Category Archives: About Resources

Saving an Endnote Library

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Many MSK staff favor Endnote as their citation management software. Saving an Endnote Library is one of the issues that requires special attention from the Endnote user.

In the desktop version of EndNote, a Library is saved with the extension .enl after its name, and its associated Data folder, with the extension .Data after its name. (NOTE: On Mac computers there is also an option to save your Library as a .enpl file, which combines both the library and the data file into one.)

The Library contains the records and the Data folder is intended for PDFs of the full text associated with the Endnote Library records, as well as anything inserted into the Image field of a reference. Even if no PDFs or images are available, the Data folder will still be there; however a Data folder should never be deleted. Data folders should never be moved or copied without first compressing them into a .enlx file. From there, the compressed zip file can be moved, copied, and shared.

Endnote library (.enl), associated data folder (.Data) and the compressed zip file of both (.enlx)

It is important to know that saving an Endnote Library to any network drive does not work well. There is a very high chance of getting a pop-up Damaged Library message at some point if the Library is saved to any drive other than your local drive, i.e. to your computer. On a PC you may consider This PC>Documents for saving an Endnote Library. If you want to save a Library to a network drive for better security you can save a backup copy either as a Compressed Library as explained above or by using the Endnote File>Save a Copy feature. You can save the backup copy to your personal drive or, as a Read Only copy, to a shared drive for your collaborators’ use (but not for their adding/removing the content). As an alternative, instead of using a shared drive for sharing your Endnote Library with others, you can use the Endnote Online companion to your desktop Endnote for collaboration.

https://youtu.be/IGO09iFYAVk

Takeaways:

  • Don’t save an Endnote Library to a network drive.
  • Never delete the .Data folders associated with Endnote Libraries.
  • Don’t try moving the Library separately from its Data Folder, use the Compressed Library feature instead.

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

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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, ClinicalTrials.gov, 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: ClinicalTrials.gov

In ClinicalTrials.gov, 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 ClinicalTrials.gov 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 ClinicalTrials.gov, they can do so by adding the following to their PubMed search strategy:

Clinicaltrials.gov[si]  

For example: clinicaltrials.gov[si] AND sarcoma – Search Results – PubMed (nih.gov)

(Note: The ClinicalTrial.gov 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 (nih.gov)

(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.

 

New Advanced Practice Providers Group Added to Synapse

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A new custom group was created to track the publications of MSK’s Advanced Practice Providers. APP’s are highly trained nurse practitioners(NPs), physicians assistants(PAs), and certified registered nurse anesthetists(CRNAs) that are an integral part of the healthcare experience at MSK.

Groups in Synapse pull the publications of selected author profiles into a single collection, allowing you to view and track the research coming out of our various departments and services. Administrators and authors can use the groups to create bibliographies for grant applications and annual reports, as well as providing an easy way to highlight your groups publications via the custom Synapse group URL. 

For more information, or to start your own Synapse Group, please contact Jeanine McSweeney.