Tag Archives: pubmed

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!

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.

 

Important NCBI Account Changes Coming in June: Choosing Your Best Third-Party Option

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NCBI announced it will transition to federated account credentials on June 1, 2021. What does this mean for you?

We’ve noted before that creating a My NCBI account is a key tool within PubMed and other NCBI databases. It retains your user information and database preferences to help you keep track of research, customize your search experience, and stay compliant with the NIH Public Access Policy. While these account changes are being implemented for privacy and security reasons, they won’t affect what you’ve stored within your NCBI account. Look to the NCBI Account Login Changes FAQs page for more information.

Starting now, if you only have a Native NCBI Account (a NCBI username and password), you will need to add a Linked Account to it. This means signing in via a third-party organization, and letting it confirm your identity. This will give you federated account credentials within NCBI, and make your account more secure. Examples of organizations that you can link through are eRA Commons, Google, ORCiD, Login.gov, Microsoft, Facebook, and NIH.

As there are 4,000+ third-party login options to choose from, it’s important you select what works best for you. See this list for a breakdown of recommendations by role, activity, or preference. Here are two common scenarios for our MSK user community:

If your work involves using NCBI within the grant application process:

If your work involves using NCBI as a researcher or clinician:

Below are instructions for adding your chosen third-party option(s). The Library recommends adding at least two in case one is disrupted.

Instructions to add a Linked Account from the main NCBI page:

  1. Go to NCBI
  2. Select an option from the list or click on “more login options” for all organizations listed alphabetically

If you’d like to add more Linked Accounts once logged in to NCBI:

  1. Click on your NCBI username in the upper right corner
  2. Select Account Settings
  3. Under Linked Accounts, select Change
  4. In the search box, search for and select your desired account
  5. Authenticate with the third-party