals (DOAJ).

Full-text access to articles will be indicated through icons on the top right of the article's page. If an article isn't yet available in PubMed Central, or if the authors aren't required to put it in PubMed Central, you can check for online access through the Caltech Connect link, or through the publisher if the Library has a subscription to that journal (the publisher link will only work on campus, or off-campus if you are using the VPN). When viewing an article's PubMed information page, full text links will be in the top right corner.

Citation Exporting to EndNote or EndNote Web

If you are interested in using EndNote to manage your citations for your Annotated Bibliography and Research Proposal, visit our EndNote LibGuide.

Directions specifically for exporting from PubMed to EndNote can be found here.

And feel free to contact your librarian with any questions!

Setting Up Alerts

PubMed allows you to set up alerts to monitor new articles that get added that match your search criteria. Here's how to set them up:

  1. In order to save searches and set up alerts, you need to create a "MyNCBI" account. From the main PubMed page, click "Sign in to NCBI".
  2. This will ask you to log in or create a new account.
  3. Once you have your account and are signed in, perform your PubMed search.
  4. Once you have your search results, under the serach box at the top of the screen will be an option to "Save Search".
  5. To save the search, click "Save".
  6. The next screen will confirm your saved search and ask if you would like email updates of new search results. Click Yes and you will be given options for frequency, day of delivery, format, number of items, and any text added to the results email. This can be helpful if you use email filters to prevent email from being marked as junk, or to direct it to a specific folder.
  7. Click Save and your preferences will be saved.
  8. To edit a saved search, click on My NCBI to bring up your My NCBI homepage. The section labeled Saved Searches will list all the searches you have saved.
  9. To edit alert options, click on the gear wheel to bring up the options screen for a particular search.
  10. Clicking on the search name will actually re-run the search.

Chemistry & Biology Librarian