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.