PubMed Changes are Coming

March Updates

By the end of March, the Strauss Health Sciences Library will transition to only linking to the new PubMed interface. So when you access PubMed from the Library, you will directed to the new interface. If you would like to access the legacy interface again before its retirement, you can use the banner in the new PubMed interface to return to the legacy view.

At some point this Spring or Summer, the National Library of Medicine will retire the legacy interface. We will post more specific information about that as we receive it.

If you have any questions about how to use the new PubMed interface, please AskUs!

February Updates

New features have been added to the new PubMed interface!

Items Per Page (see 1)

Display options now include items per page. Ten, twenty, fifty, one hundred, or two hundred results may be displayed per page.

New Sort Options: Publication Date (see 2), Reverse Sort Order (see 3)

In addition to Best match and Most recent, results may now be sorted by publication date either in ascending or descending order.

Download Results by Year as a CSV File (see 4)

The file will include the search query, the year, and the associated record count.

Similar Articles can now be displayed on a new page of results

Clicking “see all similar articles” (see 5) on any article abstract page will open a new results page listing all similar articles.

This was written by Ellie, you can contact AskUs with questions.

November Updates

A bit behind schedule but finally here, you can now find the new PubMed interface from the current PubMed browser.

Find the new PubMed interface

The new interface was built using modern web standards with a responsive layout, so it works more effectively on cell phones and tablets.

The updated Best Match sort uses a machine learning algorithm to elevate the most relevant articles to the top of your results list.

Starting in Spring 2020, this new interface will be the default for all PubMed users.

Read more about the changes to the interface from the NLM Technical Bulletin.

Have questions or feedback about the new PubMed interface? Contact NLM with your PubMed Labs Feedback.

This was written by Christi Piper, you can contact AskUs with questions.

September Updates

The new PubMed is going live this month! Are you ready?

We will use this space to keep you updated on the changes that occurring and provide tips and tricks for using the new interface. You can interact with the beta version of the new PubMed by visiting PubMed Labs. As you use the new interface, please provide NLM with your PubMed Labs Feedback as they will continue to make improvements to the interface until it becomes the default in January 2020.

Keep in mind that the beta interface is not currently a replacement for the current version of PubMed since it is not the complete database in regards to content or functionality yet.

Here are the most recent features that have been added to the new PubMed interface:

  • Filters have been added to narrow results by article type, text availability, publication date, species, language, sex, subject, journal category and age.
  • The Health Sciences Article Linker has been added! You can now get to our library holdings from the beta PubMed version.

Keep an eye on the library homepage for information about the new PubMed and quick links to access the site.

This was written by Ellie, you can contact AskUs with questions.

July Updates

In Fall/Winter 2019, PubMed will be undergoing some changes to the interface. If you want to see some of the changes that are coming before the current version of PubMed is replaced, you can visit PubMed Labs, the experimental platform that has some of the major updates already available.

Wondering what’s new? Here are some of the updated features:

Enhanced Search Results

The new version of PubMed (currently PubMed Labs) will have an enhanced relevant sort option, named Best Match, that ranks search results according to several relevance signals, including an article’s popularity, its publication date and type, and its query-document relevant score.

The search results page will now automatically include highlighted text fragments from the article abstract that are selected based on relevance to the search.

Responsive Design

Have you ever tried to use PubMed on your phone or tablet? The current version doesn’t work very well, but the new version of PubMed will feature a mobile-first responsive layout that offers better support for smaller device screens. The new interface will be compatible with any screen size no matter how you access PubMed.

Want to learn more about the new PubMed interface/PubMed Labs? Visit the NLM Technical Bulletin , where this information was taken from, for more details.

Have questions or feedback about the new PubMed interface? Contact NLM with your PubMed Labs Feedback.

This was written by Christi Piper, you can contact AskUs with questions.

PubMed Filters: Adding Institutional Filters to your NCBI Account

In a previous blog, we described some new search filters that can be used while accessing PubMed from the HSL home page. However, we realize that many of our users—especially those working with the more advanced features of PubMed—likely have their own My NCBI accounts, and won’t often be starting their search from the library’s home page. This blog will explain how to import those new filters into your existing My NCBI account, so you can use them in conjunction with your existing settings and preferences. To begin, you’ll need to either log in or create an account, which can be done at the “Sign in to NCBI” link shown below.

Sign in to NCBI link

Once logged in, continue to the Settings page (titled “My NCBI” at the top of every page) and navigate to the “Filters” module, typically at the lower-right corner of the page. If you’ve never experimented with creating your own filters, you will see a message stating “You do not have any active filters for this database.” Click the link to “Add filters for the selected database” or “Manage Filters.”

Manage Filters

On this page, select “Create custom filter” and paste the following code into the “Query terms” text box. Be sure to select all text, as even leaving off an opening or closing parenthesis may break the filter.

((inprocess[sb]) OR publisher[sb] NOT (pubstatusnihms NOT pubstatuspmcsd NOT pmcbook) OR (pubstatusaheadofprint))

Adding New Filters

This is the filter to show all articles without MeSH terms assigned, and it’s a great way to ensure you’re performing as thorough a search as possible. If your search returns 0 results when using this filter, you are likely missing the most recent literature on your subject! A consultation with an HSL librarian will be a great help to troubleshoot your search strategy, and you can schedule one via Ask Us.

Once the filter has been added, be sure to “Activate” it. This will ensure every search result page displays the filter as an option for you to choose.

Activate Filter

The second filter is much longer, but the process is the same. This filter restricts results to authors with an affiliation to CU Anschutz Medical Campus and related institutions, going back to 2014. For more information on how this filter works and why it’s restricted to this timeframe, the original blog post goes into much greater detail.

To add it, create a new custom filter, then copy and paste this code into the query terms:

 ((80045[ad]) OR (80218[ad]) OR (80206[ad]) OR (80220[ad]) OR (80262[ad]) OR (ucdenver[ad] AND (Aurora or Anschutz)) OR (uchealth[ad] AND (Aurora or Anschutz)) OR ("University of Colorado"[ad] AND Aurora[ad]) OR ("University of Colorado"[ad] AND Anschutz[ad]) OR ("University of Colorado Health Sciences Center"[ad]) OR ("University of Colorado"[ad] AND (Medicine[ad] OR SOM[ad])) OR ("University of Colorado"[ad] AND ("College of Nursing"[ad] OR "school of nursing"[ad] OR CON[ad] or SON[ad])) OR ("University of Colorado"[ad] AND "Public Health"[ad]) OR ("University of Colorado"[ad] AND "Dental Medicine"[ad]) OR ("University of Colorado"[ad] AND Pharmacy[ad]) OR (Colorado[ad] AND Denver[ad] AND AMC[ad]) OR (Colorado[ad] AND Denver[ad] AND Anschutz[ad]) OR (Colorado[ad] AND Denver[ad] AND Aurora[ad]) OR ("University of Colorado AMC"[ad]) OR (CU[ad] AND Anschutz[ad]) OR (CU[ad] AND Aurora[ad]) OR (CU[ad] AND AMC[ad]) OR ("University of Colorado Denver" AND Aurora[ad]) OR (Fitzsimons[ad]) OR ("University of Colorado Denver"[ad] AND Aurora[ad]) OR ("University of Colorado Hospital"[ad]) OR ("University of Colorado Health"[ad]) OR ("UC Health"[ad]) OR ("Children's Hospital"[ad] AND Aurora[ad]) OR ("Childrens Hospital"[ad] AND Aurora[ad]) OR ("The Children's Hospital"[ad] AND Aurora[ad]) OR ("Veterans Affairs"[ad] AND (Denver[ad] OR Aurora[ad])) OR (VAMC[ad] AND (Denver[ad] OR Aurora[ad])) OR ("VA Eastern" AND Denver[ad]) OR ("National Jewish"[ad]) OR (NJH[ad] AND Denver[ad]) OR ("Denver Health"[ad])) AND (2014:2018[crdt])

When these filters are active, they’ll show up on the top right of every search results page, displaying the number of relevant hits in parentheses.

End Result

As mentioned last time, if you have comments, questions, problems, or suggestions for other filters, please let us know by leaving a comment below or submitting a ticket via AskUs. There are a lot of other options we can help you explore, both in and out of PubMed, and we’re always happy to help!

–Jason Wardell, Education & Reference Intern

NCBI cracks 200 annotated eukaryotic genomes

The National Center for Biotechnology Information (NCBI) is the central repository for molecular data in the US. They don’t generate their own data: all of the sequences in their databases is submitted by external sources such as research labs, genomic sequencing consortia, and through the INSDC.

They do, however, provide an interface to access these data and create tools to analyze the data, which includes annotation a select set of genomes. Because NIH is primarily devoted to human health, they prioritize on eukaryotic genomes, especially mammals.

The NCBI has annotated over 200 eukaryotic genomes so far. Do you want to see your favorite organism annotated by NCBI? They take requests through their Help Desk.

  • Tobin Magle, PhD- Biomedical Sciences Research Support Specialist.