Embase: A Refresher

Embase, linked from the Library homepage under Top Databases, is a proprietary database, produced in Netherlands by Elsevier publishing company. It indexes journals in Medicine, Dentistry, Veterinary Science, Life Sciences, Public Health, Nursing, etc. While its coverage has significant overlap with PubMed (it actually indexes all of Medline), it also indexes a large number of international journals not found in PubMed. Embase also indexes supplements such as conference abstracts, clinical trials, and more.

Similar to PubMed’s MeSH terms, Embase also has the ability to map search terms to subject headings. Embase’s subject headings are called Emtree terms and their classification also has a hierarchical structure. One major difference between PubMed (MeSH) and Embase (Emtree) is that in PubMed narrower terms are automatically included, whereas in Embase, Emtree terms must be “exploded” to include all narrower terms found beneath a specific Emtree term.

Embase also includes some functions that are not found in PubMed, such as proximity searching, which besides AND, OR,and NOT, adds a layer to searches to make them more specific, using NEAR and NEXT.

Embase is typically one of the databases of choice used in searches when conducting a Systematic Review or a Meta-Analysis in biomedicine. It is recommended to specify the platform on which Embase was used. Embase is available on its native Elsevier platform (Embase.com) or on the OVID platform. MSKCC Library offers Embase on the Elsevier platform. The platform has an impact on the way the searches are conducted, so it is important to note when conducting systematic reviews.

Note: Starting July 1, 2021 Embase now requires signing into your Embase account to export citations to Endnote and other citation management tools. It is free to create an Embase/ Elsevier account and this login can be used for any Elsevier product (Embase, Scopus, etc.).


Get to Know the New Web of Science Interface!

On July 7th, 2021, Web of Science‘s new interface became the default interface for all users! The new interface had been in Beta and Preview modes since November 2020, and based on user input the new experience is faster, more intuitive, easier to use, with new functionalities and a responsive design.

Along with a large scale redesign of the interface, the new Web of Science includes two new visualization tools.

Other useful features in the new Web of Science interface are the ability to export 1,000 records at a time (previously it was 500), ability to export to RIS format from the Core Collection, and the ability to share search queries with others!

To learn more about the new interface, check out the Clarivate Blog.

Saving an Endnote Library

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.

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.