Sub-grouping PubMed Records by Their Linkages to Other NIH Resources

The National Library of Medicine (NLM), which is part of the NIH, is responsible for a wide array of information/data resources. In addition to biomedical literature databases like PubMed, PubMed Central, and the clinical trial registry,, NLM also includes computational molecular biology resources and human genome resources among its database offerings, all of which are freely-available to everyone.

One of the great strengths of NLM’s resources is that they have been designed with maximum accessibility/linkages in mind. If you are searching in one database and there is information in another NLM resource that might also be relevant, chances are pretty good that the database record you are consulting will include meaningful embedded links-out to the other tools.

These connections between resources are particularly valuable for conducting specialized searches of the biomedical literature. The ability to sub-group PubMed records according to their inclusion in a “secondary source” means that you can limit a search within PubMed to a more relevant portion of PubMed, which is a powerful way to increase the precision of your search results.

Following are two different use cases where this sub-grouping functionality can be super-useful if you are carrying out targeted information retrieval projects.

Case 1:

In, each registered clinical trial record includes a “Study Results” tab where searchers can find publication lists (when available). These lists of article citations link back to PubMed records, which in turn are indexed with identifiers. As a result of this set-up, if a searcher wishes to start in PubMed and search on their favorite topic across the published clinical trial study results identified in, they can do so by adding the following to their PubMed search strategy:[si]  

For example:[si] AND sarcoma – Search Results – PubMed (

(Note: The linkage will appear in the PubMed Abstract record in the “Associated data” section.)

Case 2: GeneRIF (Gene Reference into Function)

Another specialized literature search that is often tricky to carry out is one that limits the search results to those publications that describe a gene’s function. Luckily, NLM already has a program called GeneRIF (Gene Reference into Function) that “provides a simple mechanism to allow scientists to add to the functional annotation of genes described in Gene.” By leveraging these gene-PMID connections developed for the Gene database, PubMed searchers can limit their search results to only those PubMed records that have been tagged with a GeneRIF identifier. They can do this by adding the following to their PubMed search strategy:

“pubmed gene rif” [Filter]

For example: “pubmed gene rif” [Filter] AND sarcoma – Search Results – PubMed (

(Note: The GeneRIF linkage will appear in the PubMed Abstract record in the “Related information” section.) 

If you have any questions or would like some additional guidance on designing specialized literature searches, feel free to Ask Us at the MSK Library.