Tag Archive for PubMed

Almost Painless Biosketches

sciencv logois an online tool that assists researchers in creating and formatting biographical sketches needed for federally funded research. Because it generates reference lists from My NCBI and imports grant information from eRA Commons, it is fast!  Save your templates to modify and update later.

Formatted Biosketch

  • Developed by NCBI (NIH) for the SciENcv interagency working group: DOD,DOE, EPA, NIH, NSF, USDA
  • Used to create, save and maintain multiple NIH biosketches for grant applications and annual reports. Includes template for NIH Biosketch now, and NSF is to be added Fall, 2014.

This video from NIH demonstrates the features of SciENcv.  Prefer to read? See these detailed instructions.  Or check out this guide to get started working with My NCBI.



PubMed Commons

Would you like to see a discussion by other scientists about new findings when you read a paper abstract?  Do you wish you could join in the discussion?  Do you enjoy the commentary and letters to the editor sections of journals and newspapers?  If so, read on…


PubMed Commons

PubMed Commons is a new service that will allow researchers to post comment on specific papers in PubMed. It is designed to be a forum that will encourage constructive criticism and high quality discussions that may enhance understanding and spark collaborations.  The screenshot below shows how the discussion displays in PubMed’s abstract view. (Click to enlarge image.)


During the time the Commons is a pilot project, participation is via invitation. If you are an author with a paper in PubMed and have eRA Commons credentials, you can invite yourself. Learn how to join PubMed Commons here.

You will need to have a My NCBI account and log into it when using PubMed.  That will allow you  to both see and post comments. To see all articles with comments on a specific topic, add AND has_user_comments[sb]  to your PubMed search.  Learn more about your My NCBI account here.

According to the NCBI, comments from the first few days after the site went live included “critique or pointed to other studies or reviews with the potential to change people’s interpretations or conclusions. Some authors posted corrections or changed their own conclusions in the light of others’ subsequent work. Authors also used PubMed Commons to update people on their work – including links to databases that have moved, providing contextual information and backstories as well as new, relevant work.

Many PubMed Commons participants took the opportunity to add links to relevant papers and data, sometimes in the non-PubMed academic literature or data repositories – including complete datasets, data re-analyses, blog posts and full text pre-prints of the article.”

PubMed Commons can be viewed as another tool in an emerging field sometimes labeled “post-publication peer-review.”  Two other options for reading commentary and adding your views to the discussion on published articles follow:

  • UAB licenses Faculty of 1000 which uses experts to identify and comment on noteworthy articles.
  • PubPeer is a free website striving to create an online community for discussion of scientific papers organized into a searchable online database.  PubPeer has released a browser plugin so users can identify articles with comments when searching PubMed.

Where PubMed Commons has requirements for the people posting commentary, PubPeer encourages anonymity.  Each has strong reasons for its requirements. If you are interested in these issues, both Nature News and Retraction Watch have discussed the PubMed Commons initiative.

New! PubGet for the iPad

Many UAB researchers use Pubget, the biomedical search engine that provides the results as PDFs. PubGet includes all of PubMed and more, and provides one-click access to the articles that UAB licenses.

The PubGet Mobile website allows researchers to read articles on their cell phones and is especially useful for browsing the latest issue of key journals, but it requires the reader to be online.

The new PubGet iPad app is now free to download at the Apple app store.  This app features:

  • PubMed ArXiv, JSTOR, & IEEE abstracts and articles
  • Author, journal or topic searching
  • Advanced searching
  • Customizable list for browsing latest issues of journals
  • PDFs of the articles that UAB licenses and any freely available

PDFs can be saved to the library for viewing later even when offline. So you can read your saved articles on airplanes, which is great for travelers.

Below is a screenshot of a Pubget search result list from the app.  You can expand the screen as shown on the right, and enlarge fonts, graphs or images when reading the PDFs using your fingers on the touch screen.

You can also type notes and save them with the PDFs.














According to the team at Pubget, there are planned updates to improve the functionality of the library.  Right now, it is not possible to sort or search by author or journal, organize into folders, or delete articles that have been read.  Articles from certain publishers do not display well.  And there is no app for Android or other platforms.

In the meantime, Pubget users who would find the limitations restricting can use the Pubget Mobile website while online, and export the articles they select into another app they have downloaded.  The free Apple iBooks app works well for this, and allows deleting and sorting by title, author and category.  There is a similar free eBook app in the Android Market. Both save the PDFs for viewing offline. Another option is to search Pubget on your computer and save the PDFs you select to a cloud app like Dropbox that syncs with your tablet or smart phone for later viewing offline.

The PubGet support team is very responsive to suggestions and problem-solving. There is a support button under the Settings icon found on each page.

LigerCat: Generate Tag Clouds and Search PubMed

LigerCat is a visual approach to focusing your PubMed searches. Using Medical Subject Headings (MeSH) to refine your searching can be very useful, but often it is difficult to identify appropriate MeSH terms, even using the MeSH Database. LigerCat solves that problem for you. And it is fun to use!

"LigerCat home screen"

Enter words into the LigerCat search box and LigerCat aggegrates the articles found in PubMed, putting the associated MeSH terms into a tag cloud. In this example I searched for ‘treatment her2 positive breast cancer”:

"tag cloud"

These results are weighted for frequency and relevancy. You can click on one or more terms and search PubMed instantly from the resulting “Selected Terms” table.

The search string LigerCat generated is:

((“therapy”[Subheading] OR “therapy”[All Fields] OR “treatment”[All Fields] OR “therapeutics”[MeSH Terms] OR “therapeutics”[All Fields]) AND her2[All Fields] AND positive[All Fields] AND (“breast neoplasms”[MeSH Terms] OR (“breast”[All Fields] AND “neoplasms”[All Fields]) OR “breast neoplasms”[All Fields] OR (“breast”[All Fields] AND “cancer”[All Fields]) OR “breast cancer”[All Fields])) AND (“Breast Neoplasms”[mh] AND “Receptor, erbB-2″[mh] AND “Treatment Outcome”[mh])

A ” Publication History’ table is also created from your original search. Mouse over the year to see how many articles were published.  Or click on the year to view them in PubMed.

LigerCat evens searches for a protein sequence and returns the tag clouds and search tables as shown in the screenshots below:

Note: LigerCat searches PubMed.gov, not PubMed via LHL, so generally you will not see the UAB Article Linker buttons that provide full text.  On campus, the Publisher buttons usually work if UAB licenses the content. This YouTube video shows one easy way to get to licensed full text off campus. Or, from the PubMed screen, log into MyNCBI by creating an account or using the Google or Institutional logins. Then Set your Outside Tool preference to UAB Article Linker. (See how.) You will now see the UAB Article Linker button in PubMed. Questions? Contact me.

"PubMed Homepage showing MyNCBI log in"

About LigerCat: LigerCat stands for the Literature and Genomic Resource Catalog, and is brought to you by the Biology of Aging project at the MBLWHOI Library. It is a free resource available to all.  Read this article to learn more:

LigerCat: using “MeSH Clouds” from journal, article, or gene citations to       facilitate the identification of relevant biomedical literature. Sarkar IN, Schenk R, Miller H, Norton CN. AMIA Annu Symp Proc. 2009 Nov 14;2009:563-7.