Author Archives: Dina

Checking to What Extent PubMed and MEDLINE Index a Journal

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Understanding the extent to which a particular database indexes the contents of a journal is a crucial step towards maximizing the visibility and reach of your published work(s).

Although social media and other marketing channels have definitely helped with getting the word out about new research in scholarly publishing, the reach of bibliographic indexes in terms of providing access to content beyond an individual author’s personal and professional networks is still very significant.

There are a few factors that impact the visibility and reach of a literature database:

1) Public access versus commercial databases

Content that everyone has access to because it is not stored behind a paywall, regardless of how well-funded their institution is or if they are affiliated with a research library or not, has the potential of reaching a wide range of audiences across the globe. In the case of PubMed, for example: “On an average working day approximately 2.5 million users from around the world access PubMed to perform about 3 million searches and 9 million page views.”   

2) Syndicated/leased/shared versus proprietary content

“Syndicated content is content that is published on multiple sites beyond the source, which broadens its reach and visibility”. There are some databases, like MEDLINE, whose content is leased to other database vendors and  can be searched (in whole or in part) in other resources. For example, MEDLINE content is included in EMBASE, CINAHL, and Cochrane Library. Having a journal indexed in both MEDLINE and PubMed, therefore, increases the potential for the contents of that journal to be discovered by searchers of databases beyond NLM’s PubMed’s free search interface.  For this reason, it is helpful to understand the difference between PubMed and MEDLINE and how each of these resources is put together.

3) “Surface” versus “deep” web indexing by search engines

Another important question to ask of an online database is: Do regular web search engines, like Google, “see” the contents of this database? In the case of the vast majority of database resources on the Internet, the standard World Wide Web search engines generally stop at the front door of the database tool and do not index the actual contents within the database. In the case of PubMed, however, Google actually “crawls” the records contained within the database, increasing their findability by Google Scholar searchers who may never search the PubMed database via its native interface.

From Vine R. Google Scholar. J Med Libr Assoc. 2006 Jan;94(1):97–9. PMC1324783:

“Much of Google Scholar’s index derives from a crawl of full-text journal content provided by both commercial and open source publishers. Specialized bibliographic databases like OCLC’s Open WorldCat and the National Library of Medicine’s PubMed are also crawled. Since 2003, Google has entered into numerous individual agreements with publishers to index full-text content not otherwise accessible via the open Web. Although Google does not divulge the number or names of publishers that have entered into crawling or indexing agreements with the company, it is easy to see why publishers would be eager to boost their content’s visibility through a powerhouse like Google.”

In short, selecting a journal to publish in that is indexed in PubMed, as well as, in MEDLINE, gives your manuscript a good head start towards achieving maximum international reach and visibility.

Follow these steps to determine whether a journal is indexed in PubMed alone, in both PubMed and MEDLINE, or in neither:

Click on the “Journals” link of the PubMed homepage or go directly to the NLM Catalog to search for Journals referenced in the NCBI Databases. Once you bring up a catalog record for a journal of interest, click on the title to open the full record where you can confirm a journal’s MEDLINE “Current Indexing Status”.

Below are examples of the indexing status information provided in NLM Catalog records:

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Questions?  Ask Us at the MSK Library!

Upgrading to EndNote 20 – Important Information

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The latest version of the EndNote citation management software, EndNote 20, will become available to the MSK community on Wednesday, July 7th, 2021.

Established EndNote users should be aware that significant changes have been made to this latest release of EndNote.

Please review the information below to avoid any unexpected/unwelcome surprises and/or work disruptions on time-sensitive/critical projects.

  1. How does EndNote 20 differ from previous versions?
  2. How do I get EndNote 20?
  3. Can I upgrade to EndNote20 and keep the previous version on my machine too?
  4. What are EndNote 20’s compatibility and system requirements?
  5. Do I need to worry about my existing EndNote library files not working in EndNote 20?
  6. What should I do to avoid potential compatibility problems?
  7. If I create EndNote 20 libraries that my colleagues (who have not upgraded to EndNote 20) cannot open, what should I do?
  8. How do I get training on EndNote 20?
  9. Who should I contact if I run into any issues when upgrading to or using EndNote 20?
  10. Are there other citation management options available via MSK that I can use instead of EndNote 20?

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1. How does EndNote 20 differ from previous versions?

EndNote users familiar with a previous version can compare features and review the differences on the EndNote website (for comparisons going back to X4, see here) or read about them on the MSK Library blog post where they can also view the 2:01 min video entitled: “What’s new in EndNote 20”.

2. How do I get EndNote 20?

a) PC/Windows Desktops connected to the MSK Network (onsite workstations and VCD):

If you currently use EndNote by accessing it in the MSK User Applications folder via the Windows start menu, then EndNote 20 will simply appear there once the new version is released to all users on the MSK network. If you are a new EndNote user, you will still need to contact the Help Desk at 123-3337 or 646-227-3337 to first have EndNote added to your MSK account.

b) MSK-issued PC/Windows laptops:

If you have an earlier version of EndNote installed locally on a Windows laptop, then you can go to the MSK Self-Service Portal, listed as Company Portal in the Windows Start menu to download the app. If you do not see it listed as an app option, contact the Help Desk at 123-3337 or 646-227-3337 to have EndNote 20 added for you.

 

 

 


c) Macintosh Desktops and Laptops:

Macintosh users can use the MSK Self-Service Portal to install the upgraded EndNote 20 software. Please review the macOS and system requirements and call the Help Desk if you do not see the EndNote 20 app available to you for download.

d) Non-MSK Machines:

Current Endnote 20 policy is that the software will not be provided for use on personal computers.  Remote users can use Endnote 20 via Virtual machines.

3. Can I upgrade to EndNote 20 and keep the previous version on my machine too?

No. When you install EndNote 20 on a machine locally, this action will cause previous EndNote versions to first be uninstalled. EndNote 20 will replace previous EndNote versions on all networked PC workstations. Also, an EndNote 20 tab will appear in MS Word and this toolbar will only link with an X9.3 and later EndNote library.

4. What are EndNote 20’s compatibility and system requirements?

EndNote 20 Compatibility and System Requirements 

a) PC: Windows 10

b) Macintosh: macOS 10.14, 10.15, 11.

See full specifications at https://endnote.com/product-details/compatibility.

5. Do I need to worry about my existing EndNote library files not working in EndNote 20?

If you are using an existing EndNote library that was created in EndNote X9.2 or earlier, then you will be prompted to convert this library when you try to open it in EndNote 20 (or EndNote X9.3). 

Once you create an EndNote library in EndNote 20 (or are prompted by EndNote to convert an older library for use in EndNote version X9.3 or later) the library will NOT be compatible with earlier versions of the application (version X9.2 or earlier).

For this reason, it is strongly recommended that you upgrade to EndNote 20 on all computers that you will be using to access the EndNote desktop software.

6. What should I do to avoid potential compatibility problems?

Before converting an existing EndNote library to the new format, you may wish to create back-ups of any EndNote library files that are important to you. You may choose to back-up your libraries by using one or both of these options:

a) Sign up for an EndNote Online account and sync your important existing desktop EndNote libraries to your cloud-based EndNote Online account.

b) Save your important existing desktop EndNote libraries as “compressed” libraries (while in your current version of EndNote) by going to File > Compressed Library…

7. If I create EndNote 20 libraries that my colleagues (who have not upgraded to EndNote 20) cannot open, what should I do?

The best way to handle this situation is to share the citation records with your colleague(s) by using your EndNote Online account as an intermediary. You can sync your desktop EndNote library to your EndNote Online account and then share it with your colleague(s) just by going to File > Share… and inputting your colleague’s email (the same email that they will have used to create an EndNote Online account of their own).  They will then be able to sync these citations to their own EndNote desktop library (of an earlier version). See (1.02 min) video – In action: EndNote 20 (Windows) library sharing – Web of Science (webofsciencegroup.com)

8. How do I get training on EndNote 20?

a) MSK Library classes:

You may register for an upcoming EndNote 20 workshop offered by the MSK Library or submit a request for an individual training consultation.

b) EndNote (Clarivate Analytics) training options:

You may also wish to view short video tutorials on specific EndNote features. By going to EndNote’s YouTube training channel and selecting the EndNote 20 (Windows) essential features that includes 19 videos (all less than 2 mins in length).

Clarivate Analytics also has free live training options that you may register for and attend online or view as a recording (EndNote 20 essentials (Windows): a class recording). Also, a variety of Quick Reference Guides can be downloaded and consulted.

9. Who should I contact if I run into any issues when upgrading to or using EndNote 20?

a) MSK Library:

Research Informationists at the MSK Library are available to help you troubleshoot any EndNote issues. Feel free to contact them via the Ask-A-Librarian online form, via telephone, or Chat.

b) EndNote (Clarivate Analytics) product and technical support:

You can explore the EndNote knowledge base for answers to popular questions or contact an expert:

United States / Canada: +1 800-336-4474
EndNote.support@clarivate.com

10. Are there other citation management options available via MSK that I can use instead of EndNote 20?

For additional citation management software options, please review the MSK Library’s Citation Management LibGuide. Be sure to consult the citation manager comparison table to help you choose the citation management software tool that best fits your needs.

 Questions?  Ask Us at the MSK Library!

 

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.