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Working with Filters

Created: ; Last Revision: June 12, 2013.

NCBI databases search results can be narrowed down to smaller groups of data using filters. In My NCBI, you can select your preferred filters to be active every time you run a search.

For example, in the PubMed database, filters can be used to group results into reviews, clinical trials, or citations with free full text links, among other choices. Users may also create their own custom filters.

There is a limit of five filters (including custom filters) that can be selected for all NCBI databases, except for PubMed, where the maximum number of filters allowed is 15.

Section Contents

The Filter Display

In the figure below, a search in PubMed with the term human genetic deficiencies generated 2,473 citations. Four filters have been activated: Free Full Text, National Library of Medicine, Last 30 days and a custom filter NLM+free. Filtered results with their respective counts are displayed as links: Free Full Text (928 citations), National Library of Medicine (2057 citations– number of articles for which NLM has online access), Last 30 days (5 citations) and NLM+free (2106 citations - number of articles for which NLM has online access plus free full text).

Image workingwithfilters.G1.jpg

Note:

  • The filters shown on the right side of the above image are activated by clicking on the filter hyperlinks. For more information on using the sidebar filters, see Filters.

Setting Up Filters

To set up filters, go to the Filters portlet, select the database for which you want to establish filter preferences, and click the link Manage Filters.

Image workingwithfilters.G2.jpg

In the Filters page, users can browse a list of filters that is divided in four categories: Popular, LinkOut, Properties and Links. To select and activate a filter, click the checkbox next to the filter name.

Image workingwithfilters.G3.jpg
The "Popular" category lists the most commonly requested filters according to each NCBI database. For example, the filters Bacteria and genomic DNA/RNA are requested for Nucleotide.

The "LinkOut" category groups records that have links to resources provided by outside organizations, such as full-text publications, biological databases, consumer health information, library holdings and research tools. These links provide supplemental information related to records in NCBI databases. For example, users looking for affinity data can select the Binding database as a filter in PubMed.

Image workingwithfilters.G4.jpg

The "Properties" category groups records according to specific criteria for each database, such as languages, gender, age groups, publication type for PubMed; biosource, molecule type, RefSeq for Nucleotide among many others.

The "Links" category groups records that have links to other NCBI databases. For example, you can select "Links to Gene" to create a result link that groups all records retrieved in a search that have links to the Gene database. The result link is active every time you search any NCBI database (see image below).

Image workingwithfilters.G5.jpg

Libraries using LinkOut to display their holdings in PubMed can set up a filter for their holdings through My NCBI. In the Filters portlet click on the link “Manage Filters.” Select the radio button for LinkOut. Enter the library name in the filter search box. Check the box under the “Filter” column. In addition, to display the library icon, check the box under the “Link Icon” column.

Image workingwithfilters.G6.jpg

To view a brief animated tutorial, see Filters.

Note:

  • To deactivate filters, uncheck the box next to the filter name
  • To see your active filters and icon settings, check the Filter list for each database
  • LinkOut and Properties are divided into subcategories that may include additional subcategories. You may choose to have either a single filter added to your search results or an entire category or subcategory
  • If you know the name of a filter you are interested in, you can search for filter names and descriptions using the Search with Terms search box
  • Some databases have a default set of result filters that are active whether you have a My NCBI account or not. Default filters are replaced by your filter preferences, which can also be accessed and changed from all databases results pages. When on a results page, look for “Filter you results” and click the link “Manage Filters” to access your filter preferences list
  • Accounts that do not have any activity in two years will be deleted

Creating Custom Filters

It is possible to customize your own filters for any NCBI database. To create a custom filter:

1.

Sign into My NCBI and go to Filters, click the link Manage Filters

2.

Choose the database for which you want to create a custom filter from the drop-down list.

Image workingwithfilters.G7.jpg

3.

Click the button Image workingwithfilters.G8.jpg

4.

On the pop-up window, enter the Name for this custom filter and the Search terms that you wish to use for this filter. You can then click “Run Filter” to see the number of items retrieved by the custom filter search.

5.

If you are satisfied with the custom filter, click “Save Filter.” Your new custom filter will be automatically activated and displayed in the database filter list.

Image workingwithfilters.G9.jpg

6.

To modify a custom filter, click the gear icon Image workingwithfilters.G10.jpgand then amend the filter Name and Search terms.

7.

To deactivate filters, uncheck the box next to the filter name.

To view a brief animated tutorial, see Custom Filters.

Examples of custom filters for PubMed:

Filter typeFilter search
Address of first authormayo [ad] AND clinic [ad]
Library holdings or anything available free"loprovnlmlib"[Filter] OR free full text [sb]
Articles identified by a funding agency"loprovnlmlib"[Filter] OR free full text [sb]
Items from particular journalsBirth Defects Res A Clin Mol Teratol [ta] OR
Birth Defects Res B Dev Reprod Toxicol [ta] OR
Birth Defects Res C Embryo Today [ta] OR
Clin Dysmorphol [ta] OR
Congenit Anom Kyoto [ta]
Any termdelivery of health care [mh]
Any combination of termsclinical trial [pt] AND aged [mh]
Free text searchinghealth disparities
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