Tag Archives: Pubmed

PubMed Tip of the Month: My Bibliography

As I mentioned in my March post, the My Bibliography section of My NCBI allows you to save citations to your journal articles, book chapters, presentations, meeting abstracts, etc.  This list of citations can be shared via a stable URL, exported to a text file, or saved as a PDF.  NIH recommends using My Bibliography if you wish to include a link to a complete list of published works in your biosketch.  My Bibliography is also used to demonstrate compliance with the NIH Public Access Policy on progress reports.

Access My Bibliography

Log in to your My NCBI account, find the My Bibliography box (note: you can drag and drop the boxes in My NCBI to change the order in which they appear) and click the ‘Manage My Bibliography’ link.

Add Citations

Once you are in My Bibliography, use the buttons in the right-hand column to add a citation from PubMed (preferred method), manually (use for articles not in PubMed, or other products, such as meeting abstracts, presentations or data sets), or from a file (must be in either MEDLINE or RIS format).

Citations can also be added to My Bibliography from any PubMed results page.  Click the boxes next to the citations you wish to add, then choose My Bibliography from the Send to dropdown menu at the top of page.

Add citations from PubMed results page

PubMed Send to

Make Publicly Available

Click the ‘Edit settings’ link at the top of the My Bibliography homepage.  This will bring you to a page where you can change your sharing settings from private to public.  Once you do so, the URL will appear at the top of your My Bibliography homepage.  Note: do not copy and paste the URL that appears in your browser when you are in My Bibliography because this is different than the unique URL generated for your collection.

Public URL and edit settings for My Bibliography

My Bibliography homepage

PubMed Tip of the Month: Author Search

Go to the Advanced Search Builder by clicking the ‘Advanced’ link under the PubMed search box.

Choose Author from the All Fields drop-down menu (just Author, not Author – Last, Author – Full, or any of the other options). Enter the author’s last name, followed by 1 or 2 initials with no intervening punctuation (for example: Jones EA). If you are unsure about the inclusion of the second initial, then do not include it.

If the author has a common last name, then you probably want to narrow your search by including an affiliation. To do so, choose Affiliation from the All Fields drop-down menu below the boxes where you have entered the author’s name. Enter the name and/or location of the institution with which the author is associated. Affiliation can become complicated if the author has been (or is currently) associated with multiple institutions, or the name of the institution has several possible variations. If the author has an uncommon last name, then first try searching without an affiliation.

Check the results to ensure that they authored by the person in whom you are interested.

If you have searched for your own name, then you can send the results to the My Bibliography section of My NCBI by clicking ‘Send to:’ in the top right corner of the results page.

Author Search in PubMed Advanced Search Builder
Author Search in PubMed Advanced Search Builder

PubMed Tip of the Month: My NCBI

My NCBI is a personalized account for PubMed and other National Center for Biotechnology Information (NCBI) databases, such as Gene and Protein. This account allows you to:

  • Save searches and receive daily, weekly or monthly email alerts when new articles meeting your search criteria become available.
  • Save collections of references; in the My Bibliography section, you can save references to articles that you have authored. Collections, including My Bibliography, can be made publicly available, providing you with a URL to share with colleagues or use in grant applications.
  • Change preferences for how your results are displayed in PubMed, and select favorite filters.
  • Manage compliance with the NIH public access policy in the My Bibliography section.
  • Utilize Science Experts Network Curriculum Vitae (SciENcv) to help you create biosketches for NIH and NSF grants.

To create an NCBI account:

Click the ‘Sign in to NCBI’ link in the top-right hand corner of any PubMed page (or, click here).

Click ‘Register for an NCBI account’ link, or sign in with a 3rd party option, such as Google or eRA Commons (recommended for NIH-funded investigators who do not currently have an NCBI account). Note, you cannot user your Tufts username and password as a 3rd party sign in option.

My NCBI Sign In
My NCBI Sign In

PubMed Tip of the Month: Searching for Methods

There are several techniques that can help you find methodology articles in PubMed:

  • MeSH Headings for Methodology: “Methods” and “Research Design” are MeSH headings. You can try combining these terms with MeSH headings or keywords for your topic.
  • MeSH Headings for Particular Technique(s): Depending on your area of research, there may be a specific MeSH term for the category of techniques in which you are interested, e.g. “Cell Culture Techniques”.
  • Subheadings: Subheadings are used in conjunction with MeSH terms to further describe a particular aspect of that term. Subheadings follow a MeSH term, e.g. “Polymerase Chain Reaction/methods”[MeSH].  Subheadings can also be free-floated in a search, e.g. “DNA Replication”[MeSH] AND “Methods”[Subheading]. Two useful subheadings for methodology searches are “Isolation and Purification” and “Methods” (yes, Methods is both a heading and subheading).
  • Search Particular Journal(s): You may wish to narrow your search to one or more journals devoted to methodology. To do so, open the Advanced Search Builder by clicking the Advanced link below the PubMed search box. Select Journal from the dropdown menu and start typing the title of the journal in the adjacent search box. Choose the journal from the list of titles that appear. Enter a search term in the next search box to search the journal for articles on a specific topic, e.g. “Methods in molecular biology”[Journal] AND CRISPR.

PubMed Journal Search

PubMed Tip of the Month: Advanced Search Builder

The PubMed Advanced Search Builder allows you to view your search history, search specific fields (e.g. title, author, abstract, journal, etc.), and combine searches using Boolean operators (AND, OR, NOT). To access the Advanced Search Builder, click on the ‘Advanced’ link below the PubMed search box.

PubMed Advanced Search Builder
Use Advanced Search Builder to view search history and combine searches.

PubMed Tip of the Month: Clipboard (November 2015)

The Clipboard feature in PubMed allows you to temporarily store citations for review; items are deleted after 8 hours of inactivity. To place citations on the Clipboard, check the box to the left of an article title on the results page. Choose Clipboard from the Send to menu at the top of the page. Click Add to Clipboard. An icon will appear at the top of the page with a link showing the number of items on your Clipboard. I use this feature in a two-step review process. When I am satisfied that I have a good search, I do a first pass through the results, quickly scanning the title of each article and checking the box for any citation that may be relevant. I send these items to the Clipboard. Once I have completed the initial review, I go to the Clipboard, change the view from Summary to Abstract (menu at the top of the page) and read the abstract of each article to decide whether or not it is truly relevant.

-Laura Pavlech

PubMed Tip of the Month: Using MeSH Headings (October 2015)

Including MeSH terms in a PubMed search can help you get more precise results.

What is MeSH? Most of the more than 25 million citations in PubMed come from MEDLINE, the National Library of Medicine’s (NLM) journal citation database. Medical Subject Headings (MeSH) is a controlled vocabulary of standardized terms that indexers (actual humans!) apply to each article in MEDLINE to describe the publication type and topics covered in the article.

Why should you care about MeSH? Biomedical topics are often expressed in different ways. For example, chronic kidney disease may also be called end-stage renal disease, chronic renal failure, or abbreviated as ESRD. The MeSH term for this condition is kidney failure, chronic. Using MeSH terms in a PubMed search helps you find articles regardless of how an author referred to that topic. MeSH terms also allow you to search on all concepts in a broad category without having to enter every term. MeSH headings are arranged in a hierarchy of broader and narrower terms; when you search a broader term, all the narrower terms are automatically included in your search. For example, the MeSH term for cancer, neoplasms, can be used to search for all types of cancer.

How do I find MeSH terms? When you conduct a search in PubMed, the database will try to match your terms to MeSH headings in a process called automatic term mapping. To see how the PubMed translated your search, look for a box labeled ‘Search Details’ in the right column on the results page (you will need to scroll down the page). You can also search the MeSH database directly by choosing ‘MeSH’ from the dropdown menu to the left of the PubMed search box. See this example of the term meningitis in the MeSH database: http://www.ncbi.nlm.nih.gov/mesh/68008581.

Need help with MeSH? Contact me at laura.pavlech@tufts.edu or 617-636-0385.

-Laura Pavlech

PubMed Tip of the Month (August 2015)

http---library.tufts.edu-screens-finditattufts Use the ‘PubMed@Tufts’ link to access PubMed from either on or off campus. This will enable you to easily access full text articles available through Tufts Libraries. When you wish to access the full text of an article in PubMed, click on the title of the article and look for the blue ‘Find It@Tufts’ button at the top of the column on the right side of the page. This will either bring you directly to the article or to a page where you can search for the journal in our library catalog.

-Laura Pavlech